Rank ID GeneSet BroadUrl Description PubMedID NumGenes Contributor p.value p.adj vote.rank avg.rank med.rank min.pvalue min.rank avg.logfc avg.logfc.dir direction significance camera safe gage padog plage zscore gsva ssgsea globaltest ora fry 1 M2573 LIM_MAMMARY_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_STEM_CELL_UP.html Genes consistently up-regulated in mammary stem cells both in mouse and human species. 20346151 390/782 Daniel Hollern 7.84617440912776e-132 3.67671732811727e-128 5 29.0909090909091 2 7.13288582647966e-133 1 2.14680992581986 2.18091518484071 1 100 1 7 1 1 112 1 2 10 170 1 14 2 M2574 LIM_MAMMARY_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_STEM_CELL_DN.html Genes consistently down-regulated in mammary stem cells both in mouse and human species. 20346151 351/695 Daniel Hollern 6.45211857536171e-34 1.77850750847911e-31 5 171.545454545455 16 5.86556234123798e-35 2 1.49683333045036 -1.48477127414396 -1 16.8243009816566 2 13 16 512 646 6 5 44 506 7 130 3 M19391 LIU_PROSTATE_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_PROSTATE_CANCER_DN.html Genes down-regulated in prostate cancer samples. 16618720 318/808 Arthur Liberzon 1.68129472443829e-51 2.62618235957261e-48 5 74.9090909090909 20 1.52844974948938e-52 3 2.15661514029482 2.31203591889452 1 37.507878484617 16 20 3 3 86 15 116 40 468 4 53 4 M9192 CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_DN.html Genes down-regulated in luminal-like breast cancer cell lines compared to the mesenchymal-like ones. 16288205 330/762 Arthur Liberzon 9.82801294893252e-23 1.02342374841551e-20 10 195.727272727273 44 8.93455722630228e-24 2 1.83660163259818 1.93690645858627 1 13.4197926370882 7 229 44 108 582 2 67 32 1034 39 9 5 M13867 ONDER_CDH1_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_2_UP.html Genes up-regulated in HMLE cells (immortalized nontransformed mammary epithelium) after E-cadhedrin (CDH1) [GeneID=999] knockdown by RNAi. 18483246 193/443 Jessica Robertson 4.83013051190147e-23 5.14408899517507e-21 45 198.454545454545 44 4.39102773809223e-24 14 2.06993448322243 2.18393262035556 1 15.3507602619199 14 44 43 28 765 38 78 150 860 37 126 6 M2293 PASINI_SUZ12_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PASINI_SUZ12_TARGETS_DN.html Genes down-regulated in ES (embryonic stem cells) with defficient SUZ12 [GeneID=23512]. 17339329 257/529 Arthur Liberzon 1.16557157400087e-15 6.91375746299756e-14 35 133 52 1.05961052181897e-16 3 1.82574834445938 1.89869062764543 1 8.78264824077894 32 35 76 43 225 3 52 128 756 74 39 7 M2580 LIM_MAMMARY_LUMINAL_MATURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_LUMINAL_MATURE_DN.html Genes consistently down-regulated in mature mammary luminal cells both in mouse and human species. 20346151 102/176 Daniel Hollern 8.70243788568558e-27 1.19940070389184e-24 5 232.363636363636 62 7.91130716880504e-28 3 2.17724231287571 2.23703991781694 1 19.0373281366418 3 66 33 7 1697 41 170 62 254 19 204 8 M1655 HAN_JNK_SINGALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAN_JNK_SINGALING_DN.html Genes down-regulated in 3T3 cells (fibroblast) upon activation of JNK pathway. 12354774 29/65 John Newman 6.66352976895842e-09 1.16512315288579e-07 5 207.363636363636 64 6.05775435376494e-10 4 1.69842832843732 1.72539681912249 1 4.30454272915768 64 140 646 435 4 5 6 4 474 499 4 9 M17079 VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_UP.html Up-regulated genes distinguishing between two subtypes of gastric cancer: advanced (AGC) and early (EGC). 17297478 124/324 Arthur Liberzon 1.05673332771566e-18 8.53767650633724e-17 15 238.545454545455 75 9.60666661559694e-20 13 2.16854082163052 2.26313236870884 1 12.7369816242903 13 266 57 39 1227 42 107 63 621 75 114 10 M1804 WANG_SMARCE1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_SMARCE1_TARGETS_UP.html Genes up-regulated in BT549 cells (breast cancer) by expression of SMARCE1 [GeneID=6605] off a retroviral vector. 16135788 184/460 John Newman 1.57777907536825e-21 1.47869454943512e-19 50 210.545454545455 76 1.43434461397113e-22 20 1.93226588534011 2.07173899716283 1 13.2996208414559 63 47 49 20 536 76 260 197 900 46 122 11 M3672 TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_DN.html Genes down-regulated in lobular carcinoma vs normal ductal breast cells. 17389037 50/150 Arthur Liberzon 6.31926330259249e-18 4.85443735015548e-16 70 95.9090909090909 84 5.74478482053861e-19 10 2.88952102230124 3.12668262082995 1 16.1744608347958 135 108 59 10 66 141 245 84 50 70 87 12 M1246 LI_WILMS_TUMOR_VS_FETAL_KIDNEY_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_VS_FETAL_KIDNEY_2_DN.html Genes down-regulated in Wilm's tumor vs fetal kidney. 15531917 39/104 Arthur Liberzon 1.93216986851686e-12 7.18583174910319e-11 60 154.818181818182 89 1.7565180622896e-13 12 2.24887477966043 2.31251552252041 1 8.33821983371118 12 125 120 60 793 22 79 59 245 89 99 13 M18597 BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_AND_PAX3 http://www.broadinstitute.org/gsea/msigdb/cards/BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_AND_PAX3.html Genes up-regulated in SaOS-2 cells (osteosarcoma) upon expression of PAX3-FOXO1 [GeneID=5077;2308] but down-regulated by PAX3 expression off adenoviral vectors. 15688035 4/10 Leona Saunders 1.8046878280157e-08 2.85701593313567e-07 10 512.636363636364 90 1.80468784267174e-09 3 2.77200373823648 2.77200373823648 1 6.63074228935745 134 389 4252 110 90 47 3 9 10 565 30 14 M7439 DACOSTA_ERCC3_ALLELE_XPCS_VS_TTD_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_ERCC3_ALLELE_XPCS_VS_TTD_DN.html Genes down-regulated in fibroblasts expressing different mutant forms of ERCC3 [GeneID=2071]: XP/CS (xeroderma pigmentosum (XP) and Cockraine's syndrome (CS)) vs TTD (trichothiodystrophy). 15608684 31/72 Arthur Liberzon 1.51334778649834e-10 3.96175850700068e-09 20 118.454545454545 91 1.37577071509312e-11 9 2.14664758271865 2.15455557726777 1 6.59277825440942 9 133 172 202 332 18 20 39 227 91 60 15 M1579 BURTON_ADIPOGENESIS_8 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_8.html Progressively down-regulated 8-96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 85/182 John Newman 2.0591598807749e-07 1.93870664292301e-06 50 201.363636363636 92 1.87196370318957e-08 9 1.86899519498771 1.94095124415758 1 3.90258821348702 50 82 406 92 224 9 50 123 695 447 37 16 M13422 HUPER_BREAST_BASAL_VS_LUMINAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUPER_BREAST_BASAL_VS_LUMINAL_UP.html Genes up-regulated in basal mammary epithelial cells compared to the luminal ones. 17409405 34/100 Jessica Robertson 1.17653815307339e-12 4.5190637584442e-11 30 145.090909090909 95 1.0695801391582e-13 11 2.45394790813885 2.69281412603117 1 9.27925373015735 95 460 116 29 33 26 41 181 453 151 11 17 M14507 CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN.html Genes down-regulated in luminal-like breast cancer cell lines compared to the basal-like ones. 16288205 335/782 Arthur Liberzon 1.64445627896743e-23 1.92648053081034e-21 30 235 100 1.49496025360674e-24 24 1.85554657603864 2.00473396336641 1 14.0501507151803 100 228 39 152 393 28 333 26 1210 52 24 18 M631 REACTOME_COLLAGEN_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COLLAGEN_FORMATION.html Genes involved in Collagen formation 25/64 Reactome 3.38401128033492e-12 1.18339379549623e-10 5 174.181818181818 101 3.07637389121829e-13 4 2.57579415540017 2.57579415540017 1 9.34636569439384 4 148 128 34 1022 30 9 213 101 84 143 19 M2571 ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_DN.html Genes down-regulated during prostate cancer progression in the JOCK1 model due to inducible activation of FGFR1 [GeneID=2260] gene in prostate. 18068632 238/587 Yujin Hoshida 1.50233642746545e-38 7.82216499900347e-36 105 176.727272727273 102 1.36576038860496e-39 8 2.24589063486539 2.51497006281569 1 28.8202357602845 101 239 8 11 483 102 169 100 399 11 321 20 M2316 WIEDERSCHAIN_TARGETS_OF_BMI1_AND_PCGF2 http://www.broadinstitute.org/gsea/msigdb/cards/WIEDERSCHAIN_TARGETS_OF_BMI1_AND_PCGF2.html Genes up-regulated in DAOY cells (medulloblastoma) upon knockdown of both BMI1 and PCGF2 [GeneID=648, 7703] by RNAi. 17452456 46/110 Arthur Liberzon 7.92258158966645e-14 3.7125217329177e-12 105 212.363636363636 104 7.20234689969702e-15 10 2.35719008925634 2.51611918868465 1 9.8485583813849 102 445 95 263 715 25 104 38 421 118 10 21 M6679 BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_DN.html Genes down-regulated in SaOS-2 cells (osteosarcoma) upon expression of PAX3-FOXO1 [GeneID=5077;2308] fusion protein off an adenoviral vector. 15688035 45/91 Leona Saunders 2.41100964274656e-09 4.66859139913652e-08 95 304.636363636364 107 2.19182695035347e-10 12 2.01440162326439 2.0930841668232 1 5.39780910748798 21 593 233 214 1428 27 12 95 529 92 107 22 M12895 CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_DN.html Genes down-regulated in basal-like breast cancer cell lines as compared to the mesenchymal-like ones. 16288205 42/104 Arthur Liberzon 3.95231743062157e-08 5.75172654655052e-07 50 294 108 3.59301591056844e-09 13 1.61126033968175 1.62436407747985 1 3.67522219019049 103 130 624 231 108 50 49 13 1304 571 51 23 M17937 NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_DN.html Top 100 probe sets contrubuting to the negative side of the 1st principal component; predominantly associated with synovial sarcoma and myxoid/round cell liposarcoma samples. 17464315 51/190 Nikolaos Papanikolaou 8.17829234213675e-14 3.75720371718165e-12 70 181.909090909091 110 7.43481122012458e-15 18 2.39295605845523 2.46898150432358 1 9.99344725263545 67 110 97 18 554 215 298 158 93 73 318 24 M16114 SIMBULAN_UV_RESPONSE_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/SIMBULAN_UV_RESPONSE_NORMAL_DN.html Genes down-regulated in HFK cells (primary keratinocytes) in response to UVB irradiation. 16007217 27/56 Leona Saunders 4.37524497063324e-08 6.32790059641585e-07 15 276.454545454545 111 3.97749550695076e-09 8 2.04347014816286 2.09498266698943 1 4.63010663765664 111 733 770 536 198 11 8 14 85 562 13 25 M12432 PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_DN http://www.broadinstitute.org/gsea/msigdb/cards/PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_DN.html Genes down-regulated in unstable ateroslerotic plaques compared to the stable ones. 16741146 39/71 Arthur Liberzon 9.29035747380798e-11 2.51645174117134e-09 15 96.7272727272727 112 8.44577952200026e-12 7 2.39281838958052 2.58693241731211 1 7.52120824674558 15 127 166 194 119 7 25 67 112 175 57 26 M2124 HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_DN.html Down-regulated genes in the cancer gene signature, representing a gene signature of cellular transformation. 20385360 75/181 Arthur Liberzon 3.65801075149972e-08 5.40739381120747e-07 35 208.363636363636 115 3.32546437483876e-09 33 1.94582014158211 2.20073813810952 1 4.45740885311214 33 85 289 48 1029 80 115 90 135 241 147 27 M12602 WOO_LIVER_CANCER_RECURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WOO_LIVER_CANCER_RECURRENCE_UP.html Genes positively correlated with recurrence free survival in patients with hepatitis B-related (HBV) hepatocellular carcinoma (HCC). 18381945 90/200 Yujin Hoshida 3.30207240362224e-12 1.17024622168201e-10 65 250.727272727273 118 3.00188400329746e-13 51 2.09084969217639 2.25738563168868 1 7.59043475041135 62 283 126 85 819 118 173 51 843 101 97 28 M2030 NAKAMURA_ADIPOGENESIS_LATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_ADIPOGENESIS_LATE_DN.html Genes down-regulated in mesenchymal stem cells during late phase of adipogenesis, defined as days 7 to 14 of culturing with adipogenic hormones. 12646203 37/61 Arthur Liberzon 1.89195327873205e-10 4.84464101865486e-09 5 176.363636363636 118 1.71995752626796e-11 4 2.63073531539681 2.63073531539681 1 7.99548835723806 6 322 176 118 887 4 4 79 146 152 46 29 M8519 DAVICIONI_MOLECULAR_ARMS_VS_ERMS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_MOLECULAR_ARMS_VS_ERMS_DN.html Genes down-regulated in mARMS (molecular ARMS) compared to the mERMS (molecular ERMS) class of rhabdomyosarcoma tumors. 16849537 137/354 Arthur Liberzon 3.27613865482479e-09 6.09518107589505e-08 100 197.272727272727 120 2.97830787245769e-10 43 1.78503647556794 1.89565068344027 1 4.70764262726833 99 262 241 120 188 49 65 43 849 112 142 30 M6250 KORKOLA_YOLK_SAC_TUMOR http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_YOLK_SAC_TUMOR.html Genes predicting the yolk sac tumor (YS) subtype of nonseminomatous male germ cell tumors (NSGCT). 15870693 40/124 Leona Saunders 1.70642022598429e-13 7.40396775829849e-12 425 160.090909090909 122 1.55129111453129e-14 43 2.22043527096297 2.40996981114162 1 9.03386146409494 43 122 103 50 424 60 152 96 425 149 137 31 M75 TSENG_ADIPOGENIC_POTENTIAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TSENG_ADIPOGENIC_POTENTIAL_UP.html Genes showing increasing expression in brown preadipocytes with decreasing ability of the cells to differentiate. 15895078 24/52 John Newman 1.10399700298974e-10 2.9731781356379e-09 70 159.454545454545 126 1.00363363913195e-11 66 2.20463234674193 2.40817011542693 1 6.87132414355331 66 152 167 66 125 95 187 346 352 126 72 32 M1530 SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1B http://www.broadinstitute.org/gsea/msigdb/cards/SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1B.html Genes with some basal expression and partially methylated promoters, up-regulated by the combination of TSA and decitabine [PubChem=5562;451668] in RKO cells (colorectal cancer). 11992124 16/44 John Newman 5.00451753060862e-08 7.10641489346424e-07 15 651.454545454545 127 4.54956149495495e-09 11 2.11918111233584 2.15099254109522 1 4.76261930069078 458 638 1020 76 11 127 71 3951 115 687 12 33 M2309 AZARE_NEOPLASTIC_TRANSFORMATION_BY_STAT3_UP http://www.broadinstitute.org/gsea/msigdb/cards/AZARE_NEOPLASTIC_TRANSFORMATION_BY_STAT3_UP.html Genes up-regulated in RWPE-1 cells (prostate cancer) upon expression of constitutively active form of STAT3 [GeneID=6774]. 17438134 90/256 Arthur Liberzon 2.43590977736153e-10 6.07163468974263e-09 115 278.636363636364 128 2.21446343421022e-11 29 2.13141079135327 2.21201576220304 1 6.40152644260641 113 691 181 78 825 29 128 231 655 102 32 34 M6487 BIOCARTA_PLATELETAPP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PLATELETAPP_PATHWAY.html Platelet Amyloid Precursor Protein Pathway 11/29 BioCarta 8.38150063623005e-07 4.23525526893721e-06 95 356.545454545455 133 7.61954893581205e-08 21 2.57792710929884 2.57792710929884 1 5.0630994389905 71 516 481 93 1680 21 94 413 133 355 65 35 M158 PID_INTEGRIN4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN4_PATHWAY.html Alpha6 beta4 integrin-ligand interactions 18832364 4/12 Pathway Interaction Database 3.36861357527232e-08 5.0432342535866e-07 25 639.454545454545 134 3.36861362633632e-09 1 2.27046569871252 2.27046569871252 1 5.22622314025306 349 214 3900 68 689 134 1 23 9 1626 21 36 M4717 LI_CISPLATIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LI_CISPLATIN_RESISTANCE_UP.html Genes consistently up-regulated in ACRP cells (ovarian cancer, resistant to cisplatin [PubChem=2767]) compared to the parental sensitive A2780 cells, regardless of cisplatin exposure. 17072341 27/69 Arthur Liberzon 2.20683058915211e-07 2.02371979271366e-06 85 250.090909090909 138 2.0062098277458e-08 61 2.14047412423932 2.29763093597352 1 4.45487195173486 84 146 331 138 1278 83 61 180 130 136 184 37 M2448 SWEET_KRAS_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SWEET_KRAS_TARGETS_UP.html Genes upregulated in KRAS [GeneID=3845] knockdown vs control in a human cell line. 15608639 72/150 Aravind Subramanian 4.85978744026644e-11 1.42331024656803e-09 115 276.363636363636 138 4.41798858215798e-12 47 1.98427974516836 1.96817772216581 1 6.41657789456442 47 291 153 87 1014 51 138 111 833 202 113 38 M2129 CHICAS_RB1_TARGETS_CONFLUENT http://www.broadinstitute.org/gsea/msigdb/cards/CHICAS_RB1_TARGETS_CONFLUENT.html Genes up-regulated in confluent IMR90 cells (fibroblast) after knockdown of RB1 [GeneID=5925] by RNAi. 20385362 354/968 Arthur Liberzon 2.90405776957373e-28 4.69255679593879e-26 280 227.454545454545 138 2.64005251779428e-29 24 1.84854732244792 2.01257770587017 1 17.1143671844472 90 224 28 109 280 104 279 144 1082 24 138 39 M8645 MCCLUNG_DELTA_FOSB_TARGETS_2WK http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_DELTA_FOSB_TARGETS_2WK.html Genes up-regulated in the nucleus accumbens (a major reward center in brain) 2 weeks after induction of deltaFosB, a FOSB [GeneID=2354] splice variant. 14566342 42/105 John Newman 5.22892657864161e-07 3.20297384934831e-06 100 361.363636363636 139 4.7535707467685e-08 35 1.98551448053667 2.10677651452141 1 3.98764296459472 98 848 465 139 1197 35 74 68 689 298 64 40 M1259 SASAI_RESISTANCE_TO_NEOPLASTIC_TRANSFROMATION http://www.broadinstitute.org/gsea/msigdb/cards/SASAI_RESISTANCE_TO_NEOPLASTIC_TRANSFROMATION.html Genes down-regulated in MEF and REF cells (mouse and rat fibroblasts) but not in TIG3/T cells (human lung fibroblasts expressing TERT [GeneID=7015]) by co-expression of the SV40 early region and the activated HRAS (H-RasV12) [GeneID=3265]. 16832346 42/80 Arthur Liberzon 1.78272589332247e-14 9.08027558272726e-13 25 259.363636363636 140 1.62065990302044e-15 22 2.1706044826251 2.19998145511708 1 9.55421472310632 22 117 87 155 1079 140 62 407 316 78 390 41 M259 MANALO_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MANALO_HYPOXIA_UP.html Genes up-regulated in response to both hypoxia and overexpression of an active form of HIF1A [GeneID=3091]. 15374877 176/437 Kate Stafford 2.10395149224608e-14 1.04884220134736e-12 55 387.272727272727 140 1.91268317476917e-15 55 1.91743187009978 1.97953990752516 1 8.39595815120739 55 682 89 228 1357 61 118 212 1252 140 66 42 M13256 RIGGI_EWING_SARCOMA_PROGENITOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/RIGGI_EWING_SARCOMA_PROGENITOR_DN.html Genes down-regulated in mesenchymal stem cells (MSC) engineered to express EWS-FLI1 [GeneID=2130;2321] fusion protein. 18381423 112/259 Jessica Robertson 4.9814941116917e-13 2.02985055716411e-11 145 276.181818181818 141 4.52863101062984e-14 56 1.89164918123254 1.99765429067617 1 7.39333807747735 141 273 109 374 414 78 235 131 1156 56 71 43 M7876 CHEBOTAEV_GR_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEBOTAEV_GR_TARGETS_DN.html Genes down-regulated in follicular epithelial stem cells after transgenic expression of GR [GeneID=2908] under control of the keratin5 (K5) [GeneID=3852] promoter. 17146443 90/216 Leona Saunders 5.19337964967131e-08 7.28628055040712e-07 45 280.272727272727 142 4.72125433842512e-09 12 1.79385963831597 1.83566897727655 1 4.0243782876413 44 281 294 203 1065 12 70 116 794 142 62 44 M236 PID_DELTA_NP63_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_DELTA_NP63_PATHWAY.html Validated transcriptional targets of deltaNp63 isoforms 18832364 46/93 Pathway Interaction Database 2.55194894937869e-10 6.26095956899925e-09 120 182.454545454545 143 2.31995359061338e-11 62 2.40524164860334 2.75596710132852 1 7.21223200935009 116 119 184 62 532 137 168 143 222 235 89 45 M19256 SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_UP.html Genes up-regulated in pleura relapse of breast cancer. 18451135 6/11 Jessica Robertson 1.30791386859825e-07 1.45925818767891e-06 190 656.636363636364 144 1.307913945577e-08 26 2.59453171365061 2.59453171365061 1 5.53456744081288 187 522 4471 46 708 125 144 33 26 868 93 46 M9016 PROVENZANI_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PROVENZANI_METASTASIS_DN.html Genes down-regulated in polysomal and total RNA samples from SW480 cells (primary colorectal carcinoma, CRC) compared to the SW620 cells (lymph node metastasis from the same individual). 16531451 106/239 Arthur Liberzon 2.85104210023541e-09 5.40890011404986e-08 150 186 146 2.59185645811833e-10 40 1.90599195661893 1.96647861445099 1 5.06277891084522 146 67 237 52 40 143 140 552 292 146 231 47 M5618 TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_LOBULAR_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_LOBULAR_NORMAL_DN.html Genes down-regulated in ductal carcinoma vs normal lobular breast cells. 17389037 42/118 Arthur Liberzon 4.48486627396603e-13 1.84351608419341e-11 110 190.363636363636 149 4.07715115815178e-14 25 2.97682893547126 3.22118943865456 1 11.6801657243561 114 315 108 25 106 149 439 266 120 225 227 48 M3955 GU_PDEF_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GU_PDEF_TARGETS_UP.html Integrin, VEGF, Wnt and TGFbeta signaling pathway genes up-regulated in PC-3 cells (prostate cancer) after knockdown of PDEF [GeneID=25803] by RNAi. 17483333 58/138 Jessica Robertson 2.53031033705424e-10 6.24054433654536e-09 75 155.090909090909 150 2.30028212485933e-11 24 2.02364676230583 2.18746132359641 1 6.06905071521897 74 298 183 207 130 24 150 74 345 165 56 49 M1429 REACTOME_SMOOTH_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SMOOTH_MUSCLE_CONTRACTION.html Genes involved in Smooth Muscle Contraction 21/38 Reactome 1.8757774914195e-07 1.81926618188875e-06 130 261 151 1.7052524103211e-08 68 3.32736586107919 3.56567264433576 1 6.98135221952575 68 345 344 129 151 126 126 499 74 781 228 50 M1351 SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN.html Genes down-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 48 h. 18794802 288/749 Jessica Robertson 9.4527532467039e-25 1.23043338094596e-22 140 327.363636363636 151 8.59341204245809e-26 35 1.85256089985601 1.96733786095984 1 14.836551553446 136 536 35 151 733 87 325 261 1138 50 149 51 M3732 SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN http://www.broadinstitute.org/gsea/msigdb/cards/SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN.html Genes down-regulated in response to UVB radiation in HFK cells (keratinocytes) immortalized by overexpression of HPV E6 and E7 viral oncogenes. 16007217 28/61 Leona Saunders 1.18290133801436e-07 1.3720484331523e-06 160 493.272727272727 160 1.07536491056081e-08 7 1.74989354421177 1.84677813495016 1 3.74993212305756 160 737 1021 361 126 40 18 54 1064 1838 7 52 M17163 CAIRO_LIVER_DEVELOPMENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_LIVER_DEVELOPMENT_UP.html Genes up-regulated at early fetal liver stage (embryonic days E11.5 - E12.5) compared to the late fetal liver stage (embryonic days E14.5 - E16.5). 19061838 134/273 Arthur Liberzon 1.37504718023695e-08 2.24511187686075e-07 30 336 161 1.25004289893754e-09 8 1.67345454456827 1.79566567709673 1 4.06699799873228 27 261 269 161 1533 8 27 21 1101 234 54 53 M1167 HUMMERICH_SKIN_CANCER_PROGRESSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_SKIN_CANCER_PROGRESSION_UP.html Selected genes up-regulated during progression through benign to malignant skin tumors formed by treatment with DMBA and TPA [PubChem=6001;4792] chemicals in the two stage skin carcinogenesis model. 16247483 82/168 Arthur Liberzon 8.68745501482006e-08 1.09140520641949e-06 175 347.454545454545 171 7.89768668897641e-09 6 1.94571194120734 2.10550252178034 1 4.24024337874486 171 695 520 306 42 20 76 30 1493 463 6 54 M2899 LINDGREN_BLADDER_CANCER_HIGH_RECURRENCE http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_HIGH_RECURRENCE.html Genes up-regulated among the high recurrence rate urothelial cell carcinoma (UCC) tumors. 16532037 42/87 Arthur Liberzon 2.23157004631393e-11 6.97142482468472e-10 20 342.545454545455 172 2.02870004212416e-12 13 1.95228382323338 1.99710660458053 1 6.53431655203689 19 447 144 482 1286 13 36 355 682 172 132 55 M1229 OXFORD_RALB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALB_TARGETS_UP.html Genes up-regulated in the UMUC-3 cells (bladder cancer) after knockdown of RALB [GeneID=5899] by RNAi. 17496927 12/28 Arthur Liberzon 1.62680453594527e-08 2.61965843829536e-07 95 313.090909090909 173 1.47891322543162e-09 59 2.70819065769989 2.7443931978251 1 6.51538704407344 94 365 272 89 1290 59 296 555 96 173 155 56 M1126 HUMMERICH_MALIGNANT_SKIN_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_MALIGNANT_SKIN_TUMOR_UP.html Genes up-regulated in malignant skin tumors (squamous cell carcinoma, SCC) formed by treatment with DMBA and TPA [PubChem=6001;4792] in the two stage skin carcinogenesis model. 16247483 21/40 Leona Saunders 1.39038304629799e-09 2.89570442442327e-08 60 304.818181818182 174 1.26398458834245e-10 19 2.65248371920777 2.66667723332683 1 7.30873591883948 59 165 216 174 1553 19 60 306 523 231 47 57 M15472 VECCHI_GASTRIC_CANCER_EARLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/VECCHI_GASTRIC_CANCER_EARLY_DN.html Down-regulated genes distinguishing between early gastric cancer (EGC) and normal tissue samples. 17297478 175/696 Arthur Liberzon 6.34198445146486e-22 6.06500798766619e-20 50 280.090909090909 177 5.76544041042259e-23 15 2.00991140740117 2.12672296041898 1 14.1184027459833 207 48 48 15 118 522 795 177 644 36 471 58 M10952 KAAB_HEART_ATRIUM_VS_VENTRICLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAAB_HEART_ATRIUM_VS_VENTRICLE_UP.html Genes up-regulated in the atria of healthy hearts, compared to venticles. 15103417 208/507 John Newman 3.055505836792e-13 1.30164548647339e-11 165 235.727272727273 179 2.77773257890221e-14 58 2.07682035390034 2.22917088868962 1 8.26355371961814 163 246 105 58 452 179 329 171 549 81 260 59 M5549 TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_LOBULAR_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_LOBULAR_NORMAL_UP.html Genes up-regulated in lobular carcinoma vs normal lobular breast cells. 17389037 61/168 Arthur Liberzon 4.38176345274807e-16 2.7747220999429e-14 185 249.272727272727 184 3.98342132068006e-17 21 3.06308260274262 3.39264034040644 1 15.1786981271965 184 102 71 21 439 451 826 97 107 198 246 60 M3005 NABA_COLLAGENS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_COLLAGENS.html Genes encoding collagen proteins 22159717 17/45 Alexandra Naba 4.55504469513362e-09 8.20959209284467e-08 35 364.363636363636 185 4.14094973142248e-10 31 2.78394895546907 2.78394895546907 1 7.21044314717519 31 355 249 70 1891 119 129 510 125 185 344 61 M16774 WILCOX_RESPONSE_TO_PROGESTERONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WILCOX_RESPONSE_TO_PROGESTERONE_DN.html Genes down-regulated in primary cultures of ovarian surface epithlium cells exposed to progesterone [PubChem=5994] for 5 days. 18070364 37/163 Arthur Liberzon 3.12359019205096e-10 7.58401224867916e-09 190 261.454545454545 186 2.83962744772222e-11 45 2.57526318795615 2.58998492444278 1 7.64367653266678 85 456 186 80 1033 58 45 157 363 190 223 62 M2025 NAKAMURA_ADIPOGENESIS_EARLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_ADIPOGENESIS_EARLY_DN.html Genes down-regulated in mesenchymal stem cells during early phase of adipogenesis, defined as days 1 to 5 of culturing with adipogenic hormones. 12646203 36/62 Arthur Liberzon 3.49468819928724e-10 8.44129324838146e-09 15 242.454545454545 187 3.17698927258398e-11 10 2.60420709705974 2.60420709705974 1 7.68531219109448 11 455 187 216 1047 10 14 194 276 179 78 63 M1236 OXFORD_RALA_OR_RALB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_OR_RALB_TARGETS_DN.html Genes down-regulated after knockdown of RALA or RALB [GeneiD=5898;5899], which were also differentially expressed in bladder cancer compared to normal bladder urothelium tissue. 17496927 18/43 Arthur Liberzon 1.49625138966524e-06 6.10220540641541e-06 135 250.818181818182 189 1.36022946117102e-07 31 2.14584826983703 2.26206771792 1 4.09008214134836 131 353 413 49 888 109 31 272 189 221 103 64 M11788 CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_DN.html Selected genes down-regulated during invasion of lymphatic vessels during metastasis. 18794116 25/84 Jessica Robertson 1.38403858487205e-10 3.66418350774601e-09 40 400.363636363636 189 1.25821689541739e-11 38 2.57041842580844 2.61023651117837 1 7.92612323264851 38 734 170 534 1874 64 189 219 300 108 174 65 M1322 INGRAM_SHH_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/INGRAM_SHH_TARGETS_DN.html Genes down-regulated in 10T1/2 cells (multipotent mesoderma) by expression of SHH [GeneID=6469]. 17873912 69/144 Jessica Robertson 2.31859390995663e-10 5.8101235625972e-09 195 209.090909090909 191 2.10781264563726e-11 47 2.10473102917302 2.20737685532498 1 6.3361057545806 191 91 180 47 258 97 525 271 353 211 76 66 M6906 SENESE_HDAC2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC2_TARGETS_DN.html Genes down-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC2 [GeneID=3066] by RNAi. 17470557 87/210 Leona Saunders 3.97383362586659e-16 2.55087457134395e-14 215 240.818181818182 194 3.61257602351509e-17 63 2.03175326488331 2.10820466757004 1 10.0952125375699 142 79 70 200 194 122 214 593 759 63 213 67 M19620 COLLER_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/COLLER_MYC_TARGETS_DN.html Genes down-regulated in 293T (transformed fetal renal cell) upon expression of MYC [GeneID=4609]. 10737792 20/34 Yujin Hoshida 4.69585827825356e-08 6.72929415654318e-07 30 390 197 4.26896216225979e-09 30 2.50069115430344 2.50069115430344 1 5.64166599563942 30 960 317 225 1883 54 95 270 175 197 84 68 M1113 GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP.html Up-regulated genes from the set C (Fig. 5a): specific to cells expressing AF4-MLL [GeneID=4299;4297] fusion protein alone. 17130830 121/262 Arthur Liberzon 9.322931673207e-08 1.14065947312397e-06 200 255.363636363636 198 8.47539278934960e-09 37 1.74920986673793 2.03253921071273 1 3.79975415108617 198 554 381 206 50 37 225 156 765 193 44 69 M1399 KHETCHOUMIAN_TRIM24_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KHETCHOUMIAN_TRIM24_TARGETS_UP.html Retinoic acid-responsive genes up-regulated in hepatocellular carcinoma (HCC) samples of TRIM24 [GeneID=8805] knockout mice. 18026104 40/82 Leona Saunders 5.50793059262863e-09 9.70306870566081e-08 155 303.636363636364 199 5.00720964219845e-10 83 2.323926964838 2.50073707276956 1 5.95732362458412 152 715 254 496 758 92 139 199 302 150 83 70 M2062 NIELSEN_MALIGNAT_FIBROUS_HISTIOCYTOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_MALIGNAT_FIBROUS_HISTIOCYTOMA_DN.html Top 20 negative significant genes associated with malignant fibrous histiocytoma tumors. 11965276 21/48 Arthur Liberzon 2.54157011224036e-07 2.18528395338685e-06 80 370.818181818182 199 2.31051855077966e-08 80 2.48486701342333 2.79698791327138 1 5.14134315798429 80 158 337 128 1358 199 171 627 124 436 461 71 M1459 PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_DN http://www.broadinstitute.org/gsea/msigdb/cards/PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_DN.html Genes down-regulated in BEC (blood endothelial cells) compared to LEC (lymphatic endothelial cells). 12198161 136/274 Kevin Vogelsang 6.62157287577079e-19 5.44362991155473e-17 60 332.818181818182 200 6.01961170524616e-20 56 2.06537089271218 2.1769694365359 1 12.2785658391104 200 59 56 64 596 183 343 757 981 71 351 72 M12890 ROZANOV_MMP14_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROZANOV_MMP14_TARGETS_UP.html Genes up-regulated in HT1080 cells (fibrosarcoma) over-expressing MMP14 [GeneID=4323] compared to those with knockdown of the gene by RNAi. 18519667 225/525 Jessica Robertson 1.11933432151535e-15 6.72461619310376e-14 245 336.363636363636 201 1.01757665592305e-16 75 1.78213258011931 1.94139877063314 1 8.58068472185784 244 242 75 201 664 162 364 168 1355 107 118 73 M19128 HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS.html Genes down-regulated in tumor-conditioned vs quiescent endothelial cells and up-regulated upon treatment with decitabine and TSA [PubChem=451668;5562]. 17483324 70/176 Jessica Robertson 5.37529145643524e-10 1.22871296413929e-08 205 388.636363636364 201 4.88662859795328e-11 11 2.15612945495337 2.34210822023636 1 6.23448721625195 201 933 197 86 1181 286 704 11 455 153 68 74 M16376 KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC.html Arrhythmogenic right ventricular cardiomyopathy (ARVC) 45/95 KEGG 1.07339582708962e-08 1.80284331388601e-07 75 187 204 9.75814393024356e-10 56 2.52543709461416 2.64662763654377 1 6.22552631372779 75 118 264 56 260 75 58 276 204 434 237 75 M9972 NIELSEN_GIST_VS_SYNOVIAL_SARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_GIST_VS_SYNOVIAL_SARCOMA_UP.html Top 20 genes whose up-regulation correlated with gastrointestinal stromal tumors (GIST) compared to synovial sarcoma. 11965276 18/110 John Newman 1.79406493404259e-06 6.87407054858839e-06 130 397.545454545455 204 1.63096945188693e-07 84 2.75945745124674 2.90317370791232 1 5.20747360589463 130 963 405 224 1623 108 137 204 84 323 172 76 M1521 WESTON_VEGFA_TARGETS_6HR http://www.broadinstitute.org/gsea/msigdb/cards/WESTON_VEGFA_TARGETS_6HR.html Genes up-regulated in MMEC cells (myometrial endothelium) at 6 h after VEGFA [GeneID=7422] stimulation. 12200464 44/93 John Newman 8.74535609033988e-18 6.48925908320974e-16 35 373.363636363636 206 7.9503237184908e-19 35 2.40499298302267 2.41253590505732 1 13.3514389230369 35 307 61 428 1292 68 206 343 1111 87 169 77 M1999 WONG_ADULT_TISSUE_STEM_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/WONG_ADULT_TISSUE_STEM_MODULE.html The 'adult tissue stem' module: genes coordinately up-regulated in a compendium of adult tissue stem cells. 18397753 493/1207 Arthur Liberzon 2.05479864306837e-24 2.60237471389686e-22 75 313.363636363636 206 1.86799876642578e-25 33 1.68757998560232 1.82595167516681 1 13.31460321036 73 221 36 107 182 206 453 396 1444 33 296 78 M7617 BENPORATH_EED_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_EED_TARGETS.html Set 'Eed targets': genes identified by ChIP on chip as targets of the Polycomb protein EED [GeneID=8726] in human embryonic stem cells. 18443585 442/1581 Jessica Robertson 3.06280879154532e-27 4.34918848399435e-25 400 548.181818181818 210 2.78437162867757e-28 32 1.98695321096674 2.14110733476337 1 17.6934511926604 398 1521 32 55 1334 210 551 85 1671 67 106 79 M10593 MACLACHLAN_BRCA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MACLACHLAN_BRCA1_TARGETS_DN.html Genes down-regulated in SW480 cells (colon cancer with mutated p53 [GeneID=7157]) upon expression of BRCA1 [GeneID=672] off an adenovirus vector. 10644742 22/51 John Newman 7.11977289552079e-07 3.83485698717361e-06 70 315.454545454545 210 6.47252290878705e-08 69 3.04742496483299 3.04742496483299 1 6.03324608717086 69 486 369 97 902 85 86 717 95 354 210 80 M1637 NIELSEN_LEIOMYOSARCOMA_CNN1_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LEIOMYOSARCOMA_CNN1_UP.html Top 20 positive significant genes associated with leiomyosarcoma tumors expressing muscle gene cluster with CNN1 [GeneID=1264]. 11965276 13/32 John Newman 1.52959319619389e-06 6.20040979010774e-06 160 360.363636363636 210 1.39054023606784e-07 34 3.39989677543151 3.53115184971909 1 6.47173759150619 159 764 412 210 896 69 34 490 36 702 192 81 M835 KEGG_DILATED_CARDIOMYOPATHY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DILATED_CARDIOMYOPATHY.html Dilated cardiomyopathy 51/122 KEGG 9.85885294036101e-10 2.19993261326341e-08 120 338.181818181818 213 8.9625935861628e-11 67 2.55396723866951 2.87958181744581 1 7.14869416627219 106 116 202 67 909 117 213 619 407 609 355 82 M17299 CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP.html Genes up-regulated in luminal-like breast cancer cell lines compared to the mesenchymal-like ones. 16288205 315/712 Arthur Liberzon 1.56134362043558e-13 6.8378095377207e-12 215 356.727272727273 214 1.41940329130517e-14 23 1.67317087550984 -1.57948332567167 -1 6.82844007931122 214 23 102 370 209 84 723 881 886 59 373 83 M33 PID_GLYPICAN_1PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_GLYPICAN_1PATHWAY.html Glypican 1 network 18832364 13/37 Pathway Interaction Database 1.53407570061238e-08 2.47885473554125e-07 415 602.545454545455 219 1.39461428300873e-09 3 1.92766377991765 2.07462287198485 1 4.6544953448717 412 1216 1190 219 1935 188 145 7 42 1271 3 84 M7098 KEGG_ECM_RECEPTOR_INTERACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ECM_RECEPTOR_INTERACTION.html ECM-receptor interaction 42/94 KEGG 4.81330950032086e-09 8.60884286965784e-08 45 340.727272727273 223 4.37573591895613e-10 31 2.10734972811304 2.20649962802614 1 5.44216151161818 45 450 251 394 1390 31 48 102 698 223 116 85 M8821 REACTOME_AXON_GUIDANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AXON_GUIDANCE.html Genes involved in Axon guidance 124/342 Reactome 1.0392674836861e-07 1.2391876408532e-06 225 389.818181818182 223 9.447886661641e-09 61 1.84077614177078 2.11585894330298 1 3.97445075332009 223 1243 388 140 61 66 215 258 921 693 80 86 M3697 GOUYER_TATI_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GOUYER_TATI_TARGETS_DN.html Genes down-regulated in constitutively invasive HT-29 5M21 cells (colon cancer) vs those expressing functionally inactive TATI [GeneID=6690]. 18317448 9/22 Jessica Robertson 1.19038589986784e-08 1.98510616611413e-07 335 668.545454545455 223 1.19038590624442e-09 6 2.31616304675084 2.60464636683879 1 5.67422843846901 331 190 4318 516 970 223 164 6 59 383 194 87 M5840 SMID_BREAST_CANCER_RELAPSE_IN_LUNG_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_LUNG_UP.html Genes up-regulated in lung relapse of breast cancer. 18451135 24/105 Jessica Robertson 1.25507871235478e-08 2.07087987538539e-07 130 307.545454545455 229 1.14098065410444e-09 106 2.35452045867864 2.36710101449118 1 5.75238698308324 272 156 266 172 1091 106 127 544 293 127 229 88 M7883 CUI_TCF21_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CUI_TCF21_TARGETS_UP.html Genes most strongly up-regulated in kidney glomeruli isolated from TCF21 [GeneID=6943] knockout mice. 16207825 35/87 John Newman 1.80285679264949e-08 2.85701593313567e-07 125 393.909090909091 230 1.63896073402141e-09 85 2.50004312310042 2.5007003797528 1 5.98020176971938 121 723 274 230 1665 173 85 305 195 159 403 89 M3015 HUANG_DASATINIB_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_DASATINIB_RESISTANCE_UP.html Genes whose expression positively correlated with sensitivity of breast cancer cell lines to dasatinib [PubChem=3062316]. 17332353 74/159 Jessica Robertson 3.67886550131881e-08 5.4211206726981e-07 50 429.454545454545 230 3.34442323894294e-09 19 2.02780895270148 2.09082424736798 1 4.64440948519893 49 1010 290 541 1159 43 98 19 1233 230 52 90 M2445 PLASARI_TGFB1_TARGETS_10HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_TARGETS_10HR_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) upon stimulation with TGFB1 [GeneID=7040] for 10 h. 19752192 125/318 Arthur Liberzon 7.01789194080714e-13 2.78693573174765e-11 235 468.727272727273 231 6.37990176437217e-14 90 1.79235089984986 1.88293336499033 1 6.91504965064874 231 1000 112 600 893 120 181 374 1411 144 90 91 M2281 ISSAEVA_MLL2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ISSAEVA_MLL2_TARGETS.html Genes down-regulated in HeLa cells upon knockdown of MLL2 [GeneID=8085] by RNAi. 17178841 58/125 Arthur Liberzon 2.42445179083684e-14 1.18808794306211e-12 430 334.090909090909 232 2.20404708257896e-15 51 2.25249844766973 2.35155265445796 1 9.81855670864019 51 429 90 427 1034 195 226 232 437 76 478 92 M7137 WEINMANN_ADAPTATION_TO_HYPOXIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEINMANN_ADAPTATION_TO_HYPOXIA_DN.html Genes most down-regulated in hypoxia tolerant NCI H460 cells (lung cancer). 15897868 36/74 Arthur Liberzon 1.31225671969716e-09 2.78245927081488e-08 230 407.636363636364 233 1.19296065498172e-10 76 2.47915819221097 2.71146097192433 1 6.84684965458789 226 720 213 279 1502 230 403 76 395 233 207 93 M8544 GAUSSMANN_MLL_AF4_FUSION_TARGETS_F_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_F_UP.html Up-regualted genes from the set F (Fig. 5a): specific signature shared by cells expressing AF4-MLL [GeneID=4299;4297] alone and those expressing both AF4-MLL and MLL-AF4 fusion proteins. 17130830 145/339 Arthur Liberzon 2.43398298194542e-14 1.18808794306211e-12 165 329.363636363636 235 2.21271180176858e-15 57 2.00163880979866 2.19773701642205 1 8.72506890475516 162 57 91 209 235 438 586 237 913 97 598 94 M1950 MEISSNER_BRAIN_HCP_WITH_H3K4ME2_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_HCP_WITH_H3K4ME2_AND_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing bivalent histone H3 dimethylation mark at K4 (H3K4me2) and trimethlation mark at K27 (H3K27me3) in brain. 18600261 26/106 Arthur Liberzon 5.22982980235473e-10 1.20724051496721e-08 195 376.363636363636 237 4.75439073054359e-11 44 2.21726278199367 2.30624350024522 1 6.41746080268173 313 150 195 44 1201 237 194 835 355 93 523 95 M17082 HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_UP.html Genes up-regulated in hematopoietic progenitor cells (HPC) of T lymphocyte and NK (natural killer) lineage. 15331438 66/161 Kevin Vogelsang 8.2651717133889e-07 4.21381153484506e-06 130 376 239 7.51379528957253e-08 65 1.99767088468233 2.10807338980465 1 3.92507454400419 126 1176 433 182 684 65 239 89 459 573 110 96 M2700 SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN.html Genes down-regulated in bone relapse of breast cancer. 18451135 209/649 Jessica Robertson 2.12630714845849e-22 2.0758073536826e-20 245 257.090909090909 241 1.93300649859862e-23 38 2.22852922553194 2.29349689033819 1 16.0333676017518 241 539 47 38 340 139 367 379 592 55 91 97 M3804 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_UP.html Genes up-regulated in normal hematopoietic progenitors by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 148/368 Arthur Liberzon 6.16967370443804e-15 3.35801546936531e-13 230 362.636363636364 242 5.60879427676187e-16 65 2.16542105526118 2.17437825924548 1 9.8733484982568 227 258 81 65 987 242 526 461 777 212 153 98 M15394 BIOCARTA_AMI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AMI_PATHWAY.html Acute Myocardial Infarction 13/34 BioCarta 3.81557744339164e-06 1.1803229834245e-05 245 503.636363636364 243 3.4687127826976e-07 100 2.12491088692196 2.28992183230434 1 3.82763568692708 243 177 434 537 2339 163 100 695 196 216 440 99 M16643 VERRECCHIA_DELAYED_RESPONSE_TO_TGFB1 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_DELAYED_RESPONSE_TO_TGFB1.html ECM related genes up-regulated later than 30 min following addition of TGFB1 [GeneID=7040] in dermal fibroblasts. 11279127 42/98 John Newman 3.42430008142733e-07 2.53773838513687e-06 70 256.818181818182 244 3.11300055856343e-08 7 1.8408893587516 1.92963641668759 1 3.76521658590906 70 317 582 102 411 48 7 239 444 361 244 100 M1124 MCBRYAN_PUBERTAL_TGFB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_TGFB1_TARGETS_UP.html Pubertal genes up-regulated by TGFB1 [GeneID=7040]. 17486082 165/366 Arthur Liberzon 6.21954704883075e-13 2.49100833083939e-11 380 285.454545454545 246 5.65413368075683e-14 45 1.94639074873936 2.12440595811535 1 7.54403396897214 377 49 111 45 303 246 648 746 344 90 181 101 M12138 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_UP.html Genes up-regulated in erythroid lineage cells by RUNX1-RUNX1T1 [GeneID=861;862] fusion . 17898786 131/342 Arthur Liberzon 2.32599921678681e-12 8.51533775770546e-11 205 366 251 2.11454474253569e-13 63 1.78890303717632 1.82874621253506 1 6.58456085559659 205 63 122 271 217 275 320 251 1822 204 276 102 M7169 REACTOME_NCAM1_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NCAM1_INTERACTIONS.html Genes involved in NCAM1 interactions 20/60 Reactome 2.69958718873602e-07 2.24693882174369e-06 45 430.181818181818 252 2.45417047272581e-08 10 2.34742559754977 2.34742559754977 1 4.84660028820997 41 871 354 135 1709 74 10 684 406 196 252 103 M19130 BROWNE_HCMV_INFECTION_16HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_16HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 16 h time point that were not down-regulated at the previous time point, 14 h. 11711622 71/194 John Newman 3.23961765576741e-07 2.45845509149669e-06 235 364.181818181818 252 2.9451073934714e-08 95 1.81658046131774 1.9997497120032 1 3.72465007253254 235 96 464 95 291 192 252 691 1105 347 238 104 M9893 RODWELL_AGING_KIDNEY_NO_BLOOD_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODWELL_AGING_KIDNEY_NO_BLOOD_UP.html Genes whose expression increases with age in normal kidney, excluding those with higher expression in blood. 15562319 151/355 John Newman 3.06697335745496e-17 2.14505032134835e-15 85 304.090909090909 256 2.78815759768632e-18 31 2.08362416642181 2.18128665285794 1 11.1718782071681 165 407 65 31 1025 256 324 82 643 85 262 105 M14134 TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN.html Genes down-regulated in ductal carcinoma vs normal ductal breast cells. 17389037 120/315 Arthur Liberzon 3.43777499791935e-23 3.83557467625001e-21 650 445.090909090909 259 3.1252499981085e-24 41 2.46895691149169 2.84705529228062 1 18.4249800004612 648 264 41 189 205 1199 1278 225 259 53 535 106 M2395 SERVITJA_ISLET_HNF1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SERVITJA_ISLET_HNF1A_TARGETS_UP.html Genes up-regulated in pancreatic islets upon knockout of HNF1A [GeneID=6927]. 19289501 124/327 Arthur Liberzon 1.59235959534896e-20 1.40788623845382e-18 265 328.818181818182 263 1.44759963213542e-21 40 1.94849127463455 2.12662917889081 1 12.7142511640816 60 263 52 315 509 186 261 535 1091 40 305 107 M9387 KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION.html Vascular smooth muscle contraction 43/140 KEGG 6.01747298675929e-08 8.19705767905641e-07 155 310.363636363636 264 5.47043013759101e-09 72 2.7761103125737 2.96006735928922 1 6.17607160973873 153 319 297 126 264 72 205 729 400 738 111 108 M6239 NEWMAN_ERCC6_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NEWMAN_ERCC6_TARGETS_DN.html Genes down-regulated in Cockayne syndrome fibroblasts rescued by expression of ERCC6 [GeneID=2074] off a plasmid vector. 16772382 27/82 Leona Saunders 4.1379022812695e-11 1.22722848671069e-09 210 398.545454545455 266 3.76172934667938e-12 42 2.34941493229482 2.39310250059127 1 7.65260070245094 210 141 152 42 954 423 663 936 266 100 497 109 M8124 SMID_BREAST_CANCER_BASAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_BASAL_UP.html Genes up-regulated in basal subtype of breast cancer samles. 18451135 427/1212 Jessica Robertson 3.01309845477756e-34 8.82461209942978e-32 285 311.545454545455 268 2.73918041343418e-35 15 2.11330077540492 2.16773231066364 1 23.9884600076083 282 223 15 112 268 280 419 521 1117 34 156 110 M15549 CERVERA_SDHB_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/CERVERA_SDHB_TARGETS_1_UP.html Genes turned on in Hep3B cells (hepatocellular carcinoma, HCC) upon knockdown of SDHB [GeneID=6390] by RNAi. 18519664 72/199 Jessica Robertson 8.39735460100801e-12 2.83093551513119e-10 240 309.727272727273 269 7.63395872821825e-13 102 2.15779023406579 2.31544642503141 1 7.53085124316962 236 289 133 386 537 189 319 269 746 201 102 111 M8556 OSADA_ASCL1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OSADA_ASCL1_TARGETS_UP.html Genes up-regulated in A549 cells (lung cancer) upon expression of ASCL1 [GeneID=429] off a viral vector. 18339843 29/87 Jessica Robertson 8.77646900411096e-09 1.50096838515562e-07 155 412.454545454545 269 7.97860821738451e-10 41 2.54140191096357 2.82203841425628 1 6.33881350064823 154 617 260 41 1048 226 514 200 706 502 269 112 M17923 BOQUEST_STEM_CELL_CULTURED_VS_FRESH_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOQUEST_STEM_CELL_CULTURED_VS_FRESH_UP.html Genes up-regulated in cultured stromal stem cells from adipose tissue, compared to the freshly isolated cells. 15635089 297/758 Arthur Liberzon 1.1000065377956e-27 1.66278407616457e-25 170 412.818181818182 271 1.00000594345055e-28 30 1.96435579297557 2.12878609295627 1 17.7920526512724 169 235 30 160 1040 271 575 448 1182 51 380 113 M10605 BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN.html Genes down-regulated in medullary breast cancer (MBC) relative to ductal breast cancer (DBD). 16651414 130/309 Arthur Liberzon 5.33895725149838e-10 1.22638988630007e-08 370 340.727272727273 277 4.85359750254002e-11 108 1.95628144938583 2.24413119254167 1 5.65721080727314 367 413 196 171 384 221 108 227 1075 277 309 114 M14650 NGUYEN_NOTCH1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NGUYEN_NOTCH1_TARGETS_DN.html Genes down-regulated in primary keratinocytes by expression of constantly active NOTCH1 [GeneID=4851]. 16618808 70/163 Kevin Vogelsang 2.72090976542215e-07 2.2526825372382e-06 160 333.363636363636 277 2.47355463812556e-08 99 1.93005256266963 2.0749946931592 1 3.98409097628432 156 99 774 244 231 277 441 112 544 474 315 115 M4001 DAVICIONI_TARGETS_OF_PAX_FOXO1_FUSIONS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_TARGETS_OF_PAX_FOXO1_FUSIONS_DN.html Genes down-regulated in RD cells (embryonal rhabdomyosarcoma, ERMS) by expression of PAX3- or PAX7-FOXO1 [GeneID=5077;5081;2308] fusions off retroviral vectors. 16849537 62/139 Arthur Liberzon 2.42037246704895e-08 3.73087676993137e-07 160 349.818181818182 281 2.20033863061558e-09 158 2.15677261067035 2.3623911245104 1 5.0677158286688 158 295 281 274 457 160 251 785 381 267 539 116 M12112 VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_UP.html Angiogenic markers up-regulated in lymph endothelial cells upon infection with KSHV (Kaposi's sarcoma herpes virus). 17483315 110/272 Jessica Robertson 5.78689238619094e-19 4.84238887887335e-17 60 577.272727272727 282 5.26081126017357e-20 55 2.10120220887946 2.15255185307378 1 12.5306208445378 57 926 55 532 1452 211 183 601 1965 86 282 117 M990 CORRE_MULTIPLE_MYELOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/CORRE_MULTIPLE_MYELOMA_DN.html Genes down-regulated in multiple myeloma (MM) bone marrow mesenchymal stem cells. 17344918 44/104 Leona Saunders 1.57761956438972e-09 3.21422838205662e-08 25 413.181818181818 285 1.43419960501911e-10 24 1.94973561412006 2.00911993871918 1 5.34006151991698 24 446 221 328 1117 116 143 425 1311 129 285 118 M14043 PETRETTO_CARDIAC_HYPERTROPHY http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_CARDIAC_HYPERTROPHY.html Genes that correlated most highly with left ventricular mass (LVM) index. 18443592 36/74 Jessica Robertson 9.53113776707594e-09 1.61822143393181e-07 45 488.909090909091 285 8.66467073488003e-10 17 2.56597791356089 2.56597791356089 1 6.36947251547828 42 944 262 407 2404 17 101 285 476 316 124 119 M1797 ZHENG_GLIOBLASTOMA_PLASTICITY_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_GLIOBLASTOMA_PLASTICITY_DN.html The glioblastoma multiforme (GBM) plasticity signature: genes down-regulated in neural stem cells (NSC) with double knockout of TP53 and PTEN [GeneID=7157;5728] vs those with knockout of TP53 alone. 18948956 54/115 Jessica Robertson 2.91652429276976e-08 4.42292324787026e-07 285 321.636363636364 285 2.65138575584902e-09 96 1.97975064099582 2.04556079422717 1 4.59829484475498 96 586 285 335 370 110 392 282 728 139 215 120 M17143 SASSON_RESPONSE_TO_GONADOTROPHINS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SASSON_RESPONSE_TO_GONADOTROPHINS_DN.html Genes down-regulated in primary granulosa cells after stimulation with LH or FSH gonadotrophic hormones for 24 h. 15026540 94/168 Arthur Liberzon 2.17618417317943e-07 2.01533577777052e-06 225 596.363636363636 285 1.97834944403826e-08 86 1.85318249346865 2.08370819543549 1 3.85816618478394 222 285 723 667 175 86 97 569 1764 1766 206 121 M198 PID_SYNDECAN_1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_1_PATHWAY.html Syndecan-1-mediated signaling events 18832364 30/61 Pathway Interaction Database 8.15769932899869e-06 2.13320195623258e-05 90 569.636363636364 286 7.41611779843014e-07 86 2.52290712346578 2.59601870566978 1 4.30752104518858 86 1639 477 347 2110 153 242 284 286 406 236 122 M17787 REACTOME_GLUCURONIDATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCURONIDATION.html Genes involved in Glucuronidation 3/23 Reactome 8.57780226535512e-08 1.08243085183469e-06 290 846.363636363636 286 8.57780259645924e-09 1 3.55389468427202 3.55389468427202 1 7.74957565884798 286 907 4085 27 1815 260 410 22 1 1392 105 123 M737 LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_DN.html Genes down-regulated between two breast carcinoma subtypes: metaplastic (MCB) and ductal (DCB). 17603561 80/223 Arthur Liberzon 8.13245132053961e-11 2.24168628753227e-09 85 387 287 7.3931375644002e-12 81 1.83410598115265 -1.87203077433501 -1 5.79870376973197 287 81 163 472 557 81 861 818 481 209 247 124 M6813 IVANOVA_HEMATOPOIESIS_STEM_CELL http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_STEM_CELL.html Genes in the expression cluster 'HSC Shared': up-regulated in hematopoietic stem cells (HSC) from adult bone marrow and fetal liver. 12228721 165/530 John Newman 3.73544093712455e-07 2.6805936035782e-06 375 336 287 3.39585597397778e-08 52 1.59843281896444 1.78492640505889 1 3.25541786740564 375 52 441 59 331 113 469 105 1222 287 242 125 M1406 JECHLINGER_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_UP http://www.broadinstitute.org/gsea/msigdb/cards/JECHLINGER_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_UP.html Genes up-regulated during epithelial to mesenchymal transition (EMT) induced by TGFB1 [GeneID=7040] in the EpH4 cells (mammary epithelium cell line transformed by HRAS [GeneID=3265]). 14562044 61/132 Arthur Liberzon 7.00508582178139e-11 1.96561869226752e-09 60 515.909090909091 288 6.36825983818588e-12 58 2.01539553218746 2.19289666555534 1 6.41391474002547 58 430 160 911 1747 187 288 106 1224 253 311 126 M14555 ZHU_CMV_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_ALL_DN.html Down-regulated at any timepoint following infection of primary human foreskin fibroblasts with CMV 9826724 93/248 John Newman 2.98013499592568e-11 9.06812505903101e-10 30 463.181818181818 288 2.70921363269641e-12 28 2.2675493088313 2.35392141317166 1 7.49486245585011 28 1253 148 336 1677 101 178 302 508 276 288 127 M8417 CROMER_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROMER_METASTASIS_DN.html Metastatic propensity markers of head and neck squamous cell carcinoma (HNSCC): down-regulated in metastatic vs non-metastatic tumors. 14676830 68/149 Kevin Vogelsang 1.07377899746896e-07 1.27063848033827e-06 290 364.272727272727 289 9.76162772616469e-09 24 2.06381510747127 2.3066046754648 1 4.44780656756621 322 831 705 289 288 172 231 24 311 632 202 128 M1188 HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_UP http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer, mutated TP53 [GeneID=7157]) undergoing aberrant mitosis and necrosis after treatment with 2 nM docetaxel [PubChem=148124]. 17099726 67/163 Arthur Liberzon 1.85532056674605e-06 7.00566653970344e-06 225 493.727272727273 290 1.68665648308255e-07 135 2.07164717245497 2.09670793813006 1 3.90324528763102 224 425 501 345 2090 159 258 135 808 290 196 129 M18328 POMEROY_MEDULLOBLASTOMA_PROGNOSIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/POMEROY_MEDULLOBLASTOMA_PROGNOSIS_UP.html Top marker genes in medulloblastoma associated with good response to treatment (good outcome). 11807556 36/80 Jean Junior 1.37056332846297e-07 1.50319105270817e-06 295 281.272727272727 292 1.24596673986072e-08 22 2.06419561103254 2.1670947463725 1 4.39355262976342 292 325 632 431 85 89 121 48 413 636 22 130 M4065 ZHU_CMV_24_HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_24_HR_DN.html Down-regulated at 24 h following infection of primary human foreskin fibroblasts with CMV 9826724 64/180 John Newman 1.56864762617952e-10 4.08371265348735e-09 25 538.545454545455 292 1.42604329662852e-11 25 2.31066521495381 2.3807082680031 1 7.08538763284852 25 1175 173 491 2185 100 281 406 554 242 292 131 M2225 KANG_AR_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_AR_TARGETS_DN.html Genes down-regulated in osteoblasts from wild type male mice compared to those with AR [GeneID=367] knockout. 18838539 21/38 Arthur Liberzon 1.8624124915404e-06 7.02113027784256e-06 110 348.818181818182 297 1.69310369833606e-07 32 1.95890780039088 1.94098223288019 1 3.69014439973999 110 348 692 243 995 39 32 297 483 437 161 132 M4336 OSADA_ASCL1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OSADA_ASCL1_TARGETS_DN.html Genes down-regulated in A549 cells (lung cancer) upon expression of ASCL1 [GeneID=429] off a viral vector. 18339843 20/45 Jessica Robertson 2.57229784925957e-07 2.19144534472488e-06 300 294.090909090909 298 2.33845286365404e-08 29 2.81536784706785 2.98039257824522 1 5.82391143344815 298 344 402 113 302 291 785 47 29 542 82 133 M1991 MASRI_RESISTANCE_TO_TAMOXIFEN_AND_AROMATASE_INHIBITORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MASRI_RESISTANCE_TO_TAMOXIFEN_AND_AROMATASE_INHIBITORS_DN.html Genes down-regulated in derivatives of MCF-7aro cells (breast cancer) that developed resistance to tamoxifen [PubChem=5376] or inhibitors of aromatase (CYP19A1) [GeneID=1588]. 18559539 20/34 Leona Saunders 6.30923572322518e-08 8.54482040434486e-07 175 381.090909090909 298 5.7356690037851e-09 175 2.9324592848984 3.22474667755763 1 6.50456224633482 175 490 298 389 948 208 227 580 212 391 274 134 M12641 JIANG_TIP30_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_TIP30_TARGETS_UP.html Up-regulated genes in HepG2 cells (liver cancer) overexpressing an oncogenic variant of tumor suppressor TIP30 [GeneID=10553] compared to its wild type form. 17440068 35/76 Jessica Robertson 8.27914491273576e-07 4.21381153484506e-06 300 489 300 7.52649820762245e-08 190 1.92252944694344 1.90439788834502 1 3.77743473663386 242 855 703 296 635 285 300 190 926 725 222 135 M8448 BENPORATH_PRC2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_PRC2_TARGETS.html Set 'PRC2 targets': Polycomb Repression Complex 2 (PRC) targets; identified by ChIP on chip on human embryonic stem cells as genes that: posess the trimethylated H3K27 mark in their promoters and are bound by SUZ12 [GeneID=23512] and EED [GeneID=8726] Polycomb proteins. 18443585 240/952 Jessica Robertson 2.02485192675383e-35 8.6258692079713e-33 20 319.181818181818 301 1.84077447886712e-36 10 2.16113908829592 2.24582981654884 1 25.3292504928287 72 404 10 17 470 301 374 294 1199 20 350 136 M15422 BIOCARTA_VITCB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VITCB_PATHWAY.html Vitamin C in the Brain 11/24 BioCarta 2.32997189177027e-06 8.17654897834358e-06 65 390.363636363636 302 2.11815850854201e-07 23 2.40944193921859 2.40944193921859 1 4.48057920522939 65 372 422 302 1760 53 23 509 247 356 185 137 M13220 OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_DN http://www.broadinstitute.org/gsea/msigdb/cards/OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_DN.html Genes down-regulated in pirmary cultures of epithelial ovarian cancer (EOC): invasive (TOV) vs low malignant potential (LMP) tumors. 15940270 35/134 Leona Saunders 7.57409642460859e-08 9.77746992994927e-07 320 305.818181818182 303 6.88554244124309e-09 127 2.2889779539767 2.26124425844093 1 5.0282743507064 318 323 303 127 526 203 417 474 215 285 173 138 M16441 REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS.html Genes involved in Integrin cell surface interactions 51/114 Reactome 7.40187775046579e-11 2.06459518682635e-09 165 423.181818181818 304 6.72897977337712e-12 79 2.05639062606915 2.18337969098213 1 6.52834269622029 79 304 161 278 1253 165 318 398 1103 203 393 139 M178 CROMER_TUMORIGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROMER_TUMORIGENESIS_UP.html Tumorigenesis markers of head and neck squamous cell carcinoma (HNSCC): up-regulated in the 'early' tumors vs normal samples. 14676830 51/110 Arthur Liberzon 8.87913299463689e-10 1.99079508195543e-08 65 496.818181818182 305 8.07193908929135e-11 61 2.08911498224461 2.19604422044118 1 5.88067555919432 61 305 201 489 1792 231 88 647 990 264 397 140 M14228 RICKMAN_HEAD_AND_NECK_CANCER_A http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_A.html Cluster a: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 46/228 Jessica Robertson 4.4876477072907e-10 1.04491258071838e-08 375 321.090909090909 308 4.07967973473283e-11 114 2.35627195132232 2.4132600699059 1 6.87381158651197 308 443 193 114 477 372 741 375 129 116 264 141 M14098 BROWNE_HCMV_INFECTION_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_24HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 24 h time point that were not down-regulated at the previous time point, 20 h. 11711622 103/276 John Newman 6.8044020001106e-07 3.75356980695344e-06 215 447.727272727273 308 6.18582191331981e-08 165 2.06020386064166 2.27797590224746 1 4.08576757713767 213 1007 367 299 651 232 665 226 792 308 165 142 M13308 MURAKAMI_UV_RESPONSE_1HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/MURAKAMI_UV_RESPONSE_1HR_UP.html Genes up-regulated in primary keratinocytes at 1 h after UVB irradiation. 11532376 17/39 Arthur Liberzon 2.84429780667213e-06 9.41934948555874e-06 275 546.272727272727 308 2.58572862178651e-07 98 2.71142383574054 2.71142383574054 1 4.9812385146935 273 1052 829 595 1200 299 223 308 98 969 163 143 M5889 NABA_MATRISOME http://www.broadinstitute.org/gsea/msigdb/cards/NABA_MATRISOME.html Ensemble of genes encoding extracellular matrix and extracellular matrix-associated proteins 22159717 315/1178 Alexandra Naba 1.21342941885055e-63 2.84306512836685e-60 5 351.090909090909 309 1.1031176535005e-64 2 2.16221192985842 2.27242508476871 1 47.0621385219211 87 226 2 105 309 498 668 504 800 3 660 144 M18 PID_INTEGRIN1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN1_PATHWAY.html Beta1 integrin cell surface interactions 18832364 44/86 Pathway Interaction Database 4.92177001921866e-16 3.07512190800782e-14 10 401.272727272727 310 4.47433638110787e-17 8 2.29809001616975 2.3307920427081 1 11.3503785945694 8 310 72 318 1937 145 106 326 713 103 376 145 M4995 LINDGREN_BLADDER_CANCER_CLUSTER_2B http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_2B.html Genes specifically up-regulated in Cluster IIb of urothelial cell carcinom (UCC) tumors. 16532037 258/674 Arthur Liberzon 2.75787412573966e-30 5.38474923050669e-28 1410 463.272727272727 310 2.50715829612699e-31 23 1.92035374875104 2.01890532539817 1 19.1411075958859 40 402 23 424 1408 148 310 632 1407 47 255 146 M1295 GALIE_TUMOR_STEMNESS_GENES http://www.broadinstitute.org/gsea/msigdb/cards/GALIE_TUMOR_STEMNESS_GENES.html Stemness-related genes changed in A17 carcinomas (MTC, mesenchymal tumor cells) compared with the mesenchymal stem cells (MSC). 17998939 7/11 Jessica Robertson 4.93572777488741e-06 1.43387104434633e-05 1470 907.181818181818 310 4.93573873755557e-07 189 2.92906820517099 2.92906820517099 1 5.18569696000127 310 1470 4304 732 1467 198 191 214 231 673 189 147 M1550 SIMBULAN_PARP1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SIMBULAN_PARP1_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblasts) from PARP1 [GeneID=142] knockout mice. 11016956 23/53 John Newman 1.21267224030003e-05 2.95967818648226e-05 80 442.818181818182 310 1.10243538616247e-06 77 2.21223192116891 2.2430261208567 1 3.66208803493092 77 161 526 581 1828 88 96 457 445 302 310 148 M8728 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM.html Hypertrophic cardiomyopathy (HCM) 48/137 KEGG 5.65377738757757e-10 1.2860971280674e-08 165 371 311 5.13979762639139e-11 71 2.50824658994012 2.82116098851381 1 7.23446561510316 164 311 198 71 1090 168 246 513 323 644 353 149 M5825 VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_DN.html Angiogenic markers down-regulated in lymph endothelial cells upon infection with KSHV (Kaposi's sarcoma herpes virus). 17483315 81/220 Jessica Robertson 3.4740212054311e-15 1.93800754388692e-13 270 492.545454545455 311 3.15820109584645e-16 79 2.14752243159487 2.225154750024 1 9.97913420059663 270 825 79 220 958 311 503 748 1183 95 226 150 M15975 LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_UP.html Genes up-regulated between two breast carcinoma subtypes: metaplastic (MCB) and ductal (DCB). 17603561 46/130 Arthur Liberzon 1.24082123695543e-07 1.40786642042934e-06 60 289.181818181818 312 1.1280193699445e-08 8 1.92939033589746 1.99643291896537 1 4.12669144663121 56 444 395 480 647 16 47 25 751 312 8 151 M1954 MIKKELSEN_MCV6_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MCV6_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state). 18509334 159/697 Jessica Robertson 1.25374973958415e-34 4.19647948549382e-32 300 467.727272727273 314 1.13977249053105e-35 13 2.36136708195648 2.41404983532655 1 27.0829372425459 300 684 13 254 314 295 446 1197 1000 27 615 152 M10387 NIELSEN_SYNOVIAL_SARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_SYNOVIAL_SARCOMA_UP.html Top 20 positive significant genes associated with synovial sarcoma tumors. 11965276 23/100 Arthur Liberzon 7.17670046154689e-06 1.92870586612568e-05 140 462 315 6.52429443002805e-07 139 2.1506307631047 2.21434890760576 1 3.70631476216262 139 867 631 236 1564 222 177 315 159 389 383 153 M3837 WEST_ADRENOCORTICAL_TUMOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_TUMOR_DN.html Down-regulated genes in pediatric adrenocortical tumors (ACT) compared to the normal tissue. 17234769 364/905 Jessica Robertson 8.72626217024948e-18 6.48925908320974e-16 270 430.818181818182 317 7.93296560931769e-19 19 1.78488751440425 1.90225053749554 1 9.908892375226 266 19 60 317 1003 289 496 433 1330 61 465 154 M19068 CERVERA_SDHB_TARGETS_2 http://www.broadinstitute.org/gsea/msigdb/cards/CERVERA_SDHB_TARGETS_2.html Genes present but differentially expressed between Hep3B cells (hepatocellular carcinoma, HCC) with RNAi knockdown of SDHB [GeneID=6390] and control cells. 18519664 71/210 Jessica Robertson 1.07195490000077e-11 3.52103032381441e-10 320 324.545454545455 320 9.74504454550907e-13 113 1.98926865727195 2.21375709459948 1 6.87380994245568 443 290 136 320 319 332 597 113 572 113 335 155 M11616 ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP.html Genes whose promoters display higher levels of histone H3 trimethylation mark at K27 (H3K27me3) in hepatocellular carcinoma (HCC) compared to normal liver. 18413731 164/615 Jessica Robertson 2.57534144069224e-07 2.19144534472488e-06 325 337.272727272727 321 2.34121976560388e-08 18 1.87908620979868 2.05267381118589 1 3.88710543504878 225 406 345 324 524 55 280 235 977 321 18 156 M9167 ROZANOV_MMP14_TARGETS_SUBSET http://www.broadinstitute.org/gsea/msigdb/cards/ROZANOV_MMP14_TARGETS_SUBSET.html Genes linked to the ECM maintenance and angiogenesis that were changed in HT1080 cells (fibrosarcoma) over-expressing MMP14 [GeneID=4323] compared to those with knockdown of the gene by RNAi. 18519667 34/72 Jessica Robertson 1.51065042087162e-13 6.67821497377773e-12 30 471.818181818182 323 1.37331856442884e-14 26 2.47780631937523 2.45460512348702 1 10.1215572625706 26 605 101 387 1942 154 142 628 687 195 323 157 M19248 REACTOME_CELL_JUNCTION_ORGANIZATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_JUNCTION_ORGANIZATION.html Genes involved in Cell junction organization 42/101 Reactome 2.46508665408926e-09 4.7536609304783e-08 1405 670.181818181818 324 2.24098786986489e-10 23 2.26888298816286 2.18089012021148 1 6.07321576885985 1404 123 234 23 149 727 810 2286 324 224 1068 158 M7337 ROY_WOUND_BLOOD_VESSEL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROY_WOUND_BLOOD_VESSEL_UP.html Genes up-regulated in blood vessel cells from wound site. 17728400 42/92 Leona Saunders 1.1872641967336e-08 1.98510616611413e-07 20 415.818181818182 326 1.07933109376441e-09 18 1.89475517682895 1.89475517682895 1 4.64184666214415 18 449 326 568 900 34 22 350 1549 297 61 159 M9898 BENPORATH_SUZ12_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_SUZ12_TARGETS.html Set 'Suz12 targets': genes identified by ChIP on chip as targets of the Polycomb protein SUZ12 [GeneID=23512] in human embryonic stem cells. 18443585 411/1473 Jessica Robertson 4.43493286151784e-45 3.46368256484543e-42 10 371.454545454545 326 4.03175714683442e-46 6 1.9866389460609 2.08420019977081 1 30.1073361866332 149 398 6 9 579 263 505 486 1359 6 326 160 M2256 MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_DN.html Genes commonly down-regulated in UET-13 cells (mesenchymal progenitor) by expression of EWSR1 [GeneID=2130] fusions with ETS transcription factors FLI1 and ERG [GeneID=2313 ,2078]. 18212050 162/415 Arthur Liberzon 9.10209362715006e-14 4.14101075114808e-12 210 433.636363636364 326 8.27463057013674e-15 98 2.05158197645136 2.24035863888346 1 8.53612573568273 208 547 98 326 783 294 529 697 922 147 219 161 M4913 IZADPANAH_STEM_CELL_ADIPOSE_VS_BONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/IZADPANAH_STEM_CELL_ADIPOSE_VS_BONE_DN.html Genes down-regulated in adipose tissue mesenchymal stem cells (ASC) vs bone marrow mesenchymal stem cells (rBMSC) 18519682 105/245 Leona Saunders 7.66320540609075e-11 2.12483908478942e-09 140 540.181818181818 327 6.9665503694161e-12 137 1.69936419669824 1.78809540953523 1 5.38714585464949 137 559 162 917 1109 156 327 205 1847 189 334 162 M17275 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP.html Genes up-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 8 days after transduction. 16818636 91/298 Arthur Liberzon 1.91200846767954e-10 4.86938678236213e-09 380 292.090909090909 328 1.73818951622337e-11 27 1.865515208274 2.10018443557714 1 5.66827675793147 379 77 177 116 328 462 398 27 602 171 476 163 M1616 BURTON_ADIPOGENESIS_7 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_7.html Down-regulated at 48-96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 32/94 John Newman 7.78654648594794e-08 9.96933246807433e-07 330 515.545454545455 330 7.07867887412752e-09 36 1.49604189086088 1.43480511058661 1 3.28179007197112 232 330 716 728 36 200 200 1006 1416 480 327 164 M2451 PLASARI_TGFB1_SIGNALING_VIA_NFIC_1HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_SIGNALING_VIA_NFIC_1HR_DN.html Genes down-regulated after 1 h of TGFB1 [GeneID=7040] stimulation in MEF cells (embryonic fibroblast) with NFIC [GeneID=4782] knockout vs wild type MEFs. 19752192 71/189 Arthur Liberzon 1.27529768927334e-10 3.41488284110564e-09 135 458.636363636364 330 1.15936153577024e-11 132 2.16635980178869 2.25572402245769 1 6.70440316037796 132 423 168 330 1548 207 297 689 647 236 368 165 M1542 YAMAZAKI_TCEB3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAMAZAKI_TCEB3_TARGETS_UP.html Genes up-regulated in embryonic stem cells from TCEB3 [GeneID=6924] knockout mice. 12604609 137/290 John Newman 1.63310547957791e-10 4.22802888248734e-09 205 527.090909090909 331 1.48464134518104e-11 119 2.00096673522466 2.1658066528996 1 6.12470142042221 202 922 174 525 1513 123 331 119 1349 395 145 166 M1522 ONGUSAHA_TP53_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ONGUSAHA_TP53_TARGETS.html Genes up-regulated in MEF cells (embryonic fibroblast) lacking TP53 and BRCA1 [GeneID=7157;672] by expression of TP53; most genes are further up-regulated by simultaneous expression of BRCA1. 12802282 28/47 John Newman 3.81450083796093e-07 2.69732965324932e-06 335 366.545454545455 333 3.46772863576697e-08 73 1.95370826872371 1.92365702000522 1 3.97705253399045 333 149 673 808 341 248 287 73 346 596 178 167 M14383 SMID_BREAST_CANCER_RELAPSE_IN_BRAIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_BRAIN_UP.html Genes up-regulated in brain relapse of breast cancer. 18451135 23/112 Jessica Robertson 2.45026205403251e-07 2.14593063349835e-06 530 336.818181818182 333 2.22751120630167e-08 168 2.55877095456351 2.68131577592113 1 5.30163653936978 529 480 333 481 290 338 278 382 221 205 168 168 M18483 NAKAMURA_METASTASIS_MODEL_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_METASTASIS_MODEL_UP.html Top genes up-regulated in orthotopic tumors from highly metastatic pancreatic cancer cells. 17210693 34/65 Jessica Robertson 6.86614763965302e-08 9.1146651103156e-07 350 412.272727272727 333 6.24195259449442e-09 25 1.83535766239501 1.95892500854344 1 4.05224356448075 346 333 847 213 25 437 202 115 648 1250 119 169 M18400 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_16 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_16.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 16. 12554760 70/149 Arthur Liberzon 4.04706812564407e-10 9.62668083084675e-09 20 330.909090909091 333 3.67915284217141e-11 20 2.32240799993497 2.35860584012253 1 6.80524610092675 20 422 190 340 728 169 295 434 333 226 483 170 M9702 SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_2 http://www.broadinstitute.org/gsea/msigdb/cards/SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_2.html 50 most interesting genes up-regulated in the pancreatic cancer cell lines (AsPC1, Hs766T, MiaPaCa2, Panc1) but not in the non-neoplastic cells (HPDE) by decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 12839967 23/61 John Newman 2.96715605610824e-07 2.33632760673967e-06 335 392.090909090909 335 2.69741496026438e-08 33 2.30652133416106 2.45433506332402 1 4.74786337134443 380 623 343 33 262 335 335 1218 184 301 299 171 M2310 DANG_REGULATED_BY_MYC_DN http://www.broadinstitute.org/gsea/msigdb/cards/DANG_REGULATED_BY_MYC_DN.html Genes down-regulated by MYC [GeneID=4609], according to the MYC Target Gene Database. 14519204 188/435 Chi Dang 9.5512831195113e-07 4.60984738132019e-06 230 512.636363636364 336 8.68298842381459e-08 228 1.7558898679882 1.89916386547377 1 3.42497854381232 228 253 374 239 908 322 566 415 1704 336 294 172 M2108 VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_DN.html Down-regulated genes distinguishing between two subtypes of gastric cancer: advanced (AGC) and early (EGC). 17297478 70/210 Arthur Liberzon 4.33500457349366e-07 2.84557418794994e-06 100 382.272727272727 337 3.94091402517068e-08 95 1.6519858824049 -1.61432923794543 -1 3.34882259728511 97 95 504 476 399 166 180 229 1237 337 485 173 M8910 LY_AGING_OLD_UP http://www.broadinstitute.org/gsea/msigdb/cards/LY_AGING_OLD_UP.html Genes up-regulated in fibroblasts from old individuals, compared to those from young donors. 10741968 4/11 Arthur Liberzon 1.39879344366285e-07 1.52231708717588e-06 340 800.272727272727 337 1.3987935317109e-08 29 2.70236796347415 2.70236796347415 1 5.74645147563691 337 391 4603 438 1624 151 29 37 34 984 175 174 M11615 CHANDRAN_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANDRAN_METASTASIS_DN.html Genes down-regulated in metastatic tumors from the whole panel of patients with prostate cancer. 17430594 187/480 Arthur Liberzon 6.66106136268677e-11 1.89174142700304e-09 450 320.454545454545 338 6.0555103298986e-12 24 2.03728434033157 2.3476766072393 1 6.49596463353189 449 540 158 24 113 420 702 242 338 164 375 175 M16101 BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN.html Genes down-regulated in NIH3T3 cells (fibroblasts) transfrormed by expression of constitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector; their expression did NOT reverted completely after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins. 17213802 34/71 Leona Saunders 1.49197569919057e-06 6.0900680543615e-06 35 484.636363636364 339 1.35634246455077e-07 33 2.22023773863692 2.23816953105863 1 4.23257350789769 151 1358 531 468 1257 33 33 301 785 339 75 176 M11948 WEINMANN_ADAPTATION_TO_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEINMANN_ADAPTATION_TO_HYPOXIA_UP.html Genes most up-regulated in hypoxia tolerant NCI H460 cells (lung cancer). 15897868 35/64 Arthur Liberzon 2.63577701438092e-07 2.21827056578335e-06 240 471.727272727273 339 2.39616120924388e-08 57 2.2788694945629 2.68358864604634 1 4.70970162957758 240 724 339 290 1449 266 690 57 587 359 188 177 M16338 NIELSEN_LEIOMYOSARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LEIOMYOSARCOMA_UP.html Top 20 positive significant genes associated with CNN1 [GeneID=1264] negative leiomyosarcoma tumors. 11965276 21/41 John Newman 2.90187994100708e-07 2.31211682689763e-06 240 406.545454545455 341 2.63807302161423e-08 117 2.23352030087978 2.28017481576791 1 4.60128766945134 117 346 341 237 1116 238 158 589 519 329 482 178 M10773 LI_WILMS_TUMOR http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR.html 'Wilm's tumor signature': genes highly expressed in Wilm's tumor samples compared to normal fetal kidney and a heterologous tumor, Burkit lymphoma. 12057921 18/109 Arthur Liberzon 3.31871102269179e-09 6.14682998115958e-08 55 457.454545454545 341 3.01701002518008e-10 54 2.35702686687424 2.35786538844254 1 6.21298471929988 54 351 243 341 1876 261 271 604 463 109 459 179 M53 PID_INTEGRIN3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN3_PATHWAY.html Beta3 integrin cell surface interactions 18832364 34/73 Pathway Interaction Database 3.19736211419378e-09 5.99313554684482e-08 95 499.818181818182 342 2.90669283530968e-10 93 2.14921599085316 2.24330660616778 1 5.67384670516714 93 462 240 342 1826 171 197 367 1072 194 534 180 M2948 SESTO_RESPONSE_TO_UV_C8 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C8.html Cluster 8: genes changed in primary keratinocytes by UVB irradiation. 11867738 70/168 John Newman 6.05157302432584e-06 1.68431282435188e-05 140 476.545454545455 342 5.50144515503882e-07 99 1.84494086118216 2.0584808050706 1 3.21918291810041 138 932 578 247 1503 99 111 342 516 475 301 181 M2452 PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_UP.html Genes up-regulated after 10 h of TGFB1 [GeneID=7040] stimulation in MEF cells (embryonic fibroblast) with NFIC [GeneID=4782] knockout vs wild type MEFs. 19752192 41/119 Arthur Liberzon 3.24905145318797e-07 2.45845509149669e-06 95 546.818181818182 342 2.95368357547408e-08 71 2.35193995234373 2.43238958486702 1 4.82233157384981 92 847 342 701 2199 71 157 386 708 271 241 182 M18438 LEE_LIVER_CANCER_E2F1_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_E2F1_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) induced by overexpression of E2F1 [GeneID=1869]. 15565109 52/147 Yujin Hoshida 1.71681152012952e-09 3.45278059370255e-08 845 672 344 1.56073774679024e-10 217 2.45920859039419 2.75332638235086 1 6.70748990051737 844 303 224 217 1529 909 1765 240 299 344 718 183 M5485 REACTOME_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MUSCLE_CONTRACTION.html Genes involved in Muscle contraction 36/77 Reactome 2.62111849140668e-08 4.00083428362596e-07 85 406.454545454545 345 2.38283502057739e-09 81 2.975166286065 3.26423174570899 1 6.95768095099798 81 606 283 396 345 216 212 844 210 771 507 184 M15412 OSAWA_TNF_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/OSAWA_TNF_TARGETS.html Genes up-regulated in Hc cells (normal hepatocyte) by TNF [GeneID=7124]. 12682234 13/29 Yujin Hoshida 3.4978125492812e-07 2.56908301033412e-06 365 434 346 3.17983009582156e-08 141 2.57884010389592 2.56407866012059 1 5.26954005713842 176 364 346 286 1500 365 342 587 141 217 450 185 M17807 KEGG_BASAL_CELL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASAL_CELL_CARCINOMA.html Basal cell carcinoma 26/60 KEGG 1.25812891363562e-06 5.5461825863561e-06 350 392.545454545455 349 1.14375421193719e-07 51 2.62029367719968 2.70053657025025 1 5.03413732310954 433 339 392 319 865 348 51 570 143 509 349 186 M4594 GENTILE_UV_LOW_DOSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_LOW_DOSE_DN.html Selected genes down-regulated in WS1 (fibroblast) in response to irradiation with low dose UV-C. 12907719 47/123 John Newman 2.25362973794935e-06 7.99432925967499e-06 355 772.909090909091 352 2.0487564059268e-07 145 2.35125027400748 2.67025450007836 1 4.380778701662 352 2272 916 1285 1572 268 221 145 199 1029 243 187 M5883 NABA_SECRETED_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_SECRETED_FACTORS.html Genes encoding secreted soluble factors 22159717 89/379 Alexandra Naba 1.83769562140647e-21 1.68851797684524e-19 485 312.818181818182 353 1.67063238309679e-22 12 2.19775581908049 2.37244816387431 1 15.0806711775983 483 76 50 12 359 353 618 488 605 57 340 188 M1778 ZHANG_GATA6_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_GATA6_TARGETS_DN.html Genes down-regulated after cre-lox knockout of GATA6 [GeneID=2627] in airway epithelium. 18536717 57/129 Jessica Robertson 1.72920977197926e-09 3.46285341516872e-08 355 486.909090909091 354 1.57200888485311e-10 106 1.82695507352809 1.82862900042375 1 4.98217397365516 354 106 225 270 165 503 812 1109 1142 132 538 189 M9325 MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_DN.html Down-regulated 'cooperation response genes': responded synergystically to the combination of mutant TP53 and HRAS [GeneID=7157;3265] in YAMC cells (colon). 18500333 52/122 Jessica Robertson 2.02323055109828e-09 3.95035765101938e-08 235 448.454545454545 354 1.83930050268994e-10 177 2.17837831241102 2.41766705346892 1 5.89497046349209 450 708 231 259 555 659 1053 354 255 177 232 190 M9450 REACTOME_PLATELET_ADHESION_TO_EXPOSED_COLLAGEN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_ADHESION_TO_EXPOSED_COLLAGEN.html Genes involved in Platelet Adhesion to exposed collagen 15/34 Reactome 6.55985445472128e-06 1.79030157104391e-05 90 431.727272727273 355 5.96352183151112e-07 77 2.42163578725665 2.42163578725665 1 4.2019807708898 88 503 517 355 1532 77 122 421 279 620 235 191 M9143 FRIDMAN_SENESCENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FRIDMAN_SENESCENCE_UP.html Genes up-regulated in senescent cells. 18711403 68/146 Jessica Robertson 5.31230540028777e-08 7.3867843043764e-07 455 531.454545454545 356 4.82936866233015e-09 83 2.26601911848893 2.54823284806608 1 5.07870176369657 451 701 296 83 829 919 1536 101 325 249 356 192 M6967 HU_ANGIOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HU_ANGIOGENESIS_UP.html Up-regulated genes that separate angiogenic from non-angiogenic non-small cell lung carcinoma (NSCLC) samples. 15592519 21/48 Leona Saunders 1.31144109275911e-07 1.45971804291429e-06 255 443.545454545455 358 1.19221924630488e-08 83 2.05165640818785 2.30000978295952 1 4.37642155111 253 349 815 99 83 358 449 1154 225 592 502 193 M610 REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION.html Genes involved in Extracellular matrix organization 40/134 Reactome 2.51941992683738e-10 6.24054433654536e-09 80 336.818181818182 359 2.29038175193263e-11 61 2.36409001424096 2.51871522358473 1 7.09006258386436 78 452 182 61 809 376 426 359 277 120 565 194 M17004 LU_TUMOR_ENDOTHELIAL_MARKERS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LU_TUMOR_ENDOTHELIAL_MARKERS_UP.html Genes specifically up-regulated in tumor endothelium. 17308118 20/48 Jessica Robertson 1.84990134629736e-06 6.99647918381715e-06 120 601.727272727273 360 1.681729910741e-07 21 2.31587918074693 2.31587918074693 1 4.36389172347482 120 1550 566 360 2516 62 21 182 613 543 86 195 M15057 HENDRICKS_SMARCA4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HENDRICKS_SMARCA4_TARGETS_UP.html Genes up-regulated in ALAB cells (breast cancer) upon reintroduction of SMARCA4 [GeneID=6597] expressed off adenoviral vector. 14673169 54/109 John Newman 4.02468892985765e-07 2.7734841654872e-06 280 373.545454545455 362 3.65880878739642e-08 84 2.23339495066653 2.21583528552152 1 4.53652354628036 279 840 507 84 362 152 289 469 541 385 201 196 M10372 CHIBA_RESPONSE_TO_TSA_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIBA_RESPONSE_TO_TSA_UP.html Cancer related genes up-regulated in any of four hepatoma cell lines following 24 h treatment with TSA [PubChem=5562]. 15452378 52/110 John Newman 5.82642502181472e-09 1.02257032405332e-07 130 620.454545454545 363 5.29675003385935e-10 127 2.47177583358694 2.49969993251668 1 6.3157447589825 127 1587 255 579 2070 363 248 215 692 283 406 197 M274 PID_LYMPH_ANGIOGENESIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LYMPH_ANGIOGENESIS_PATHWAY.html VEGFR3 signaling in lymphatic endothelium 18832364 31/57 Pathway Interaction Database 1.38835864600592e-06 5.85584933859922e-06 120 502.363636363636 365 1.26214502014647e-07 67 2.32041268747759 2.47345621041107 1 4.43798936965736 119 1193 795 365 849 67 238 120 560 1086 134 198 M10276 LEE_NEURAL_CREST_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_NEURAL_CREST_STEM_CELL_DN.html Genes down-regulated in the neural crest stem cells (NCS), defined as p75+/HNK1+ [GeneID=4804;27087]. 18037878 91/239 Arthur Liberzon 4.38026982734589e-10 1.02629722054714e-08 155 462.545454545455 365 3.98206348019819e-11 74 2.20380846513708 2.3861043738627 1 6.43532773492955 155 1093 192 74 746 494 846 176 636 311 365 199 M1951 MEISSNER_NPC_HCP_WITH_H3K4ME2 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_HCP_WITH_H3K4ME2.html Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation mark at K4 (H3K4me2) in neural precursor cells (NPC). 18600261 266/753 Arthur Liberzon 2.4617443880856e-33 6.07143905398374e-31 365 298.454545454545 365 2.23794944371419e-34 5 1.96561499760404 2.16386486261187 1 21.7102518085852 365 32 18 5 95 440 564 598 571 12 583 200 M12795 CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP.html Genes up-regulated in basal-like breast cancer cell lines as compared to the mesenchymal-like ones. 16288205 89/215 Arthur Liberzon 3.77900549202217e-12 1.31173479523081e-10 1875 948.272727272727 367 3.43545953820788e-13 96 2.13574331602985 -1.80683004768417 -1 7.71471562842747 1874 277 129 192 284 682 2927 2751 367 96 852 201 M9858 VALK_AML_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_3.html Top 40 genes from cluster 3 of acute myeloid leukemia (AML) expression profile; 84% of the samples are FAB M1 or M2 subtypes, 52% bear intern tandem duplication in FLT3 [GeneID=2322]. 15084694 19/76 Jessica Robertson 2.22003119039013e-07 2.03184885901722e-06 40 471.181818181818 368 2.01821037674058e-08 39 2.17175709274704 2.17175709274704 1 4.51859769521342 39 628 368 614 1152 57 114 693 1031 352 135 202 M2576 LIM_MAMMARY_LUMINAL_PROGENITOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_LUMINAL_PROGENITOR_DN.html Genes consistently down-regulated in mammary luminal progenitor cells both in mouse and human species. 20346151 16/33 Daniel Hollern 9.60632105570152e-07 4.61694568892485e-06 50 383.727272727273 368 8.73302295483034e-08 15 2.20662528552304 2.20662528552304 1 4.30362861595834 46 637 579 563 1056 46 15 244 368 496 171 203 M19218 LIU_CDX2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_CDX2_TARGETS_DN.html Genes down-regulated in HET1A cells (esophagus epithelium) engineered to stably express CDX2 [GeneID=1045]. 16990345 7/19 Arthur Liberzon 1.03278300774084e-06 4.83478638788567e-06 495 675.181818181818 370 1.03278348772948e-07 22 3.23102816318 3.46306683413833 1 6.27789636598408 495 196 4154 22 770 370 299 260 31 401 429 204 M6744 COLDREN_GEFITINIB_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/COLDREN_GEFITINIB_RESISTANCE_DN.html Genes down-regulated in NSCLC (non-small cell lung carcinoma) cell lines resistant to gefitinib [PubChem=123631] compared to the sensitive ones. 16877703 158/386 Arthur Liberzon 8.09065343166101e-14 3.75374277037262e-12 190 340.090909090909 371 7.35513948332845e-15 50 1.84194009632528 -1.75245019008333 -1 7.69256750761515 190 50 96 371 435 107 651 755 612 69 405 205 M1614 DAVICIONI_RHABDOMYOSARCOMA_PAX_FOXO1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_RHABDOMYOSARCOMA_PAX_FOXO1_FUSION_DN.html Genes down-regulated in RMS cells (rhabdomyosarcoma) expressing PAX3 or PAX7 fusions with FOXO1 [GeneID=5077;5081;2308] compared to the fusion negative cell lines. 16849537 18/41 Arthur Liberzon 4.6312207261143e-06 1.36747954143488e-05 190 444.636363636364 373 4.21020952302483e-07 118 2.38891760068869 2.57746244669379 1 4.24737938703776 186 749 585 142 1395 121 393 373 118 612 217 206 M5315 TAKAYAMA_BOUND_BY_AR http://www.broadinstitute.org/gsea/msigdb/cards/TAKAYAMA_BOUND_BY_AR.html Genes whose promoters bound AR [GeneID=367] in LNCaP cells (prostate cancer) after exposure to the synthetic androgen R1881 [PubChem=13766], based on ChIP-chip analysis. 17297473 11/26 Leona Saunders 1.57648720208341e-07 1.63800865387203e-06 800 479.272727272727 373 1.43317028641104e-08 16 2.29993681858327 2.83469974430232 1 4.86395839699429 798 881 496 373 109 842 1130 149 16 357 121 207 M1561 LINDVALL_IMMORTALIZED_BY_TERT_DN http://www.broadinstitute.org/gsea/msigdb/cards/LINDVALL_IMMORTALIZED_BY_TERT_DN.html Genes down-regulated in BJ cells (foreskin fibroblasts) immortalized by expression of TERT [GeneID=7015]. 12702554 64/152 John Newman 9.70016517623205e-07 4.65147070024235e-06 170 652.181818181818 375 8.8183358665441e-08 164 2.26486824297867 2.38329235750651 1 4.41454251152012 170 1481 375 455 1912 302 313 164 1208 425 369 208 M12170 AMIT_EGF_RESPONSE_480_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_480_MCF10A.html Genes whose expression peaked at 480 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 27/56 Leona Saunders 1.06235548184475e-06 4.91916777462895e-06 340 576.363636363636 376 9.65778177131562e-08 149 2.27050231109771 2.36752256948563 1 4.40535568891955 376 1037 1160 572 745 340 149 165 337 1092 367 209 M10427 TSENG_IRS1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TSENG_IRS1_TARGETS_UP.html Up-regulated in brown preadipocytes with IRS1 [GeneID=3667] knockout vs wild type controls; the knockouts have severe defects in adipocyte differentiation. 15895078 87/177 John Newman 4.43345429561427e-08 6.37275056111917e-07 445 449.090909090909 377 4.03041307723413e-09 10 2.01628537069927 2.21304618229533 1 4.56625061080368 442 80 359 122 10 1031 1005 377 821 252 441 210 M2476 LIU_IL13_PRIMING_MODEL http://www.broadinstitute.org/gsea/msigdb/cards/LIU_IL13_PRIMING_MODEL.html Genes up-regulated in BEAS-2B cells (bronchial epithelium) stimulated with IL13 [GeneID=3596] on days 1 to 3, rested on days 4 and 5, and then restimulated on day 6 for 1 h before lysis (priming model). 20123980 11/30 Arthur Liberzon 1.32911812375777e-09 2.80551690447248e-08 510 533.363636363636 377 1.20828920414613e-10 1 1.67286338081882 1.92402190358019 1 4.61786215586409 507 377 1389 178 627 347 254 1 634 1525 28 211 M12848 CASTELLANO_NRAS_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_NRAS_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) isolated from NRAS [GeneID=4893] knockout mice. 16909116 11/24 Leona Saunders 8.64974965677193e-09 1.4847152707558e-07 370 617.181818181818 378 7.86340880980015e-10 5 2.56517808216794 2.56517808216794 1 6.40254999881222 369 1145 1283 284 1499 537 153 5 71 1065 378 212 M5547 LU_AGING_BRAIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/LU_AGING_BRAIN_UP.html Age up-regulated genes in the human frontal cortex. 15190254 186/458 John Newman 6.06547609099178e-10 1.37308313827959e-08 690 599.454545454545 379 5.51406917514915e-11 199 1.87507090483484 1.9889554168302 1 5.38873381466262 690 919 199 221 1294 379 759 265 1324 278 266 213 M10263 LOPEZ_MESOTHELIOMA_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_DN.html Top genes associated with unfavorable survival after surgery of patients with epithelioid mesothelioma. 16540645 14/37 Arthur Liberzon 1.39805171165455e-05 3.32551792934681e-05 360 536.363636363636 379 1.27096417822305e-06 118 2.39837980547838 2.39837980547838 1 3.9258612319314 118 507 532 356 1812 191 326 833 359 379 487 214 M2061 NIELSEN_LEIOMYOSARCOMA_CNN1_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LEIOMYOSARCOMA_CNN1_DN.html Top 20 negative significant genes associated with leiomyosarcoma tumors expressing muscle gene cluster with CNN1 [GeneID=1264]. 11965276 15/43 John Newman 5.41263960019541e-07 3.27556613442881e-06 710 571.727272727273 379 4.92058266532961e-08 69 1.60701726780342 1.74036732538995 1 3.22176419393541 706 640 963 379 1212 305 270 69 180 1488 77 215 M8570 DOANE_BREAST_CANCER_ESR1_DN http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_BREAST_CANCER_ESR1_DN.html Genes down-regulated in breast cancer samples positive for ESR1 [GeneID=2099] compared to the ESR1 negative tumors. 16491124 31/77 Arthur Liberzon 1.57174475755709e-09 3.21422838205662e-08 740 486.454545454545 380 1.42885887152727e-10 62 2.50036448961289 2.45617365889418 1 6.84815936121883 739 142 220 380 62 649 821 756 1001 342 239 216 M12924 SASSON_RESPONSE_TO_FORSKOLIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/SASSON_RESPONSE_TO_FORSKOLIN_DN.html Genes down-regulated in primary granulosa cells in response to forskolin [PubChem=47936]. 15026540 92/157 Arthur Liberzon 4.18634051658454e-07 2.81856202021769e-06 170 616.818181818182 380 3.80576483017815e-08 63 1.92845850980906 2.14083391525211 1 3.91219391953705 167 823 671 973 380 70 63 338 1677 1466 157 217 M2302 VANDESLUIS_COMMD1_TARGETS_GROUP_4_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_COMMD1_TARGETS_GROUP_4_DN.html Genes down-regulated in 9.5 days post coitus (dpc) embryos with COMMD1 [GeneID=150684] knockout and in normal 8.5 dpc embryos compared to normal 9.5 dpc embryos. 17371845 14/41 Arthur Liberzon 5.07364427818973e-07 3.13655634401017e-06 345 673.090909090909 380 4.61240495297722e-08 179 2.43660053206561 2.5105174649982 1 4.90169469516608 342 361 380 179 453 1163 1336 1381 334 258 1217 218 M509 REACTOME_DEVELOPMENTAL_BIOLOGY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEVELOPMENTAL_BIOLOGY.html Genes involved in Developmental Biology 192/520 Reactome 1.95425147915852e-07 1.87272442358626e-06 430 547.545454545455 381 1.77659241159449e-08 49 1.7107425170868 1.97296157534152 1 3.58154966867599 426 1674 595 357 158 91 381 281 1216 795 49 219 M2506 LEE_NEURAL_CREST_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_NEURAL_CREST_STEM_CELL_UP.html Genes up-regulated in the neural crest stem cells (NCS), defined as p75+/HNK1+ [GeneID=4804;27087]. 18037878 87/284 Arthur Liberzon 3.66560389065678e-13 1.52009025058563e-11 250 626 382 3.33236717332489e-14 107 2.15893122404575 2.4636519668898 1 8.53709824153619 249 280 107 382 1927 884 987 344 535 251 940 220 M1501 SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1A http://www.broadinstitute.org/gsea/msigdb/cards/SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1A.html Genes basally silent, with hypermethylated promoters, up-regulated by the combination of TSA and decitabine [PubChem=5562;451668] in RKO cells (colorectal cancer). 11992124 9/38 John Newman 1.40498620550084e-05 3.33862340718912e-05 255 953.909090909091 384 1.40499508851795e-06 69 1.88717985124242 1.88465625645348 1 3.08790967371574 251 376 4396 1151 1847 136 69 538 1029 384 316 221 M2352 WINZEN_DEGRADED_VIA_KHSRP http://www.broadinstitute.org/gsea/msigdb/cards/WINZEN_DEGRADED_VIA_KHSRP.html Transcripts (mRNA molecules) rapidly degraded upon interaction with KHSRP [GeneID=8570]. 17908789 58/146 Arthur Liberzon 1.97611318197525e-09 3.89078418938488e-08 280 454.818181818182 384 1.79646653068206e-10 59 2.07047565745172 2.04241572355324 1 5.60796649746562 276 434 229 384 703 279 637 623 1051 328 59 222 M5882 NABA_PROTEOGLYCANS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_PROTEOGLYCANS.html Genes encoding proteoglycans 22159717 10/35 Alexandra Naba 4.95944153142946e-07 3.09688721232308e-06 415 670.090909090909 385 4.50858422675687e-08 234 2.46730169869402 2.5739668230897 1 4.96844129129942 411 373 385 769 444 269 719 3207 250 310 234 223 M6100 SENESE_HDAC1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC1_TARGETS_DN.html Genes down-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC1 [GeneID=3065] by RNAi. 17470557 182/452 Leona Saunders 2.06890886021137e-08 3.24244378560217e-07 135 373.454545454545 387 1.88082625424332e-09 130 1.79018701567328 1.83114165005878 1 4.24623439301407 133 543 277 130 404 181 395 495 917 246 387 224 M1373 GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_UP.html Genes up-regulated in MMH-RT cells (hepatocytes displaying an invasive, metastatic phenotype) during epithelial to mesenchymal transition (EMT). 16607286 67/135 Jessica Robertson 1.14382148301507e-09 2.49299882298076e-08 495 392.454545454545 388 1.03983771237251e-10 141 2.31100679546366 2.53441139521306 1 6.42275474697858 324 428 207 141 493 388 369 492 685 291 499 225 M3063 DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN http://www.broadinstitute.org/gsea/msigdb/cards/DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN.html Genes down-regulated in HEK293 cells (embryonic kidney) at 6 h, 12 h or 24 h after infection with reovirus strain T3A (known as a strong inducer of apoptosis). 12885910 218/538 John Newman 1.07668703359867e-07 1.27087038776911e-06 365 464.818181818182 389 9.78806442083708e-09 42 1.62509625236107 1.78412797468403 1 3.50225976783555 361 42 389 133 65 705 758 438 1264 192 766 226 M523 KEGG_THYROID_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_THYROID_CANCER.html Thyroid cancer 19/43 KEGG 1.33212368815541e-07 1.47224801950384e-06 280 475.181818181818 391 1.21102160801541e-08 29 3.10625646608247 3.4099170324814 1 6.62179135326361 280 1047 589 137 1093 391 552 29 66 860 183 227 M2502 PHONG_TNF_RESPONSE_VIA_P38_PARTIAL http://www.broadinstitute.org/gsea/msigdb/cards/PHONG_TNF_RESPONSE_VIA_P38_PARTIAL.html Genes whose expression changes in Calu-6 cells (lung cancer) by TNF [GeneID=7124] were blocked partially by p38 inhibitor LY479754. 20516219 117/268 Arthur Liberzon 2.34928437307522e-08 3.63324969380544e-07 395 578.545454545455 391 2.13571308923838e-09 258 1.90314357618737 2.02000221945689 1 4.47978076069826 391 274 280 285 1017 664 1189 456 1228 322 258 228 M902 REACTOME_CGMP_EFFECTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CGMP_EFFECTS.html Genes involved in cGMP effects 5/21 Reactome 1.46321683933062e-06 6.03576946223879e-06 395 872.363636363636 393 1.46321780278309e-07 15 2.7842565536843 2.7842565536843 1 5.31175512018077 393 1324 4048 684 1230 282 185 127 15 1158 150 229 M4263 CHEBOTAEV_GR_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEBOTAEV_GR_TARGETS_UP.html Genes up-regulated in follicular epithelial stem cells after transgenic expression of GR [GeneID=2908] under control of the keratin5 (K5) [GeneID=3852] promoter. 17146443 53/124 Leona Saunders 2.28603851587836e-06 8.07792108336594e-06 325 541.272727272727 394 2.07821899211244e-07 113 1.70788943728065 1.86637326930331 1 3.1792679364917 325 113 502 322 1089 317 415 151 1882 444 394 230 M1941 MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation at K4 (H3K4me2) and trimethylation at K27 (H3K27me3) in brain. 18600261 553/1553 Jessica Robertson 3.37985673890962e-40 1.97975108481631e-37 5 724.090909090909 395 3.37985673890963e-41 2 2.02532394430658 2.18599643433882 1 27.1718944703638 395 5 4554 2 93 464 708 394 879 2 469 231 M15694 WATTEL_AUTONOMOUS_THYROID_ADENOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/WATTEL_AUTONOMOUS_THYROID_ADENOMA_DN.html Down-regulated genes characteristic for autonomous thyroid adenoma. 16027733 30/85 Arthur Liberzon 3.07037816366383e-08 4.641223249977e-07 590 651.545454545455 396 2.79125291501348e-09 134 2.07557495596008 1.87976378027446 1 4.80498862871279 587 134 286 375 180 937 1039 2066 396 237 930 232 M5329 KIM_MYCL1_AMPLIFICATION_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYCL1_AMPLIFICATION_TARGETS_UP.html Genes positively correlated with amplifications of MYCL1 [GeneID=4610] in SCLC (small cell lung cancer) cell lines. 16116477 6/19 Arthur Liberzon 1.53907081887163e-06 6.22805341729919e-06 400 777.272727272727 397 1.53907188480521e-07 35 2.17679183830748 2.2946245749772 1 4.14200788871534 397 201 4278 672 941 184 35 1024 104 548 166 233 M5301 KONDO_EZH2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_EZH2_TARGETS.html Genes up-regulated in PC3 cells (prostate cancer) after EZH2 [GeneID=2146] knockdown by RNAi. 18488029 146/457 Jessica Robertson 2.55338985890444e-06 8.66528384925486e-06 260 597 397 2.32126620223146e-07 250 1.76911727016071 1.98632012062957 1 3.27353243335133 260 551 479 957 1150 250 366 307 1552 397 298 234 M6470 VERRECCHIA_RESPONSE_TO_TGFB1_C5 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C5.html Cluster 5: ECM related genes up-regulated in dermal fibroblasts later than 30 min after TGFB1 [GeneID=7040] addition; decreased slowly after the peak at 120 min time point. 11279127 26/50 John Newman 4.32116183980982e-07 2.84395567153776e-06 125 586.090909090909 398 3.92832971687029e-08 11 1.8212220717268 1.8212220717268 1 3.69205416793093 123 1368 1470 844 398 63 11 93 633 1304 140 235 M7140 ZHOU_INFLAMMATORY_RESPONSE_FIMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_INFLAMMATORY_RESPONSE_FIMA_UP.html Genes up-regulated in macrophages by P.gingivalis FimA pathogen. 18025224 269/856 Arthur Liberzon 2.56898956483754e-15 1.48620803713935e-13 675 515.181818181818 399 2.33544505894321e-16 34 1.79903144998949 1.91758544375408 1 8.43556667216905 675 34 78 157 103 586 1262 1030 1285 58 399 236 M15997 BIOCARTA_INTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INTRINSIC_PATHWAY.html Intrinsic Prothrombin Activation Pathway 14/36 BioCarta 1.6269719992027e-06 6.48828316484466e-06 260 637.272727272727 400 1.47906654763908e-07 168 2.17981618712199 2.3570283103266 1 4.13359787870412 259 759 400 1034 2479 245 216 583 331 168 536 237 M19636 MCBRYAN_PUBERTAL_BREAST_6_7WK_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_6_7WK_DN.html Genes down-regulated during pubertal mammary gland development between week 6 and 7. 17486082 60/121 Arthur Liberzon 1.53829347037408e-12 5.81326064691367e-11 400 381.636363636364 400 1.39844860943197e-13 36 2.48410854576272 2.6497916911676 1 9.29399180321639 400 705 118 36 89 429 436 779 349 353 504 238 M2226 PILON_KLF1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PILON_KLF1_TARGETS_UP.html Genes up-regulated in erythroid progenitor cells from fetal livers of E13.5 embryos with KLF1 [GeneID=10661] knockout compared to those from the wild type embryos. 18852285 332/853 Arthur Liberzon 1.97408548817349e-12 7.28390913195351e-11 125 452.272727272727 401 1.79462317106841e-13 121 1.88529886375051 2.0038148636949 1 6.98612138857734 461 231 121 124 658 314 543 401 1522 180 420 239 M1736 GAVIN_FOXP3_TARGETS_CLUSTER_P7 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_P7.html Cluster P7 of genes with similar expression profiles in peripheral T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 78/177 Jessica Robertson 4.35914885483723e-07 2.85691909563178e-06 255 401.454545454545 402 3.96286338052078e-08 29 1.75035126009629 1.86835486684754 1 3.54711834436672 254 697 800 485 402 56 125 104 804 660 29 240 M5360 KANG_IMMORTALIZED_BY_TERT_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_IMMORTALIZED_BY_TERT_UP.html Up-regulated genes in the signature of adipose stromal cells (ADSC) immortalized by forced expression of telomerase (TERT) [GeneID=7015]. 15579653 69/177 Kevin Vogelsang 1.48437320054788e-06 6.07483098661735e-06 110 400.454545454545 403 1.34943109279802e-07 73 2.12898462663868 2.36961743576502 1 4.05945882114558 109 573 403 613 884 73 81 327 619 453 270 241 M1541 DELASERNA_MYOD_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DELASERNA_MYOD_TARGETS_DN.html Genes down-regulated in NIH 3T3 cells (fibroblasts) 24 h after inducing MyoD [GeneID=4654] differentiation program. 15870273 63/154 John Newman 8.06183850097617e-06 2.11758829683713e-05 215 495.454545454545 405 7.32897094864505e-07 212 2.09104850382608 2.18585700110454 1 3.57261970901799 212 297 485 240 1613 350 406 405 606 504 332 242 M18784 VALK_AML_CLUSTER_10 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_10.html Top 40 genes from cluster 10 of acute myeloid leukemia (AML) expression profile; 41% of the samples are FAB M1 subtype, 45% have up-regulated EVI1 [GeneID=2122] expression; indicate poor survival. 15084694 16/54 Jessica Robertson 2.11530072929378e-07 1.97206191965366e-06 240 506.272727272727 408 1.92300084789095e-08 13 2.15889249362199 2.14148953811672 1 4.50206710312717 239 760 650 1192 172 52 13 408 1135 915 33 243 M5539 KEGG_AXON_GUIDANCE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AXON_GUIDANCE.html Axon guidance 61/153 KEGG 4.50940572967457e-07 2.91061642551722e-06 410 577.363636363636 409 4.09946059452836e-08 146 1.71959567162266 1.83191687198341 1 3.47970841785485 366 1101 810 409 410 227 211 146 1585 783 303 244 M10371 BENPORATH_ES_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_ES_WITH_H3K27ME3.html Set 'H3K27 bound': genes posessing the trimethylated H3K27 (H3K27me3) mark in their promoters in human embryonic stem cells, as identified by ChIP on chip. 18443585 439/1630 Jessica Robertson 3.42215948194601e-45 3.2072478664798e-42 250 423.909090909091 409 3.11105407449638e-46 5 2.02502237112 2.13480190169789 1 30.7137603670715 248 533 5 13 590 361 680 463 1353 8 409 245 M7253 KEGG_FOCAL_ADHESION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FOCAL_ADHESION.html Focal adhesion 101/245 KEGG 3.97783085492199e-07 2.76826476128525e-06 260 475.636363636364 411 3.61621052195975e-08 258 1.91889725544276 2.13987035802514 1 3.89828234274741 258 416 377 411 355 357 791 395 936 433 503 246 M2255 MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_UP.html Genes commonly up-regulated in UET-13 cells (mesenchymal progenitor) by expression of EWSR1 [GeneID=2130] fusions with ETS transcription factors FLI1 and ERG [GeneID=2313 ,2078]. 18212050 191/464 Arthur Liberzon 2.75116988652799e-17 1.95333061943488e-15 65 474.727272727273 413 2.50106353320727e-18 45 1.78840654554812 1.82249973918393 1 9.61557523128293 304 45 64 153 763 413 513 1106 1290 62 509 247 M10091 WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN http://www.broadinstitute.org/gsea/msigdb/cards/WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN.html Genes down-regulated in mucinous ovarian carcinoma tumors of low malignant potential (LMP) compared to normal ovarian surface epithelium tissue. 16467078 127/317 Arthur Liberzon 3.63309697318701e-07 2.631328039622e-06 105 554.090909090909 415 3.30281597559963e-08 104 1.72714932408738 1.83813326011704 1 3.52265179364946 104 415 832 734 325 229 377 568 1398 742 371 248 M1769 JI_CARCINOGENESIS_BY_KRAS_AND_STK11_UP http://www.broadinstitute.org/gsea/msigdb/cards/JI_CARCINOGENESIS_BY_KRAS_AND_STK11_UP.html Cluster A: genes up-regulated in primary lung tumors driven by KRAS [GeneID=3845] activation and loss of STK11 [GeneID=6794]; also up-regulated in human squamous cell carcinoma (SCC) vs adenocarcinoma subtype of NSCLC (non-small cell lung cancer). 17676035 12/24 Jessica Robertson 4.09728746170043e-07 2.79255907977434e-06 325 402.272727272727 415 3.72480747707348e-08 22 2.76861682735132 3.22559389091802 1 5.62066620731881 321 180 539 477 371 581 550 352 22 415 617 249 M9806 ZHU_CMV_8_HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_8_HR_DN.html Down-regulated at 8 h following infection of primary human foreskin fibroblasts with CMV 9826724 38/93 John Newman 4.33576604822078e-07 2.84557418794994e-06 355 832.636363636364 417 3.94160627519543e-08 91 2.11252121443399 2.2182268184917 1 4.28239663323846 351 2449 1176 1252 400 417 302 91 547 1833 341 250 M1949 MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation mark at K4 (H3K4me2) and trimethylation mark at K27 (H3K27me3) in neural precursor cells (NPC). 18600261 122/536 Arthur Liberzon 2.45493153894523e-25 3.2868026261421e-23 35 878.181818181818 417 2.23175594449566e-26 21 2.3754201190208 2.59941145688674 1 19.5217305594209 1436 267 34 106 21 2545 1766 1345 417 32 1691 251 M19432 MCBRYAN_PUBERTAL_BREAST_4_5WK_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_4_5WK_UP.html Genes up-regulated during pubertal mammary gland development between week 4 and 5. 17486082 225/469 Arthur Liberzon 6.17229524475189e-43 4.13191078812962e-40 5 1082.54545454545 418 5.61117749522902e-44 4 2.19555707189937 -2.13716503070854 -1 31.606917272145 2362 36 7 4 418 1238 3099 2314 226 5 2199 252 M4767 VERRECCHIA_RESPONSE_TO_TGFB1_C2 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C2.html Cluster 2: ECM related genes up-regulated in dermal fibroblasts within 30 min after TGFB1 [GeneID=7040] addition; reached a plateau after that. 11279127 30/76 John Newman 1.37253370632993e-06 5.83638198535578e-06 115 423.909090909091 418 1.24775869329598e-07 111 2.01570933832963 1.98584049155631 1 3.85628348152175 363 151 773 418 842 111 112 531 686 530 146 253 M1842 LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP.html Up-regulated genes in NMuMG cells (mammary epithelium) after stimulation with both TGFB1 and WNT3A [GeneID=7040;89780]. 17210685 86/219 Jessica Robertson 1.25247197059984e-09 2.66776529737765e-08 560 455.090909090909 418 1.1386108830117e-10 160 2.12096045835517 2.48755627432647 1 5.87176490156127 560 418 212 205 343 699 901 656 521 160 331 254 M9951 WANG_METHYLATED_IN_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/WANG_METHYLATED_IN_BREAST_CANCER.html Genes up-regulated in MDA468 cells (breast cancer) vs DU99 cells (normal breast) after treatment with azacytidine [PubChem=9444]. 15735726 39/88 Leona Saunders 3.02656554954166e-06 9.87638312336507e-06 185 639.363636363636 419 2.75142701202823e-07 88 1.95742829951897 2.05975130661208 1 3.58132786854241 181 1637 691 245 1506 112 141 419 1278 735 88 255 M15327 AMUNDSON_POOR_SURVIVAL_AFTER_GAMMA_RADIATION_2G http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_POOR_SURVIVAL_AFTER_GAMMA_RADIATION_2G.html Genes with basal expression distinguishing NCI-60 cell lines with poor survival after 2 Gy gamma irradiation. 18199535 117/292 Jessica Robertson 3.58965446452146e-08 5.32313950023658e-07 425 881.090909090909 421 3.26332229372042e-09 7 1.40926375395637 1.54421480193498 1 3.2317996386011 421 925 1613 1132 7 334 362 134 2388 2029 347 256 M12950 BIOCARTA_ACE2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ACE2_PATHWAY.html Angiotensin-converting enzyme 2 regulates heart function 10/27 BioCarta 4.77144526847472e-06 1.39482174223784e-05 255 615.363636363636 422 4.33768692454688e-07 174 2.53903884016695 2.55986121885254 1 4.50630808432113 255 374 450 410 1778 422 701 1135 174 309 761 257 M3228 KEGG_SMALL_CELL_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SMALL_CELL_LUNG_CANCER.html Small cell lung cancer 55/124 KEGG 4.85054362517749e-07 3.053666136433e-06 255 549.727272727273 423 4.40958608602006e-08 64 1.89449128877313 2.13175221956989 1 3.81919147223069 323 1016 423 348 1097 255 714 64 947 607 253 258 M1545 WESTON_VEGFA_TARGETS_12HR http://www.broadinstitute.org/gsea/msigdb/cards/WESTON_VEGFA_TARGETS_12HR.html Genes up-regulated in MMEC cells (myometrial endothelium) at 12 h after VEGFA [GeneID=7422] stimulation. 12200464 29/62 John Newman 3.4842110314364e-11 1.05335567053619e-09 55 581.818181818182 424 3.16746457408325e-12 52 2.39452792107167 2.45036140249529 1 7.85761850816944 52 467 149 495 2315 177 229 489 1389 214 424 259 M1852 QI_PLASMACYTOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/QI_PLASMACYTOMA_DN.html Down-regulated genes that best disciminate plasmablastic plasmacytoma from plasmacytic plasmacytoma tumors. 17363561 76/179 Jessica Robertson 5.1913505746971e-07 3.18829210917833e-06 425 449.090909090909 425 4.71941072700273e-08 90 1.79957744648681 2.04105607695041 1 3.61552553692524 425 90 467 395 462 362 819 163 814 254 689 260 M986 SMIRNOV_CIRCULATING_ENDOTHELIOCYTES_IN_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_CIRCULATING_ENDOTHELIOCYTES_IN_CANCER_UP.html Genes up-regulated in circulating endothelial cells (CEC) from cancer patients compared to those from healthy donors. 16540638 131/329 Arthur Liberzon 1.4859769213265e-09 3.08110082006018e-08 480 517.454545454545 428 1.35088811120928e-10 99 1.83371157629593 2.10169134280063 1 5.03460083464629 480 1167 217 185 495 428 745 99 1368 247 261 261 M18274 VANHARANTA_UTERINE_FIBROID_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANHARANTA_UTERINE_FIBROID_UP.html Genes up-regulated in uterine fibroids vs normal myometrium samples. 15940248 38/88 Leona Saunders 1.24368366185493e-06 5.50106086641434e-06 95 628.454545454545 428 1.13062214993022e-07 91 2.12107846962104 2.32820429261348 1 4.07779010081355 91 1026 390 570 2164 410 266 428 527 350 691 262 M5681 MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_UP.html Genes up-regulated in apoptotic tissues (neuroepithelium) after MDM4 [GeneID=4194] knockout. 15608685 127/276 Arthur Liberzon 1.17096475343524e-07 1.36157340808872e-06 430 472 428 1.0645134688733e-08 70 1.84938160943375 1.82091548870066 1 3.96537992575901 428 923 567 334 70 252 136 615 1253 505 109 263 M6154 MAHAJAN_RESPONSE_TO_IL1A_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAHAJAN_RESPONSE_TO_IL1A_UP.html Genes up-regulated in corneal fibroblasts after treatment with IL1A [GeneID=3552]. 12091409 60/143 John Newman 2.47265352703605e-07 2.14969469901502e-06 410 627.636363636364 430 2.24786709540536e-08 218 2.00331109669733 2.09862039198661 1 4.15019609661841 409 1100 335 830 693 394 900 218 1289 306 430 264 M6767 POOLA_INVASIVE_BREAST_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/POOLA_INVASIVE_BREAST_CANCER_DN.html Genes down-regulated in atypical ductal hyperplastic tissues from patients with (ADHC) breast cancer vs those without the cancer (ADH). 15864312 100/269 Jessica Robertson 1.2889790294322e-15 7.55019466489911e-14 430 389.727272727273 430 1.17179911766563e-16 37 2.19945730594851 2.52425368346049 1 10.5496051533258 430 276 77 37 203 590 652 852 505 98 567 265 M6362 NAKAMURA_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_LUNG_CANCER.html Genes up-regulated in lung adenocarcinoma cell lines and not expressed in non-cancerous lung epithelial cells. 16491115 12/26 Arthur Liberzon 1.0164846488449e-06 4.79199905884023e-06 335 591.272727272727 431 9.24077380454744e-08 146 2.54802927205356 2.55986121885254 1 4.95442332039189 334 514 379 146 1879 431 807 663 585 414 352 266 M12107 MAHAJAN_RESPONSE_TO_IL1A_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAHAJAN_RESPONSE_TO_IL1A_DN.html Genes down-regulated in corneal fibroblasts after treatment with IL1A [GeneID=3552]. 12091409 69/175 John Newman 2.88629561301201e-06 9.53820962099739e-06 385 526.636363636364 431 2.62390854518351e-07 167 1.82978812837622 2.09581328103332 1 3.35791651072751 385 580 868 308 1204 249 431 183 542 876 167 267 M4665 BAELDE_DIABETIC_NEPHROPATHY_DN http://www.broadinstitute.org/gsea/msigdb/cards/BAELDE_DIABETIC_NEPHROPATHY_DN.html Genes down-regulated in glomeruli of kidneys from patients with diabetic nephropathy (type 2 diabetes mellitus). 15042541 328/758 John Newman 3.801556094184e-07 2.69640744894893e-06 435 529.363636363636 431 3.45596068280497e-08 180 1.80596430101551 1.93052597148813 1 3.67639659702043 246 800 383 180 338 356 882 435 1288 484 431 268 M4592 JEON_SMAD6_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JEON_SMAD6_TARGETS_UP.html Genes up-regulated in H1299 cells (lung cancer) upon knockdown of SMAD6 [GeneID=4091] by RNAi. 19047146 10/36 Jessica Robertson 5.13093722033363e-09 9.14204251501269e-08 560 373 432 4.66448839300019e-10 3 2.1366913657302 2.44249305296163 1 5.49755196412199 559 191 806 162 559 432 654 3 28 704 5 269 M3645 DELYS_THYROID_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/DELYS_THYROID_CANCER_UP.html Genes up-regulated in papillary thyroid carcinoma (PTC) compared to normal tissue. 17621275 324/768 Aravind Subramanian 8.64000942443805e-32 1.92795638871032e-29 425 384.181818181818 433 7.85455402221641e-33 20 1.92322457374208 2.08264575291448 1 20.1862942954497 422 22 20 149 433 504 645 542 915 28 546 270 M1234 OXFORD_RALA_AND_RALB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_AND_RALB_TARGETS_DN.html Genes down-regulated in the UMUC-3 cells (bladder cancer) after knockdown of both RALA and RALB [GeneID=5898;5899] by RNAi. 17496927 14/25 Arthur Liberzon 1.33167467756346e-06 5.7407797047492e-06 125 446.909090909091 433 1.21061407603247e-07 125 2.25625403728379 2.24224139736277 1 4.32238870233035 125 501 447 619 826 142 433 810 305 378 330 271 M3021 KOBAYASHI_RESPONSE_TO_ROMIDEPSIN http://www.broadinstitute.org/gsea/msigdb/cards/KOBAYASHI_RESPONSE_TO_ROMIDEPSIN.html Genes up-regulated in MM-LH cells (malignant melanoma) after treatment with the HDAC inhibitor romidepsin (FK228) [PubChem=5352062]. 16186804 12/24 Arthur Liberzon 4.17723311027209e-07 2.81825276987931e-06 435 595.909090909091 434 3.79748536674658e-08 94 2.7591481343785 2.91207801436305 1 5.59743192969024 434 1937 885 275 378 459 845 280 94 856 112 272 M14072 WINTER_HYPOXIA_METAGENE http://www.broadinstitute.org/gsea/msigdb/cards/WINTER_HYPOXIA_METAGENE.html Genes regulated by hypoxia, based on literature searches. 17409455 178/364 Jessica Robertson 3.28016950607465e-08 4.94240331365461e-07 500 620.090909090909 434 2.98197232271048e-09 186 1.93030695427789 2.17882931322106 1 4.44942457884514 497 1412 287 303 587 434 1054 385 1350 326 186 273 M1472 PETROVA_PROX1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PETROVA_PROX1_TARGETS_DN.html Genes specific to BEC (blood endothelium cells) repressed in BEC by expression of PROX1 [GeneID=5629] off adenovirus vector. 12198161 65/111 Kevin Vogelsang 4.10711561761753e-10 9.72017362836149e-09 235 646.636363636364 437 3.73374147125844e-11 191 1.93631133159496 1.94617014599638 1 5.67091382144528 234 574 191 437 1642 253 228 1124 1536 256 638 274 M863 LEI_MYB_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LEI_MYB_TARGETS.html Myb-regulated genes in MCF7 (breast cancer) and lung epithelial cell lines overexpressing MYBL2, MYBL1 or MYB [GeneID=4605;4603;4602]. 15105423 248/532 Kevin Vogelsang 5.0305700702944e-12 1.73332730510291e-10 685 439.454545454545 438 4.57324551845991e-13 54 1.97670600156002 2.20307782642158 1 7.05279007765886 683 403 130 63 54 618 929 707 625 184 438 275 M5885 NABA_MATRISOME_ASSOCIATED http://www.broadinstitute.org/gsea/msigdb/cards/NABA_MATRISOME_ASSOCIATED.html Ensemble of genes encoding ECM-associated proteins including ECM-affilaited proteins, ECM regulators and secreted factors 22159717 209/882 Alexandra Naba 3.38939060547535e-35 1.32355703143813e-32 440 493.363636363636 438 3.08126418679581e-36 11 2.06760236610369 2.16796359925602 1 24.0924431726617 438 244 11 253 138 808 820 752 1032 16 915 276 M16312 REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL.html Genes involved in Cell surface interactions at the vascular wall 51/131 Reactome 2.04663592767954e-07 1.93870664292301e-06 260 722 439 1.86057828915988e-08 224 1.86656109462498 1.90835863131445 1 3.89750564750938 256 439 328 834 1205 224 317 1223 2221 399 496 277 M15908 BACOLOD_RESISTANCE_TO_ALKYLATING_AGENTS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BACOLOD_RESISTANCE_TO_ALKYLATING_AGENTS_UP.html Genes up-regulated in D-341 MED (OBR) cells (medulloblastoma) resistant to both carmustine and O6-BG [PubChem=2578;4578]. 12479369 24/57 John Newman 2.46053946664649e-07 2.14593063349835e-06 415 621.636363636364 439 2.23685431076356e-08 17 2.59767885903455 2.67623522836234 1 5.38225163612786 414 2052 439 81 868 138 330 518 1038 943 17 278 M15103 DOUGLAS_BMI1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DOUGLAS_BMI1_TARGETS_UP.html Genes up-regulated in A4573 cells (Ewing's sarcoma, ESFT) after knockdown of BMI1 [GeneID=648] by RNAi. 18701473 378/940 Jessica Robertson 2.29153193507793e-07 2.06900166623799e-06 940 584 440 2.08321106705925e-08 18 1.64110873499468 1.77673478500383 1 3.4098003396098 938 18 440 269 189 980 941 378 1300 343 628 279 M19982 WAMUNYOKOLI_OVARIAN_CANCER_LMP_UP http://www.broadinstitute.org/gsea/msigdb/cards/WAMUNYOKOLI_OVARIAN_CANCER_LMP_UP.html Genes up-regulated in mucinous ovarian carcinoma tumors of low malignant potential (LMP) compared to normal ovarian surface epithelium tissue. 16467078 188/404 Arthur Liberzon 2.59535843751414e-07 2.19924948249389e-06 260 567.818181818182 441 2.3594170397189e-08 23 1.45402000524187 -1.35403949869683 -1 3.00698668454007 257 541 1630 807 220 23 341 441 1172 722 92 280 M9564 SMID_BREAST_CANCER_NORMAL_LIKE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_NORMAL_LIKE_DN.html Genes down-regulated in the normal-like subtype of breast cancer. 18451135 12/24 Jessica Robertson 2.26069355251425e-06 8.0072637846423e-06 475 593.727272727273 442 2.05517806870828e-07 144 2.38616150780629 2.55986121885254 1 4.44521188148658 471 182 414 144 1858 589 442 999 271 282 879 281 M10702 JAEGER_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JAEGER_METASTASIS_DN.html Genes down-regulated in metastases from malignant melanoma compared to the primary tumors. 17289871 179/478 Leona Saunders 2.30494540952914e-33 6.00054121614086e-31 10 482.909090909091 443 2.09540491775379e-34 6 2.2012626072454 2.52484177667352 1 24.3170882962366 866 46 17 6 96 1260 1447 528 443 10 593 282 M308 TSAI_RESPONSE_TO_RADIATION_THERAPY http://www.broadinstitute.org/gsea/msigdb/cards/TSAI_RESPONSE_TO_RADIATION_THERAPY.html Genes up-regulated in response to both single dose and fractionated radiation that were common to all three cell lines studied. 17440099 32/76 Jessica Robertson 2.9918854165822e-06 9.79048537856439e-06 215 463 443 2.71989953218026e-07 124 1.87592037344915 1.95397079975532 1 3.43480159777743 124 608 486 501 1222 213 182 443 776 213 325 283 M10010 VALK_AML_WITH_FLT3_ITD http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_WITH_FLT3_ITD.html Genes that best predicted acute myeloid leukemia (AML) with internal tandem duplications (IDT) in FLT3 [GeneID=2322]. 15084694 31/73 Jessica Robertson 7.06268977621082e-07 3.8227912014599e-06 90 574.636363636364 443 6.42062913050609e-08 89 2.14056763386905 2.10965510184287 1 4.23893442561044 89 954 371 656 578 164 427 870 1383 443 386 284 M19541 REN_ALVEOLAR_RHABDOMYOSARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/REN_ALVEOLAR_RHABDOMYOSARCOMA_DN.html Genes commonly down-regulated in human alveolar rhabdomyosarcoma (ARMS) and its mouse model overexpressing PAX3-FOXO1 [GeneID=5077;2308] fusion. 18701482 342/636 Jessica Robertson 4.96321446106409e-07 3.09688721232308e-06 340 455.181818181818 445 4.51201416433535e-08 25 1.70446229129497 1.90430612311189 1 3.43230048868551 339 25 547 75 445 531 942 222 1168 250 463 285 M17228 SASAI_TARGETS_OF_CXCR6_AND_PTCH1_DN http://www.broadinstitute.org/gsea/msigdb/cards/SASAI_TARGETS_OF_CXCR6_AND_PTCH1_DN.html Down-regulated genes in medulloblastoma tumors from heterozygotic CXCR6 [GeneID=10663] knockout mice compared to those from PTCH1 [GeneID=5727] heterozygotic knockout mice. 17413002 2/9 Jessica Robertson 2.96370966950328e-06 9.74592527108237e-06 635 1084.5 445 3.29301508146853e-07 5 2.09250232797659 2.09250232797659 1 3.83287747391605 634 531 4515 NA 2109 359 89 174 5 2173 256 286 M11825 BRUECKNER_TARGETS_OF_MIRLET7A3_DN http://www.broadinstitute.org/gsea/msigdb/cards/BRUECKNER_TARGETS_OF_MIRLET7A3_DN.html Genes down-regulated in A549 cells (lung cancer) expressing MIRLET7A3 [GeneID=406883] microRNA off a plasmid vector. 17308078 60/144 Jessica Robertson 1.19550868192683e-07 1.38324782308868e-06 450 551.636363636364 447 1.08682613353849e-08 178 2.09041695145741 2.36722217097697 1 4.47695861365635 178 299 312 447 1738 395 521 392 817 522 447 287 M5884 NABA_CORE_MATRISOME http://www.broadinstitute.org/gsea/msigdb/cards/NABA_CORE_MATRISOME.html Ensemble of genes encoding core extracellular matrix including ECM glycoproteins, collagens and proteoglycans 22159717 108/301 Alexandra Naba 4.9517736024603e-30 9.28160444045159e-28 25 467 447 4.501612365873e-31 15 2.31023256021867 2.40886457605059 1 22.8275438525612 23 271 24 368 1165 447 803 921 460 15 640 288 M566 VERRECCHIA_RESPONSE_TO_TGFB1_C4 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C4.html Cluster 4: ECM related genes up-regulated in dermal fibroblasts later than 30 min after TGFB1 [GeneID=7040] addition; kept increasing with time. 11279127 23/55 John Newman 6.85505561796272e-06 1.85837695054818e-05 305 633.636363636364 448 6.2318881617812e-07 188 1.98006810833944 2.16277455896305 1 3.42404957321017 305 342 570 188 1546 656 448 1148 371 303 1093 289 M1758 SANSOM_WNT_PATHWAY_REQUIRE_MYC http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_WNT_PATHWAY_REQUIRE_MYC.html Wnt target genes up-regulated after Cre-lox knockout of APC [GeneID=324] in the small intestine that require functional MYC [GeneID=4609]. 17377531 51/97 Jessica Robertson 4.68770379820262e-07 2.98054002691689e-06 430 503.090909090909 452 4.26154981549714e-08 140 2.53931095044134 2.65768018343134 1 5.12888350508856 476 1344 427 452 426 545 259 140 579 611 275 290 M6391 KEGG_PEROXISOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PEROXISOME.html Peroxisome 45/92 KEGG 1.71119806500167e-06 6.67110992728605e-06 135 1538.63636363636 453 1.5556358145478e-07 36 0.807661727894874 -0.807661727894874 -1 1.52801071538048 283 453 3550 3100 1391 36 56 133 3808 3984 131 291 M9940 HONRADO_BREAST_CANCER_BRCA1_VS_BRCA2 http://www.broadinstitute.org/gsea/msigdb/cards/HONRADO_BREAST_CANCER_BRCA1_VS_BRCA2.html Genes distinguishing between breast cancer tumors bearing mutations in BRCA1 [GeneID=672] and those with mutated BRCA2 [GeneID=675]. 16998498 13/36 Arthur Liberzon 1.12760927454318e-06 5.12509899176465e-06 455 704.545454545455 454 1.02509986590851e-07 241 2.99055745408706 3.53535055950618 1 5.78297767918601 454 1796 955 298 767 453 241 477 264 1752 293 292 M11654 LIEN_BREAST_CARCINOMA_METAPLASTIC http://www.broadinstitute.org/gsea/msigdb/cards/LIEN_BREAST_CARCINOMA_METAPLASTIC.html Genes up-regulated in metaplastic carcinoma of the breast (MCB) subclass 2 compared to the MCB subclass 1. 17603561 36/78 Arthur Liberzon 3.90966616137031e-11 1.16692328867397e-09 80 591.909090909091 454 3.55424196494528e-12 76 2.22143825525919 2.27605172003057 1 7.25351935452265 76 454 151 442 2174 355 629 909 524 110 687 293 M4737 VERRECCHIA_EARLY_RESPONSE_TO_TGFB1 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_EARLY_RESPONSE_TO_TGFB1.html ECM related genes up-regulated early (within 30 min) in dermal fibroblasts after addition of TGFB1 [GeneID=7040]. 11279127 69/173 John Newman 1.35378098648023e-06 5.80295291630298e-06 395 477.272727272727 454 1.23071074503349e-07 241 1.94557345504456 1.988498591824 1 3.72387958283198 392 294 627 251 833 241 519 685 705 454 249 294 M13639 CORRE_MULTIPLE_MYELOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/CORRE_MULTIPLE_MYELOMA_UP.html Genes up-regulated in multiple myeloma (MM) bone marrow mesenchymal stem cells. 17344918 35/139 Leona Saunders 3.93334557423682e-07 2.75510573406185e-06 390 746.090909090909 456 3.57576934315791e-08 350 2.08794486574779 2.20657502223076 1 4.24328564382268 405 1542 456 1065 350 390 437 508 1762 904 388 295 M12527 RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN.html Down-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: well vs poorly differentiated tumors. 18679425 273/587 Jessica Robertson 2.26890856641992e-07 2.06048557020227e-06 615 567.090909090909 456 2.06264436401591e-08 185 1.64222351900527 1.85544920200573 1 3.41319182652646 615 238 393 283 185 456 822 874 1412 511 449 296 M2223 KANG_AR_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_AR_TARGETS_UP.html Genes up-regulated in osteoblasts from wild type male mice compared to those with AR [GeneID=367] knockout. 18838539 12/35 Arthur Liberzon 4.57801413022961e-05 9.25078663831649e-05 185 642.181818181818 456 4.16191763419207e-06 172 2.22609413661118 2.39198713675667 1 3.28230878275988 183 883 604 456 2187 331 172 888 229 417 714 297 M16334 BIOCARTA_EPHA4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPHA4_PATHWAY.html Eph Kinases and ephrins support platelet aggregation 19/36 BioCarta 3.16604908054038e-06 1.020364923756e-05 180 688.636363636364 458 2.87823057895695e-07 133 2.8663351624662 2.8663351624662 1 5.22943855742264 179 1499 888 312 1244 182 133 797 458 1449 434 298 M820 REACTOME_CELL_CELL_JUNCTION_ORGANIZATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CELL_JUNCTION_ORGANIZATION.html Genes involved in Cell-cell junction organization 25/69 Reactome 2.53013202368653e-07 2.17979909250208e-06 355 1400 459 2.30012028606086e-08 157 2.42697416525763 -2.41963537202512 -1 5.02252749884358 2915 157 336 376 459 2268 4620 1717 351 351 1850 299 M11504 TOMLINS_PROSTATE_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/TOMLINS_PROSTATE_CANCER_DN.html Genes down-regulated in prostate cancer vs benign prostate tissue, based on a meta-analysis of five gene expression profiling studies. 17173048 22/67 Leona Saunders 1.83767450557979e-06 6.97587836865205e-06 460 517.181818181818 459 1.67061458236656e-07 272 2.39691310140265 2.49351070511034 1 4.51770878059918 459 487 407 272 980 401 768 391 475 651 398 300 M5312 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_DN.html Genes down-regulated in NIH3T3 cells (fibroblasts) transformed by activated KRAS [GeneID=3845] vs those reverted to normal cells upon over-expression of a dominant negative form of CDC25 [GeneID=5923]. 16607279 33/75 Lauren Kazmierski 2.08791705853146e-06 7.59625724866338e-06 370 565.090909090909 461 1.89810821825316e-07 170 1.82963698883903 1.80409684830515 1 3.42375969169727 370 461 601 681 1049 312 368 170 1238 510 456 301 M14614 SAKAI_TUMOR_INFILTRATING_MONOCYTES_UP http://www.broadinstitute.org/gsea/msigdb/cards/SAKAI_TUMOR_INFILTRATING_MONOCYTES_UP.html Selected genes up-regulated in inflammatory monocytes infiltrating hepatocellular carcinoma (HCC). 19074895 17/47 Jessica Robertson 2.39921059825101e-06 8.34647428612045e-06 180 635.090909090909 461 2.18110292246798e-07 74 1.87070462513284 2.18262552525443 1 3.47263921733322 482 360 1258 176 1517 550 461 228 176 1704 74 302 M3258 LIU_TARGETS_OF_VMYB_VS_CMYB_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_TARGETS_OF_VMYB_VS_CMYB_DN.html Gene regulated in the opposite directions by v-MYB (DN) and c-MYB (UP) variants of CMYB [GeneID=4602] overexpressed in primary monocyte cultures off adenoviral vectors. 16205643 35/80 Arthur Liberzon 7.86403608648619e-07 4.09504663003896e-06 285 375.090909090909 463 7.14912627048721e-08 42 1.96709792192123 2.08952694651924 1 3.87393163355349 284 463 534 526 613 150 515 148 567 284 42 303 M1199 TERAMOTO_OPN_TARGETS_CLUSTER_4 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_4.html Cluster 4: genes whose up-regulation peaked 4 days after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 16/33 Arthur Liberzon 4.19469889805103e-06 1.2681521958882e-05 260 562.636363636364 463 3.81336990547854e-07 160 2.06244822983587 2.21988020026224 1 3.691621880028 161 968 891 463 1355 257 160 590 256 686 402 304 M4680 DAVICIONI_TARGETS_OF_PAX_FOXO1_FUSIONS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_TARGETS_OF_PAX_FOXO1_FUSIONS_UP.html Genes up-regulated in RD cells (embryonal rhabdomyosarcoma, ERMS) by expression of PAX3- or PAX7-FOXO1 [GeneID=5077;5081;2308] fusions off retroviral vectors. 16849537 186/462 Arthur Liberzon 2.01113530335205e-09 3.9431715613003e-08 310 617.545454545455 464 1.82830482290049e-10 132 1.74846281943286 1.82117309645164 1 4.73206949857047 306 807 230 692 1157 378 771 132 1646 210 464 305 M2485 GUILLAUMOND_KLF10_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUILLAUMOND_KLF10_TARGETS_UP.html Genes up-regulated in the liver tissue from 10 week old male mice with KLF10 [GeneID=7071] compared to wild-type littermates. 20385766 35/96 Arthur Liberzon 2.81185106123797e-05 6.07764486760199e-05 200 603.545454545455 465 2.55626090958769e-06 179 2.17857816048463 2.30460977801653 1 3.35753278757132 196 948 612 294 2027 290 179 465 412 726 490 306 M160 PID_AVB3_INTEGRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AVB3_INTEGRIN_PATHWAY.html Integrins in angiogenesis 18832364 54/117 Pathway Interaction Database 2.12741688034845e-06 7.68033551719015e-06 470 647.363636363636 466 1.93401721598152e-07 139 2.14991252229941 2.25228081529405 1 4.01932751290284 195 1484 569 466 1794 157 466 139 932 698 221 307 M4383 BIOCARTA_NO1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NO1_PATHWAY.html Actions of Nitric Oxide in the Heart 19/50 BioCarta 1.28242797467168e-06 5.59499629414704e-06 235 604 468 1.16584429293411e-07 40 2.19558050382825 2.19558050382825 1 4.21511946361553 233 1379 1055 187 813 130 40 468 490 1448 401 308 M16300 HAEGERSTRAND_RESPONSE_TO_IMATINIB http://www.broadinstitute.org/gsea/msigdb/cards/HAEGERSTRAND_RESPONSE_TO_IMATINIB.html Genes with the highest differential expression in primary tissue cultures of high grade glioma: responders vs non-responders to imatinib [PubChem=5291] treatment. 16547494 20/32 Arthur Liberzon 1.05601541695814e-09 2.33419256786125e-08 35 571.727272727273 469 9.60014015877307e-11 24 2.40946057120644 2.40946057120644 1 6.72155347568308 34 959 204 688 2397 103 24 572 469 295 544 309 M9066 BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_DN.html Genes down-regulated in A172 cells (glioma, does not express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 48 h. 15980968 30/67 John Newman 5.61812513189195e-07 3.3409307573662e-06 285 423 470 5.10738778780844e-08 124 2.219478970691 2.44922517542116 1 4.44267183611446 285 613 768 229 488 234 124 650 261 531 470 310 M1878 HUNSBERGER_EXERCISE_REGULATED_GENES http://www.broadinstitute.org/gsea/msigdb/cards/HUNSBERGER_EXERCISE_REGULATED_GENES.html Exercise regulated genes in hyppocampus. 18059283 22/53 Jessica Robertson 2.67712936767274e-07 2.23619041299723e-06 190 472.545454545455 470 2.43375426676955e-08 14 1.92694415279396 1.92158059835464 1 3.97992220231925 188 166 954 771 665 14 26 1273 470 652 19 311 M1834 BOQUEST_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOQUEST_STEM_CELL_UP.html Genes up-regulated in freshly isolated CD31- [GeneID=5175] (stromal stem cells from adipose tissue) versus the CD31+ (non-stem) counterparts. 15635089 185/494 Arthur Liberzon 1.15451260981741e-32 2.7050230448022e-30 40 487.636363636364 471 1.04955691801584e-33 19 2.04399142130767 2.10321487726259 1 22.0911211637178 36 248 19 471 1323 354 677 614 979 25 618 312 M165 PID_SYNDECAN_4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_4_PATHWAY.html Syndecan-4-mediated signaling events 18832364 29/62 Pathway Interaction Database 3.44689205772612e-07 2.54765554929094e-06 475 568.818181818182 472 3.13353872524967e-08 55 1.88545968085913 1.92352160537258 1 3.85520998391652 472 622 896 143 1265 337 253 55 1010 809 395 313 M3034 BERENJENO_TRANSFORMED_BY_RHOA_REVERSIBLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_REVERSIBLY_DN.html Genes down-regulated in NIH3T3 cells (fibroblasts) transformed by expression of contitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector; their expression reverted completely after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins. 17213802 29/52 Leona Saunders 7.84270359308351e-07 4.09418433400279e-06 615 463 472 7.12973308082097e-08 57 2.16827867096623 2.16827867096623 1 4.27020222541392 115 472 946 458 611 98 57 533 614 990 199 314 M16944 WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN.html Genes down-regulated in esophageal adenocarcinoma (EAC) and Barret's esophagus (BE) relative to normal esophagi. 16449976 26/80 Leona Saunders 5.57656964834257e-08 7.63225151371406e-07 1935 1079.27272727273 473 5.06960889972519e-09 18 2.19871775485085 2.32675509028236 1 4.91645278877388 1932 473 452 195 18 2412 1712 2291 148 305 1934 315 M1348 SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP.html Genes up-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 12 h. 18794802 94/214 Jessica Robertson 5.49826834832512e-13 2.22111081726306e-11 110 566.909090909091 473 4.99842577120589e-14 106 2.16705670570049 2.37265510986985 1 8.43876656716531 384 1336 110 493 905 472 1177 241 539 106 473 316 M12225 PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP.html Up-regulated genes in angioimmunoblastic lymphoma (AILT) compared to normal T lymphocytes. 18006812 138/361 Arthur Liberzon 2.27314568321598e-28 3.80427166841074e-26 40 559.272727272727 474 2.0664960756509e-29 27 2.16361410428876 2.30898477197911 1 20.1034207287972 37 260 27 474 1556 461 658 736 1251 48 644 317 M13907 TSENG_IRS1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TSENG_IRS1_TARGETS_DN.html Down-regulated in brown preadipocytes with IRS1 [GeneID=3667] knockout vs wild type controls; the knockouts have severe defects in adipocyte differentiation. 15895078 121/236 John Newman 5.42379301497276e-07 3.27556613442881e-06 345 575.090909090909 474 4.93072213830336e-08 343 1.93323595422352 2.07046717024808 1 3.87577065979227 343 556 387 787 474 400 384 901 875 410 809 318 M5887 NABA_BASEMENT_MEMBRANES http://www.broadinstitute.org/gsea/msigdb/cards/NABA_BASEMENT_MEMBRANES.html Genes encoding structural components of basement membranes 22159717 23/56 Alexandra Naba 1.63948815763957e-09 3.32581883406885e-08 50 621.272727272727 475 1.49044378078305e-10 48 2.310102120088 2.39079842004431 1 6.31454088556737 48 475 222 726 2524 380 435 571 563 206 684 319 M12769 LU_TUMOR_VASCULATURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LU_TUMOR_VASCULATURE_UP.html Genes up-regulated in endothelial cells derived from invasive ovarian cancer tissue. 17308118 25/59 Arthur Liberzon 5.26647496427309e-08 7.36677662166677e-07 540 670.272727272727 476 4.78770462758611e-09 234 2.43135539975742 2.31587918074693 1 5.45030755754387 536 476 295 234 1890 615 463 1566 423 265 610 320 M15107 JAATINEN_HEMATOPOIETIC_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/JAATINEN_HEMATOPOIETIC_STEM_CELL_UP.html Genes up-regulated in CD133+ [GeneID=8842] cells (hematopoietic stem cells, HSC) compared to the CD133- cells. 16210406 180/523 Arthur Liberzon 7.76763488218227e-07 4.0714918409291e-06 45 735.363636363636 476 7.06148874975997e-08 41 1.70206213837783 1.76012086689876 1 3.35353838918131 216 1714 813 880 1810 44 476 210 1545 340 41 321 M15491 HAN_SATB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAN_SATB1_TARGETS_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer) after knockdown of SATB1 [GeneID=6304] by RNAi. 18337816 311/767 Jessica Robertson 5.21286602149702e-07 3.19731546815904e-06 925 647.272727272727 476 4.73897023334362e-08 218 1.63719228193364 1.78558575233628 1 3.28854348682976 925 236 476 218 463 665 1155 660 1538 345 439 322 M19944 GEISS_RESPONSE_TO_DSRNA_DN http://www.broadinstitute.org/gsea/msigdb/cards/GEISS_RESPONSE_TO_DSRNA_DN.html Genes down-pregulated by dsRNA in GRE cells (glioma; no interferon system). 11487589 14/25 John Newman 1.29737092435723e-06 5.63436529336234e-06 120 804.363636363636 478 1.17942880857793e-07 117 2.69785078236716 2.69785078236716 1 5.17638503231544 455 1217 1089 1127 1886 273 120 117 478 1899 187 323 M2084 WANG_METASTASIS_OF_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/WANG_METASTASIS_OF_BREAST_CANCER.html Genes whose expression in primary ER(-) [GeneID=2099] breast cancer tumors negatively correlates with developing distant metastases. 15721472 15/45 Arthur Liberzon 1.13183243216507e-05 2.79587073122063e-05 515 556.363636363636 479 1.0289438683066e-06 117 2.53750831011529 2.99100410968464 1 4.22347993042908 479 498 513 238 1729 513 339 471 117 432 791 324 M15326 HUANG_FOXA2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_FOXA2_TARGETS_UP.html Genes up-regulated in H358 cells (lung cancer) by inducible expression of FOXA2 [GeneID=3170] in a Tet-off system. 18593902 31/77 Leona Saunders 6.06573295439107e-07 3.47495592160468e-06 805 378.454545454545 482 5.51430420618736e-08 38 2.25658981240325 2.61568990639871 1 4.50286577489357 801 138 482 69 570 706 556 72 156 575 38 325 M7761 KEGG_MELANOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MELANOGENESIS.html Melanogenesis 48/110 KEGG 3.58307597859942e-07 2.61124324039143e-06 485 528.909090909091 483 3.25734232924064e-08 58 1.82806716866199 1.8273324820544 1 3.73070494826231 555 309 483 483 321 147 267 1323 1113 759 58 326 M2447 PLASARI_NFIC_TARGETS_BASAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_NFIC_TARGETS_BASAL_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) upon knockout of NFIC [GeneID=4782]. 19752192 26/64 Arthur Liberzon 2.34536057679022e-09 4.56031521279626e-08 215 527.636363636364 483 2.13214598117322e-10 119 2.25221182712444 2.32482903028514 1 6.04343719652878 211 147 232 433 1131 483 554 1125 586 119 783 327 M872 REACTOME_L1CAM_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_L1CAM_INTERACTIONS.html Genes involved in L1CAM interactions 46/131 Reactome 1.23774084889253e-07 1.40786642042934e-06 535 624.090909090909 486 1.12521901684455e-08 77 1.85948832756861 2.30811016765421 1 3.97718099525622 533 1349 985 291 77 486 617 122 433 1699 273 328 M16596 WATTEL_AUTONOMOUS_THYROID_ADENOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/WATTEL_AUTONOMOUS_THYROID_ADENOMA_UP.html Up-regulated genes characteristic for autonomous thyroid adenoma. 16027733 39/124 Arthur Liberzon 5.6324396794897e-07 3.34397885467784e-06 850 681.727272727273 489 5.12040101955212e-08 131 2.17445013339284 2.44598779125319 1 4.35222402723861 847 131 399 175 489 1528 1318 781 242 371 1218 329 M15069 ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_UP.html Genes up-regulated in A549 cells (lung carcinoma) upon infection with RSV (respiratory syncytial virus) and up-regulated by further treatment with ribavirin [PubChem=5064]. 12719586 26/82 John Newman 7.86177785644102e-08 1.00382264401315e-06 490 563.272727272727 490 7.14707103398588e-09 37 2.30972446641767 2.30571129494635 1 5.06419852315724 490 1731 830 789 37 336 285 66 669 838 125 330 M6220 BIOCARTA_AGR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AGR_PATHWAY.html Agrin in Postsynaptic Differentiation 22/59 BioCarta 2.72995311159632e-07 2.25439753774636e-06 530 522.818181818182 491 2.48177586395721e-08 70 2.8247805653563 3.3177941390586 1 5.83068271149091 527 491 793 94 232 508 734 409 70 1711 182 331 M17967 REACTOME_TIGHT_JUNCTION_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TIGHT_JUNCTION_INTERACTIONS.html Genes involved in Tight junction interactions 17/35 Reactome 2.04655803580251e-06 7.48647225274829e-06 610 505.454545454545 491 1.86050903602098e-07 233 2.38907053848646 -2.58073145201498 -1 4.47613665859332 609 635 491 720 1042 265 283 314 233 556 412 332 M253 BONOME_OVARIAN_CANCER_SURVIVAL_SUBOPTIMAL_DEBULKING http://www.broadinstitute.org/gsea/msigdb/cards/BONOME_OVARIAN_CANCER_SURVIVAL_SUBOPTIMAL_DEBULKING.html Genes whose expression in suboptimally debulked ovarian tumors is associated with survival prognosis. 18593951 333/779 Jessica Robertson 3.03736183711688e-07 2.360377706257e-06 470 797.090909090909 491 2.76123841496446e-08 233 1.47263023486701 1.61094806558916 1 3.02894443116048 585 233 1506 1356 272 369 468 466 1969 1053 491 333 M6920 MCCLUNG_CREB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_CREB1_TARGETS_UP.html Genes up-regulated in the nucleus accumbens (a major reward center in the brain) 8 weeks after induction of CREB1 [GeneID=1385] expression in a transgenic Tet-Off system. 14566342 61/159 John Newman 5.55411435677261e-08 7.63225151371406e-07 495 642.454545454545 493 5.04919499726514e-09 17 1.67832593062642 1.86351556047856 1 3.75282829410931 493 587 939 346 17 270 455 512 2144 1225 79 334 M12166 KRASNOSELSKAYA_ILF3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KRASNOSELSKAYA_ILF3_TARGETS_DN.html Down-regulated in GHOST(3)CXCR4 cells (osteosarcoma) upon ectopic expression of ILF3 [GeneID=3609]. 12036489 32/90 John Newman 1.93729568516269e-06 7.2106176176905e-06 205 552.727272727273 494 1.76117944647814e-07 203 2.48613609178694 2.72466840309391 1 4.67281456272058 203 727 409 226 1298 602 813 494 270 367 671 335 M522 REACTOME_CELL_CELL_COMMUNICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CELL_COMMUNICATION.html Genes involved in Cell-Cell communication 67/162 Reactome 8.85170629906822e-09 1.50833075336122e-07 3670 1855 495 8.04700575880278e-10 26 1.97427732626679 -1.87493726041552 -1 4.9227469202967 3666 292 261 26 421 3621 2392 4538 495 289 4404 336 M2578 LIM_MAMMARY_LUMINAL_MATURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_LUMINAL_MATURE_UP.html Genes consistently up-regulated in mature mammary luminal cells both in mouse and human species. 20346151 84/201 Daniel Hollern 3.29536343474332e-08 4.94938238948949e-07 30 560.454545454545 497 2.99578498554938e-09 29 1.84616563804658 -1.90323605071012 -1 4.25506237269342 29 561 316 594 2243 197 700 304 497 148 576 337 M8697 NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_UP.html Top 20 genes whose up-regulation correlated with gastrointestinal stromal tumors (GIST) and synovial sarcoma compared to other tumors. 11965276 15/52 John Newman 6.46181231097885e-06 1.7697283745907e-05 185 696.818181818182 498 5.87439208237335e-07 182 2.5276280992745 2.54984958904245 1 4.39053447629237 182 1383 468 706 2202 244 204 822 498 431 525 338 M10202 TSUNODA_CISPLATIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TSUNODA_CISPLATIN_RESISTANCE_UP.html Genes up-regulated in bladder cancer cells resistant to cisplatin [PubChem=2767] compared to the parental cells sensitive to the drug. 15608674 14/21 Leona Saunders 9.4496808865796e-07 4.5792352259061e-06 405 546 499 8.59062267773858e-08 216 2.40431991473941 2.40431991473941 1 4.69232696688948 401 882 657 329 698 499 1049 216 252 764 259 339 M1686 ZHONG_SECRETOME_OF_LUNG_CANCER_AND_ENDOTHELIUM http://www.broadinstitute.org/gsea/msigdb/cards/ZHONG_SECRETOME_OF_LUNG_CANCER_AND_ENDOTHELIUM.html Proteins secreted in co-culture of LKR-13 tumor cells (non-small cell lung cancer, NSCLC) and MEC stroma cells (endothelium). 18757440 81/177 Jessica Robertson 7.79727643613158e-09 1.35326064369306e-07 790 581.363636363636 500 7.08843314887894e-10 101 2.29273461059051 2.77820543943307 1 5.75628695703461 789 569 257 101 249 1122 1329 362 500 376 741 340 M11319 GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_UP.html Up-regulated genes from the set E (Fig. 5a): specific signature shared by cells expressing either MLL-AF4 [GeneID=4297;4299] or AF4-MLL fusion proteins alone, and those expressing both fusion proteins. 17130830 71/170 Arthur Liberzon 3.79271790588197e-07 2.69640744894893e-06 275 718.818181818182 501 3.44792596339322e-08 275 2.07292745550836 2.17452534035917 1 4.21985276203717 275 1860 352 784 1281 473 501 365 1045 411 560 341 M6977 BROWNE_HCMV_INFECTION_30MIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_30MIN_UP.html Genes up-regulated in primary fibroblast cell culture at 30 min time point after infection with HCMV (AD169 strain). 11711622 38/94 Arthur Liberzon 1.15185064841303e-05 2.83337120129315e-05 285 652.454545454545 501 1.04714243562193e-06 220 1.91234833663161 1.95511241764943 1 3.17890631141689 281 324 1180 626 1737 240 220 480 883 705 501 342 M9626 BOYERINAS_ONCOFETAL_TARGETS_OF_LET7A1 http://www.broadinstitute.org/gsea/msigdb/cards/BOYERINAS_ONCOFETAL_TARGETS_OF_LET7A1.html Embryonic genes targeted by LET7A1 [GeneID=406881] and which are up-regulated in many human cancers. 18413726 15/36 Jessica Robertson 4.5779198989693e-05 9.25078663831649e-05 470 651.363636363636 502 4.16183196584463e-06 244 2.48500052951187 2.55986121885254 1 3.66405846432973 467 502 767 661 2186 327 277 646 244 622 466 343 M2185 PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_UP http://www.broadinstitute.org/gsea/msigdb/cards/PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_UP.html Genes up-regulated in ovarian tumors from mouse models for the BMP SMAD signaling (gonad specific double knockout of SMAD1 and SMAD5 [GeneID=4086, 4090]). 17967875 98/227 Arthur Liberzon 2.95210225821577e-10 7.20497457395787e-09 330 554.909090909091 503 2.68372932601082e-11 72 1.61050972624817 1.79089391369878 1 4.79328558393558 330 72 185 718 349 580 549 503 1698 338 782 344 M1666 BURTON_ADIPOGENESIS_9 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_9.html Strongly down-regulated at 8-96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 75/142 John Newman 9.57161876633211e-07 4.60984738132019e-06 505 651.181818181818 505 8.70147539153917e-08 173 1.68890381855818 1.70285853673248 1 3.29431785356312 192 931 890 1007 701 258 291 173 1712 503 505 345 M1402 LEI_HOXC8_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEI_HOXC8_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblasts) by overexpression of HOXC8 [GeneID=3224]. 15699330 8/28 Kate Stafford 2.06305836838707e-06 7.53053726046618e-06 195 1049.18181818182 507 2.06306028368399e-07 147 1.93258022784452 1.93258022784452 1 3.61906090459675 193 1468 4364 954 1475 308 356 147 1436 507 333 346 M7581 NAKAMURA_CANCER_MICROENVIRONMENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_CANCER_MICROENVIRONMENT_UP.html Genes up-regulated in pancreatic cancer cells grown in orthotopic xenograft tumors compared to those grown in vitro. 17210693 24/63 Arthur Liberzon 1.21513637525706e-06 5.43332925043375e-06 510 605.090909090909 510 1.10467004219962e-07 114 2.33840969145983 2.44114663963636 1 4.50021001826739 437 482 636 510 1838 510 489 114 646 578 416 347 M16468 SEIDEN_MET_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/SEIDEN_MET_SIGNALING.html Genes down-regulated both in vivo and in vitro upon activation of MET [GeneID=4233] signaling. 16158056 15/41 Arthur Liberzon 1.2194369852795e-08 2.02634103298573e-07 1485 956.272727272727 510 1.10857908367156e-09 2 1.25008525071384 1.25008525071384 1 3.05842868897765 340 510 2311 1483 2 209 147 976 2635 1483 423 348 M1791 NADELLA_PRKAR1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NADELLA_PRKAR1A_TARGETS_DN.html Epithelial and mesenchymal markers down-regulated in MEF cells (embryonic fibroblasts) after knockout of PRKAR1A [GeneID=5573]. 18413734 7/22 Jessica Robertson 5.34294719421323e-06 1.52721495651653e-05 370 920.272727272727 511 5.34296004044483e-07 25 4.09632620432503 4.09632620432503 1 7.21122862891218 368 666 4468 300 1495 328 400 511 25 1009 553 349 M17068 BARRIER_CANCER_RELAPSE_TUMOR_SAMPLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_CANCER_RELAPSE_TUMOR_SAMPLE_DN.html Down-regulated genes in tumor samples from colon cancer patients who developed recurrence of the disease. 16091735 5/17 Leona Saunders 5.38393378897964e-07 3.26801991388064e-06 620 829.636363636364 513 5.38393509338352e-08 64 1.34527118849395 1.51943650979704 1 2.69750560968698 619 788 4170 941 513 205 64 429 73 1162 162 350 M16402 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_24 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_24.html Amplification hot spot 24: colocalized fragile sites and cancer genes in the 1q21-q24 region. 16751803 14/23 Arthur Liberzon 1.42842105925498e-06 5.93929111239472e-06 335 601.454545454545 517 1.29856544245849e-07 106 2.53300312432643 2.42032644088435 1 4.83889763824108 332 1304 972 745 867 228 232 517 106 1023 290 351 M10861 LI_PROSTATE_CANCER_EPIGENETIC http://www.broadinstitute.org/gsea/msigdb/cards/LI_PROSTATE_CANCER_EPIGENETIC.html Genes affected by epigenetic aberrations in prostate cancer. 15657340 21/46 Jessica Robertson 3.07295945065956e-06 9.98605269472308e-06 520 796.545454545455 517 2.79360340270631e-07 300 1.90413131000779 1.98300096188215 1 3.48047721550278 517 1294 1219 1306 1234 416 396 300 404 1254 422 352 M15588 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_UP.html Genes up-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 16 days after transduction. 16818636 80/276 Arthur Liberzon 2.4586050766621e-07 2.14593063349835e-06 645 539.363636363636 520 2.23509577402092e-08 87 1.78442371355108 1.92304600812736 1 3.69723047825623 645 87 334 520 960 539 739 184 1462 362 101 353 M750 REACTOME_ADENYLATE_CYCLASE_INHIBITORY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADENYLATE_CYCLASE_INHIBITORY_PATHWAY.html Genes involved in Adenylate cyclase inhibitory pathway 6/14 Reactome 2.89287745359022e-07 2.31211682689763e-06 430 1305.81818181818 523 2.89287783018359e-08 155 1.37029215133039 1.37029215133039 1 2.82294652769795 429 523 3993 878 285 155 190 1613 4089 2051 158 354 M10253 BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_DN.html Genes down-regulated in NIH3T3 cells (fibroblasts) after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins; the changes did not depend on expression of constitutively active (Q63L) form of RHOA [GeneID=387]. 17213802 39/107 Leona Saunders 3.52195351916828e-08 5.23932513994366e-07 175 678.363636363636 526 3.20177597777347e-09 172 3.03866772384774 3.27793778933783 1 6.97609229087232 172 1593 288 464 1904 344 563 526 362 593 653 355 M6937 CUI_TCF21_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CUI_TCF21_TARGETS_DN.html Genes most strongly down-regulated in kidney glomeruli isolated from TCF21 [GeneID=6943] knockout mice. 16207825 28/82 John Newman 1.3179639446835e-06 5.7079288768825e-06 385 543.727272727273 526 1.19814975840252e-07 55 2.38182850536998 2.35345345331376 1 4.56512619837012 383 1194 588 305 1037 174 294 828 526 597 55 356 M1419 MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_UP.html Up-regulated genes discriminating multiple myeloma samples by type of immunoglobulin they produce: IgG vs IgA. 12623842 23/51 Kate Stafford 5.96278683648423e-06 1.66418219867571e-05 415 739.181818181818 527 5.42072999802772e-07 343 2.33416528134478 2.24856657108364 1 4.07727149737603 415 343 463 506 1655 900 888 1256 503 527 675 357 M2612 ZWANG_CLASS_2_TRANSIENTLY_INDUCED_BY_EGF http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_CLASS_2_TRANSIENTLY_INDUCED_BY_EGF.html Class II of genes transiently induced by EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 21/64 Yaara Zwang 2.39121418192747e-07 2.12220258646063e-06 530 499.454545454545 528 2.17383131075663e-08 45 1.89448093435556 2.05896721092546 1 3.92860704489322 528 347 707 561 704 466 755 45 447 782 152 358 M15484 ONDER_CDH1_SIGNALING_VIA_CTNNB1 http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_SIGNALING_VIA_CTNNB1.html Genes changed in HMLE cells (mmortalized nontransformed mammary epithelium) after RNAi knockdown of both CDH1 and CTNNB1 [GeneID=999;1499], compared to the knockdown of CDH1 alone. 18483246 73/178 Jessica Robertson 8.3225421340898e-13 3.24995270336207e-11 445 549.272727272727 529 7.56594739462996e-14 92 2.18860364599527 2.34601283563997 1 8.3904284670007 444 92 114 223 1178 529 850 1182 627 105 698 359 M10381 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN.html Genes down-regulated in transformed NIH3T3 cells (fibroblasts transformed by activated KRAS [GeneID=3845]) vs normal cells. 16607279 131/252 Lauren Kazmierski 1.47510959844359e-06 6.06395169132821e-06 450 651.818181818182 531 1.34100962501085e-07 61 1.53709412878353 1.63646608253532 1 2.93130416160885 448 61 724 531 880 497 510 929 1535 372 683 360 M12868 KEGG_PATHWAYS_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PATHWAYS_IN_CANCER.html Pathways in cancer 189/425 KEGG 3.27781824824062e-09 6.09518107589505e-08 535 522.454545454545 532 2.97983477556755e-10 91 1.8247398337634 2.13625279474893 1 4.81235153608687 532 680 242 91 315 783 973 166 1019 374 572 361 M8349 MARCHINI_TRABECTEDIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARCHINI_TRABECTEDIN_RESISTANCE_DN.html Genes down-regulated in chondrosarcoma and ovarian carcinoma cell lines which developed resistance to trabectedin [PubChem=3199]. 15661559 75/164 John Newman 6.36928353833318e-06 1.75052566924512e-05 300 771.363636363636 534 5.79027452573149e-07 144 2.21062146383849 2.47989622793764 1 3.8437169791652 296 2575 618 252 1670 217 404 534 1080 695 144 362 M19025 MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP.html Up-regulated genes distinguishing in multiple myeloma (MM) samples with higher expression of TACI [GeneID=23495]. 15827134 303/758 Kevin Vogelsang 2.08401541627452e-11 6.59844340585299e-10 535 656.727272727273 535 1.89455946935842e-12 90 1.77465478307382 1.82379334235975 1 5.95528070467949 835 674 142 90 171 533 535 1656 1534 170 884 363 M7657 AMUNDSON_GAMMA_RADIATION_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_GAMMA_RADIATION_RESISTANCE.html Gene predicting resistance of the NCI-60 cell lines to gamma radiation. 18199535 27/64 Jessica Robertson 9.08046651514292e-08 1.11819282849268e-06 445 618.272727272727 536 8.25496989994347e-09 305 2.429540997146 2.46017986432779 1 5.28528853724838 441 338 305 786 760 801 1304 536 429 327 774 364 M17572 SMID_BREAST_CANCER_LUMINAL_B_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_LUMINAL_B_DN.html Genes down-regulated in the luminal B subtype of breast cancer. 18451135 326/967 Jessica Robertson 3.76132695164109e-49 4.40639452384754e-46 160 531.909090909091 536 3.41938813785556e-50 4 2.16632678956724 2.25233814166926 1 35.9151073804706 157 230 4 421 1132 536 655 683 1463 14 556 365 M159 PID_AMB2_NEUTROPHILS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AMB2_NEUTROPHILS_PATHWAY.html amb2 Integrin signaling 18832364 26/76 Pathway Interaction Database 6.37614946056079e-07 3.60301743795935e-06 490 604.454545454545 538 5.79650118957173e-08 184 2.07344792595202 2.06412282409926 1 4.12550708464596 488 1039 555 184 538 339 685 452 1454 670 245 366 M8245 REACTOME_CRMPS_IN_SEMA3A_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CRMPS_IN_SEMA3A_SIGNALING.html Genes involved in CRMPs in Sema3A signaling 12/29 Reactome 1.00131819196844e-05 2.52267583202372e-05 390 684.727272727273 540 9.1029340858499e-07 134 1.97607087467976 1.99748315685866 1 3.32126723456126 388 652 862 540 1999 316 134 259 712 1175 495 367 M7923 REACTOME_SEMAPHORIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMAPHORIN_INTERACTIONS.html Genes involved in Semaphorin interactions 39/106 Reactome 3.98460790536321e-07 2.76826476128525e-06 265 559.909090909091 543 3.62237147913615e-08 45 2.02187709840488 2.22263757026396 1 4.10748817829933 262 602 611 543 1123 93 130 60 1132 1558 45 368 M1098 GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN.html Genes down-regulated in ME-A cells (breast cancer) undergoing apoptosis upon serum starvation (5% to 0% FCS) for 22 hr. 17160024 170/346 Arthur Liberzon 3.6618421942278e-09 6.70288770396541e-08 1000 706.545454545455 543 3.32894745483895e-10 134 1.76182406000252 1.87433295412434 1 4.61984390304152 999 1475 246 634 365 543 494 981 1401 134 500 369 M12596 SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_DN.html Genes down-regulated in prostate cancer samples bearing the fusion of TMPRSS2 with ERG [GeneID=7113;2078]. 18505969 7/42 Jessica Robertson 2.30308458188796e-06 8.11447695543383e-06 395 968.818181818182 543 2.30308696878081e-07 210 1.75118884786437 1.75118884786437 1 3.25861539331735 394 520 4577 1026 1146 278 210 703 543 1010 250 370 M15368 ROSS_AML_WITH_PML_RARA_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_AML_WITH_PML_RARA_FUSION.html Top 100 probe sets for pediatric acute myeloid leukemia (AML) subtype t(15;17): has PML RARA fusion [GeneID=5371;5914]. 15226186 56/135 Kate Stafford 2.33344814779231e-07 2.0907338471424e-06 525 756 544 2.12131672299223e-08 332 2.08840116567885 2.30956881183484 1 4.33569446465724 521 589 332 544 2089 476 546 422 1404 519 874 371 M19522 REACTOME_ADENYLATE_CYCLASE_ACTIVATING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADENYLATE_CYCLASE_ACTIVATING_PATHWAY.html Genes involved in Adenylate cyclase activating pathway 5/11 Reactome 3.82208043055388e-07 2.69732965324932e-06 545 1368.54545454545 545 3.82208108792748e-08 219 1.77216024446095 1.77216024446095 1 3.60748557160408 545 390 3992 1385 382 284 219 1637 4090 1862 268 372 M6750 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_DN.html Genes down-regulated in nasopharyngeal carcinoma (NPC) positive for LMP1 [GeneID=9260], a latent gene of Epstein-Barr virus (EBV). 16912175 73/300 Arthur Liberzon 8.86283784305214e-18 6.48925908320974e-16 1065 984.545454545455 545 8.05712531186554e-19 58 2.37967810220146 2.43819465826928 1 13.2109020950463 1063 89 62 150 58 2099 2727 2499 545 104 1434 373 M14780 KUNINGER_IGF1_VS_PDGFB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KUNINGER_IGF1_VS_PDGFB_TARGETS_DN.html Genes down-regulated in C2AS12 cells (myoblast) by IGF1 [GeneID=3479] vs PDGFB [GeneID=5155]. 15475267 32/67 John Newman 3.99348480287842e-07 2.76826476128525e-06 550 623.363636363636 546 3.63044138889463e-08 328 1.62737385244237 1.6285247181395 1 3.30604608220013 546 328 545 522 358 595 764 1099 1048 366 686 374 M9334 VALK_AML_CLUSTER_11 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_11.html Top 40 genes from cluster 11 of acute myeloid leukemia (AML) expression profile; 67% of the samples are FAB M4 or M5. 15084694 31/75 Jessica Robertson 3.83741086000577e-06 1.18381219815583e-05 350 667.636363636364 546 3.48856141230197e-07 331 1.91768834202136 1.68721104852482 1 3.4534638277459 347 331 546 446 1322 424 351 1502 830 576 669 375 M14791 SABATES_COLORECTAL_ADENOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SABATES_COLORECTAL_ADENOMA_DN.html Genes down-regulated in colorectal adenoma compared to normal mucosa samples. 18171984 154/566 Leona Saunders 2.15373344590532e-23 2.46155973841764e-21 185 635 548 1.95793949627756e-24 40 2.01007128435945 2.04077210116962 1 15.1419983939946 185 548 40 193 1111 518 703 1162 1600 68 857 376 M14557 DORSEY_GAB2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/DORSEY_GAB2_TARGETS.html Genes up-regulated by expression of GAB2 [GeneID=9846] in K562 cells (chronic myeloid leukemia (CML) cell line with p210 BCR-ABL [GeneID=613;25]). 11830491 25/76 Kevin Vogelsang 5.61732105655691e-07 3.3409307573662e-06 250 655.454545454545 548 5.10665680985782e-08 187 2.24334125109074 2.26238875110004 1 4.49043632612324 247 1035 362 699 2169 341 203 672 548 187 747 377 M14833 GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_UP.html Up-regulated genes from the set B (Fig. 5a): specific signature shared by cells expressing either AF4-MLL or MLL-AF4 [GeneID=4299;4297] fusion proteins. 17130830 23/59 Arthur Liberzon 7.60285763528646e-06 2.01624170226103e-05 470 592.636363636364 549 6.91171264518764e-07 159 2.14446330604035 2.13994915613303 1 3.68057587551039 468 159 553 611 1594 549 276 556 348 300 1105 378 M515 LEE_METASTASIS_AND_ALTERNATIVE_SPLICING_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_METASTASIS_AND_ALTERNATIVE_SPLICING_UP.html Up-regulated genes displaying alternative splicing in MDA-MB-435 cells (breast cancer) whose metastatic potential has been reduced by expression of NME1 [GeneID=4830]. 18245461 66/152 Jessica Robertson 6.52971134972928e-07 3.63831479011075e-06 490 727.545454545455 550 5.93610298889224e-08 275 1.81095695492883 1.91821543877246 1 3.6004302331208 486 426 473 1169 550 506 588 1014 1726 275 790 379 M2207 FUKUSHIMA_TNFSF11_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/FUKUSHIMA_TNFSF11_TARGETS.html Genes up-regulated in RAW 264.7 cells (macrophage) upon stimulation with TNFSF11 [GeneID=8600]. 18710934 6/16 Arthur Liberzon 5.48756199863622e-08 7.5854618069644e-07 725 794.090909090909 550 5.48756213414623e-09 16 2.41192221991757 2.69186545847558 1 5.39554410064895 613 203 4630 54 724 724 1093 16 33 550 95 380 M115 PID_REG_GR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_REG_GR_PATHWAY.html Glucocorticoid receptor regulatory network 18832364 57/143 Pathway Interaction Database 9.73123743932774e-07 4.6578732012962e-06 885 578 551 8.84658340339879e-08 117 1.89271400549043 2.0655058522251 1 3.68874897225816 881 435 907 403 707 442 376 609 551 930 117 381 M14812 SEMBA_FHIT_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SEMBA_FHIT_TARGETS_UP.html Genes up-regulated in H1299 cells (non-small cell lung cancer, NSCLC) expressing the Y144F mutant form of FHIT [GeneID=2272]. 16407838 17/40 Leona Saunders 1.40763302858765e-06 5.89469917065392e-06 460 559.090909090909 551 1.27966720839891e-07 284 2.04275865111207 2.30616227771572 1 3.90480779246985 456 497 684 586 857 786 509 383 284 557 551 382 M10770 ZHAN_MULTIPLE_MYELOMA_MF_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_MF_UP.html Top 50 up-regulated genes in cluster MF of multiple myeloma samples with characteristic expression spike of MAF family transcription factors. 16728703 40/98 Kevin Vogelsang 8.14582023883085e-08 1.03445294415071e-06 465 623.090909090909 552 7.40529140040155e-09 20 1.9741787068924 2.29054600052353 1 4.31907611695722 464 1111 552 292 996 619 1207 20 504 775 314 383 M8729 AMIT_EGF_RESPONSE_480_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_480_HELA.html Genes whose expression peaked at 480 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 141/275 Leona Saunders 2.85054076935428e-07 2.29907642774426e-06 695 528.454545454545 554 2.59140103518092e-08 62 1.70286970682313 2.05426709311694 1 3.50962036241917 695 62 554 351 248 817 698 175 1095 663 455 384 M1439 ABBUD_LIF_SIGNALING_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/ABBUD_LIF_SIGNALING_2_UP.html Genes up-regulated in GH3 cells (pituitary cancer) after treatment with LIF [GeneID=3976]. 14576184 18/45 Kevin Vogelsang 4.6823729500431e-06 1.37478694510664e-05 300 693.545454545455 556 4.25671174164322e-07 299 2.29624023610238 2.42166621933602 1 4.08066083881078 299 634 487 509 1407 556 478 1310 514 614 821 385 M2401 KOHOUTEK_CCNT1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KOHOUTEK_CCNT1_TARGETS.html Genes down-regulated in E14 ES (embryonic stem) cells upon knockdown of CYCT1 [GeneID=904] by RNAi. 19364821 47/86 Arthur Liberzon 3.52807401700524e-11 1.05977915664657e-09 160 1192.45454545455 556 3.20734001551074e-12 115 2.20620586669982 2.50466742425275 1 7.23751240265834 1907 115 150 158 556 3689 2448 1200 446 157 2291 386 M17471 SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP.html Genes up-regulated in invasive ductal carcinoma (IDC) relative to ductal carcinoma in situ (DCIS, non-invasive). 16707453 224/604 Arthur Liberzon 1.24021680175503e-34 4.19647948549382e-32 680 688.363636363636 559 1.12746981977731e-35 5 1.87927318081931 1.91957043741657 1 21.5537169149886 5 676 12 802 2125 325 350 677 1992 49 559 387 M2581 DURAND_STROMA_S_UP http://www.broadinstitute.org/gsea/msigdb/cards/DURAND_STROMA_S_UP.html Genes up-regulated in the HSC supportive stromal cell lines. 197/546 Charles Durand 1.21019534612726e-20 1.09057219076007e-18 145 551.090909090909 560 1.10017758738842e-21 38 1.92265192634021 2.08223307932104 1 12.6235924673979 144 247 51 475 560 678 832 883 1267 38 887 388 M7585 TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_UP.html Genes up-regulated in ductal carcinoma vs normal ductal breast cells. 17389037 39/114 Arthur Liberzon 6.77378760571097e-07 3.74315668872189e-06 615 555.545454545455 561 6.15799062850661e-08 220 1.86421342479054 1.90972820968143 1 3.69790420310978 612 851 666 246 561 414 545 397 865 734 220 389 M8510 POMEROY_MEDULLOBLASTOMA_DESMOPLASIC_VS_CLASSIC_DN http://www.broadinstitute.org/gsea/msigdb/cards/POMEROY_MEDULLOBLASTOMA_DESMOPLASIC_VS_CLASSIC_DN.html Top down-regulated marker genes for medulloblastoma classification: desmoplastic vs classic morphology. 11807556 49/113 Jean Junior 2.32648472176698e-05 5.16923063357045e-05 495 691.090909090909 561 2.11500847685963e-06 230 2.09484889297848 2.34800853447584 1 3.28233033613053 230 844 690 657 2200 492 718 358 561 358 494 390 M1253 INAMURA_LUNG_CANCER_SCC_UP http://www.broadinstitute.org/gsea/msigdb/cards/INAMURA_LUNG_CANCER_SCC_UP.html Up-regulated genes characteristic to the squamous cell carcinoma (SCC) type of non-small cell lung cancer (NSCLC). 16007138 17/33 Arthur Liberzon 1.0360444624246e-06 4.84521392307551e-06 175 686.181818181818 563 9.41859045753286e-08 174 2.94867149720257 2.94867149720257 1 5.72826813040301 174 2315 494 443 735 573 237 708 558 748 563 391 M9483 SUNG_METASTASIS_STROMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SUNG_METASTASIS_STROMA_UP.html Genes up-regulated in metastatic vs non-metastatic stromal cells originated from either bone or prostate tissues. 19047182 93/236 Jessica Robertson 6.08180755833748e-07 3.4755305144353e-06 240 635.727272727273 563 5.52891749057116e-08 131 1.53925441309086 1.7074425220713 1 3.07143319018437 238 563 997 416 523 441 131 744 1609 710 621 392 M2271 STEGER_ADIPOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/STEGER_ADIPOGENESIS_DN.html Genes down-regulated during adipogenesis of 3T3-L1 cells (fibroblast). 18285465 16/34 Arthur Liberzon 4.51769898883382e-05 9.1520361246926e-05 220 726.272727272727 564 4.10708342038995e-06 218 2.10176471960191 2.16466993888624 1 3.1025695731166 218 496 564 675 2279 540 585 1151 246 495 740 393 M17400 BIOCARTA_ALK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ALK_PATHWAY.html ALK in cardiac myocytes 24/51 BioCarta 8.11581888295288e-07 4.16091108156643e-06 295 640.272727272727 565 7.37801988807908e-08 55 1.79022682365688 1.9792995479297 1 3.52107352498698 291 1375 1203 915 1087 129 55 88 565 1187 148 394 M12144 BROWNE_HCMV_INFECTION_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_48HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 48 h time point that were not down-regulated at the previous time point, 24 h. 11711622 310/965 John Newman 1.42263262494996e-13 6.41005430818801e-12 565 454.636363636364 565 1.29330238631823e-14 26 1.83973778078724 2.03038065379705 1 7.52708893017303 565 26 99 57 139 709 966 669 997 124 650 395 M1275 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2.html Cluster PAM2: genes up-regulated in hepatocellular carcinoma (HCC) vs normal liver tissue from mice deficient for TXNIP [GeneID=10628]. 16607285 108/290 Leona Saunders 9.63467865854117e-08 1.16964000502394e-06 1090 711.454545454545 566 8.75879916407475e-09 55 1.75752305106846 2.02335667545668 1 3.81081266457896 1090 69 351 535 55 1404 1528 277 976 566 975 396 M14566 PEREZ_TP53_AND_TP63_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/PEREZ_TP53_AND_TP63_TARGETS.html Genes up-regulated in HMEC cells (primary mammary epithelium) upon expression of both of TP53 [GeneID=7157] and the transcriptionally active isoform of TP63 [GeneID=8626] off adenoviral vectors. 17563751 138/385 Leona Saunders 1.21572444965764e-09 2.61324989499802e-08 570 607.909090909091 569 1.10520404575404e-10 165 1.85920608124388 1.81462100040655 1 5.15320565456214 569 552 210 165 542 601 910 1138 1118 169 713 397 M47 PID_INTEGRIN_CS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN_CS_PATHWAY.html Integrin family cell surface interactions 18832364 14/27 Pathway Interaction Database 8.97050879338233e-08 1.11259227184017e-06 575 547.727272727273 573 8.15500832650471e-09 46 2.05342258236038 2.55612577903784 1 4.46870723145569 610 369 1073 227 46 605 573 574 365 1371 212 398 M9331 YAUCH_HEDGEHOG_SIGNALING_PARACRINE_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAUCH_HEDGEHOG_SIGNALING_PARACRINE_DN.html Genes down-regulated in mouse stroma of pancreatic adenocarcinoma zenografts after treatment with HhAntag, a hedgehog (Hh) pathway inhibitor. 18754008 132/465 Jessica Robertson 1.27256862491795e-07 1.43347513854941e-06 575 636.454545454545 573 1.15688063502587e-08 80 2.11187778629802 2.36272427708959 1 4.51096278148191 573 1168 361 408 80 386 487 1474 762 665 637 399 M2003 MIKKELSEN_ES_ICP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_ICP_WITH_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 K27 trimethylation mark (H3K27me3) in embryonic stem cells (ES). 17603471 33/100 Arthur Liberzon 6.49406636557732e-08 8.71954011148864e-07 550 731.818181818182 573 5.90369687024758e-09 135 2.35989571076748 2.4001230394332 1 5.22696162161067 550 135 299 573 450 690 775 2334 630 319 1295 400 M915 REACTOME_NITRIC_OXIDE_STIMULATES_GUANYLATE_CYCLASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NITRIC_OXIDE_STIMULATES_GUANYLATE_CYCLASE.html Genes involved in Nitric oxide stimulates guanylate cyclase 7/27 Reactome 7.98082189335309e-07 4.11774058972012e-06 275 843.636363636364 576 7.98082475956283e-08 85 2.69891691656998 2.69891691656998 1 5.31278174916686 274 1075 4052 683 969 212 256 94 576 1004 85 401 M929 SABATES_COLORECTAL_ADENOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SABATES_COLORECTAL_ADENOMA_UP.html Genes up-regulated in colorectal adenoma compared to normal mucosa samples. 18171984 74/249 Leona Saunders 6.64016429505121e-17 4.44511569808714e-15 2415 1131.63636363636 578 6.03651299550107e-18 67 2.14737077925095 2.56868648983981 1 11.2652868225609 2414 86 67 256 568 3340 2478 894 578 77 1690 402 M1277 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM3 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM3.html Cluster PAM3: genes most highly up-regulated in hepatocellular carcinoma (HCC) vs normal liver tissue from mice deficient for TXNIP [GeneID=10628]. 16607285 62/153 Leona Saunders 3.44081216784951e-09 6.32299836021286e-08 410 788.818181818182 580 3.12801106657359e-10 245 2.54643540938566 2.65335914951387 1 6.70083200203469 406 2107 245 505 1823 652 879 414 675 580 391 403 M10165 TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP.html Genes up-regulated in lobular carcinoma vs normal ductal breast cells. 17389037 50/129 Arthur Liberzon 1.77114021811699e-07 1.76962965076679e-06 110 950.909090909091 581 1.61012760064099e-08 108 2.20909795363957 2.26932390359797 1 4.64474612735494 108 2005 323 1172 2733 307 375 594 1745 581 517 404 M16488 DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY http://www.broadinstitute.org/gsea/msigdb/cards/DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY.html The lung adenocarcinoma TSP (tumor sequencing project) genes that were found significantly mutated by at least one method. 18948947 26/58 Jessica Robertson 5.99316713480392e-07 3.46715817206064e-06 655 546.727272727273 582 5.44833524313026e-08 100 2.34427242053757 2.3266029854721 1 4.67866625891719 654 1195 721 100 516 582 387 347 183 672 657 405 M11363 NIELSEN_GIST http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_GIST.html A cluster of genes specifically up-regulated in gastrointestinal stromal tumors (GIST). 11965276 65/182 Arthur Liberzon 1.04832641669442e-06 4.87830942267135e-06 320 617 582 9.53024469304436e-08 50 1.75318139653161 1.73918001914374 1 3.40394198054053 320 582 881 1074 752 96 105 310 1408 1209 50 406 M16003 LOPEZ_MESOTHELIOMA_SURVIVAL_OVERALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_OVERALL_DN.html Top genes associated with unfavorable overall survival of mesothelioma patients after surgery. 16540645 16/40 Arthur Liberzon 7.3374249090109e-05 0.000140976972562184 195 721.454545454545 583 6.67060876157298e-06 194 2.75882726470007 2.75882726470007 1 3.88329664132224 194 755 626 550 2533 583 473 532 200 690 800 407 M14183 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_17 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_17.html Amplification hot spot 17: colocalized fragile sites and cancer genes in the 1q11-q44 region. 16751803 17/31 Arthur Liberzon 1.4771522057568e-06 6.06655147780573e-06 885 833.545454545455 584 1.342866543242e-07 128 2.53300312432643 2.42032644088435 1 4.83037280150807 402 2241 1208 883 881 477 582 584 128 1265 518 408 M1955 MIKKELSEN_MCV6_ICP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MCV6_ICP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the bivalent trimethylation marks at H3K4 (H3K4me3) and H3K27 (H3K27me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state). 18509334 20/64 Jessica Robertson 3.76982779590397e-07 2.69293216693181e-06 345 771.818181818182 587 3.42711676535092e-08 260 2.74723125287295 2.90951491889266 1 5.59309361129521 344 489 350 587 2056 859 957 1028 260 296 1264 409 M1255 INAMURA_LUNG_CANCER_SCC_DN http://www.broadinstitute.org/gsea/msigdb/cards/INAMURA_LUNG_CANCER_SCC_DN.html Down-regulated genes characteristic to the squamous cell carcinoma (SCC) type of non-small cell lung cancer (NSCLC). 16007138 8/24 Arthur Liberzon 2.29240837702187e-05 5.10804833795744e-05 360 1083.18181818182 588 2.29243202547797e-06 234 1.90028841390736 1.90028841390736 1 2.98107347875825 358 664 4276 1644 1990 274 234 573 588 788 526 410 M15374 VERRECCHIA_RESPONSE_TO_TGFB1_C6 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C6.html Cluster 6: ECM related genes up-regulated in dermal fibroblasts later than 30 min after TGFB1 [GeneID=7040] addition; slowly increased up to 120 min time point, then reached a plateau. 11279127 9/19 Arthur Liberzon 1.00319871598936e-05 2.52491901949986e-05 590 1342.90909090909 589 1.00320324485262e-06 82 1.67322568081543 1.67322568081543 1 2.81202621769697 589 2405 4605 1490 1722 398 82 579 528 1825 549 411 M181 PID_BMP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BMP_PATHWAY.html BMP receptor signaling 18832364 26/54 Pathway Interaction Database 5.86101542768293e-06 1.63968467427595e-05 495 1433.63636363636 591 5.32821003823653e-07 174 1.81872127796118 1.96557056493587 1 3.18118621553964 494 3643 2191 2821 1765 480 174 208 380 3023 591 412 M1632 BURTON_ADIPOGENESIS_11 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_11.html Strongly down-regulated at 2-96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 53/129 John Newman 6.50256830573872e-07 3.63616170413981e-06 200 680.727272727273 591 5.91142747973818e-08 75 1.70499653441439 1.94180212190253 1 3.38992663766862 199 591 1130 1016 1440 131 240 75 1587 940 139 413 M2575 LIM_MAMMARY_LUMINAL_PROGENITOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_LUMINAL_PROGENITOR_UP.html Genes consistently up-regulated in mammary luminal progenitor cells both in mouse and human species. 20346151 44/91 Daniel Hollern 1.2013175993776e-12 4.57672704933614e-11 20 666.454545454545 592 1.09210690852569e-13 17 2.00497319364752 -2.04049776592515 -1 7.57748434629339 17 1019 117 979 2358 225 338 592 822 88 776 414 M1350 SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP.html Genes up-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 48 h. 18794802 327/800 Jessica Robertson 5.95055028431687e-30 1.0724722550888e-27 25 1135.45454545455 593 5.40959116756085e-31 18 1.88290449512263 -1.71985118650266 -1 18.5618933255785 2201 21 25 148 533 1111 3428 2409 593 18 2003 415 M10508 HARRIS_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/HARRIS_HYPOXIA.html Genes known to be induced by hypoxia 11902584 72/148 John Newman 1.97728547170072e-06 7.32455313864788e-06 330 639.818181818182 593 1.79753386256378e-07 70 2.04561805961742 2.20278752145261 1 3.83974830897711 329 1532 593 665 1134 214 407 249 1226 619 70 416 M2712 TRAYNOR_RETT_SYNDROM_UP http://www.broadinstitute.org/gsea/msigdb/cards/TRAYNOR_RETT_SYNDROM_UP.html Genes up-regulated in primary fibroblasts from Rett syndrom patients who carry mutations inactivating MECP2 [GeneID=4204]. 12418965 28/68 John Newman 1.40016787147419e-07 1.52231708717588e-06 595 724.272727272727 594 1.27287996416952e-08 27 2.33733915839968 2.43974968595858 1 4.97023582159648 355 2396 672 1069 1377 313 538 31 594 595 27 417 M16756 MURAKAMI_UV_RESPONSE_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/MURAKAMI_UV_RESPONSE_6HR_DN.html Genes down-regulated in primary keratinocytes at 6 h after UVB irradiation. 11532376 17/31 John Newman 2.66571572466159e-06 8.95451174606755e-06 315 769.909090909091 595 2.42338086789582e-07 308 2.19434509987054 2.30711957914367 1 4.04892675189854 312 1500 991 1504 1175 409 308 417 509 749 595 418 M1499 WHITESIDE_CISPLATIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WHITESIDE_CISPLATIN_RESISTANCE_UP.html Genes up-regulated in NCI-H2170 cells (lung cancer) upon induction of resistance to cisplatin [PubChem=2767]. 14737109 11/25 John Newman 3.16467596365595e-07 2.41919601397908e-06 910 1003.63636363636 597 2.87697856262838e-08 189 1.48135957354078 1.35692694322875 1 3.04111101949257 907 189 1687 582 283 597 303 4196 342 1068 886 419 M2611 ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF.html Class I of genes transiently induced by EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 330/861 Yaara Zwang 8.52387620262564e-07 4.26956588478944e-06 525 709.909090909091 598 7.74898136835822e-08 27 1.56341987178153 1.72667383936654 1 3.06858480150933 522 27 667 542 650 568 1105 720 1921 598 489 420 M10156 BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_UP.html Genes up-regulated in SaOS-2 cells (osteosarcoma) upon expression of PAX3-FOXO1 [GeneID=5077;2308] fusion protein off an adenoviral vector. 15688035 43/118 Leona Saunders 3.95126440826869e-07 2.75940760315158e-06 180 560.545454545455 600 3.59205919811593e-08 28 1.78890139408055 1.81362726167961 1 3.63510293152525 180 1109 727 961 352 105 28 896 1013 600 195 421 M4621 ROSS_AML_OF_FAB_M7_TYPE http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_AML_OF_FAB_M7_TYPE.html Top 100 probe sets for pediatric acute myeloid leukemia (AML) subtype FAB M7 (also known as acute megakaryoblastic leukemia, AMKL). 15226186 49/126 Jean-Pierre Bourquin 3.15378573551304e-06 1.01851412519739e-05 600 788.090909090909 600 2.8670820514517e-07 167 1.99802719066475 2.38921060642972 1 3.64584404465397 600 1429 607 882 2141 516 353 167 1144 441 389 422 M945 MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_UP.html Genes up-regulated in normal bone marrow plasma cells (BMPC) compared to polyclonal plasmablasts (PPC) that also distinguished multiple myeloma (MM) samples by expression of levels of TACI (TNFRSF13B) [GeneID=23495]. 15827134 83/185 Kevin Vogelsang 7.18067502161851e-06 1.92870586612568e-05 585 761.909090909091 600 6.52790769003723e-07 326 1.77141457341598 1.87023228717226 1 3.05278809143523 378 930 600 932 1565 326 416 750 1316 583 585 423 M67 PID_ARF6_TRAFFICKING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF6_TRAFFICKING_PATHWAY.html Arf6 trafficking events 18832364 29/75 Pathway Interaction Database 2.89553393145612e-07 2.31211682689763e-06 605 672.272727272727 601 2.63230392050218e-08 63 2.09883575945538 2.72684042133405 1 4.32382329193049 601 1284 1090 832 252 176 155 169 842 1931 63 424 M9128 KIM_WT1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_UP.html Genes up-regulated in UB27 cells (osteosarcoma) at any time point after inducing the expression of a mutant form of WT1 [GeneID=7490]. 17430890 163/336 Arthur Liberzon 3.30156129988568e-07 2.47466829669015e-06 605 690.545454545455 603 3.00141981395844e-08 298 1.89520307170227 1.98106513465279 1 3.88387739764875 603 1242 475 754 298 403 497 877 1272 647 528 425 M12314 KANG_GIST_WITH_PDGFRA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_GIST_WITH_PDGFRA_UP.html Genes up-regulated in gastrointestinal stromal tumors (GIST) with PDGFRA [GeneID=5156] mutations. 15690055 37/116 Arthur Liberzon 4.01241358979371e-07 2.7690972138105e-06 265 620.090909090909 605 3.64764938326151e-08 61 2.03086471226875 2.19788393507114 1 4.12564978237129 261 945 605 1110 1777 158 113 61 679 971 141 426 M2259 KIM_GLIS2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_GLIS2_TARGETS_UP.html Partial list of genes up-regulated in the kidney of GLIS2 [GeneID=84662] knockout mice compared to the wild type. 18227149 79/190 Arthur Liberzon 5.74067979921647e-12 1.96356390796558e-10 85 697 607 5.21879981748313e-13 82 2.01671776631649 2.04011455181291 1 7.15562197691639 82 696 131 777 2092 329 306 880 1523 244 607 427 M17175 MURAKAMI_UV_RESPONSE_24HR http://www.broadinstitute.org/gsea/msigdb/cards/MURAKAMI_UV_RESPONSE_24HR.html Genes down-regulated in primary keratinocytes at 24 h after UVB irradiation. 11532376 17/40 John Newman 1.33847348433853e-06 5.74893377416163e-06 295 698.818181818182 608 1.21679481696593e-07 293 2.21864122349697 2.3344527182234 1 4.24983255069871 293 1133 979 1547 831 385 304 368 489 750 608 428 M2423 PARK_OSTEOBLAST_DIFFERENTIATION_BY_PHENYLAMIL_DN http://www.broadinstitute.org/gsea/msigdb/cards/PARK_OSTEOBLAST_DIFFERENTIATION_BY_PHENYLAMIL_DN.html Genes down-regulated in M2-10B4 cells (osteoblast) in response to phenylamil [PubChem=4755]. 19433444 6/13 Arthur Liberzon 3.38341736297296e-06 1.07416624409833e-05 725 1106.54545454545 608 3.38342251436487e-07 104 1.99943401445907 2.20514671468852 1 3.63152529875736 721 207 4665 1375 2618 608 151 334 520 869 104 429 M1223 DARWICHE_PAPILLOMA_RISK_HIGH_VS_LOW_DN http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_HIGH_VS_LOW_DN.html Genes that classify skin lesions into low risk papilloma. 17525749 27/58 Arthur Liberzon 5.52526219623756e-06 1.5653796040852e-05 1040 776.181818181818 609 5.02297824807947e-07 320 1.7187847594227 1.9108632270432 1 3.01903752245705 577 340 1038 1474 1476 320 348 1038 609 900 418 430 M1111 GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_DN.html Down-regulated genes from the set A (Fig. 5a): specific to cells expressing MLL-AF4 [GeneID=4297;4299] fusion protein alone. 17130830 68/206 Arthur Liberzon 9.10327035765339e-07 4.46212603514265e-06 840 589.181818181818 610 8.27570374950223e-08 82 1.77661178781325 1.9156885013705 1 3.47458357688823 840 100 557 82 680 610 1023 696 862 518 513 431 M8191 ALONSO_METASTASIS_EMT_UP http://www.broadinstitute.org/gsea/msigdb/cards/ALONSO_METASTASIS_EMT_UP.html EMT (epithelial-mesenchymal transition) genes up-regulated genes in melanoma tumous that developed metastatic disease compared to primary melanoma that did not. 17409456 36/69 Jessica Robertson 4.67826374685173e-07 2.97857933665043e-06 535 659.181818181818 610 4.25296794697918e-08 172 2.31778443091316 2.45510804597453 1 4.68168782386026 534 1439 358 610 768 402 1116 172 1039 637 176 432 M18679 SCIAN_CELL_CYCLE_TARGETS_OF_TP53_AND_TP73_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCIAN_CELL_CYCLE_TARGETS_OF_TP53_AND_TP73_UP.html Cell cycle genes up-regulated in H1299 cells (lung cancer) after overexpression of either P53 or P73 [GeneID=7157;7161]. 17982488 10/17 Jessica Robertson 5.12462373508829e-08 7.23312856103124e-07 600 884.909090909091 611 4.65874895859997e-09 15 3.22949172204469 3.22949172204469 1 7.2488557090812 597 2087 1091 1319 1934 415 611 15 206 1365 94 433 M695 REACTOME_GLYCOSAMINOGLYCAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOSAMINOGLYCAN_METABOLISM.html Genes involved in Glycosaminoglycan metabolism 51/122 Reactome 2.63501205066722e-06 8.87682708082428e-06 290 794.818181818182 612 2.39546836973885e-07 288 1.6648535839659 1.77105104942076 1 3.07423086662305 288 438 786 1416 1170 501 430 321 1763 1018 612 434 M2386 GILDEA_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/GILDEA_METASTASIS.html Top genes down-regulated in metastatic (T24T) vs non-metastatic (T24) bladder cancer cell lines. 12438227 29/78 Kevin Vogelsang 1.32703248142993e-05 3.18406257449087e-05 375 735.545454545455 612 1.2064004419201e-06 299 2.05143999853613 2.14403760245163 1 3.37211777578801 372 612 512 497 1786 628 792 1104 315 299 1174 435 M2687 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_15 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_15.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 15. 12554760 30/75 Arthur Liberzon 6.21709110402366e-06 1.72040678779681e-05 405 815.363636363636 615 5.65191697571354e-07 353 2.07284311710773 2.21783058798917 1 3.60986583370168 404 615 525 353 1512 848 456 1790 747 533 1186 436 M7409 MODY_HIPPOCAMPUS_NEONATAL http://www.broadinstitute.org/gsea/msigdb/cards/MODY_HIPPOCAMPUS_NEONATAL.html Genes highly expressed in the neonatal hippocampus (clusters 4 and 8). 11438693 39/85 John Newman 3.5036725844055e-06 1.10411632350532e-05 620 750.272727272727 617 3.18516196753762e-07 419 2.44872293747716 2.74978243789085 1 4.43686811250869 617 458 537 419 1285 725 1118 1009 486 1057 542 437 M7396 SWEET_LUNG_CANCER_KRAS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SWEET_LUNG_CANCER_KRAS_DN.html Genes down-regulated in the Kras2LA mouse lung cancer model with mutated KRAS [GeneID=3845]. 15608639 296/758 Arthur Liberzon 2.75813145079702e-29 4.78689036238327e-27 85 725.363636363636 619 2.5073922279973e-30 26 1.72842131725852 1.7633382754047 1 16.62853033521 83 232 26 719 1373 563 619 1274 2148 35 907 438 M5466 WINTER_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/WINTER_HYPOXIA_UP.html Genes up-regulated in head and neck tumor samples which clustered around known hypoxia genes. 17409455 81/174 Arthur Liberzon 2.18577030966819e-06 7.82775852839293e-06 515 660.181818181818 621 1.98706589209443e-07 155 1.78113174649994 2.08789064105481 1 3.32450464243118 511 698 621 350 1068 1038 943 155 903 375 600 439 M16201 WONG_ENDMETRIUM_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WONG_ENDMETRIUM_CANCER_UP.html Genes up-regulated in cancer endometrium samples compared to the normal endometrium. 17043662 19/52 Arthur Liberzon 1.39219877657927e-06 5.86253407200259e-06 960 679.454545454545 622 1.26563605235271e-07 201 2.08427876684066 -2.19291074055845 -1 3.98598539253312 959 869 622 1022 850 571 1210 224 201 489 457 440 M16009 ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN.html Genes whose DNA is hyper-methylated in hepatocellular carcinoma (HCC) compared to normal liver. 18413731 385/1587 Jessica Robertson 1.39122526733381e-14 7.32503550868114e-13 115 528.545454545455 622 1.26475024303074e-15 84 1.85751606796163 2.00878734262308 1 8.23945373864505 622 992 84 115 628 170 891 864 1204 115 129 441 M11980 REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS.html Genes involved in Adherens junctions interactions 8/34 Reactome 1.32045959901e-07 1.46627338411395e-06 660 791.272727272727 623 1.32045967747262e-08 34 2.52173323218556 2.98535539887866 1 5.3773563226596 658 784 4015 648 297 220 84 34 623 1130 211 442 M1270 CALVET_IRINOTECAN_SENSITIVE_VS_RESISTANT_DN http://www.broadinstitute.org/gsea/msigdb/cards/CALVET_IRINOTECAN_SENSITIVE_VS_RESISTANT_DN.html Genes down-regulated in neuroblastoma xenografts: sensitive vs resistant to the topoisomerase inhibitor irinotecan [GeneID=3750]. 16501609 3/7 Arthur Liberzon 5.5189845056313e-08 7.6064592333495e-07 495 1096.54545454545 624 5.51898464269766e-09 3 5.03253732493544 5.03253732493544 1 11.2557322162374 492 1232 4287 287 2058 624 1099 17 3 1395 568 443 M1794 WILSON_PROTEASES_AT_TUMOR_BONE_INTERFACE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WILSON_PROTEASES_AT_TUMOR_BONE_INTERFACE_DN.html Protease genes down-regulated at tumor-bone interface compared to the tumor alone area. 18632634 2/7 Jessica Robertson 1.43294053515885e-05 3.39643871914737e-05 615 1043.2 624.5 1.59216629011281e-06 72 2.57893913983638 -2.57893913983638 -1 4.21277619043993 614 670 4477 NA 2160 319 77 324 72 1084 635 444 M8364 TSENG_ADIPOGENIC_POTENTIAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/TSENG_ADIPOGENIC_POTENTIAL_DN.html Genes showing decreasing expression in brown preadipocytes with increasing ability of the cells to differentiate. 15895078 44/93 John Newman 4.60251856785179e-09 8.26337241722355e-08 145 677.363636363636 625 4.18410779770955e-10 143 2.24114592866069 2.27434715417216 1 5.80225727293462 143 1187 250 867 2244 276 161 625 652 335 711 445 M10150 LI_CISPLATIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LI_CISPLATIN_RESISTANCE_DN.html Genes consistently down-regulated in ACRP cells (ovarian cancer, resistant to cisplatin [PubChem=2767]) compared to the parental sensitive A2780 cells, regardless of cisplatin exposure. 17072341 22/61 Arthur Liberzon 1.52838932188144e-08 2.47821189008181e-07 400 863.545454545455 626 1.38944484772682e-09 271 2.3744690595672 2.16568181240734 1 5.73343949169845 399 626 271 429 1787 784 1035 1930 1320 481 437 446 M6900 MAHADEVAN_GIST_MORPHOLOGICAL_SWITCH http://www.broadinstitute.org/gsea/msigdb/cards/MAHADEVAN_GIST_MORPHOLOGICAL_SWITCH.html Genes up-regulated in the GIST (gastrointestinal stromal tumor) cell line resistant to imatinib [PubChem=5291] that may correlate with the morphological switch in these cells. 17325667 12/32 Arthur Liberzon 2.19966364432389e-07 2.02299711222616e-06 620 572 628 1.99969442205151e-08 123 2.29571891741326 2.54082564406379 1 4.77810608151065 618 1057 789 123 177 643 746 954 273 628 284 447 M3102 SMID_BREAST_CANCER_ERBB2_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_ERBB2_UP.html Genes up-regulated in the erbb2 subype of breast cancer samples, characterized by higher expression of ERBB2 [GeneID=2064]. 18451135 102/290 Jessica Robertson 9.34078918636665e-07 4.54055374764669e-06 845 626.272727272727 629 8.49163013844879e-08 73 1.56545454133527 -1.71618932047425 -1 3.05728580586712 752 73 845 566 692 219 843 629 1440 240 590 448 M1935 MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 trimethylation marks at k4 (H3K4me3) and K27 ((H3K27me3) in neural precursor cells (NPC). 18600261 70/261 Jessica Robertson 1.23989703663032e-07 1.40786642042934e-06 710 643.636363636364 630 1.12717918773602e-08 197 2.17888607125442 2.20639506507298 1 4.66032733065151 708 1173 313 197 817 630 459 963 326 394 1100 449 M2142 HOELZEL_NF1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOELZEL_NF1_TARGETS_UP.html Genes up-regulated in SH-SY5Y cells (neuroblastoma) after knockdown of NF1 [GeneID=4763] by RNAi. 20655465 85/230 Arthur Liberzon 1.37843410374669e-06 5.84912142521847e-06 600 736.727272727273 630 1.25312269765495e-07 118 1.72373521661631 1.97801021812276 1 3.29710681841131 596 567 751 984 1496 397 717 118 1531 630 317 450 M13715 LANDIS_ERBB2_BREAST_TUMORS_65_DN http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_TUMORS_65_DN.html Down-regulated genes from the 65 most significantly changed (p<0.01) genes identified by two analytical methods in the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 31/55 Leona Saunders 3.28031667450505e-07 2.46734573623285e-06 600 781.727272727273 631 2.98210651237979e-08 263 2.06193110948863 2.34959747147016 1 4.22652647548416 598 329 415 680 296 1223 1658 1334 631 263 1172 451 M13186 MCBRYAN_PUBERTAL_BREAST_3_4WK_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_3_4WK_UP.html Genes up-regulated during pubertal mammary gland development between weeks 3 and 4. 17486082 174/374 Arthur Liberzon 3.97536437225069e-23 4.33222266241087e-21 45 1876.54545454545 631 3.61396761113698e-24 42 2.11576522345426 -2.14894644783884 -1 15.7483353711181 4644 251 42 559 631 3223 4435 2762 584 45 3466 452 M12224 MARTINEZ_RB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RB1_TARGETS_UP.html Genes up-regulated in mice with skin specific knockout of RB1 [GeneID=5925] by Cre-lox. 18245467 486/1078 Jessica Robertson 9.99340917287896e-13 3.87017482513313e-11 635 646 631 9.08491742989409e-14 115 1.80916895630148 2.03368708016391 1 6.88563146372682 631 1233 115 173 836 669 886 412 1382 145 624 453 M2572 ANASTASSIOU_CANCER_MESENCHYMAL_TRANSITION_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/ANASTASSIOU_CANCER_MESENCHYMAL_TRANSITION_SIGNATURE.html Genes in the 'mesenchymal transition signature' common to all invasive cancer types. 22208948 48/125 Dimitris Anastassiou 3.32144147425752e-12 1.17024622168201e-10 10 650.181818181818 631 3.01949224932957e-13 10 2.3485312390685 2.3485312390685 1 8.52589891880727 10 1179 127 644 2455 254 290 739 656 167 631 454 M18299 YANG_BREAST_CANCER_ESR1_UP http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_UP.html Genes up-regulated in early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative ones. 16261164 28/67 Leona Saunders 3.57965243292542e-07 2.61124324039143e-06 3540 1708.54545454545 634 3.25423001397826e-08 134 1.87886030598525 -1.64823211352284 -1 3.83436317925588 3539 143 634 258 320 4202 2875 2714 134 594 3381 455 M11187 REACTOME_NCAM_SIGNALING_FOR_NEURITE_OUT_GROWTH http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NCAM_SIGNALING_FOR_NEURITE_OUT_GROWTH.html Genes involved in NCAM signaling for neurite out-growth 32/96 Reactome 3.00061794178858e-06 9.80536657965224e-06 665 616.181818181818 635 2.72783821308269e-07 103 2.03730159715389 2.11176280230442 1 3.7297986731534 219 1033 665 103 1225 527 309 918 635 479 665 456 M9487 FRIDMAN_SENESCENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRIDMAN_SENESCENCE_DN.html Genes down-regulated in senescent cells. 18711403 16/38 Jessica Robertson 4.6436084698467e-06 1.36855026979256e-05 355 826 636 4.22147115571325e-07 349 2.66529032585089 2.70471959394088 1 4.73842550120742 353 636 446 349 2082 1166 1337 765 374 493 1085 457 M15125 FARMER_BREAST_CANCER_CLUSTER_4 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_4.html Cluster 4: selected stromal genes clustered together across breast cancer samples. 15897907 20/55 Leona Saunders 1.50850783276678e-08 2.45446795289762e-07 55 878.727272727273 636 1.371370766464e-09 53 2.52114694107829 2.52114694107829 1 6.09146382903421 53 1291 270 650 3083 636 626 1026 616 392 1023 458 M2512 FOSTER_KDM1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FOSTER_KDM1A_TARGETS_UP.html Genes up-regulated in ES cells (embryonic stem) heterozygotic for KDM1A [GeneID=23028] loss of function mutant compared to the homozygotic loss of the gene. 20713442 159/576 Arthur Liberzon 1.1773317377537e-23 1.41460936490098e-21 255 781.818181818182 637 1.07030157977609e-24 31 2.04220527950697 2.09081861163071 1 15.5636496424442 1002 255 38 255 31 1590 1168 2093 637 41 1490 459 M969 SCHUHMACHER_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHUHMACHER_MYC_TARGETS_DN.html Genes down-regulated in P493-6 cells (Burkitt's lymphoma) induced to express MYC [GeneID=4609]. 11139609 2/8 Yujin Hoshida 1.15092839856614e-05 2.83258953554672e-05 840 1337.9 639 1.27881587320079e-06 83 1.67316281527115 1.67316281527115 1 2.78138029509486 836 392 4367 NA 1814 321 83 442 3713 1082 329 460 M19467 SANA_TNF_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/SANA_TNF_SIGNALING_DN.html Genes down-regulated in five primary endothelial cell types (lung, aortic, iliac, dermal, and colon) by TNF [GeneID=7124]. 15749026 60/138 Yujin Hoshida 5.3476140920175e-07 3.25018412907834e-06 265 902.909090909091 639 4.86146853807318e-08 265 2.08678776982544 2.06582049812873 1 4.18618983723611 265 1956 360 1070 1218 502 540 970 1879 639 533 461 M797 REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS.html Genes involved in Class B/2 (Secretin family receptors) 32/92 Reactome 1.53132542583774e-09 3.1611413856721e-08 995 625.727272727273 640 1.39211402445785e-10 39 2.29143472955878 2.48866177790022 1 6.28198713707375 992 137 218 111 39 1128 867 1432 640 292 1027 462 M13008 DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN.html Genes exclusively down-regulated in fibroblasts expressing the TTD mutant form of ERCC3 [GeneID=2071], after UVC irradiation. 15608684 56/151 Arthur Liberzon 1.77224785465222e-06 6.81275918531608e-06 220 615.363636363636 640 1.61113571119871e-07 94 1.87802745020689 2.15292684864281 1 3.54676566126675 220 1342 651 1001 964 94 192 268 1299 640 98 463 M1565 WESTON_VEGFA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WESTON_VEGFA_TARGETS.html Genes up-regulated in MMEC cells (myometrial endothelium) by VEGFA [GeneID=7422] stimulation. 12200464 74/171 John Newman 2.3392915863597e-18 1.82698672894693e-16 265 713.090909090909 640 2.12662871487245e-19 58 2.20919731785464 2.24553113572037 1 12.7089772029747 264 421 58 484 1073 640 986 1263 1673 133 849 464 M7061 CROMER_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROMER_METASTASIS_UP.html Metastatic propensity markers of head and neck squamous cell carcinoma (HNSCC): up-regulated in metastatic vs non-metastatic tumors. 14676830 65/157 Kevin Vogelsang 4.09609374725805e-06 1.2447662321434e-05 430 755.090909090909 641 3.72372852148571e-07 357 1.70788117229834 1.81229889942615 1 3.06202081869184 357 427 1029 590 1347 641 428 458 1184 1026 819 465 M2299 VANDESLUIS_COMMD1_TARGETS_GROUP_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_COMMD1_TARGETS_GROUP_3_UP.html Genes up-regulated in 9.5 days post coitus (dpc) embryos with COMMD1 [GeneID=150684] knockout compared to normal 9.5 dpc embryos. 17371845 58/143 Arthur Liberzon 9.78617586277711e-09 1.65552419108208e-07 2745 1264.45454545455 641 8.89652355118964e-10 107 1.98153296091904 -1.8970855797211 -1 4.91154836046804 2742 107 263 632 455 1784 3108 1614 641 259 2304 466 M2582 DURAND_STROMA_NS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DURAND_STROMA_NS_UP.html Genes up-regulated in the HSC non-supportive stromal cell lines. 120/268 Charles Durand 9.15526647239463e-07 4.47824412209199e-06 575 747.454545454545 641 8.32297298395186e-08 292 1.65855029466813 1.75499187362787 1 3.242737130468 1008 924 572 733 685 572 292 641 1826 458 511 467 M13796 THUM_MIR21_TARGETS_HEART_DISEASE_UP http://www.broadinstitute.org/gsea/msigdb/cards/THUM_MIR21_TARGETS_HEART_DISEASE_UP.html Genes up-regulated in a mouse model of heart disease whose expression reverted to normal by silencing of MIR21 [GeneID=406991] microRNA. 19043405 16/34 Jessica Robertson 4.0609805569327e-09 7.40457388707651e-08 210 714.636363636364 643 3.69180051311714e-10 158 2.37398355975484 2.54228086606134 1 6.18752458381734 206 170 247 643 2271 670 932 1121 356 158 1087 468 M1226 OXFORD_RALA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_TARGETS_DN.html Genes down-regulated in the UMUC-3 cells (bladder cancer) after knockdown of RALA [GeneID=5898] by RNAi. 17496927 13/32 Arthur Liberzon 3.24532479908556e-05 6.88340082549742e-05 390 704.363636363636 645 2.95033879400574e-06 309 2.12651327546741 2.55986121885254 1 3.23526585567255 389 645 655 888 2074 309 512 709 358 701 508 469 M16708 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 5. 12554760 27/62 Arthur Liberzon 7.59865664026372e-06 2.01624170226103e-05 850 742.090909090909 645 6.9078935324141e-07 304 2.24442472302047 2.48332790787771 1 3.85214121727312 846 738 625 304 1593 741 1181 506 645 563 421 470 M65 PID_FRA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FRA_PATHWAY.html Validated transcriptional targets of AP1 family members Fra1 and Fra2 18832364 32/66 Pathway Interaction Database 7.19045912958082e-06 1.92870586612568e-05 340 900.363636363636 646 6.5368023917425e-07 336 2.08605567919242 2.21061762423563 1 3.59502853349244 336 1638 471 1137 1845 552 646 476 1508 617 678 471 M5200 VALK_AML_WITH_EVI1 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_WITH_EVI1.html Genes that best predicted acute myeloid leukemia (AML) with the up-regulated expression of EVI1 [GeneID=2122]. 15084694 13/41 Jessica Robertson 1.42772461297143e-06 5.93929111239472e-06 115 808.545454545455 647 1.29793230865148e-07 44 1.6133246457795 1.50209322304961 1 3.08199888959949 360 647 836 1497 866 114 44 576 2558 1281 115 472 M10991 NIKOLSKY_OVERCONNECTED_IN_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_OVERCONNECTED_IN_BREAST_CANCER.html Overconnected mutated transcription factors regulating genes within the breast cancer amplicome. 19010930 16/38 Leona Saunders 1.51319243891947e-06 6.16057321353313e-06 650 659.454545454545 648 1.37563043610595e-07 109 2.28520531997301 2.51583976947957 1 4.35224947323144 649 967 1083 398 1352 648 357 124 109 1206 361 473 M5465 MCCABE_HOXC6_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCCABE_HOXC6_TARGETS_DN.html Genes with promoters bound by HOXC6 [GeneID=3223] in LNCaP cells (prostate cancer) and down-regulated upon loss of function (LOF) of HOXC6. 18339881 12/38 Jessica Robertson 5.50960192768803e-06 1.56188715264042e-05 650 718.363636363636 649 5.00874156889814e-07 159 1.85145116626903 2.01116739838853 1 3.25272192068079 301 886 1086 1189 1474 345 159 309 649 857 647 474 M2407 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_1 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_1.html Genes regulated in MCF7 cells (breast cancer) by expression of full-length and truncated (611-CTF) forms of ERBB2 [GeneID=2064] at both 15 h and 60 h time points. 19364815 41/82 Arthur Liberzon 2.76257152192192e-07 2.26714713690475e-06 715 655.090909090909 649 2.51142897165641e-08 236 1.85924833646028 1.87957480917338 1 3.83604497891318 714 717 812 702 236 463 414 649 1485 537 477 475 M2171 FIGUEROA_AML_METHYLATION_CLUSTER_4_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_4_DN.html Cluster 4 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 13/34 Arthur Liberzon 4.9288788650977e-06 1.43279940209974e-05 625 1232 650 4.48080900708182e-07 91 1.80091219943221 1.80091219943221 1 3.18859457631601 623 3426 2081 2278 1426 300 91 578 650 1757 342 476 M16123 EBAUER_MYOGENIC_TARGETS_OF_PAX3_FOXO1_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/EBAUER_MYOGENIC_TARGETS_OF_PAX3_FOXO1_FUSION.html Muscle development genes up-regulated in Rh4 cells (alveolar rhabdomyosarcoma, ARMS) but not in the RD cells (embryonal rhabdomyosarcoma, ERMS) after knockdown of PAX3-FOXO1 [GeneID=5077;2308] fusion by RNAi for 72 hr. 17525748 38/86 Leona Saunders 6.47620662692249e-07 3.6257472226713e-06 295 606.272727272727 651 5.88746230303986e-08 294 2.57700401274012 2.90808066512184 1 5.12485214423687 294 947 364 651 761 489 340 919 341 843 720 477 M16524 LEE_LIVER_CANCER_DENA_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_DENA_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) induced by diethylnitrosamine (DENA) [PubChem=5921]. 15565109 38/123 Yujin Hoshida 9.74219435192467e-07 4.65835946256316e-06 645 764.727272727273 651 8.85654424184925e-08 132 1.98569610850988 2.07757266705752 1 3.86993078545894 643 132 376 233 1483 1200 1755 651 724 208 1007 478 M2467 KRIEG_HYPOXIA_VIA_KDM3A http://www.broadinstitute.org/gsea/msigdb/cards/KRIEG_HYPOXIA_VIA_KDM3A.html Genes dependent on KDM3A [GeneID=55818] for hypoxic induction in RCC4 cells (renal carcinoma) expressing VHL [GeneID=7428]. 19858293 49/103 Arthur Liberzon 6.44924443817171e-08 8.68424121760708e-07 415 913.727272727273 654 5.86294966111788e-09 18 1.91396657936568 2.05586317894606 1 4.24050027891355 413 1590 654 1630 2006 262 355 18 1991 1107 25 479 M14171 KEGG_STARCH_AND_SUCROSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STARCH_AND_SUCROSE_METABOLISM.html Starch and sucrose metabolism 15/58 KEGG 1.73868851398342e-07 1.75214932828522e-06 400 889.818181818182 655 1.58062604672203e-08 41 2.55214549935003 2.55214549935003 1 5.3700437541247 396 1792 1532 649 2016 655 898 41 80 1475 254 480 M14859 COLIN_PILOCYTIC_ASTROCYTOMA_VS_GLIOBLASTOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/COLIN_PILOCYTIC_ASTROCYTOMA_VS_GLIOBLASTOMA_DN.html Genes down-regulated in pilocytic astrocytoma compared to glioblastoma samples. 16314830 23/60 Jessica Robertson 4.49402959137302e-05 9.12040825689649e-05 170 705.545454545455 655 4.08556490488278e-06 144 2.51181255836237 2.54934566367828 1 3.70925173073846 166 868 610 839 2193 144 344 655 704 892 346 481 M830 REACTOME_RECEPTOR_LIGAND_BINDING_INITIATES_THE_SECOND_PROTEOLYTIC_CLEAVAGE_OF_NOTCH_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RECEPTOR_LIGAND_BINDING_INITIATES_THE_SECOND_PROTEOLYTIC_CLEAVAGE_OF_NOTCH_RECEPTOR.html Genes involved in Receptor-ligand binding initiates the second proteolytic cleavage of Notch receptor 5/18 Reactome 2.79875316870119e-09 5.33128347501373e-08 40 854.909090909091 656 2.79875317222605e-10 2 2.62338261184033 3.0671270605586 1 6.97436253704069 656 903 4025 267 1179 609 956 2 38 729 40 482 M1902 SCHRAETS_MLL_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHRAETS_MLL_TARGETS_UP.html Genes up-regulated in fibroblasts from MLL [GeneID=4297] knockout mice. 12789274 33/77 Arthur Liberzon 6.64516258979397e-06 1.80831776398226e-05 180 778.909090909091 657 6.04107514707409e-07 177 2.3766870645697 2.58189050779698 1 4.12020874340256 177 952 469 1259 2393 264 257 945 723 657 472 483 M7346 KORKOLA_EMBRYONIC_CARCINOMA_VS_SEMINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_EMBRYONIC_CARCINOMA_VS_SEMINOMA_UP.html Top 25 most highly expressed genes in embryonic carcinoma relative to seminoma tumors. 16424014 10/29 Arthur Liberzon 5.09135519913122e-07 3.14335842728971e-06 3045 1701.90909090909 658 4.62850579763608e-08 53 2.34540328478502 2.48830590314783 1 4.71742717386704 3042 658 615 261 454 4190 2561 4495 53 457 1935 484 M1185 HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_DN http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_DN.html Genes down-regulated in MCF7 cells (breast cancer, normal TP53 [GeneID=7157]) undergoing aberrant mitosis and necrosis after treatment wiht 4 nM docetaxel [PubChem=148124]. 17099726 5/11 Arthur Liberzon 2.68675904864277e-05 5.8422983303666e-05 665 1233.36363636364 662 2.68679153322937e-06 388 1.56318335308395 1.56318335308395 1 2.41891243048449 662 388 4244 1383 2038 647 599 743 436 1873 554 485 M17162 NAKAMURA_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_METASTASIS.html Genes up-regulated in highly metastatic pancreatic cancer cells. 17210693 28/70 Jessica Robertson 2.56128509407525e-08 3.92228168327994e-07 995 719.454545454545 662 2.32844102172205e-09 2 1.80157303878979 1.96443193631602 1 4.21880377442183 993 341 1275 77 662 840 1401 109 373 1841 2 486 M4957 FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP.html Genes up-regulated in thyroid tumors of uncertain malignancy (T-UM) compared to other thyroid tumors. 17968324 25/58 Arthur Liberzon 2.43545271083318e-07 2.14593063349835e-06 485 1020.09090909091 662 2.2140481640397e-08 117 2.3671258884666 -2.170226359458 -1 4.90455821411305 2077 481 662 117 201 1182 3583 481 319 798 1320 487 M8629 NADERI_BREAST_CANCER_PROGNOSIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NADERI_BREAST_CANCER_PROGNOSIS_DN.html Down-regulated genes in the breast cancer prognostic signature of 70 genes that significantly correlated with survival. 16936776 15/23 Arthur Liberzon 3.96033311044421e-07 2.76162514219369e-06 1390 1130.09090909091 664 3.60030347578574e-08 353 1.8891332143492 1.7459850505314 1 3.83853618306836 1386 500 664 479 353 1819 2641 2545 658 429 957 488 M1956 MIKKELSEN_MCV6_ICP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MCV6_ICP_WITH_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state). 18509334 35/125 Jessica Robertson 3.58097166645225e-06 1.12504417218126e-05 295 727.727272727273 664 3.25543408660424e-07 295 2.14997745862687 2.33014805315182 1 3.88915927792194 295 852 431 1208 1295 382 397 857 1036 588 664 489 M1720 LEIN_MIDBRAIN_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_MIDBRAIN_MARKERS.html Top 100 ranked genes most specific to midbrain region of adult mouse brain. 17151600 53/141 Jessica Robertson 8.58611509890853e-07 4.283031975493e-06 665 686.636363636364 665 7.80556222716531e-08 119 2.18119281076196 2.33598086865008 1 4.28002133885474 665 1104 488 119 656 805 923 1059 457 445 832 490 M1417 JECHLINGER_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN http://www.broadinstitute.org/gsea/msigdb/cards/JECHLINGER_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN.html Genes down-regulated during epithelial to mesenchymal transition (EMT) induced by TGFB1 [GeneID=7040] in the EpH4 cells (mammary epithelium cell line transformed by HRAS [GeneID=3265]). 14562044 53/124 Arthur Liberzon 4.1000440607869e-07 2.79255907977434e-06 1475 1001.54545454545 666 3.72731347717676e-08 360 2.16057084238835 2.54180376592123 1 4.386250708754 1473 588 577 397 372 2101 1949 1092 360 666 1442 491 M1712 LEIN_NEURON_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_NEURON_MARKERS.html Genes enriched in neurons in the adult mouse brain identified through correlation-based searches seeded with neuron cell-type specific gene expression patterns. 17151600 40/110 Jessica Robertson 8.38259809067761e-07 4.23525526893721e-06 645 1061.45454545455 666 7.6205466224337e-08 527 1.46044478134509 1.52424990794668 1 2.86834221356561 561 1827 2188 757 643 666 664 644 864 2335 527 492 M10117 VERHAAK_AML_WITH_NPM1_MUTATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_AML_WITH_NPM1_MUTATED_DN.html Genes down-regulated in acute myeloid leukemia (AML) patients with mutated NPM1 [GeneID=4869]. 16109776 146/470 Kevin Vogelsang 5.50570571467647e-17 3.73909231579332e-15 215 639.727272727273 667 5.00518701334225e-18 66 2.01172475359619 2.20743138692445 1 10.6089128189097 215 409 66 560 1289 802 667 706 1246 83 994 493 M2456 WANG_MLL_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WANG_MLL_TARGETS.html Genes requiring MLL [GeneID=4297] for H3K4me3 and expression in MEF cells (embryonic fibroblast). 19703992 178/461 Arthur Liberzon 2.21435845351448e-19 1.88663340239434e-17 55 617.363636363636 669 2.01305313955862e-20 54 2.043692743698 2.15873852293606 1 12.4934713986544 326 542 54 801 669 412 724 1134 1187 54 888 494 M6315 IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_DN.html Cluster 2: genes down-regulated in lung tissue samples from mice with oncogenic form of KRAS [GeneID=3845] and inactivated PTEN [GeneID=5728]. 18281487 215/575 Jessica Robertson 1.55796068309623e-09 3.2020191934162e-08 315 886 670 1.41632789472684e-10 219 1.8976355008682 2.16221749474208 1 5.19851281619422 315 1240 219 1469 1376 600 650 716 1983 508 670 495 M4303 WOTTON_RUNX_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WOTTON_RUNX_TARGETS_DN.html Common target genes down-regulated by all three Runx family members (RUNX1, RUNX2, and RUNX3 [GeneID=861;860;864]) in MEF cells (embryonic fibroblasts). 18560354 19/53 Jessica Robertson 7.02207858364418e-07 3.81051980858506e-06 270 783.636363636364 671 6.38370984090008e-08 30 1.90127931959851 2.05919051497935 1 3.76604573809722 268 1131 1356 746 1661 45 30 252 671 2424 36 496 M19829 BIOCARTA_AGPCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AGPCR_PATHWAY.html Attenuation of GPCR Signaling 9/21 BioCarta 3.27800862975918e-07 2.46734573623285e-06 435 1182.72727272727 673 3.2780091132996e-08 199 1.14943298172044 1.14943298172044 1 2.35609662468374 435 1148 3816 1176 322 204 199 673 2191 2560 286 497 M8924 WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP.html Genes up-regulated in esophageal adenocarcinoma (EAC) and Barret's esophagus (BE) relative to normal esophagi. 16449976 24/59 Leona Saunders 5.77677612658261e-06 1.624848315076e-05 360 690.727272727273 673 5.25162845030862e-07 359 2.31339715180666 2.47828382889221 1 4.04977838312867 359 740 461 451 1611 673 1029 773 709 422 370 498 M19612 LEE_LIVER_CANCER_ACOX1_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_ACOX1_UP.html Genes up-regulated in hepatocellular carcinoma of ACOX1 [GeneID=51] knockout mice. 15565109 48/148 Yujin Hoshida 2.39984083740647e-12 8.71756136750908e-11 2610 1332.54545454545 674 2.18167348855372e-13 114 2.1498077380796 2.5476846646975 1 7.90496224050855 2608 114 123 198 802 4053 3154 674 559 166 2207 499 M1617 KEEN_RESPONSE_TO_ROSIGLITAZONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KEEN_RESPONSE_TO_ROSIGLITAZONE_DN.html Genes down-regulated in aorta biopsies from mice treated with rosiglitazone [PubChem=77999]. 15054141 85/202 John Newman 1.80822478918677e-12 6.77867308970337e-11 390 649.090909090909 676 1.64384071744387e-13 119 2.17560891387705 2.39933403325998 1 8.08671519426837 387 284 119 400 1591 765 1085 965 730 138 676 500 M1721 LEIN_PONS_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_PONS_MARKERS.html Top 100 ranked genes most specific to pons region (P) of the adult mouse brain. 17151600 56/143 Jessica Robertson 4.24362908678095e-07 2.82649481163302e-06 670 702.545454545455 676 3.85784536849477e-08 387 1.87686742899972 1.93844116693582 1 3.80669557779968 666 1178 834 856 387 604 752 676 599 420 756 501 M18841 MULLIGHAN_MLL_SIGNATURE_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_MLL_SIGNATURE_1_DN.html The 'MLL signature 1': genes down-regulated in pediatric AML (acute myeloid leukemia) with rearranged MLL [GeneID=4297] compared to all AML cases with the intact gene. 17597811 165/408 Arthur Liberzon 2.20559030912614e-06 7.8703867605922e-06 250 740.454545454545 677 2.00508410938552e-07 201 1.62477391715764 1.69834503168947 1 3.03126000034488 509 998 620 824 1074 201 250 860 1884 677 248 502 M2377 IKEDA_MIR133_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR133_TARGETS_UP.html Genes up-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-133 microRNA. 19188439 36/94 Arthur Liberzon 2.1866273823445e-06 7.82775852839293e-06 385 1315.54545454545 677 1.98784505062143e-07 73 1.65541999223132 1.74888166041274 1 3.08986208343948 382 3119 2142 2376 2403 79 163 196 677 2861 73 503 M9246 ENGELMANN_CANCER_PROGENITORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ENGELMANN_CANCER_PROGENITORS_DN.html Down-regulated genes in the cancer progenitor (stem) cells corresponding to side population (SP) MCF7 cells (breast cancer) positive for MUC1 [GeneID=4582]. 18381450 44/118 Jessica Robertson 2.25585821390937e-07 2.05660536777807e-06 2190 1579 678 2.05078040474806e-08 183 2.02620952604608 2.09311206862816 1 4.21187334186792 2190 318 373 430 183 3533 3377 4382 678 261 1644 504 M3654 THUM_SYSTOLIC_HEART_FAILURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/THUM_SYSTOLIC_HEART_FAILURE_UP.html Genes up-regulated in samples with systolic heart failure compared to normal hearts. 17606841 293/717 Arthur Liberzon 2.56771844781829e-06 8.70646067038822e-06 535 1010 680 2.33429222247481e-07 437 1.79263002854488 1.84108820794846 1 3.31569081131057 531 2328 437 627 1155 674 1203 991 2014 470 680 505 M7375 DORN_ADENOVIRUS_INFECTION_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_48HR_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) 48 h after infection with adenovirus Ad12. 15681441 45/94 Arthur Liberzon 8.56348222008364e-06 2.21758760607268e-05 125 699.818181818182 680 7.78501413959148e-07 122 2.24487454878749 2.24487454878749 1 3.81899271605482 122 1537 680 975 1650 243 483 234 767 807 200 506 M12212 WANG_ESOPHAGUS_CANCER_VS_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_ESOPHAGUS_CANCER_VS_NORMAL_DN.html Down-regulated genes specific to esophageal adenocarcinoma (EAC) relative to normal tissue. 16449976 81/168 Arthur Liberzon 2.12790260656734e-07 1.97452507215338e-06 1190 697.363636363636 681 1.93445710216743e-08 88 1.73795292489127 1.90690430946362 1 3.62391236581255 1189 88 603 436 174 734 681 1205 1185 963 413 507 M11951 HINATA_NFKB_TARGETS_KERATINOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HINATA_NFKB_TARGETS_KERATINOCYTE_UP.html Genes up-regulated in primary keratinocytes by expression of p50 (NFKB1) and p65 (RELA) [GeneID=4790;5970] components of NFKB. 12673201 77/152 Arthur Liberzon 1.79028099606204e-07 1.78494824415888e-06 2995 1770.81818181818 683 1.62752831068064e-08 83 1.9638395150356 2.13187725963609 1 4.1263901613653 2992 83 324 163 683 4632 3457 2896 448 269 3532 508 M16297 SCHLESINGER_H3K27ME3_IN_NORMAL_AND_METHYLATED_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SCHLESINGER_H3K27ME3_IN_NORMAL_AND_METHYLATED_IN_CANCER.html Genes bearing the H3K27me3 mark in normal cells; their DNA is methylated in cancer cells. 17200670 15/73 Leona Saunders 7.19102926034084e-08 9.36032308721033e-07 685 874.818181818182 684 6.53729954126399e-09 199 2.44313233608158 2.53444758832186 1 5.38382054328905 684 358 302 604 1356 1206 1097 1755 522 199 1540 509 M16033 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_8 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_8.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 8. 12554760 30/77 Arthur Liberzon 2.27464003873342e-06 8.05057645128763e-06 550 748.636363636364 684 2.06785671868113e-07 337 1.87991670187698 1.94459131752142 1 3.50051181829248 547 337 766 402 1085 911 576 653 1475 684 799 510 M19384 YAUCH_HEDGEHOG_SIGNALING_PARACRINE_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAUCH_HEDGEHOG_SIGNALING_PARACRINE_UP.html Genes up-regulated in mouse stroma of pancreatic adenocarcinoma zenografts after treatment with HhAntag, a hedgehog (Hh) pathway inhibitor. 18754008 79/243 Jessica Robertson 8.82445331788261e-08 1.10565209218176e-06 1005 692.454545454545 685 8.02223061076512e-09 43 2.02576312995991 2.18065007720739 1 4.41052633501397 1001 1338 825 277 43 936 628 1008 449 685 427 511 M18467 MATTIOLI_MULTIPLE_MYELOMA_WITH_14Q32_TRANSLOCATIONS http://www.broadinstitute.org/gsea/msigdb/cards/MATTIOLI_MULTIPLE_MYELOMA_WITH_14Q32_TRANSLOCATIONS.html Genes expressed in multiple myeloma (MM) patients carrying specific translocations involving the immunoglobulin heavy chain (IGH) locus at 14q32. 15735737 29/80 Leona Saunders 7.61278825270055e-06 2.01773335702233e-05 500 803.090909090909 686 6.92074054163924e-07 315 2.01447757592851 1.87714242353617 1 3.45724283603012 498 1871 820 352 1595 399 315 686 422 991 885 512 M9377 ALCALAY_AML_BY_NPM1_LOCALIZATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/ALCALAY_AML_BY_NPM1_LOCALIZATION_UP.html Genes up-regulated in acute myeloid leukemia (AML) with respect to cellular localization of NPM1 [GeneID=4869]: cytoplasmic vs. nucleolar. 15831697 117/271 Kevin Vogelsang 1.45968975112502e-10 3.84275627739992e-09 690 747.636363636364 687 1.32699068292897e-11 171 1.89410736274615 2.14816927026739 1 5.82634765946754 501 686 171 687 1563 804 870 298 1530 413 701 513 M2282 ITO_PTTG1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ITO_PTTG1_TARGETS_UP.html Genes up-regulated in HSA/c and KYSE140 cells (esophageal squamous cell carcinoma, ESCC) after knockdown of PTTG1 [GeneID=9232] by RNAi. 18451147 9/30 Jessica Robertson 6.73774052117495e-07 3.72763306755913e-06 690 1117.45454545455 687 6.73774256404745e-08 83 2.60837459175476 3.016192787434 1 5.17576323590349 687 1893 4474 605 1460 481 992 83 234 1247 136 514 M15590 DORN_ADENOVIRUS_INFECTION_32HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_32HR_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) 32 h after infection with adenovirus Ad12. 15681441 43/90 Arthur Liberzon 8.08184393908055e-06 2.12165382064602e-05 140 709.545454545455 687 7.34715784401428e-07 140 2.2781905943256 2.2781905943256 1 3.89166397094857 140 1353 687 898 1614 364 587 274 717 880 291 515 M212 PID_INTEGRIN5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN5_PATHWAY.html Beta5 beta6 beta7 and beta8 integrin cell surface interactions 18832364 14/26 Pathway Interaction Database 1.55580771677602e-07 1.62734708946706e-06 420 690.363636363636 689 1.4143707516368e-08 105 2.1050238049513 2.29847810102425 1 4.45393408732796 417 1303 877 779 105 689 492 335 771 1372 454 516 M2133 QI_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/QI_HYPOXIA.html Genes up-regulated by hypoxia in TRAMP-C cells (prostatic cancer). 20609350 114/201 Arthur Liberzon 1.50276655657222e-07 1.5968172526298e-06 1070 853.636363636364 690 1.36615150838415e-08 70 1.62096039718169 1.78474325584116 1 3.43459738329945 1069 70 581 393 99 1221 1215 2242 1479 331 690 517 M2894 AMIT_EGF_RESPONSE_240_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_240_MCF10A.html Genes whose expression peaked at 240 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 15/28 Leona Saunders 1.89046146185102e-07 1.82277827371068e-06 1030 717.454545454545 691 1.71860147663502e-08 155 2.16743191003044 2.54645894935285 1 4.54695942644424 1027 1610 1167 690 155 691 709 440 291 835 277 518 M507 REACTOME_GPCR_LIGAND_BINDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GPCR_LIGAND_BINDING.html Genes involved in GPCR ligand binding 100/454 Reactome 6.48894259587163e-15 3.45536193230164e-13 410 835.909090909091 692 5.89903872351966e-16 83 2.17939925779279 2.34038401774103 1 9.92719598744027 408 692 83 1606 317 635 790 1424 2268 262 710 519 M1484 IGLESIAS_E2F_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IGLESIAS_E2F_TARGETS_UP.html Genes up-regulated in pancreatic cells from mice with double knockout of E2F1 [GeneID=1869] and E2F2 [GeneID=1870] compared to wild type. 15146237 128/271 Kevin Vogelsang 4.21607024041781e-07 2.82649481163302e-06 150 941.636363636364 692 3.83279186216714e-08 148 1.99756338145048 2.03107791698888 1 4.05149323456033 148 1717 355 1183 2324 293 323 692 1915 960 448 520 M1099 GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP.html Genes up-regulated in ME-A cells (breast cancer, sensitive to apoptotic stimuli) upon serum deprivation for 22 hr in the presence of medium concentrate (MC) from ME-C cells (breast cancer, resistant to apoptotic stimuli). 17160024 179/538 Arthur Liberzon 7.87641394204105e-09 1.36195113403706e-07 365 720.818181818182 694 7.16037633658189e-10 258 1.81797526730974 2.09601040307307 1 4.56247820682962 364 683 258 694 955 938 1055 423 1461 368 730 521 M10331 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_FGF3 http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_FGF3.html Genes whose expression is coregulated with that of FGF3 [GeneID=2248] in hematopoietic stem cells (HSC). 15711547 6/12 Jean Junior 7.40684438215965e-05 0.000142131338144145 460 1304.72727272727 694 7.40709126978789e-06 123 2.11649960195129 2.11649960195129 1 2.97642292117101 457 2460 4366 1376 2342 405 218 694 123 1322 589 522 M7514 BERENJENO_TRANSFORMED_BY_RHOA_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_DN.html Genes down-regulated in NIH3T3 cells (fibroblasts) transformed by expression of contitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector. 17213802 307/655 Leona Saunders 5.91201136842247e-07 3.43292258642226e-06 420 802.545454545455 696 5.374557233768e-08 31 1.61050278502328 1.78907272190522 1 3.21675604571819 416 31 643 696 512 1172 1326 891 1451 418 1272 523 M19508 HATADA_METHYLATED_IN_LUNG_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/HATADA_METHYLATED_IN_LUNG_CANCER_UP.html Genes with hypermethylated DNA in lung cancer samples. 16407832 213/744 Arthur Liberzon 3.15531938406541e-09 5.93808298543395e-08 700 729.636363636364 698 2.86847217144625e-10 239 1.80189967552063 2.04512831417579 1 4.75958486068976 475 1239 239 942 696 698 532 800 1376 281 748 524 M2442 STEINER_ERYTHROCYTE_MEMBRANE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/STEINER_ERYTHROCYTE_MEMBRANE_GENES.html Major erythrocyte membrane genes. 19687298 12/27 Arthur Liberzon 7.94856563955298e-07 4.11774058972012e-06 700 703.818181818182 698 7.22597137396254e-08 61 2.96903827675237 3.08375912585129 1 5.84451202367502 698 884 790 297 619 574 633 1179 61 1181 826 525 M2533 BOSCO_EPITHELIAL_DIFFERENTIATION_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/BOSCO_EPITHELIAL_DIFFERENTIATION_MODULE.html Genes representing epithelial differentiation module in sputum during asthma exacerbations. 20336062 26/95 Antony Bosco 1.33952119364066e-10 3.56647517806827e-09 1365 846.272727272727 698 1.21774653974747e-11 156 2.43726691377033 -2.49359250235784 -1 7.52599544928299 1364 616 169 671 775 870 2414 698 405 156 1171 526 M2523 ZHAN_MULTIPLE_MYELOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_DN.html Genes most significantly down-regulated in multiple myeloma samples, compared to normal bone marrow plasma cells. 11861292 40/90 Kevin Vogelsang 9.53900262698746e-12 3.17019619220307e-10 105 738 699 8.67182057002621e-13 105 2.38329307501012 2.4130231958761 1 8.2750504645368 105 1432 135 783 1536 578 530 699 1160 188 972 527 M708 REACTOME_A_TETRASACCHARIDE_LINKER_SEQUENCE_IS_REQUIRED_FOR_GAG_SYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_A_TETRASACCHARIDE_LINKER_SEQUENCE_IS_REQUIRED_FOR_GAG_SYNTHESIS.html Genes involved in A tetrasaccharide linker sequence is required for GAG synthesis 9/26 Reactome 7.0778900114757e-05 0.000136602111176998 590 1353.63636363636 700 7.07811545595326e-06 458 1.74632027041522 1.74632027041522 1 2.4668414837927 588 1316 3962 1986 2473 567 458 539 700 1808 493 528 M1414 MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_DN.html Down-regulated genes discriminating multiple myeloma samples by type of immunoglobulin they produce: IgG vs IgA. 12623842 22/46 Kate Stafford 1.91593110854765e-06 7.1687063813697e-06 705 1047.90909090909 701 1.74175707008319e-07 175 2.27543552602148 2.27543552602148 1 4.278898203403 701 1837 1466 2450 1006 267 175 399 691 2190 345 529 M2385 KATSANOU_ELAVL1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KATSANOU_ELAVL1_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) with ELAVL1 [GeneID=1994] knocked out. 19307312 127/297 Arthur Liberzon 6.77585155895449e-11 1.91274942200366e-09 340 651.545454545455 704 6.15986505378471e-12 159 1.97134658709199 2.20692271906398 1 6.28226328264881 338 269 159 1109 990 714 788 553 1249 294 704 530 M13273 DELYS_THYROID_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/DELYS_THYROID_CANCER_DN.html Genes down-regulated in papillary thyroid carcinoma (PTC) compared to normal tissue. 17621275 147/388 Aravind Subramanian 6.23447174209949e-15 3.35801546936531e-13 210 829 705 5.66770158372683e-16 82 1.81523541601686 1.80945590468533 1 8.27665909340748 209 1330 82 519 1439 697 705 1111 1894 121 1012 531 M1998 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS.html Genes trans-regulated by the hematopoietic stem cell (HSC) proliferation QTL (quantitative trait locus) Scp2. 15711547 25/62 Arthur Liberzon 8.52400552815007e-06 2.20926382217429e-05 505 897.363636363636 706 7.74912595908865e-07 366 2.18905419778651 2.43437564201712 1 3.72533765516474 505 1730 706 1439 1636 524 1011 682 806 466 366 532 M2010 MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing the bivalent histone H3 trimethylation mark at K4 and K27 (H3K4me3 and H3K27me3) in neural progenitor cells (NPC). 17603471 92/329 Arthur Liberzon 3.90737460736897e-14 1.88762447527124e-12 1510 833 706 3.55215873397185e-15 19 2.32444453640037 2.36846615911193 1 9.96133107807598 1508 78 92 19 706 1700 1583 1550 379 181 1367 533 M9815 AKL_HTLV1_INFECTION_DN http://www.broadinstitute.org/gsea/msigdb/cards/AKL_HTLV1_INFECTION_DN.html Genes down-regulated in WE17/10 cells (CD4+ [GeneID=920] T lymphocytes) infected by HTLV1 (and thus displaying low CD7 [GeneID=924]) compared to the uninfected (i.e., CD7+) cells. 17287851 46/136 Arthur Liberzon 3.91236507893816e-08 5.71132173205738e-07 175 701.272727272727 708 3.55669558955782e-09 12 2.05069169916101 2.16433142539562 1 4.67984296308922 173 1347 738 974 2341 235 236 12 757 708 193 534 M828 MASSARWEH_TAMOXIFEN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MASSARWEH_TAMOXIFEN_RESISTANCE_DN.html Genes down-regulated in breast cancer tumors (formed by MCF-7 xenografts) resistant to tamoxifen [PubChem=5376]. 18245484 149/377 Jessica Robertson 1.64816290516905e-06 6.51656844989384e-06 925 815 708 1.49833103628749e-07 381 1.71905217744913 1.81076555175349 1 3.25866138077571 922 410 598 578 930 983 1020 631 1804 381 708 535 M10161 BROWNE_HCMV_INFECTION_4HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_4HR_UP.html Genes up-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 4 h time point that were not up-regulated at the previous time point, 2 h. 11711622 41/108 Arthur Liberzon 1.14129360238279e-06 5.17224547462841e-06 540 804.727272727273 708 1.03754017677445e-07 107 1.99496128608562 2.18647484229208 1 3.85484786841826 537 1592 708 1130 1724 342 1062 107 820 419 411 536 M1984 NAKAYAMA_FGF2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_FGF2_TARGETS.html Genes down-regulated in S-17 cells (bone marrow stroma) after stimulation with FGF2 [GeneID=2247]. 17284717 27/57 Jessica Robertson 1.73031371432394e-05 3.99028054395766e-05 200 756.636363636364 711 1.57302483954456e-06 197 2.44680780739069 2.60326239286232 1 3.934347636881 197 864 510 711 2036 454 394 1095 389 717 956 537 M2009 MIKKELSEN_NPC_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 trimethylation mark at K27 (H3K27me3) in neural progenitor cells (NPC). 17603471 131/551 Arthur Liberzon 1.07567486202457e-23 1.32647694827556e-21 1045 697.090909090909 711 9.77886238204154e-25 31 2.28363351772123 2.52684041691253 1 17.4268943089427 1042 1165 37 190 52 1245 711 1272 540 31 1383 538 M5493 WNT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/WNT_SIGNALING.html Genes related to Wnt-mediated signal transduction 53/137 SuperArray 1.07097795479641e-06 4.94931232364493e-06 890 629.272727272727 712 9.73616796506882e-08 131 2.33947172364159 2.56892542053412 1 4.53690512571722 890 712 661 131 749 755 613 820 350 939 302 539 M7012 SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN.html Genes down-regulated in invasive ductal carcinoma (IDC) relative to ductal carcinoma in situ (DCIS, non-invasive). 16707453 59/148 Arthur Liberzon 2.55792231378012e-17 1.84406522498056e-15 100 1720.54545454545 716 2.32538392161828e-18 16 2.62133196032368 -2.20112329878946 -1 14.1178490166603 4305 98 63 16 716 3255 3181 3080 168 99 3945 540 M4435 YAO_HOXA10_TARGETS_VIA_PROGESTERONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAO_HOXA10_TARGETS_VIA_PROGESTERONE_DN.html Genes down-regulated in the uteri of ovariectomized mice 6 h after progesterone [PubChem=5994] injection: HOXA10 [GeneID=3206] knockout vs wild type animals. 12554760 15/36 Kevin Vogelsang 3.40860633711046e-06 1.08069886980376e-05 675 793 719 3.09873783482041e-07 344 3.18131202048072 3.31988799370568 1 5.77508069072717 674 642 429 344 1652 994 1076 890 467 836 719 541 M5098 CLIMENT_BREAST_CANCER_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/CLIMENT_BREAST_CANCER_COPY_NUMBER_DN.html Genes from the most frequent genomic losses and homozygous deletions in a panel of patients with lymph node negative breast cancer (NNBC). 17234794 5/12 Jessica Robertson 3.86058322819712e-06 1.18861320678921e-05 605 1102.36363636364 719 3.86058993505981e-07 166 3.21030473443472 3.21030473443472 1 5.77920591343335 604 667 4497 166 1360 778 495 732 719 1878 230 542 M18517 MATSUDA_NATURAL_KILLER_DIFFERENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/MATSUDA_NATURAL_KILLER_DIFFERENTIATION.html Genes changed between developmental stages of Valpha14i natural killer T lymphocyte cells (NKT). 16357323 344/792 Kevin Vogelsang 2.08626582630317e-07 1.95134564112907e-06 720 853 720 1.89660547649486e-08 170 1.70620798584074 1.93231425272558 1 3.56091747770941 720 1522 490 622 170 1198 1065 483 1619 696 798 543 M2396 SERVITJA_ISLET_HNF1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SERVITJA_ISLET_HNF1A_TARGETS_DN.html Genes down-regulated in pancreatic islets upon knockout of HNF1A [GeneID=6927]. 19289501 52/171 Arthur Liberzon 7.96234442508106e-07 4.11774058972012e-06 3930 1662.45454545455 722 7.23849755168364e-08 262 1.95865814144233 -1.93951171239388 -1 3.85559227907117 3926 306 459 262 620 2365 3804 2228 722 517 3078 544 M19056 REACTOME_AMINO_ACID_AND_OLIGOPEPTIDE_SLC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINO_ACID_AND_OLIGOPEPTIDE_SLC_TRANSPORTERS.html Genes involved in Amino acid and oligopeptide SLC transporters 21/55 Reactome 7.96649750710375e-07 4.11774058972012e-06 1130 937.636363636364 724 7.24227308352881e-08 493 1.88284372934095 1.95364949623744 1 3.70635262571268 1126 493 892 853 621 1746 2137 724 600 591 531 545 M18685 ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP.html Genes up-regulated in macrophage by live P.gingivalis. 18025224 240/771 Arthur Liberzon 5.90969081002022e-11 1.69894546845121e-09 725 650.545454545455 724 5.3724461910718e-12 38 1.72389152562162 1.88636298149973 1 5.52611467067526 724 38 156 377 339 885 1627 788 1379 94 749 546 M2143 HOELZEL_NF1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOELZEL_NF1_TARGETS_DN.html Genes down-regulated in SH-SY5Y cells (neuroblastoma) after knockdown of NF1 [GeneID=4763] by RNAi. 20655465 66/179 Arthur Liberzon 5.1750594079143e-09 9.18573044904788e-08 740 831.363636363636 725 4.70459947280691e-10 189 1.9781942863955 2.10086531851154 1 5.08825335571709 189 703 252 725 2377 575 738 1196 1319 333 738 547 M16948 CROMER_TUMORIGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROMER_TUMORIGENESIS_DN.html Tumorigenesis markers of head and neck squamous cell carcinoma (HNSCC): down-regulated in the 'early' tumors vs normal samples. 14676830 29/90 Arthur Liberzon 1.13620706569703e-11 3.6719077999009e-10 2270 1333.36363636364 728 1.03291551427536e-12 139 2.70950623849388 -2.37330283353446 -1 9.34450481735498 2270 728 139 154 145 1665 2146 4301 303 215 2601 548 M2513 ELVIDGE_HIF1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HIF1A_TARGETS_DN.html Genes down-regulated in MCF7 cells (breast cancer) after knockdown of HIF1A [GeneID=3091] by RNAi. 16565084 62/150 Arthur Liberzon 1.56445915632592e-07 1.63071584833658e-06 635 717.090909090909 729 1.42223569779764e-08 107 1.89248975106638 2.12281212444187 1 4.00362067731147 979 1013 462 729 107 1042 1187 633 773 330 633 549 M6641 BROWNE_HCMV_INFECTION_18HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_18HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 18 h time point that were not down-regulated at the previous time point, 16 h. 11711622 127/356 John Newman 1.42220517752458e-06 5.92922905861225e-06 865 680.727272727273 729 1.29291463356342e-07 181 1.83255424444864 1.96015737865702 1 3.50129526549639 543 268 432 181 863 861 1252 834 729 506 1019 550 M1349 SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_DN.html Genes down-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 12 h. 18794802 36/94 Jessica Robertson 6.96674900409331e-08 9.17880044260113e-07 490 789.181818181818 730 6.33340838609968e-09 132 2.16757101740057 2.26897696833976 1 4.78331697981078 489 853 301 132 1869 730 1048 882 1213 498 666 551 M11288 SCHLESINGER_METHYLATED_DE_NOVO_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SCHLESINGER_METHYLATED_DE_NOVO_IN_CANCER.html Genes bearing H3K27me3 mark or whose promoters are bound by the polycomb proteins SUZ12 or EED [GeneID=23512;8726]; their DNA is methylated de novo in cancer. 17200670 47/126 Leona Saunders 4.00015338064006e-06 1.21956530524914e-05 735 746.636363636364 731 3.63650968540328e-07 179 2.13216138126613 2.18130282837932 1 3.82962590354882 267 1430 436 735 1419 509 762 718 1027 731 179 552 M5929 CROONQUIST_STROMAL_STIMULATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_STROMAL_STIMULATION_UP.html Genes up-regulated in ANBL-6 cell line (multiple myeloma, MM) co-cultured with bone marrow stromal cells compared to those grown in the presence of IL6 [GeneID=3569]. 12791645 59/137 Arthur Liberzon 5.39419374144334e-09 9.5385629707183e-08 310 820.090909090909 732 4.90381250424492e-10 253 2.28431003159255 2.55767787668833 1 5.86196735862308 307 707 253 359 1609 1209 1165 1241 732 279 1160 553 M9326 VALK_AML_CLUSTER_9 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_9.html Top 40 genes from cluster 9 of acute myeloid leukemia (AML) expression profile; 87% of the samples are FAB M4 or M5 subtype, all have inv(16) inversion producing the CBFB-MYH11 fusion [GeneID=865;4629]; indicate good survival. 15084694 23/49 Jessica Robertson 4.00666583830508e-05 8.26011267852953e-05 440 945.727272727273 733 3.64248982730406e-06 360 2.54166860474965 2.70228020378288 1 3.79331621034444 436 1779 965 1203 2702 493 360 431 408 893 733 554 M11885 NIELSEN_SCHWANNOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_SCHWANNOMA_DN.html Top 20 negative significant genes associated with schwannoma tumors. 11965276 11/31 Arthur Liberzon 2.50571268151359e-06 8.57525404595596e-06 375 1235.45454545455 733 2.27792321402312e-07 154 1.46271420073893 1.46271420073893 1 2.70899661163705 733 375 1871 1207 2596 373 358 154 2073 3571 279 555 M1527 MCDOWELL_ACUTE_LUNG_INJURY_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCDOWELL_ACUTE_LUNG_INJURY_UP.html Genes up-regulated in the mouse model of acute lung injury induced by inhaling nickel sulfate [PubChem=24586]. 12540486 37/112 John Newman 2.54807124049315e-06 8.66492150431849e-06 735 877.181818181818 735 2.31643108337293e-07 191 2.30596251341621 2.63019812263865 1 4.26691338489002 735 1356 449 459 1148 1261 1799 643 518 191 1090 556 M1642 SIMBULAN_PARP1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SIMBULAN_PARP1_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) from PARP1 [GeneID=142] knockout mice. 11016956 11/25 John Newman 7.40870405633533e-06 1.97144731447969e-05 645 804.090909090909 735 6.73520818722821e-07 339 2.78832188794415 2.91118334342913 1 4.79558524226846 641 1506 740 445 1586 1028 595 339 439 791 735 557 M19766 WU_SILENCED_BY_METHYLATION_IN_BLADDER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/WU_SILENCED_BY_METHYLATION_IN_BLADDER_CANCER.html Genes silenced by DNA methylation in bladder cancer cell lines. 17456585 35/106 Jessica Robertson 2.68731652915818e-09 5.13990418597357e-08 115 824.090909090909 735 2.44301502949159e-10 112 2.23089901512482 2.26952253248743 1 5.94387670631136 112 457 236 646 2280 735 841 1392 877 360 1129 558 M5576 BIOCARTA_PLCE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PLCE_PATHWAY.html Phospholipase C-epsilon pathway 6/16 BioCarta 3.78563237019411e-06 1.17324558774667e-05 420 1104.54545454545 736 3.78563881916517e-07 159 1.18561428603098 1.18561428603098 1 2.13679776331223 420 1152 3854 1516 1354 233 188 493 736 2045 159 559 M1278 MCLACHLAN_DENTAL_CARIES_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCLACHLAN_DENTAL_CARIES_DN.html Genes down-regulated in pulpal tissue extracted from carious teeth. 15869869 65/178 John Newman 6.85687952944473e-06 1.85837695054818e-05 485 755.181818181818 736 6.23354627346299e-07 465 1.84636618367087 2.05022716062765 1 3.19284438566591 485 833 642 502 1547 465 796 825 818 658 736 560 M1967 MIKKELSEN_IPS_WITH_HCP_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_WITH_HCP_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV8.1 (induced pluripotent cells, iPS). 18509334 39/196 Jessica Robertson 1.26857637157599e-06 5.56085021253985e-06 395 997.454545454545 736 1.15325191188202e-07 374 2.38135560203462 2.56816354078444 1 4.57408840332459 374 2336 394 1607 1380 446 391 1098 1694 736 516 561 M2550 HOLLEMAN_VINCRISTINE_RESISTANCE_B_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_VINCRISTINE_RESISTANCE_B_ALL_UP.html Genes distinguishing vincristine [PubChem=5978] resistant and sensitive B-lineage ALL; here - genes up-regulated in the drug resistant samples. 15295046 29/60 Arthur Liberzon 1.7677152662343e-07 1.76962965076679e-06 495 817.272727272727 736 1.60701400751951e-08 137 1.77960622568907 1.90054119548842 1 3.74171688973598 491 736 1741 1119 137 832 1079 562 320 1541 432 562 M17761 ST_WNT_BETA_CATENIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_WNT_BETA_CATENIN_PATHWAY.html Wnt/beta-catenin Pathway 20/54 Signaling Transduction KE 5.59621802977453e-07 3.33637120706405e-06 730 989.909090909091 737 5.08747223027715e-08 70 2.21791082048547 2.45887525997173 1 4.44001374959636 726 2661 1222 737 1209 865 547 70 347 2007 498 563 M8719 BIOCARTA_MCALPAIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MCALPAIN_PATHWAY.html mCalpain and friends in Cell motility 21/49 BioCarta 1.74938967268518e-06 6.76068727228936e-06 730 795.636363636364 747 1.59035551251035e-07 230 2.45394703620034 2.8062496285059 1 4.63741270459114 730 747 1058 417 956 520 539 1167 230 1611 777 564 M4904 REACTOME_G_ALPHA_S_SIGNALLING_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_ALPHA_S_SIGNALLING_EVENTS.html Genes involved in G alpha (s) signalling events 33/145 Reactome 5.46753666061882e-08 7.58014106262124e-07 570 898.363636363636 749 4.97048799681859e-09 16 1.80366578172219 1.8926996417885 1 4.03505667257369 570 468 693 950 16 687 749 1682 2456 816 795 565 M1867 WANG_NEOPLASTIC_TRANSFORMATION_BY_CCND1_MYC http://www.broadinstitute.org/gsea/msigdb/cards/WANG_NEOPLASTIC_TRANSFORMATION_BY_CCND1_MYC.html Selected genes changed in NMuMG cells (mammary epithelium) transformed by overexpression of CCND1 [GeneID=595] vs those transformed by overexpression of CCND1 and MYC [GeneID=4609]. 17440082 18/42 Jessica Robertson 2.02647691519191e-06 7.43041535570367e-06 485 859.454545454545 751 1.84225343803148e-07 134 2.72653815371055 2.64735427124964 1 5.11166542843297 484 751 410 134 1782 1271 1937 839 281 439 1126 566 M5311 HOSHIDA_LIVER_CANCER_SUBCLASS_S1 http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_SUBCLASS_S1.html Genes from 'subtype S1' signature of hepatocellular carcinoma (HCC): aberrant activation of the WNT signaling pathway. 19723656 189/406 Jessica Robertson 2.41088186971605e-06 8.37464228427682e-06 335 950.636363636364 751 2.19171319245274e-07 335 1.73604734430523 1.92929032259465 1 3.22174278247297 335 1474 417 842 1953 626 687 719 1827 826 751 567 M9138 CHANG_POU5F1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_POU5F1_TARGETS_UP.html Genes up-regulated by POU5F1 [GeneID=5460] in bladder cancer cell lines. 18676852 18/36 Jessica Robertson 3.75860044648257e-05 7.82443433683578e-05 500 909.909090909091 752 3.41696787455119e-06 220 2.4233764829699 2.49111631804551 1 3.63761676271628 500 752 562 584 2118 1069 1496 942 220 613 1153 568 M1466 AFFAR_YY1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/AFFAR_YY1_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) expressing ~25% of YY1 [GeneID=7528]. 16611997 174/415 Kevin Vogelsang 1.32715151183937e-08 2.1744867078599e-07 820 734.454545454545 752 1.20650138167766e-09 268 1.85557824170548 2.0774478317124 1 4.51902850784785 820 545 268 412 1050 866 712 841 1354 459 752 569 M7404 FRIDMAN_IMMORTALIZATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRIDMAN_IMMORTALIZATION_DN.html Genes down-regulated in immortalized cell lines. 18711403 24/63 Jessica Robertson 1.20641127106531e-06 5.40463022582414e-06 755 977.090909090909 753 1.09673812056734e-07 152 2.58425626001153 2.88652585417603 1 4.97550814117335 753 1962 701 222 787 1793 2554 152 179 579 1066 570 M638 KEGG_ADHERENS_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ADHERENS_JUNCTION.html Adherens junction 53/111 KEGG 2.91506145763221e-07 2.31211682689763e-06 790 641.727272727273 754 2.6500562217146e-08 145 2.01513498723395 2.43493985729369 1 4.15139086266413 786 842 993 145 256 482 614 932 317 938 754 571 M1334 HASEGAWA_TUMORIGENESIS_BY_RET_C634R http://www.broadinstitute.org/gsea/msigdb/cards/HASEGAWA_TUMORIGENESIS_BY_RET_C634R.html Genes up-regulated in salivary, thyroid and mammary gland carcinomas developed in transgenic mice carrying RET [GeneID=5979] allele with the MEN2A mutation (C634R). 18542059 15/35 Jessica Robertson 4.03087246553176e-05 8.29906343298851e-05 905 920.727272727273 756 3.66449665606037e-06 213 2.10629313839562 2.55986121885254 1 3.14196659252936 903 756 694 248 2139 1267 1939 664 213 430 875 572 M8395 REACTOME_HEMOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HEMOSTASIS.html Genes involved in Hemostasis 244/615 Reactome 2.79986902747017e-06 9.30194568921026e-06 390 1079.90909090909 757 2.54533871889046e-07 386 1.62321975454547 1.67505314896837 1 2.98529790886105 386 2102 442 1230 1194 455 506 1427 2625 755 757 573 M12315 TSAI_DNAJB4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TSAI_DNAJB4_TARGETS_DN.html Genes down-regulated in CL1-5 cells (lung cancer) overexpressing DNAJB4 [GeneID=11080] off a plasmid vector. 16788156 5/9 Jessica Robertson 0.000145480158786704 0.000259603969563783 560 1410.09090909091 757 1.45489683678785e-05 122 3.0010656672933 3.0010656672933 1 3.93339288586171 557 1518 4579 1209 2950 732 757 661 122 1881 545 574 M13339 CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP http://www.broadinstitute.org/gsea/msigdb/cards/CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP.html Genes up-regulated in secondary APL (acute promyelocytic leukemia) compared to the de novo tumors. 16990782 32/65 Leona Saunders 7.90407000398232e-08 1.00648021844188e-06 820 789.636363636364 761 7.18551844359686e-09 38 1.9252412254297 2.02485512607709 1 4.22038971255691 816 611 682 601 38 1272 1147 328 1245 761 1185 575 M11457 GHO_ATF5_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GHO_ATF5_TARGETS_DN.html Genes down-regulated in HEP3B cells (liver cancer) overexpressing ATF5 [GeneID=22809] off a plasmid vector. 18701499 20/32 Jessica Robertson 3.55555724471088e-07 2.60333457011175e-06 650 874.454545454545 761 3.23232529031527e-08 173 1.7163160428574 2.02494706814309 1 3.50347058669256 647 173 1820 761 318 654 399 799 1201 2014 833 576 M735 REACTOME_NEURONAL_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEURONAL_SYSTEM.html Genes involved in Neuronal System 98/338 Reactome 1.11414226632119e-06 5.08361310611597e-06 605 929.454545454545 762 1.01285711868615e-07 519 1.67404522120184 1.75060324621337 1 3.23933767640005 602 1251 973 916 762 519 577 1257 1957 715 695 577 M878 REACTOME_SIGNAL_TRANSDUCTION_BY_L1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_TRANSDUCTION_BY_L1.html Genes involved in Signal transduction by L1 24/53 Reactome 3.62923192011051e-07 2.631328039622e-06 765 1011.90909090909 762 3.29930228982474e-08 300 1.61479127104614 2.05815554110577 1 3.29348903872224 762 1601 2047 845 324 435 346 602 995 2874 300 578 M5278 NIKOLSKY_BREAST_CANCER_7Q21_Q22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_7Q21_Q22_AMPLICON.html Genes within amplicon 7q21-q22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 37/105 Jessica Robertson 3.47333055197181e-06 1.09606456061272e-05 465 776.909090909091 764 3.15757821421064e-07 304 1.94097436099214 2.0842615046052 1 3.5191280779635 465 946 901 927 1282 579 1450 403 764 525 304 579 M12486 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_RUNX1 http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_RUNX1.html Genes whose expression is coregulated with that of RUNX1 [GeneID=861] in hematopoietic stem cells (HSC). 15711547 8/22 Jean Junior 2.11031356509628e-05 4.74061810452596e-05 760 1452.81818181818 766 2.11033360576917e-06 154 2.04428163572242 2.04428163572242 1 3.23118807872055 759 2795 4371 1680 1967 606 154 766 533 1665 685 580 M9678 STEIN_ESR1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESR1_TARGETS.html Genes regulated by ESR1 [GeneID=2099] in MCF-7 cells (breast cancer). 18974123 44/113 Arthur Liberzon 1.12583671457024e-06 5.12420814378806e-06 290 803.636363636364 766 1.02348844610072e-07 108 1.61825467286366 1.79442521185207 1 3.1293377047379 289 1275 1373 1554 766 132 123 317 1974 929 108 581 M6145 LEE_LIVER_CANCER_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_SURVIVAL_UP.html Genes highly expressed in hepatocellular carcinoma with good survival. 15349906 90/349 Yujin Hoshida 5.77841041673434e-07 3.4051419593832e-06 3580 1946.36363636364 768 5.25310175860309e-08 288 1.73040529541581 -1.54857051352287 -1 3.45847668000971 3580 560 580 768 498 4438 3220 3478 720 288 3280 582 M2542 GENTLES_LEUKEMIC_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/GENTLES_LEUKEMIC_STEM_CELL_UP.html Genes up-regulated in LSC (leukemic stem) cells compared to LPC (leukemia progenitor) cells from AML (acute myeloid leukemia) tumor samples. 21177505 14/51 Andrew Gentles 1.52480138209082e-06 6.19169781323881e-06 455 965.818181818182 768 1.38618403538071e-07 87 1.76355464885227 1.76355464885227 1 3.35733758587691 452 1559 1228 1700 2257 296 87 125 1998 768 154 583 M1687 ZHONG_SECRETOME_OF_LUNG_CANCER_AND_FIBROBLAST http://www.broadinstitute.org/gsea/msigdb/cards/ZHONG_SECRETOME_OF_LUNG_CANCER_AND_FIBROBLAST.html Proteins secreted in co-culture of LKR-13 tumor cells (non-small cell lung cancer, NSCLC) and MLg stroma cells (fibroblasts). 18757440 118/257 Jessica Robertson 6.45646674293974e-07 3.62335367154678e-06 860 801 770 5.86951694341546e-08 414 2.10462078486303 2.53893466683356 1 4.18565079999882 856 1091 596 414 545 1323 1191 546 770 662 817 584 M6939 HOSHIDA_LIVER_CANCER_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_SURVIVAL_UP.html Survival signature genes defined in adjacent liver tissue: genes correlated with poor survival of hepatocellular carcinoma (HCC) patients. 18923165 57/169 Yujin Hoshida 3.06240353850737e-09 5.78646087961514e-08 345 678.181818181818 770 2.78400322070021e-10 177 2.19680062900428 2.42547969167276 1 5.81170672809414 341 839 238 177 1346 770 571 957 908 449 864 585 M2402 KOHOUTEK_CCNT2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KOHOUTEK_CCNT2_TARGETS.html Genes down-regulated in E14 ES (embryonic stem) cells upon knockdown of CYCT2 [GeneID=905] by RNAi. 19364821 27/179 Arthur Liberzon 2.7199537671053e-07 2.2526825372382e-06 2755 1513.72727272727 770 2.47268554853167e-08 153 2.1635858975035 2.30540367034955 1 4.46615973979296 2752 153 458 770 230 3327 2271 2928 464 564 2734 586 M13398 OHM_EMBRYONIC_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/OHM_EMBRYONIC_CARCINOMA_DN.html Genes with low to medium basal transcription state in undifferentiated embryonic carcinoma cells. 17211412 4/14 Leona Saunders 1.03228608413751e-05 2.57988938147647e-05 775 1337 771 1.03229087943438e-06 18 3.28620872458034 3.28620872458034 1 5.51157299046127 771 2098 4301 1788 2983 387 90 273 18 1634 364 587 M11011 ASTON_MAJOR_DEPRESSIVE_DISORDER_DN http://www.broadinstitute.org/gsea/msigdb/cards/ASTON_MAJOR_DEPRESSIVE_DISORDER_DN.html Genes down-regulated in the temporal cortex samples from patients with major depressive disorder. 15303102 116/304 Jean Junior 2.51579142812456e-06 8.5863063599357e-06 500 837.909090909091 771 2.28708573185565e-07 496 1.74662914769469 1.93791373959279 1 3.23445964807266 496 687 1140 625 1142 771 524 648 1473 802 909 588 M5880 NABA_ECM_AFFILIATED http://www.broadinstitute.org/gsea/msigdb/cards/NABA_ECM_AFFILIATED.html Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins 22159717 47/185 Alexandra Naba 3.00527561582142e-07 2.34712025595653e-06 775 1137.90909090909 772 2.73206911486589e-08 270 1.99592248576573 1.76206072558925 1 4.10705026723809 772 314 372 721 270 1683 1117 3052 1831 733 1652 589 M2043 RICKMAN_HEAD_AND_NECK_CANCER_F http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_F.html Cluster f: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 36/93 Jessica Robertson 8.34535768490381e-06 2.17499144112677e-05 290 871 773 7.58671758353435e-07 290 2.51343705045673 2.73778827458031 1 4.28361136162632 290 1029 521 1170 1626 622 477 1347 651 773 1075 590 M16325 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_4 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_4.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 4. 12554760 6/18 Arthur Liberzon 1.31331567564669e-06 5.69833079266702e-06 760 1120.09090909091 774 1.31331645180646e-07 169 1.67687490925628 1.67687490925628 1 3.21442648554109 760 205 4599 169 871 774 776 737 1717 1328 385 591 M920 REACTOME_AQUAPORIN_MEDIATED_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AQUAPORIN_MEDIATED_TRANSPORT.html Genes involved in Aquaporin-mediated transport 23/54 Reactome 7.23168998336716e-06 1.93643995783191e-05 660 1215.81818181818 775 6.5742852318134e-07 363 1.8983904513655 1.78153851749042 1 3.27040741691632 657 485 506 775 1573 646 363 3622 2770 891 1086 592 M3008 NABA_ECM_GLYCOPROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_ECM_GLYCOPROTEINS.html Genes encoding structural ECM glycoproteins 22159717 81/221 Alexandra Naba 1.22452525697532e-16 8.08186669603711e-15 130 700.636363636364 775 1.11320477906847e-17 68 2.14881047066501 2.23171534910684 1 11.0689148246882 128 562 68 372 1311 939 1346 1143 775 72 991 593 M18876 MAHADEVAN_IMATINIB_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAHADEVAN_IMATINIB_RESISTANCE_UP.html Top genes up-regulated in the GIST (gastrointestinal stromal tumor) cell line resistant to imatinib [PubChem=5291] compared to the parental cell line sensitive to the drug. 17325667 9/31 Arthur Liberzon 1.23869659268996e-05 3.00597215605653e-05 745 1249 776 1.23870349740575e-06 167 2.42651448391638 2.57672732559782 1 4.01082895449469 741 776 4181 167 1799 1345 1993 728 366 603 1040 594 M8901 LANDIS_ERBB2_BREAST_TUMORS_324_DN http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_TUMORS_324_DN.html Down-regulated genes from the 324 genes identified by two analytical methods as changed in the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 114/229 Leona Saunders 9.48844852394811e-12 3.17019619220307e-10 430 892.181818181818 780 8.62586229453547e-13 134 1.97166419979003 2.15878322606304 1 6.84583063775074 427 275 134 642 780 1422 1501 1516 1437 239 1441 595 M10953 BOYAULT_LIVER_CANCER_SUBCLASS_G2 http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G2.html Genes in hepatocellular carcinoma (HCC) subclass G2, defined by unsupervised clustering. 17187432 26/52 Yujin Hoshida 1.50934188840753e-06 6.15024007745884e-06 715 735.363636363636 780 1.37212993083127e-07 126 1.79726095162601 1.90490589925298 1 3.42342215811883 712 957 1298 762 890 551 132 126 835 1046 780 596 M15835 RIGGINS_TAMOXIFEN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/RIGGINS_TAMOXIFEN_RESISTANCE_DN.html Genes down-regulated SUM44/LCCTam cells (breast cancer) resistant to 4-hydroxytamoxifen [PubChem=63062] relative to the parental SUM44 cells sensitive to the drug. 18974135 153/395 Leona Saunders 7.29942853652143e-07 3.89579978612066e-06 920 833.181818181818 781 6.63584632583278e-08 492 1.77052247438002 1.98267209053911 1 3.50082225854158 919 1331 645 499 591 781 1254 1210 919 492 524 597 M10457 LUCAS_HNF4A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LUCAS_HNF4A_TARGETS_DN.html Genes down-regulated in Tet-On HEK293 cells (embryonic kidney) by expression of HNF4A [GeneID=3172]. 16007190 3/18 Leona Saunders 3.14307422977855e-05 6.70999810512178e-05 575 1121.45454545455 783 3.14311868578377e-06 80 1.66199029021467 1.66199029021467 1 2.53527460954443 574 911 4175 928 2229 287 80 783 1146 777 446 598 M3238 SMID_BREAST_CANCER_RELAPSE_IN_BONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_BONE_UP.html Genes up-regulated in bone relapse of breast cancer. 18451135 68/168 Jessica Robertson 1.34595128936085e-07 1.48403005692823e-06 2735 1482.18181818182 783 1.22359215609602e-08 97 1.89011226407832 -1.84615640926449 -1 4.0268728892394 2732 97 315 388 593 2437 4581 2012 783 161 2205 599 M11695 STOSSI_RESPONSE_TO_ESTRADIOL http://www.broadinstitute.org/gsea/msigdb/cards/STOSSI_RESPONSE_TO_ESTRADIOL.html Genes up-regulated by estradiol (E2) [PubChem=5757] in U2OS cells (osteosarcoma) expressing ESR1 or ESR2 [GeneID=2099;2100]. 15033914 31/92 Kevin Vogelsang 6.05399454983099e-07 3.47495592160468e-06 940 907.454545454545 785 5.50363292343579e-08 35 1.73706626788461 1.77538532745334 1 3.46619319224707 936 732 763 785 1754 495 849 245 2300 1088 35 600 M2193 OHGUCHI_LIVER_HNF4A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OHGUCHI_LIVER_HNF4A_TARGETS_UP.html Genes up-regulated in liver samples of liver-specific knockout of HNF4A [GeneID=3172]. 18426912 39/91 Arthur Liberzon 1.21758315938234e-06 5.43907977584904e-06 785 1345.63636363636 789 1.10689439386407e-07 719 1.78520738693653 -1.73801863798429 -1 3.43528646201887 2155 719 784 782 789 726 1548 4136 1458 737 968 601 M14728 BROWNE_HCMV_INFECTION_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_6HR_UP.html Genes up-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 6 h time point that were not up-regulated at the previous time point, 4 h. 11711622 58/171 John Newman 1.64930648347718e-06 6.51656844989384e-06 475 889.090909090909 790 1.49937065448948e-07 472 2.02349633267632 2.15101380179929 1 3.83577033930707 1214 936 528 621 931 1386 1817 610 790 472 475 602 M16478 LEE_TARGETS_OF_PTCH1_AND_SUFU_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_TARGETS_OF_PTCH1_AND_SUFU_DN.html Genes down-regulated in medulloblastoma tumors from animals with inactivating mutations of one copy of PTCH1 or SUFU [GeneID=5727;51684] in conjunction with TP53 [GeneID=7157] loss. 17452975 58/167 Jessica Robertson 1.67581417816989e-07 1.70714461715307e-06 450 818.181818181818 792 1.52346755074756e-08 123 1.7167369512097 1.82764094258825 1 3.61932767632283 446 838 792 948 123 471 534 2079 1447 387 935 603 M3432 LEE_LIVER_CANCER_MYC_TGFA_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_TGFA_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) tissue of MYC and TGFA [GeneID=4609;7039] double transgenic mice. 15565109 51/124 Yujin Hoshida 1.22414019441773e-06 5.45796474885013e-06 1495 1006.18181818182 792 1.11285534142123e-07 437 1.9477278813701 -1.702179483129 -1 3.74695403999087 1495 437 697 494 792 988 2328 1441 688 610 1098 604 M19529 RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN.html Genes down-regulated in anaplastic thyroid carcinoma (ATC) compared to normal thyroid tissue. 17406368 312/761 Arthur Liberzon 4.45079327976926e-06 1.32421697199992e-05 755 922.727272727273 793 4.04618389467326e-07 527 1.47512670630314 1.65926181705246 1 2.63023170796367 755 801 1136 527 1384 701 918 793 1825 680 630 605 M773 REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE.html Genes involved in GPVI-mediated activation cascade 28/59 Reactome 1.07668768955707e-06 4.95128411507793e-06 965 860.909090909091 797 9.78807469538312e-08 250 1.95268546106211 2.03480292553635 1 3.7866924099732 963 730 797 250 751 1369 1220 1044 375 756 1215 606 M1574 LEE_AGING_MUSCLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_MUSCLE_DN.html Downregulated in the gastrocnemius muscle of aged adult mice (30-month) vs young adult (5-month) 10464095 40/102 John Newman 4.75945480979509e-06 1.39365569125892e-05 935 994.454545454545 798 4.3267864603421e-07 193 2.48623291553881 2.73553585115873 1 4.41291775773685 606 2838 878 934 2372 511 470 193 798 932 407 607 M2488 FORTSCHEGGER_PHF8_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FORTSCHEGGER_PHF8_TARGETS_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) upon knockdown of PHF8 [GeneID=23133] by RNAi. 20421419 504/1186 Arthur Liberzon 1.64970858521389e-07 1.69158302632654e-06 1085 1163.90909090909 798 1.64970870768313e-08 142 1.5909090430749 1.80172358016052 1 3.3563624443731 1084 798 4676 392 142 976 1242 764 1569 448 712 608 M11405 TAKADA_GASTRIC_CANCER_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKADA_GASTRIC_CANCER_COPY_NUMBER_DN.html Candidate genes in the regions of copy number loss in gastric cancer cell lines. 16103878 13/41 Arthur Liberzon 5.42825655306556e-06 1.54537121553252e-05 1765 968.727272727273 799 4.93479086066744e-07 513 1.77644417297447 1.77016459596962 1 3.12394377256583 1763 513 1045 524 1466 1180 799 688 791 699 1188 609 M9908 LANDIS_BREAST_CANCER_PROGRESSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_BREAST_CANCER_PROGRESSION_DN.html Genes down-regulated in preneoplastic mammary tissues and whose expression is maintained in tumors. 16434967 60/108 Lauren Kazmierski 1.9504359606831e-08 3.0670278227386e-07 865 794.818181818182 801 1.77312361634084e-09 129 2.03613075596672 2.16913351180869 1 4.84757810577391 129 836 276 861 2124 521 531 801 1378 424 862 610 M1784 KAN_RESPONSE_TO_ARSENIC_TRIOXIDE http://www.broadinstitute.org/gsea/msigdb/cards/KAN_RESPONSE_TO_ARSENIC_TRIOXIDE.html Genes changed in U373-MG cells (malignant glioma) upon treatment with arsenic trioxide [PubChem=14888], a chemical that can cause autophagic cell death. 15592527 84/179 Arthur Liberzon 1.24459089307951e-06 5.50106086641434e-06 320 1220.81818181818 801 1.13144690652176e-07 265 1.92015479822495 1.91020160573857 1 3.69151275637117 319 3795 879 2344 801 310 265 318 2495 1560 343 611 M13202 FOURNIER_ACINAR_DEVELOPMENT_LATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FOURNIER_ACINAR_DEVELOPMENT_LATE_DN.html Genes down-regulated late in HMEC cells (mammary epithelium) during acinar development in vitro. 16849555 29/50 Arthur Liberzon 1.59313355269704e-06 6.40409354248728e-06 595 842.454545454545 802 1.44830427851677e-07 42 2.35046007956982 2.72226935089327 1 4.46206411049922 592 1690 1435 937 910 306 42 802 488 1533 532 612 M12029 BILD_HRAS_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/BILD_HRAS_ONCOGENIC_SIGNATURE.html Genes selected in supervised analyses to discriminate cells expressing activated HRAS [GeneID=3265] oncogene from control cells expressing GFP. 16273092 192/465 Arthur Liberzon 5.86034264922388e-07 3.4235028683673e-06 805 964 802 5.32758564572538e-08 359 1.63142677452917 1.78163458961945 1 3.25926042325555 802 1854 713 1177 506 614 836 559 2042 1142 359 613 M19877 KEGG_ENDOMETRIAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ENDOMETRIAL_CANCER.html Endometrial cancer 26/61 KEGG 3.02931260738414e-05 6.49375977959839e-05 625 1065.18181818182 803 2.75395847329046e-06 139 2.12360509735503 2.54264857229928 1 3.25048541501988 621 1449 1552 895 2051 744 507 410 139 2546 803 614 M13206 KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN.html Genes down-regulated in TC71 and EWS502 cells (Ewing's sarcoma) by EWSR1-FLI1 [GeneID=2130;2314] as inferred from RNAi knockdown of this fusion protein. 17114343 267/623 Leona Saunders 1.16518103258965e-07 1.35821848724256e-06 420 740.545454545455 804 1.05925554027352e-08 96 1.67151515120981 1.78977942403865 1 3.58465945494662 419 537 311 96 1075 933 883 804 1790 408 890 615 M2469 KRIEG_HYPOXIA_NOT_VIA_KDM3A http://www.broadinstitute.org/gsea/msigdb/cards/KRIEG_HYPOXIA_NOT_VIA_KDM3A.html Genes induced under hypoxia independently of KDM3A [GeneID=55818] in RCC4 cells (renal carcinoma) expressing VHL [GeneID=7428]. 19858293 505/1187 Arthur Liberzon 2.15919523340791e-06 7.75170183355026e-06 655 1258.27272727273 804 2.15919733136661e-07 267 1.57800402995333 1.73669892741212 1 2.94781007510959 655 1763 4670 930 1110 562 557 459 2064 804 267 616 M3854 MARTINEZ_RB1_AND_TP53_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RB1_AND_TP53_TARGETS_DN.html Genes down-regulated in mice with skin specific double knockout of both RB1 and TP53 [GeneID=5925;7157] by Cre-lox. 18245467 417/992 Jessica Robertson 3.98705251402872e-10 9.53231024527479e-09 1650 854.545454545455 805 3.62459319522845e-11 15 1.80025527990333 2.11779812589187 1 5.27802119908539 1646 15 189 53 334 2090 1792 1175 805 266 1035 617 M16692 COWLING_MYCN_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/COWLING_MYCN_TARGETS.html Genes down-regulated by MYCN [GeneID=4613] but not by its transactivation-defficient, trunkated form N-Myc-delta-73. 17704800 35/86 Jessica Robertson 2.50223856546947e-06 8.57525404595596e-06 545 804.090909090909 808 2.27476491952092e-07 326 1.63343685486123 1.88629831872881 1 3.0251807928121 542 326 838 1180 1138 367 644 808 1498 905 599 618 M16369 HUANG_DASATINIB_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_DASATINIB_RESISTANCE_DN.html Genes whose expression negatively correlated with resistance of breast cancer cell lines to dasatinib [PubChem=3062316]. 17332353 50/100 Jessica Robertson 8.54642082785425e-07 4.26956588478944e-06 1250 997.727272727273 809 7.76947649810504e-08 505 1.62429318674597 -1.50924323126911 -1 3.18806321712773 1247 711 1349 809 654 505 1430 1535 665 1353 717 619 M2599 GHANDHI_BYSTANDER_IRRADIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GHANDHI_BYSTANDER_IRRADIATION_DN.html Genes significantly (FDR < 10%) down-regulated in IMR-90 cells (fibroblast) in response to bystander irradiation. 19108712 16/32 Itai Pashtan 3.6804571486247e-05 7.6856605162457e-05 555 1240.90909090909 810 3.34592611065918e-06 241 2.22623799087711 2.44230042393131 1 3.34802568110236 552 2922 1407 2531 2628 587 349 416 241 1207 810 620 M7517 SMID_BREAST_CANCER_LUMINAL_A_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_LUMINAL_A_UP.html Genes up-regulated in the luminal A subtype of breast cancer. 18451135 52/160 Jessica Robertson 2.68866065303436e-12 9.67623284837993e-11 815 825.818181818182 811 2.44423695730694e-13 124 2.1717870889405 2.37558233073691 1 7.94981132041863 811 302 124 199 412 1636 1564 1303 1020 222 1491 621 M4716 CONCANNON_APOPTOSIS_BY_EPOXOMICIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/CONCANNON_APOPTOSIS_BY_EPOXOMICIN_UP.html Genes up-regulated in SH-SY5Y cells (neuroblastoma) after treatment with epoxomicin [PubChem=3035402], a protease inhibitor causing apoptosis. 16983338 168/404 Leona Saunders 1.15903838050172e-06 5.23242182180256e-06 665 1132.63636363636 813 1.05367181011353e-07 519 1.74228456586546 1.91785328267518 1 3.36340334493712 661 2296 619 1573 776 813 1182 519 2331 1055 634 622 M16941 DACOSTA_ERCC3_ALLELE_XPCS_VS_TTD_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_ERCC3_ALLELE_XPCS_VS_TTD_UP.html Genes up-regulated in fibroblasts expressing different mutant forms of ERCC3 [GeneID=2071]: XP/CS (xeroderma pigmentosum (XP) and Cockraine's syndrome (CS)) vs TTD (trichothiodystrophy). 15608684 19/33 Arthur Liberzon 1.66948624479414e-06 6.56860834853513e-06 915 1024.72727272727 817 1.51771591972495e-07 401 2.36487152827399 2.64224004236561 1 4.47990026633734 912 495 401 805 1630 2051 1604 817 702 490 1365 623 M1623 SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_DN.html Down-regulated in murine dorsal skin cells at 6 h after treatment with the phorbol ester carcinogen TPA [PubChem=4792]. 12640676 33/68 John Newman 5.29260743674887e-05 0.000105402288349363 390 1032.18181818182 817 4.81157706083349e-06 390 2.04682361384193 2.12423340148807 1 2.97558003183514 390 726 594 700 2223 1086 716 1300 1380 817 1422 624 M1618 LIU_SMARCA4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LIU_SMARCA4_TARGETS.html Genes up-regulated in SW-13 cells (kidney cancer) by transient expression of SMARCA4 [GeneID=6597] at 24 h off a plasmid vector. 11509180 47/109 John Newman 1.29500905733758e-06 5.62932508597765e-06 640 1116.09090909091 818 1.17728165421178e-07 583 1.81169732299901 2.04068887487881 1 3.47637362221845 640 596 583 1830 818 1158 669 1823 2079 605 1476 625 M6225 WANG_BARRETTS_ESOPHAGUS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_BARRETTS_ESOPHAGUS_UP.html Genes up-regulated in Barrett's esophagus compared to the normal tissue. 16449976 37/102 Arthur Liberzon 1.73124190865785e-07 1.7484050827523e-06 1265 880.454545454545 819 1.57385640444924e-08 132 1.57201532660961 -1.81340989476085 -1 3.30825712928951 1263 459 1026 1071 132 773 1808 527 1139 819 668 626 M13788 MCBRYAN_PUBERTAL_BREAST_5_6WK_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_5_6WK_UP.html Genes up-regulated during pubertal mammary gland development between week 5 and 6. 17486082 85/174 Arthur Liberzon 7.33690136884525e-13 2.88913611885789e-11 2110 1037.54545454545 820 6.66991033531607e-14 113 2.06655874676434 -2.04390915764035 -1 7.96115300609829 2107 565 113 426 820 1089 2533 1225 734 137 1664 627 M1170 HUMMERICH_SKIN_CANCER_PROGRESSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_SKIN_CANCER_PROGRESSION_DN.html Selected genes down-regulated during progression through benign to malignant skin tumors formed by treatment with DMBA and TPA [PubChem=6001;4792] chemicals in the two stage skin carcinogenesis model. 16247483 102/194 Arthur Liberzon 4.11086864021909e-06 1.24683044971305e-05 620 807.909090909091 821 3.73716029246578e-07 250 2.00337004176617 2.15542471948707 1 3.59126905368832 250 1418 438 929 1424 616 467 821 994 616 914 628 M19428 KEGG_WNT_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_WNT_SIGNALING_PATHWAY.html Wnt signaling pathway 77/178 KEGG 5.93903449199926e-07 3.44008845853011e-06 825 830.181818181818 822 5.39912372298049e-08 69 2.18047658770966 2.39409925095246 1 4.35447791672188 822 2414 1012 836 663 346 537 71 889 1473 69 629 M2088 LI_INDUCED_T_TO_NATURAL_KILLER_DN http://www.broadinstitute.org/gsea/msigdb/cards/LI_INDUCED_T_TO_NATURAL_KILLER_DN.html Genes down-regulated in ITNK cells (T-lymphocyte progenitors (DN3 cells) reprogrammed to natural killer (NK) cells by ablation of BCL11B [GeneID=64919] gene), compared to the parental DN3 cells. 20538915 94/199 Arthur Liberzon 2.32921197538112e-07 2.0907338471424e-06 675 998.818181818182 822 2.11746565634767e-08 193 2.00198513573763 2.1279733879081 1 4.15628760117406 671 417 448 822 193 1972 1402 1552 1081 540 1889 630 M16591 MCCABE_HOXC6_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCCABE_HOXC6_TARGETS_UP.html Genes with promoters bound by HOXC6 [GeneID=3223] in LNCaP cells (prostate cancer) and up-regulated upon loss of function (LOF) of HOXC6. 18339881 4/14 Jessica Robertson 3.60025242149939e-07 2.61589047989435e-06 825 1062.09090909091 823 3.6002530047813e-08 4 4.39652522647246 4.39652522647246 1 8.97115273266992 823 215 4464 265 1468 1142 1161 58 4 1639 444 631 M4577 MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_DN http://www.broadinstitute.org/gsea/msigdb/cards/MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_DN.html Top genes down-regulated in mesenchyme stem cells (MSC) grown in a tumor conditioned medium, which leads to carcinoma-associated fibroblast phenotype. 18519693 22/40 Leona Saunders 1.69581287959594e-07 1.72003877787588e-06 1055 883.636363636364 823 1.54164819119389e-08 129 2.35453145934117 2.53156090654623 1 4.9611517427082 1052 1201 426 440 129 1516 1973 823 532 260 1368 632 M15592 NGUYEN_NOTCH1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NGUYEN_NOTCH1_TARGETS_UP.html Genes up-regulated in primary keratinocytes by expression of constantly active NOTCH1 [GeneID=4851]. 16618808 19/56 Kevin Vogelsang 3.66698451060457e-06 1.14633018123369e-05 825 803.363636363636 824 3.33362783889952e-07 282 1.66856834272661 1.86351266368785 1 3.0133590296731 554 873 824 821 1300 685 282 319 1362 862 955 633 M2089 NOUSHMEHR_GBM_SOMATIC_MUTATED http://www.broadinstitute.org/gsea/msigdb/cards/NOUSHMEHR_GBM_SOMATIC_MUTATED.html Genes showing significantly elevated somatic mutation frequencies in proneural G-CIMP (a CpG island methylator phenotype) GBM (glyoblastoma multiforme) tumors. 20399149 14/29 Arthur Liberzon 2.36949761634344e-05 5.25234902090131e-05 675 1084.09090909091 824 2.15411194297179e-06 278 2.15198876050758 2.15198876050758 1 3.36641101322587 672 2788 1358 1262 2037 542 409 371 824 1384 278 634 M1131 DARWICHE_SKIN_TUMOR_PROMOTER_UP http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_SKIN_TUMOR_PROMOTER_UP.html Genes up-regulated during skin tumor progression: epidermis treated with the carcinogen DMBA [PubChem=6001] followed by 20 weekly applications of the tumor promoter TPA [PubChem=4792], compared to the untreated skin. 17525749 105/260 Arthur Liberzon 2.30725979905234e-07 2.07520526264093e-06 1040 954.454545454545 825 2.09750912820662e-08 191 1.67019118203247 1.95529295470509 1 3.46943237397988 1040 818 683 1594 191 892 825 745 1905 1078 728 635 M1193 HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer, mutated TP53 [GeneID=7157]) undergoing mitotic arrest and apoptosis after treatment with 100 nM docetaxel [PubChem=148124]. 17099726 11/33 Arthur Liberzon 8.48591267248956e-07 4.25749323161521e-06 785 828.363636363636 825 7.71446904155054e-08 92 2.95012890852863 3.43372355383491 1 5.79165850316077 781 1314 944 1390 1406 479 230 92 825 1518 133 636 M8831 BRUECKNER_TARGETS_OF_MIRLET7A3_UP http://www.broadinstitute.org/gsea/msigdb/cards/BRUECKNER_TARGETS_OF_MIRLET7A3_UP.html Genes up-regulated in A549 cells (lung cancer) expressing MIRLET7A3 [GeneID=406883] microRNA off a plasmid vector. 17308078 73/201 Jessica Robertson 7.32945277790883e-07 3.90737380173843e-06 4290 1722.54545454545 826 6.66314110888006e-08 451 1.73500085106566 -1.56237848437182 -1 3.42976894559684 4290 826 737 686 592 1151 2003 4371 769 451 3072 637 M19837 RICKMAN_HEAD_AND_NECK_CANCER_E http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_E.html Cluster e: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 46/189 Jessica Robertson 4.50431799626789e-10 1.04491258071838e-08 1040 913.272727272727 827 4.09483454290011e-11 117 2.24961382559135 -2.346420590666 -1 6.56266419954529 1038 594 194 518 428 1602 2200 950 827 117 1578 638 M6670 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_UP.html Genes up-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 3 days after transduction. 16818636 102/331 Arthur Liberzon 9.57187687158461e-07 4.60984738132019e-06 925 995.727272727273 828 8.70171003288198e-08 478 1.54522129776992 1.74902023846118 1 3.01405565714037 924 688 478 828 702 1629 1333 680 1916 526 1249 639 M8512 TSAI_RESPONSE_TO_IONIZING_RADIATION http://www.broadinstitute.org/gsea/msigdb/cards/TSAI_RESPONSE_TO_IONIZING_RADIATION.html Genes up-regulated in TK6, WTK1, and NH32 cell lines (lymphoblast) in response to ionizing radiation. 16247478 122/274 Arthur Liberzon 7.06653782060382e-07 3.8227912014599e-06 515 765.545454545455 828 6.42412735492823e-08 80 1.81761260305289 2.15188865298007 1 3.59939135443145 514 1004 559 242 1266 946 1427 80 1322 828 233 640 M17673 KEGG_CARDIAC_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CARDIAC_MUSCLE_CONTRACTION.html Cardiac muscle contraction 33/118 KEGG 1.50849928530303e-05 3.55396060881347e-05 830 860.454545454545 830 1.37137238991159e-06 219 2.89880578480821 3.4303437180019 1 4.71442605786512 830 335 573 546 1836 908 697 1309 219 986 1226 641 M169 PID_INTEGRIN2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN2_PATHWAY.html Beta2 integrin cell surface interactions 18832364 14/38 Pathway Interaction Database 6.32986503259316e-06 1.74173502893315e-05 830 985 831 5.7544393136602e-07 181 1.90301714029982 2.11127934333926 1 3.31039097945672 826 181 630 986 1523 806 736 831 2380 1020 916 642 M2465 DELACROIX_RAR_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DELACROIX_RAR_TARGETS_DN.html Genes bound by RARG [GeneID=5916] and down-regulated by tretinoin (all-trans retinoic acid, ATRA) [PubChem=444795] in MEF cells (embryonic fibroblast). 19884340 14/35 Arthur Liberzon 4.13293106593027e-06 1.25190142048799e-05 690 998 831 3.75721711826889e-07 401 2.87458925023244 2.70653873154979 1 5.15117657556837 688 1459 731 1339 1351 546 401 1539 831 1386 707 643 M12459 CHIBA_RESPONSE_TO_TSA_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIBA_RESPONSE_TO_TSA_DN.html Cancer related genes down-regulated in any of four hepatoma cell lines following 24 h treatment with TSA [PubChem=5562]. 15452378 28/53 John Newman 1.70070104985779e-06 6.64677658017817e-06 670 1073.27272727273 833 1.5460930587084e-07 594 2.25857971195924 2.351243701942 1 4.27430455017555 668 2160 897 833 944 793 743 1555 779 1840 594 644 M17607 DER_IFN_BETA_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_BETA_RESPONSE_DN.html Genes down-regulated in HT1080 (fibrosarcoma) cells by treatment with interferon beta for 6 h. 9861020 3/11 Yujin Hoshida 1.72755164818447e-06 6.71252655339338e-06 585 1139.09090909091 834 1.72755299118155e-07 137 1.11788374795563 -1.11788374795563 -1 2.113819696156 581 908 4369 1610 1771 239 196 137 834 1399 486 645 M1627 JACKSON_DNMT1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JACKSON_DNMT1_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) upon Cre-lox knockout of DNMT1 [GeneID=1786]. 11137995 24/53 John Newman 1.04670062863674e-05 2.61034547407757e-05 280 854.545454545455 834 9.51550553262753e-07 167 2.18549167612253 2.12633032868583 1 3.66139751642636 278 167 489 1052 1984 834 434 1617 1219 423 903 646 M2346 TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_TOP20_UP http://www.broadinstitute.org/gsea/msigdb/cards/TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_TOP20_UP.html Top 20 up-regulated genes in leukemic progenitor cells expressing activated fusion of ESWR1 and FLI1 [GeneID=2130, 2313] compared to normal hematopoetic progenitors. 17875932 12/36 Arthur Liberzon 6.90844177520498e-07 3.78631089574392e-06 790 1129.54545454545 835 6.28040358599579e-08 421 2.40466978747354 2.4852489434753 1 4.76559232041882 788 2819 835 1985 567 588 421 1281 1358 1180 603 647 M2410 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4.html Genes regulated in MCF7 cells (breast cancer) by expression of the full-length and truncated (611-CTF) forms of ERBB2 [GeneID=2064] at 60 h time point. 19364815 66/188 Arthur Liberzon 1.67054682101983e-07 1.7054863623745e-06 935 810.454545454545 835 1.51867904351915e-08 73 2.0388150970387 1.96262472827522 1 4.29866665495916 932 835 321 73 208 971 1186 2521 959 334 575 648 M15047 MULLIGHAN_NPM1_SIGNATURE_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_SIGNATURE_3_DN.html The 'NPM1 signature 3': genes down-regulated in pediatric AML (acute myeloid leukemia) with mutated NPM1 [GeneID=4869] compared to the AML cases with intact NPM1 and MLL [GeneID=4297]. 17597811 129/372 Arthur Liberzon 5.58656054034128e-08 7.63225151371406e-07 840 812.363636363636 838 5.07869152927577e-09 19 1.82572740408526 2.01496256170915 1 4.08242602620663 838 814 516 449 19 1233 1290 1269 1046 535 927 649 M791 REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_GLUCAGON_LIKE_PEPTIDE1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_GLUCAGON_LIKE_PEPTIDE1.html Genes involved in Regulation of Insulin Secretion by Glucagon-like Peptide-1 21/55 Reactome 1.23613361519959e-05 3.00211711665109e-05 1765 1444.81818181818 839 1.12376414620762e-06 717 1.45251825207002 1.4126827853032 1 2.40118915806829 717 746 839 742 1763 923 732 3891 2996 780 1764 650 M11302 SMID_BREAST_CANCER_RELAPSE_IN_LUNG_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_LUNG_DN.html Genes down-regulated in lung relapse of breast cancer. 18451135 26/60 Jessica Robertson 5.47896563517022e-06 1.55696985848439e-05 595 1203.72727272727 839 4.98089025477007e-07 479 1.62189363141041 1.66990795491892 1 2.85023564384348 594 479 798 1855 1471 787 730 2194 2260 839 1234 651 M17268 SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN.html Genes down-regulated in 293 cells (embryonic kidney) upon expression of KHSV (Kaposi sarcoma-associated herpesvirus) microRNAs. 17500590 41/111 Arthur Liberzon 1.02776134953477e-06 4.82091059451446e-06 4340 2102.18181818182 841 9.34328936062224e-08 321 1.81828984243997 -1.6159502447875 -1 3.53377163270975 4340 321 527 599 732 3030 4506 3732 841 536 3960 652 M10660 YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP.html Genes up-regulated in the uteri of ovariectomized mice 6 h after progesterone [PubChem=5994] injection: HOXA10 [GeneID=3206] knockout vs wild type animals. 12554760 54/127 Kevin Vogelsang 3.8942664997697e-08 5.70266650560025e-07 255 826.636363636364 841 3.54024233518449e-09 252 2.29668652134763 2.3729962549691 1 5.24177581905656 252 841 292 823 1188 667 902 1080 1449 467 1132 653 M5354 FIRESTEIN_PROLIFERATION http://www.broadinstitute.org/gsea/msigdb/cards/FIRESTEIN_PROLIFERATION.html Genes required for proliferation of DLD-1 cell (colon cancer with APC [GeneID=324] deletions), based on shRNA screen. 18794900 108/296 Jessica Robertson 5.46400196722779e-07 3.29104283013232e-06 845 904.909090909091 841 4.96727574935285e-08 280 1.36997441414512 1.52125870483417 1 2.74551318248481 841 1247 1364 551 479 315 541 1213 1950 1173 280 654 M174 PID_UPA_UPAR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_UPA_UPAR_PATHWAY.html Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling 18832364 31/84 Pathway Interaction Database 1.29620268940249e-07 1.4496433896277e-06 910 858.545454545455 842 1.17836615070233e-08 82 1.60474675717808 1.68800081231133 1 3.42487563498844 804 862 906 1044 82 612 842 524 2299 907 562 655 M13547 TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_LOBULAR_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_LOBULAR_NORMAL_DN.html Genes down-regulated in lobular carcinoma vs normal lobular breast cells. 17389037 47/135 Arthur Liberzon 5.22624853492072e-06 1.50523667084441e-05 145 961.818181818182 842 4.75114631842569e-07 145 1.90046358020023 1.927230610936 1 3.34997526977855 145 1186 454 1462 2578 448 605 879 1490 491 842 656 M5389 RODWELL_AGING_KIDNEY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODWELL_AGING_KIDNEY_UP.html Genes whose expression increases with age in normal kidney. 15562319 313/819 John Newman 1.23680266671938e-11 3.9696282851007e-10 440 723.272727272727 842 1.1243660606603e-12 140 1.7482490513197 1.96176524279959 1 6.00769893631701 440 400 140 391 897 1119 1064 842 1471 174 1018 657 M6754 ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_UP.html Genes whose promoters display higher histone H3 trimethylation mark at K9 (H3K9me3) in hepatocellular carcinoma (HCC) compared to normal liver. 18413731 47/208 Jessica Robertson 5.89661641433114e-07 3.42823132972155e-06 640 917.909090909091 843 5.36056181344558e-08 177 1.73265809081185 1.8662169891523 1 3.46112046500511 638 1273 1595 1200 511 318 640 843 1161 1741 177 658 M2115 VERHAAK_GLIOBLASTOMA_PRONEURAL http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_GLIOBLASTOMA_PRONEURAL.html Genes correlated with proneural type of glioblastoma multiforme tumors. 20129251 109/333 Arthur Liberzon 1.75747599969964e-05 4.04098750470684e-05 570 963.454545454545 844 1.59771821772874e-06 438 1.76835836329989 1.91084693397962 1 2.83988920367373 568 1856 1034 963 1889 460 438 478 1442 844 626 659 M15898 KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM.html Fructose and mannose metabolism 15/41 KEGG 7.9826059215259e-07 4.11774058972012e-06 845 1177.90909090909 845 7.25691710725617e-08 67 1.11133414531391 -1.17361706653439 -1 2.18764635745097 845 1215 2697 2171 623 193 293 505 1746 2602 67 660 M12399 BIOCARTA_CFTR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CFTR_PATHWAY.html Cystic Fibrosis Transmembrane Conductance Regulator And Beta 2 Adrenergic Receptor Pathway 6/17 BioCarta 8.2907462008202e-06 2.16316462678416e-05 500 1172.09090909091 845 8.29077713239526e-07 148 1.18561428603098 1.18561428603098 1 2.02165006015928 499 1665 3825 1009 1654 383 148 845 510 2043 312 661 M13143 BIOCARTA_UCALPAIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_UCALPAIN_PATHWAY.html uCalpain and friends in Cell spread 24/44 BioCarta 2.67689119437591e-06 8.97917833704045e-06 1110 878.545454545455 848 2.43354041048995e-07 366 2.43832720473504 3.00374953300826 1 4.49804897429916 1107 744 1162 366 1177 683 763 949 376 1489 848 662 M7815 RADMACHER_AML_PROGNOSIS http://www.broadinstitute.org/gsea/msigdb/cards/RADMACHER_AML_PROGNOSIS.html The 'Bullinger validation signature' [PMID=15084693] used to validate prediction of prognostic outcome of acute myeloid leukemia (AML) patients with a normal karyotype. 16670265 68/181 Kevin Vogelsang 7.81949654691957e-07 4.09409618087878e-06 735 867.636363636364 848 7.10863575110692e-08 575 1.54854008330124 1.71976449016737 1 3.04969599801066 734 575 822 663 609 891 1146 1141 1119 848 996 663 M50 PID_PTP1B_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PTP1B_PATHWAY.html Signaling events mediated by PTP1B 18832364 43/115 Pathway Interaction Database 3.54803316216348e-07 2.60189098558655e-06 905 806.181818181818 849 3.22548521306358e-08 291 1.732178430242 1.80228399480898 1 3.53600257965728 904 849 1142 894 316 484 828 291 1360 1248 552 664 M167 PID_AP1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AP1_PATHWAY.html AP-1 transcription factor network 18832364 70/143 Pathway Interaction Database 0.000123733967339689 0.000223867710792967 640 1218.18181818182 849 1.12491751837856e-05 617 2.33912000896975 2.61962772280335 1 3.12079782839144 639 2534 685 849 2515 1408 1219 617 758 794 1382 665 M1404 LEI_HOXC8_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEI_HOXC8_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) by overexpression of HOXC8 [GeneID=3224]. 15699330 14/30 Kate Stafford 1.54226794314931e-05 3.6207753414818e-05 850 971.909090909091 850 1.40207159548183e-06 267 2.47165978560085 2.73456234720548 1 4.01243600422503 850 973 952 703 1846 810 684 1403 267 765 1438 666 M1847 LIN_TUMOR_ESCAPE_FROM_IMMUNE_ATTACK http://www.broadinstitute.org/gsea/msigdb/cards/LIN_TUMOR_ESCAPE_FROM_IMMUNE_ATTACK.html Genes up-regulated in highly immune-resistant cancer cell line developed from a susceptible cancer using an in vivo selection strategy. 17308126 12/33 Jessica Robertson 0.000112572754450172 0.000205259115701754 265 1174 852 1.02344104679062e-05 263 2.21841838820723 2.21841838820723 1 2.9903223107953 263 1974 720 1156 3256 852 696 603 1834 858 702 667 M6724 REACTOME_NA_CL_DEPENDENT_NEUROTRANSMITTER_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NA_CL_DEPENDENT_NEUROTRANSMITTER_TRANSPORTERS.html Genes involved in Na+/Cl- dependent neurotransmitter transporters 5/23 Reactome 1.27708198252723e-06 5.58768083111353e-06 580 1328.72727272727 855 1.27708271645009e-07 75 1.66561063290065 1.66561063290065 1 3.19801862313485 576 1568 4026 2198 855 559 75 264 2520 1157 818 668 M16389 ZEMBUTSU_SENSITIVITY_TO_METHOTREXATE http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_METHOTREXATE.html Top genes associated with chemosensitivity to methotrexate [PubChem=4112] across 85 tumor xenografts. 11809704 19/41 Arthur Liberzon 5.1826019321837e-06 1.49460272210961e-05 315 781.545454545455 857 4.71146740093203e-07 314 2.18452546839605 2.32346511188205 1 3.85315396963042 314 633 857 1012 1443 645 569 925 462 865 872 669 M4991 DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP.html 'PAX-FKHR signature': genes up-regulated by PAX3- or PAX7-FOXO1 [GeneID=5081;5077;2308] fusion in primary alveolar rhabdomyosarcoma(ARMS) tumors. 16849537 32/95 Arthur Liberzon 8.05537811295421e-07 4.14508109582784e-06 855 887.454545454545 858 7.32307369314639e-08 86 1.79871643262648 1.91688509800944 1 3.53885954380293 761 1118 855 953 858 822 1115 86 1195 1145 854 670 M3603 OUILLETTE_CLL_13Q14_DELETION_DN http://www.broadinstitute.org/gsea/msigdb/cards/OUILLETTE_CLL_13Q14_DELETION_DN.html Genes down-regulated in chronic lymphocytic leukemia (CLL) samples bearing deletions in the 13q14 region. 18281475 37/98 Jessica Robertson 3.35882161827539e-06 1.06852940279963e-05 965 1081.45454545455 859 3.05347886029448e-07 605 1.5478449084621 1.53671710874361 1 2.81260737090428 964 721 1213 815 1271 766 859 2275 1743 664 605 671 M2236 JOHNSTONE_PARVB_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_1_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer) upon overexpression of PARVB [GeneID=29780] under all three culture conditions. 17998334 2/13 Arthur Liberzon 3.5939652721879e-06 1.12801883894658e-05 1025 1412.8 859 3.99330112545105e-07 27 2.69370803272258 -2.69370803272258 -1 4.8716008218457 1025 1326 4632 NA 2826 693 662 188 27 2175 574 672 M2435 WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP.html Genes up-regulated in mucinous ovarian carcinoma tumors of grades 1 and 2 compared to the normal ovarian survace epithelium tissue. 16467078 99/221 Arthur Liberzon 1.4265174319776e-07 1.54380154416791e-06 1155 840.818181818182 860 1.29683411315948e-08 75 1.44813268944818 -1.46332214381334 -1 3.07616066146586 1152 75 1035 860 88 259 2030 1016 1711 649 374 673 M11790 ONDER_CDH1_TARGETS_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_3_DN.html Genes down-regulated in HMLE cells (immortalized nontransformed mammary epithelial) cells after loss of function of E-cadhedrin (CDH1) [GeneID=999], which was achieved either by RNAi knockdown or by expression of a dominan-negative form of CDH1. 18483246 29/94 Jessica Robertson 5.16784982896025e-07 3.17802418615587e-06 2770 1590.63636363636 860 4.69804640263661e-08 396 2.53111342433759 2.81092989366516 1 5.08654833483449 2769 860 396 486 461 3261 2642 2666 591 810 2555 674 M15981 RIGGI_EWING_SARCOMA_PROGENITOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/RIGGI_EWING_SARCOMA_PROGENITOR_UP.html Genes up-regulated in mesenchymal stem cells (MSC) engineered to express EWS-FLI1 [GeneID=2130;2321] fusion protein. 18381423 308/830 Jessica Robertson 2.00594528905544e-22 1.99997013287527e-20 675 728.909090909091 860 1.82358662641403e-23 46 1.89251631359069 2.11096014722354 1 13.6270718028813 673 234 46 156 1115 1284 1151 946 1474 79 860 675 M77 PID_WNT_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_WNT_SIGNALING_PATHWAY.html Wnt signaling network 18832364 19/34 Pathway Interaction Database 6.06597085760271e-07 3.47495592160468e-06 1540 1093.45454545455 861 5.51452048195356e-08 169 1.7145838036042 1.73898691023736 1 3.42133102082916 1537 169 893 678 521 1969 1927 2203 845 861 425 676 M746 REACTOME_SIGNALING_BY_GPCR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_GPCR.html Genes involved in Signaling by GPCR 212/1438 Reactome 8.32332720134536e-11 2.2808836997371e-09 640 971.363636363636 862 7.5666610924184e-12 124 1.77661594896176 1.84296499500326 1 5.61205457457011 636 805 164 862 124 1064 997 1773 2512 377 1371 677 M12827 BOQUEST_STEM_CELL_CULTURED_VS_FRESH_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOQUEST_STEM_CELL_CULTURED_VS_FRESH_DN.html Genes down-regulated in cultured stromal stem cells from adipose tissue, compared to the freshly isolated cells. 15635089 19/44 Arthur Liberzon 4.66529268101409e-06 1.37126688371108e-05 565 887.181818181818 863 4.24118415836835e-07 354 2.07543421900486 2.12620495258492 1 3.68910994537667 519 354 500 562 1401 1123 1390 565 1505 863 977 678 M18938 SENESE_HDAC1_AND_HDAC2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC1_AND_HDAC2_TARGETS_UP.html Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of both HDAC1 and HDAC2 [GeneID=3065;3066] by RNAi. 17470557 128/454 Leona Saunders 6.3005287169238e-08 8.54482040434486e-07 865 970.636363636364 864 5.72775354305742e-09 20 1.70472964373294 1.77215676625026 1 3.78130401868863 864 1002 1078 1359 20 407 833 637 2729 1465 283 679 M916 REACTOME_PLATELET_HOMEOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_HOMEOSTASIS.html Genes involved in Platelet homeostasis 31/91 Reactome 1.62780744293737e-07 1.6764627862867e-06 550 955.909090909091 866 1.47982505761898e-08 116 1.80035402217829 1.88221876431905 1 3.80079747436115 548 144 745 866 116 1002 1090 1957 2284 574 1189 680 M1732 GAVIN_FOXP3_TARGETS_CLUSTER_P2 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_P2.html Cluster P2 of genes with similar expression profiles in peripheral T ymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 47/145 Jessica Robertson 9.09158061578552e-08 1.11819282849268e-06 1270 764.090909090909 866 8.26507362863492e-09 49 1.89300128467939 2.06579971399317 1 4.1180856802587 1270 1274 900 990 49 888 423 136 854 866 755 681 M15780 GRADE_COLON_AND_RECTAL_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_AND_RECTAL_CANCER_DN.html Down-regulated genes in both rectal and colon carcinoma compared to normal mucosa samples. 17210682 66/198 Jessica Robertson 1.12631975845107e-06 5.12420814378806e-06 600 888.727272727273 866 1.02392757735102e-07 332 1.98332973025712 2.06182306703917 1 3.83531010943673 599 830 386 487 1312 1115 866 1366 924 332 1559 682 M240 PID_SYNDECAN_2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_2_PATHWAY.html Syndecan-2-mediated signaling events 18832364 34/68 Pathway Interaction Database 5.86909382473693e-06 1.64096501567525e-05 730 1321.09090909091 867 5.33555407471579e-07 209 1.86730887900648 2.03763815631669 1 3.26594103902324 727 2542 2112 767 2448 867 686 209 1002 2755 417 683 M2023 YIH_RESPONSE_TO_ARSENITE_C5 http://www.broadinstitute.org/gsea/msigdb/cards/YIH_RESPONSE_TO_ARSENITE_C5.html Genes in cluster 5: slowly down-regulated in HFW cells (fibroblast) by sodium arsenite [PubChem=26435]. 12016162 8/17 Arthur Liberzon 6.22428120361093e-06 1.72040678779681e-05 460 1207.81818181818 868 6.22429863743407e-07 168 3.41417558047048 3.41417558047048 1 5.94580249652756 460 1806 4600 168 1545 671 868 267 912 1669 320 684 M96 BIOCARTA_FREE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FREE_PATHWAY.html Free Radical Induced Apoptosis 5/19 BioCarta 0.000123008785284982 0.000222641625278263 870 1528.63636363636 869 1.23015594838055e-05 264 2.12928364302657 -2.12928364302657 -1 2.84269552394289 869 1758 3837 2213 3291 517 264 634 761 1857 814 685 M2001 WU_CELL_MIGRATION http://www.broadinstitute.org/gsea/msigdb/cards/WU_CELL_MIGRATION.html Genes associated with migration rate of 40 human bladder cancer cells. 18724390 145/340 Jessica Robertson 3.25447820157978e-28 5.08349495086762e-26 1450 1065.90909090909 869 2.95861654689072e-29 17 2.06792144296385 2.27581696627646 1 19.1191250197008 1447 53 29 191 869 2497 2650 1431 624 17 1917 686 M1189 DING_LUNG_CANCER_BY_MUTATION_RATE http://www.broadinstitute.org/gsea/msigdb/cards/DING_LUNG_CANCER_BY_MUTATION_RATE.html The lung adenocarcinoma TSP (tumor sequencing project) genes mutations in which show positive correlation with the higher overall mutation rate. 18948947 19/47 Arthur Liberzon 5.75822928796561e-06 1.62060435095537e-05 835 947.545454545455 869 5.23476759952495e-07 207 2.26186379727761 2.44759784965054 1 3.96050437771557 831 1132 1084 1315 1715 869 856 207 253 1455 706 687 M17428 GAL_LEUKEMIC_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAL_LEUKEMIC_STEM_CELL_UP.html Genes up-regulated in leukemic stem cells (LSC), defined as CD34+CD38- [GeneID=947;952] cells from AML (acute myeloid leukemia patients) compared to the CD34+CD38+ cells. 17039238 79/232 Leona Saunders 7.09600053645819e-08 9.30349643972164e-07 720 977.181818181818 871 6.45090978666953e-09 28 1.85554136161652 2.16945440157622 1 4.09076654279647 716 2143 840 1561 28 1243 871 537 1169 912 729 688 M10122 REACTOME_RETROGRADE_NEUROTROPHIN_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RETROGRADE_NEUROTROPHIN_SIGNALLING.html Genes involved in Retrograde neurotrophin signalling 10/19 Reactome 4.5864877218293e-07 2.94012058337785e-06 465 820.272727272727 872 4.16953516182316e-08 44 2.03697935027338 2.339218758311 1 4.11869261933691 463 1064 1335 1235 417 872 735 923 44 1362 573 689 M2214 CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN.html Genes down-regulated in CD4+ [GeneID=920] T lymphocytes after stimulation with prostaglandin E2 [PubChem=5280360]. 16424048 233/562 Arthur Liberzon 1.54997938944334e-07 1.62487772235604e-06 2535 1126.18181818182 873 1.40907227149545e-08 39 1.57227492278263 -1.59125057017833 -1 3.32709146153012 2531 39 319 423 161 873 3367 2231 1196 130 1118 690 M1626 BURTON_ADIPOGENESIS_PEAK_AT_0HR http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_PEAK_AT_0HR.html Cluster 1: genes progressively down-regulated over 24 h (peak at 0 h timepoint) during differentiation of 3T3-L1 fibroblasts into adipocytes in response to adipogenic hormones. 12137940 69/149 John Newman 1.91838621473274e-06 7.1687063813697e-06 880 1091.63636363636 876 1.74398898868685e-07 221 2.24437698158716 2.33640665162343 1 4.22049340638003 221 2003 408 1270 2830 700 876 776 1220 877 827 691 M1938 MEISSNER_BRAIN_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing the H3K27 tri-methylation (H3K27me3) mark in brain. 18600261 81/357 Jessica Robertson 6.01025289318678e-16 3.70579540229911e-14 3485 1731.09090909091 876 5.46386626653342e-17 73 2.19769284772208 -2.10425734936775 -1 10.7894281720712 3481 84 73 717 121 2943 4318 2911 876 111 3407 692 M2232 BHAT_ESR1_TARGETS_NOT_VIA_AKT1_DN http://www.broadinstitute.org/gsea/msigdb/cards/BHAT_ESR1_TARGETS_NOT_VIA_AKT1_DN.html Genes bound by ESR1 [GeneID=2099] and down-regulated by estradiol [PubChem=5757] in MCF-7 cells (breast cancer). 18838536 74/157 Arthur Liberzon 1.28352987968589e-06 5.59499629414704e-06 880 1005.36363636364 876 1.16684602593357e-07 539 1.79175262779936 1.81822980020332 1 3.43984261179546 876 828 649 539 814 1766 1415 931 1058 668 1515 693 M2369 GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN.html Genes down-regulated during differentiation of Oli-Neu cells (oligodendroglial precursor) in response to PD174265 [PubChem=4709]. 19139271 694/1785 Arthur Liberzon 7.56563201793196e-07 3.99690548320509e-06 780 1137.63636363636 876 7.56563459367864e-08 1 1.50163476877236 1.70194631380571 1 2.96304782092121 776 1 4657 434 639 1045 1083 876 1559 325 1119 694 M11594 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_22 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_22.html Amplification hot spot 22: colocolized fragile sites and cancer genes in the 22q11.1-q13s region. 16751803 5/25 Arthur Liberzon 1.62326333452961e-05 3.7712503647029e-05 875 1375.09090909091 877 1.62327519207885e-06 79 2.75660311004845 2.75660311004845 1 4.45718808290359 871 2096 4236 1701 1895 490 484 525 79 1872 877 695 M2919 KIM_MYCN_AMPLIFICATION_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYCN_AMPLIFICATION_TARGETS_DN.html Genes negatively correlated with amplifications of MYCN [GeneID=4613] in the SCLC (small cell lung cancer) cell lines. 16116477 69/256 Arthur Liberzon 2.11177390166079e-05 4.74162554057617e-05 985 1088.45454545455 877 1.91981288435668e-06 257 1.84600724786471 2.06014908650703 1 2.91773364890144 985 2146 804 1360 1958 790 877 348 1574 874 257 696 M749 REACTOME_CA_DEPENDENT_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CA_DEPENDENT_EVENTS.html Genes involved in Ca-dependent events 15/33 Reactome 2.71445174826102e-07 2.2526825372382e-06 585 1048.36363636364 878 2.46768371198315e-08 72 1.23639915098298 1.43137476820838 1 2.55222411790539 584 878 1636 1388 229 161 72 1325 2988 1984 287 697 M7184 GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_UP.html Genes up-regulated in glioblastoma cell lines displaying spherical growth (cluster-1) compared to those displaying semiadherent or adherent growth phenotype (cluster-2). 18037961 11/35 Jessica Robertson 1.67452424283741e-05 3.87880405434311e-05 670 876.818181818182 878 1.52230635324607e-06 142 2.34166769599552 2.62510015938646 1 3.77582034020172 669 976 1182 1072 1870 797 657 336 142 1066 878 698 M999 HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_DN.html Genes down-regulated in hematopoietic progenitor cells (HPC) of T lymphocyte and NK (natural killer) lineage. 15331438 30/109 Kevin Vogelsang 8.40174610694712e-07 4.23795288021036e-06 725 1037.27272727273 878 7.6379539232319e-08 397 2.08587114447467 2.38548868522781 1 4.09648102650054 725 1281 397 1064 645 1050 878 1635 2213 845 677 699 M2273 ZHU_SKIL_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_SKIL_TARGETS_UP.html Genes up-regulated in A549 cells (lung adenocarcinoma) upon SKIL [GeneID=6498] knockdown by RNAi. 17074815 20/36 Arthur Liberzon 4.541855169759e-06 1.34788684771948e-05 1205 916.909090909091 881 4.12896776941231e-07 452 1.61482525961446 1.54301958147176 1 2.87478023565237 667 1205 1059 881 1387 638 574 811 1211 1201 452 700 M3952 BIOCARTA_LAIR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LAIR_PATHWAY.html Cells and Molecules involved in local acute inflammatory response 9/23 BioCarta 3.37625971001349e-06 1.07262054244903e-05 665 1175.27272727273 882 3.37626483963279e-07 194 2.06572129284781 1.91213152610002 1 3.752393551793 663 194 3822 810 1309 922 857 1494 1137 882 838 701 M16173 BIOCARTA_PS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PS1_PATHWAY.html Presenilin action in Notch and Wnt signaling 9/27 BioCarta 1.01863773224971e-05 2.55942971223708e-05 695 1207.81818181818 883 1.01864240158257e-06 191 2.05223960317019 2.24226218754135 1 3.44457503553274 693 1749 3856 1281 2052 719 572 283 1007 883 191 702 M5888 RASHI_RESPONSE_TO_IONIZING_RADIATION_2 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_2.html Cluster 2: late ATM [GeneID=472] dependent genes induced by ionizing radiation treatment. 16314843 98/231 Arthur Liberzon 1.21136687921543e-07 1.39129048921654e-06 75 1503.63636363636 885 1.10124267810534e-08 74 1.72335496626239 -1.87573575038867 -1 3.68925124427285 3346 74 757 343 74 1967 3136 2429 885 529 3000 703 M2541 PARK_APL_PATHOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PARK_APL_PATHOGENESIS_DN.html Genes down-regulated in U937 cells (acute promyelocytic leukemia, APL) expressing RARA [GeneID=5914] fused with either PML or PLZF [GeneID=5371;7704]. 12893766 41/116 Arthur Liberzon 2.23213009131965e-05 4.98558703904856e-05 345 1009.36363636364 885 2.02922976266877e-06 345 1.68083913168176 1.81461649765713 1 2.64328776369503 345 943 686 1136 1956 530 405 885 2220 1152 845 704 M19233 EPPERT_CE_HSC_LSC http://www.broadinstitute.org/gsea/msigdb/cards/EPPERT_CE_HSC_LSC.html Shared human hematopoietic stem cell (HSC) and acute myeloid leukemia (AML) stem cell (LSC) genes: HSC genes that are highly expressed in LSC versus other leukemic cells. 21873988 23/67 Kolja Eppert 1.44972015562143e-06 6.01097981436963e-06 410 934.636363636364 886 1.31792828266844e-07 120 1.81069272350696 1.76369067764177 1 3.4555903498723 407 1494 886 1586 2234 421 337 121 1248 1427 120 705 M1053 KEGG_HEDGEHOG_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HEDGEHOG_SIGNALING_PATHWAY.html Hedgehog signaling pathway 22/61 KEGG 2.91605003136257e-07 2.31211682689763e-06 1415 820.272727272727 887 2.65095492534404e-08 40 2.68358984550735 2.84897608474547 1 5.52847845705394 1414 350 887 212 257 1167 797 1410 40 1334 1155 706 M16697 BIOCARTA_CD40_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CD40_PATHWAY.html CD40L Signaling Pathway 11/19 BioCarta 5.80811105116748e-06 1.62877369154822e-05 540 1110.81818181818 887 5.28011489539137e-07 304 1.15404180373661 -1.15404180373661 -1 2.01979625999521 540 887 2532 925 1490 304 747 616 1512 2095 571 707 M12085 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINDED_IN_ERYTHROCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINDED_IN_ERYTHROCYTE_UP.html Genes up-regulated by RUNX1-RUNX1T1 [GeneID=861;862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing erythroid lineage. 17898786 29/83 Arthur Liberzon 2.90123971877725e-07 2.31211682689763e-06 580 821.090909090909 887 2.63749100125177e-08 207 1.67947989484593 1.69696679271628 1 3.4599059284156 578 1034 1011 1283 253 541 207 887 1805 1219 214 708 M6856 KEGG_HEMATOPOIETIC_CELL_LINEAGE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HEMATOPOIETIC_CELL_LINEAGE.html Hematopoietic cell lineage 35/107 KEGG 2.80195028398562e-06 9.30194568921026e-06 830 1192.27272727273 889 2.54723077508585e-07 467 1.8885560571683 2.01908548537772 1 3.4732835359602 828 2072 749 2243 1195 695 707 889 2367 903 467 709 M7013 KAYO_CALORIE_RESTRICTION_MUSCLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAYO_CALORIE_RESTRICTION_MUSCLE_UP.html Upregulated in the vastus lateralis muscle of middle aged rhesus monkeys subjected to caloric restriction since young adulthood vs age matched controls 11309484 83/232 John Newman 4.9117975629276e-06 1.42872025945864e-05 505 968.545454545455 889 4.4652804811039e-07 503 2.00907868318277 2.20294033161711 1 3.55807181964479 504 1721 503 1185 1425 757 767 854 1152 897 889 710 M512 REACTOME_DAG_AND_IP3_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DAG_AND_IP3_SIGNALING.html Genes involved in DAG and IP3 signaling 18/37 Reactome 3.35322073609507e-07 2.49812279321805e-06 895 1195.18181818182 891 3.04838295199105e-08 208 1.38748198402527 1.43137476820838 1 2.84131672656484 891 754 1512 1125 305 333 208 3288 2416 1775 540 711 M10619 KAAB_FAILED_HEART_ATRIUM_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAAB_FAILED_HEART_ATRIUM_DN.html Genes down-regulated in atria of failing hearts (DCM and ICM) compared to healthy controls. 15103417 131/274 John Newman 1.9698553108603e-06 7.30858431250307e-06 655 1107.09090909091 891 1.79077915877168e-07 444 1.83298004714448 2.03784054945017 1 3.44124902973925 651 2187 1791 469 1018 929 860 444 891 2374 564 712 M2019 MIKKELSEN_MEF_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 trimethylation mark at K27 (H3K27me3) in MEF cells (embryonic fibroblast). 17603471 212/986 Arthur Liberzon 3.34709887989608e-31 6.81935015269262e-29 25 1797 892 3.04281716354191e-32 14 2.05082669632065 -2.05784048902082 -1 21.1143322167447 4487 245 22 14 192 3338 3879 2269 892 23 4406 713 M16963 RAMASWAMY_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAMASWAMY_METASTASIS_DN.html Down-regulated genes in metastatic vs primary solid tumors. 12469122 41/105 John Newman 5.30156688698089e-06 1.51945825274571e-05 800 1112 893 4.81961787523315e-07 633 2.35488316298359 2.7439380017659 1 4.14747201041236 800 1355 754 1963 1456 633 742 1393 893 1408 835 714 M13334 WU_ALZHEIMER_DISEASE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WU_ALZHEIMER_DISEASE_DN.html Genes down-regulated in brain endothelial cells from patients with Alzheimer disease. 16116430 14/44 Jessica Robertson 9.9003946917032e-09 1.66882192537127e-07 895 1068.90909090909 893 9.00035885114252e-10 1 1.62675959363533 1.52835186745909 1 4.03011946884737 893 1504 1774 887 1 613 858 1741 1363 1378 746 715 M605 KEGG_ASCORBATE_AND_ALDARATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ASCORBATE_AND_ALDARATE_METABOLISM.html Ascorbate and aldarate metabolism 4/30 KEGG 3.19956877131084e-07 2.43791532721343e-06 1710 1169.63636363636 894 3.19956923198674e-08 7 3.15254851655832 3.55389468427202 1 6.46806880515909 1709 211 3786 35 894 2207 2858 159 7 977 23 716 M11857 RODRIGUES_NTN1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_NTN1_TARGETS_DN.html Genes down-regulated in HCT8/S11 cells (colon cancer) engineered to stably express NTN1 [GeneID=1630] off a plasmid vector. 17334389 115/305 Arthur Liberzon 5.0499813686711e-07 3.12605187497923e-06 2575 1400.27272727273 894 4.59089320715225e-08 341 1.86336204704346 -1.74851382783981 -1 3.74950658428975 2573 558 499 641 451 1504 3405 2219 894 341 2318 717 M11581 COLIN_PILOCYTIC_ASTROCYTOMA_VS_GLIOBLASTOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/COLIN_PILOCYTIC_ASTROCYTOMA_VS_GLIOBLASTOMA_UP.html Genes up-regulated in pilocytic astrocytoma compared to glioblastoma samples. 16314830 37/104 Jessica Robertson 0.000283177960813215 0.000478188080854315 1490 1136.81818181818 895 2.57467652066144e-05 466 2.25784225523385 2.28652446733552 1 2.74033347529971 895 1488 734 492 2704 1651 1488 769 466 524 1294 718 M6946 SHI_SPARC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHI_SPARC_TARGETS_DN.html Genes down-regulated in glioma cell lines after knockdown of SPARC [GeneID=6678] by RNAi. 17213807 7/16 Arthur Liberzon 4.52004192576418e-06 1.34311455067412e-05 875 1309.45454545455 896 4.52005111964105e-07 481 2.15547300312118 2.49507875857338 1 3.83847785984149 872 896 4247 1510 1429 743 481 1578 789 1006 853 719 M4306 ONDER_CDH1_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_2_DN.html Genes down-regulated in HMLE cells (immortalized nontransformed mammary epithelium) after E-cadhedrin (CDH1) [GeneID=999] knockdown by RNAi. 18483246 316/793 Jessica Robertson 2.75660706217697e-34 8.61164046224085e-32 25 1248.27272727273 896 2.50600642016089e-35 8 1.93764049268295 2.18703327636351 1 22.0020227567915 2080 24 14 8 210 3409 2557 2309 896 21 2203 720 M257 PID_EPHRINB_REV_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHRINB_REV_PATHWAY.html Ephrin B reverse signaling 18832364 27/52 Pathway Interaction Database 7.84126928048704e-07 4.09418433400279e-06 900 978.727272727273 897 7.12842915934916e-08 610 1.44275671392259 1.66210380284248 1 2.84136121971542 700 1446 1469 713 610 838 656 1267 1271 899 897 721 M78 EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_UP.html Genes up-regulated in Rh4 cells (alveolar rhabdomyosarcoma, ARMS) after knockdown of the PAX3-FOXO1 [GeneiD=5077;2308] fusion protein by RNAi for 72 hr. 17525748 148/388 Leona Saunders 2.87402875666376e-07 2.30751325380193e-06 1015 784.090909090909 898 2.61275375647296e-08 251 1.96477716238585 2.31375591297717 1 4.04827006000047 1013 1088 347 1220 251 754 935 898 971 487 661 722 M10765 BIOCARTA_TCRA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCRA_PATHWAY.html Lck and Fyn tyrosine kinases in initiation of TCR Activation 4/20 BioCarta 0.000135799097596452 0.000243347828427141 575 1418.45454545455 899 1.35807396937963e-05 316 1.3955313486285 1.3955313486285 1 1.84340032034812 572 794 3845 1917 2501 396 316 899 2140 1622 601 723 M17374 SASAKI_TARGETS_OF_TP73_AND_TP63 http://www.broadinstitute.org/gsea/msigdb/cards/SASAKI_TARGETS_OF_TP73_AND_TP63.html Genes up-regulated in DLD1 cells (colon cancer) by p73 beta [GeneID=7161] or by and p63 gamma [GeneID=8626] but not by p53 [GeneID=7157]. 15856012 8/13 Arthur Liberzon 2.06932682037419e-06 7.5403308555781e-06 900 1097.54545454545 899 2.06932874732778e-07 225 1.49720131813313 1.68056213696144 1 2.80343641323852 899 1072 4264 792 1086 902 516 340 314 1663 225 724 M2103 STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_UP http://www.broadinstitute.org/gsea/msigdb/cards/STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_UP.html Genes induced in SKBR3 cells (breast cancer) by 25-hydroxyvitamin D3 [PubChem=1593]. 20227041 57/173 Arthur Liberzon 7.71986679993465e-08 9.9110399519161e-07 1675 1176.27272727273 899 7.01806097347921e-09 35 1.87308399506847 -1.74381171311673 -1 4.11063165876092 1675 111 542 727 35 1421 1626 3729 899 450 1724 725 M14353 CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN.html All marker genes down-regulated in the 'interferon' subclass of hepatocellular carcinoma (HCC). 18701503 20/68 Yujin Hoshida 1.54775839587736e-06 6.25780486892259e-06 3860 2102.54545454545 901 1.4070540770614e-07 352 2.14330540225787 2.40440120389673 1 4.07666830196881 3858 352 864 679 901 4512 4454 3252 479 719 3058 726 M840 REACTOME_CELL_EXTRACELLULAR_MATRIX_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_EXTRACELLULAR_MATRIX_INTERACTIONS.html Genes involved in Cell-extracellular matrix interactions 12/22 Reactome 1.16607033995827e-06 5.25404385869661e-06 1180 1037.27272727273 903 1.06006450728481e-07 653 1.91513713306688 1.87991671214096 1 3.69583386319376 865 653 1368 819 779 903 851 1086 1734 1176 1176 727 M3270 ST_INTEGRIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_INTEGRIN_SIGNALING_PATHWAY.html Integrin Signaling Pathway 61/127 Signaling Transduction KE 1.5532436811652e-06 6.26916441855309e-06 775 1223.27272727273 904 1.41204070707924e-07 392 1.59914054141709 1.74770186914427 1 3.04118058477275 775 2448 1759 897 904 392 488 1866 1528 1954 445 728 M15912 HAMAI_APOPTOSIS_VIA_TRAIL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAMAI_APOPTOSIS_VIA_TRAIL_DN.html Genes down-regulated in T1 cells (primary melanoma, sensitive to TRAIL [GeneID=8743]) compared to G1 cells (metastatic melanoma, resistant to TRAIL). 16983347 134/337 Leona Saunders 3.37133057292799e-07 2.50762778805406e-06 1000 943.181818181818 904 3.06484644505323e-08 306 1.72308236507321 2.04377336830834 1 3.5275279363266 998 553 484 740 306 1644 1041 943 1892 870 904 729 M1366 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX6_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX6_DN.html Early prostate development genes (down-regulated at 48 hr dihydrotestosterone [PubChem=10635]) which are also down-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 4/7 Jessica Robertson 1.06612877142202e-05 2.64752486639299e-05 620 1210.63636363636 905 1.06613388629406e-06 243 2.44957351505199 -2.44957351505199 -1 4.09831954878611 620 905 4331 1030 2270 384 1144 275 243 1636 479 730 M9270 VALK_AML_WITH_11Q23_REARRANGED http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_WITH_11Q23_REARRANGED.html Genes that best predicted acute myeloid leukemia (AML) with the 11q23 rearrangements. 15084694 14/39 Jessica Robertson 7.94511490228214e-07 4.11774058972012e-06 985 881.727272727273 906 7.22283433781363e-08 390 1.90027580801163 2.30098445602671 1 3.74066743876765 982 646 1271 1236 618 906 949 390 888 1380 433 731 M12522 CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1 http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1.html The 'group 1 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 and ERBB2 [GeneID=2099;2064]. 18794137 352/837 Jessica Robertson 1.75806247509794e-07 1.76408581548371e-06 1360 1119.54545454545 907 1.59823874144375e-08 121 1.69772330448243 1.96300516133554 1 3.57039931429491 1358 671 411 121 134 3027 2350 907 1167 515 1654 732 M11548 AMUNDSON_POOR_SURVIVAL_AFTER_GAMMA_RADIATION_8G http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_POOR_SURVIVAL_AFTER_GAMMA_RADIATION_8G.html Genes with basal expression distinguishing NCI-60 cell lines with poor survival after 8 Gy gamma irradiation. 18199535 75/152 Jessica Robertson 3.48686736621163e-08 5.20364983377952e-07 1025 788.818181818182 908 3.16987947406942e-09 6 1.36269599591129 1.53966152768338 1 3.12991912175237 1021 93 1300 908 6 912 808 203 1374 1409 643 733 M292 DASU_IL6_SIGNALING_SCAR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DASU_IL6_SIGNALING_SCAR_UP.html Genes up-regulated in hypertrophic scar fibroblasts in response to IL6 [GeneID=3569]. 15095275 19/49 John Newman 1.40008795351867e-06 5.87886393386064e-06 1115 873.636363636364 909 1.27280804049136e-07 172 2.20023882421942 2.50688054847925 1 4.20677644778855 1114 172 1003 909 853 956 839 733 318 1119 1594 734 M6875 LANDIS_BREAST_CANCER_PROGRESSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_BREAST_CANCER_PROGRESSION_UP.html Genes up-regulated in preneoplastic mammary tissues and whose expression is maintained in tumors. 16434967 36/57 Lauren Kazmierski 3.15832502167418e-06 1.01927762063121e-05 305 975 910 2.87120868707446e-07 288 1.50485713771249 -1.59784977835578 -1 2.74576682087352 303 1539 1482 1585 1242 288 450 585 910 1686 655 735 M1713 LEIN_ASTROCYTE_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_ASTROCYTE_MARKERS.html Genes enriched in astrocytes in the adult mouse brain identified through correlation-based searches seeded with the astrocyte cell-type specific gene expression patterns. 17151600 29/75 Jessica Robertson 1.59363268262758e-06 6.40409354248728e-06 1710 1340.45454545455 911 1.44875803365636e-07 469 1.9143087322806 1.92287792418063 1 3.63408354142486 1707 469 549 565 911 1945 1882 2916 826 501 2474 736 M1802 ZHENG_IL22_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_IL22_SIGNALING_DN.html Genes down-regulated in ex-vivo colonic tissue after treatment with IL22 [GeneID=50616]. 18264109 31/105 Jessica Robertson 1.22025599922593e-05 2.9689094560606e-05 1250 1202.18181818182 911 1.10932978870236e-06 470 2.17665102977724 2.52370785187406 1 3.60211203057448 1248 731 911 1665 1759 1868 1944 470 823 909 896 737 M5686 MARKEY_RB1_CHRONIC_LOF_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARKEY_RB1_CHRONIC_LOF_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) isolated from RB1 [GeneID=5925] knockout mice: chronic loss of function (LOF) of RB1. 17452985 82/188 Arthur Liberzon 1.0115325092838e-07 1.21539521500099e-06 810 916.272727272727 912 9.19575050720724e-09 286 2.1235296082408 2.38940832170655 1 4.59148383736021 807 286 308 772 1415 1324 912 1235 1074 462 1484 738 M10959 REACTOME_OTHER_SEMAPHORIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OTHER_SEMAPHORIN_INTERACTIONS.html Genes involved in Other semaphorin interactions 12/29 Reactome 3.72991805782162e-05 7.77508719704276e-05 270 1105.90909090909 913 3.3908920881806e-06 269 2.42541784134051 2.42541784134051 1 3.6431169219545 269 1656 913 991 2652 360 286 636 1838 2240 324 739 M6712 ROVERSI_GLIOMA_LOH_REGIONS http://www.broadinstitute.org/gsea/msigdb/cards/ROVERSI_GLIOMA_LOH_REGIONS.html Genes in the most frequently heterozygous deleted loci of a panel of glioma cell lines. 16247447 31/83 Arthur Liberzon 2.61086672981928e-06 8.82085183556822e-06 700 1036.27272727273 913 2.37351802571852e-07 198 1.52018042410366 1.69481361740816 1 2.8086115815912 697 1192 1197 1396 1164 478 198 913 2656 721 787 740 M11771 DOANE_BREAST_CANCER_CLASSES_DN http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_BREAST_CANCER_CLASSES_DN.html Genes down-regulated in ER(-) / PR(-) breast tumors (do not express ESR1 and PGR [GeneID=2099;5241]) with molecular similarity to ER(+) (class A) relative to the rest of the ER(-) / PR(-) samples (class B). 16491124 26/53 Arthur Liberzon 1.04143080406589e-06 4.8607019400924e-06 710 827.090909090909 915 9.46755724596614e-08 146 1.98024751433057 2.18591395246133 1 3.8459456934918 709 1367 1150 1308 737 408 146 915 1099 1043 216 741 M1647 WENG_POR_TARGETS_LIVER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WENG_POR_TARGETS_LIVER_UP.html Genes up-regulated in liver from mice with liver specific knockout of POR [GeneID=5447]. 16006652 25/96 John Newman 1.09015737614327e-06 5.00340593987009e-06 1315 830.636363636364 917 9.91052651222778e-08 160 2.07643707697227 1.96742626725509 1 4.02322256033582 1167 160 996 1313 754 560 247 1313 472 1238 917 742 M684 REACTOME_SYNTHESIS_OF_PC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PC.html Genes involved in Synthesis of PC 9/19 Reactome 1.36022371583034e-05 3.25204506754131e-05 1185 1274.45454545455 919 1.36023204184057e-06 208 1.80811136120589 -1.65855618637711 -1 2.96607496919431 1184 1146 3956 904 1830 653 919 790 208 884 1545 743 M2449 PLASARI_NFIC_TARGETS_BASAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_NFIC_TARGETS_BASAL_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) upon knockout of NFIC [GeneID=4782]. 19752192 16/37 Arthur Liberzon 4.38091079596245e-05 8.92562956081742e-05 330 1071.18181818182 919 3.98272548771163e-06 92 2.03618757115838 2.03618757115838 1 3.01386325445447 328 2622 1391 1758 2250 175 92 462 1432 919 354 744 M6815 AMIT_EGF_RESPONSE_60_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_60_MCF10A.html Genes whose expression peaked at 60 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 34/58 Leona Saunders 1.2641470624683e-05 3.05823083878495e-05 520 1048.45454545455 921 1.14923120588296e-06 369 2.09181663905528 2.40303457012137 1 3.45187755181049 520 2541 921 791 1768 858 1153 944 369 1027 641 745 M14447 MASSARWEH_RESPONSE_TO_ESTRADIOL http://www.broadinstitute.org/gsea/msigdb/cards/MASSARWEH_RESPONSE_TO_ESTRADIOL.html Genes rapidly up-regulated in breast cancer cell cultures by estradiol [PubChem=5757]. 18245484 38/105 Jessica Robertson 1.38660647574509e-06 5.85372787868602e-06 925 1083.72727272727 921 1.26055213608199e-07 289 1.52370066495275 1.5876921860021 1 2.91429656504079 921 2304 1315 1049 848 458 500 381 2349 1507 289 746 M16130 RICKMAN_HEAD_AND_NECK_CANCER_C http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_C.html Cluster c: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 56/231 Jessica Robertson 1.11832456529309e-11 3.63921452289125e-10 880 1039.72727272727 922 1.01665869572615e-12 138 2.21666874426204 2.70581354074621 1 7.64796130484996 879 432 138 685 2462 1429 1919 1308 970 293 922 747 M3342 BIOCARTA_INTEGRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INTEGRIN_PATHWAY.html Integrin Signaling Pathway 35/74 BioCarta 4.66098031374528e-06 1.37126688371108e-05 925 1066.63636363636 923 4.23726380786841e-07 540 1.77117819587689 2.11662127026848 1 3.1482911079832 923 854 1498 555 1400 821 1037 540 748 2371 986 748 M12004 SENESE_HDAC1_AND_HDAC2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC1_AND_HDAC2_TARGETS_DN.html Genes down-regulated in U2OS cells (osteosarcoma) upon knockdown of both HDAC1 and HDAC2 [GeneID=3065;3066] by RNAi. 17470557 177/422 Leona Saunders 1.46525229648218e-14 7.62908029035055e-13 85 677.727272727273 924 1.33204754225653e-15 82 1.73205847253165 1.87413875270013 1 7.67177443168855 754 252 85 264 991 966 1066 940 1131 82 924 749 M19695 FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP.html Genes up-regulated in kidney biopsies from patients with acute transplant rejection compared to the biopsies from patients with well functioning kidneys more than 1-year post transplant. 15307835 76/208 Jean Junior 2.26489706364398e-07 2.06048557020227e-06 625 972.272727272727 924 2.05899754255896e-08 184 1.86368929809157 2.06695059929238 1 3.87348555553631 625 1820 635 1142 184 924 693 670 1964 958 1080 750 M8760 MCGARVEY_SILENCED_BY_METHYLATION_IN_COLON_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/MCGARVEY_SILENCED_BY_METHYLATION_IN_COLON_CANCER.html Genes silenced in HCT116 cells (colon cancer) by methylation of CpG islands in their promoters. 18632628 29/86 Jessica Robertson 2.43644865739147e-07 2.14593063349835e-06 745 967.818181818182 926 2.21495357020228e-08 202 2.28943966904284 2.47786446455877 1 4.7435965231467 742 2339 968 843 202 1023 926 254 951 1537 861 751 M2267 SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_2FC_UP http://www.broadinstitute.org/gsea/msigdb/cards/SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_2FC_UP.html Genes up-regulated more than two-fold in lymphoblastoid cell lines from European population compared to those from Asian population. 17206142 10/37 Leona Saunders 2.16041882087423e-06 7.75170183355026e-06 805 1163.90909090909 927 1.96401903856992e-07 142 3.09412194221844 3.09412194221844 1 5.78001301928431 803 2559 1256 1867 1952 780 927 142 214 1967 336 752 M10679 REACTOME_INHIBITION_OF_INSULIN_SECRETION_BY_ADRENALINE_NORADRENALINE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INHIBITION_OF_INSULIN_SECRETION_BY_ADRENALINE_NORADRENALINE.html Genes involved in Inhibition of Insulin Secretion by Adrenaline/Noradrenaline 12/36 Reactome 1.64492772540349e-06 6.51433174142389e-06 930 1306.09090909091 928 1.49538995937096e-07 371 1.5262515227022 1.52113611358058 1 2.8932687105402 926 371 876 868 928 972 1199 2905 2940 625 1757 753 M18292 MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_UP http://www.broadinstitute.org/gsea/msigdb/cards/MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_UP.html Top genes up-regulated in mesenchyme stem cells (MSC) grown in a tumor conditioned medium, which leads to carcinoma-associated fibroblast phenotype. 18519693 20/39 Leona Saunders 0.000145108511356124 0.000259039422558017 205 1247.63636363636 928 1.31925530333941e-05 204 1.98291387528743 1.98291387528743 1 2.59962185683452 204 2341 613 1515 2925 717 454 928 2360 936 731 754 M5899 LOPEZ_MESOTELIOMA_SURVIVAL_TIME_DN http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTELIOMA_SURVIVAL_TIME_DN.html Top genes higher expressed in long term mesothelioma survivors. 16540645 2/13 Arthur Liberzon 0.000265613100560776 0.000451291874266785 780 1289.2 930.5 2.95160512781177e-05 237 2.94977565048583 -2.94977565048583 -1 3.60723790772168 778 1406 4132 NA 2679 445 273 902 237 1081 959 755 M11213 SATO_SILENCED_BY_DEACETYLATION_IN_PANCREATIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SATO_SILENCED_BY_DEACETYLATION_IN_PANCREATIC_CANCER.html 50 most interesting genes up-regulated in pancreatic cancer cell lines (AsPC1, Hs766T, MiaPaCa2, Panc1) but not in the non-neoplastic cells (HPDE) by TSA [PubChem=5562]. 12839967 30/89 John Newman 9.72185950004021e-08 1.17717399527619e-06 1980 1614.18181818182 931 8.83805448150164e-09 56 1.95941720019891 2.32398635906327 1 4.24657978696303 1979 336 571 521 56 3961 4050 3419 931 532 1400 756 M6189 ELVIDGE_HIF1A_AND_HIF2A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HIF1A_AND_HIF2A_TARGETS_DN.html Genes down-regulated in MCF7 cells (breast cancer) after knockdown of both HIF1A and HIF2A [GeneID=3091;2034] by RNAi. 16565084 72/165 Arthur Liberzon 1.36218720389356e-07 1.49840592428292e-06 1025 789 934 1.2383520802154e-08 84 1.85434235302296 1.98846392707125 1 3.94782745519935 1023 1098 444 736 84 1048 1270 934 1065 315 662 757 M8231 HEIDENBLAD_AMPLICON_12P11_12_UP http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLICON_12P11_12_UP.html Up-regulated genes whose expression is associated with amplification of the 12p11-12 chromosome in pancreatic cancer cell lines. 15688027 20/48 Arthur Liberzon 3.48863624488761e-07 2.56636568972423e-06 570 888.909090909091 935 3.17148799826913e-08 313 1.70056090921065 1.68683396297184 1 3.47517108677303 567 1296 1252 1028 313 756 968 989 850 935 824 758 M1722 LEIN_MEDULLA_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_MEDULLA_MARKERS.html Top 100 ranked genes most specific to medulla (myelencephalon) hindbrain region of adult mouse brain. 17151600 48/121 Jessica Robertson 1.68182044990097e-06 6.60051141393297e-06 1320 938.272727272727 938 1.52892885053934e-07 276 1.8394761831926 1.6888646323498 1 3.48320145619862 1316 1108 1036 276 938 1120 1432 917 664 645 869 759 M2358 RAFFEL_VEGFA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAFFEL_VEGFA_TARGETS_DN.html Genes down-regulated in hearts of E18.5 embryos upon knockout of VEGFA [GeneID=7422]. 18981216 2/5 Arthur Liberzon 0.000189888148908215 0.000331773253461556 1145 1483.3 939 2.11004640426754e-05 21 2.54304047385828 -2.54304047385828 -1 3.23405017122932 1145 913 4655 NA 2958 712 553 735 21 2176 965 760 M14718 TURJANSKI_MAPK14_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TURJANSKI_MAPK14_TARGETS.html Examples of transcription factors whose activities are regulated by MAPK14 [GeneID=1432] phosphorylation. 17496919 8/13 Arthur Liberzon 3.30416791672793e-07 2.47466829669015e-06 945 1471 942 3.30416840801667e-08 56 4.23380450123343 4.23380450123343 1 8.67641988245431 942 2092 4204 1369 2730 879 600 56 65 2401 843 761 M11575 REACTOME_GLUCAGON_SIGNALING_IN_METABOLIC_REGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCAGON_SIGNALING_IN_METABOLIC_REGULATION.html Genes involved in Glucagon signaling in metabolic regulation 14/36 Reactome 4.43840850032887e-06 1.32221120359448e-05 350 1075.45454545455 945 4.03492495878065e-07 350 1.58825035762938 1.52302842184037 1 2.83231955872261 350 366 945 780 1382 526 471 2367 2616 1021 1006 762 M203 PID_ALK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALK2_PATHWAY.html ALK2 signaling events 18832364 5/13 Pathway Interaction Database 1.73135941882976e-08 2.75957491042049e-07 10 1312.63636363636 948 1.73135943231898e-09 6 3.13978420181193 3.13978420181193 1 7.52778367844187 737 2378 3903 1032 2686 948 389 8 6 1860 492 763 M6656 HASINA_NOL7_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HASINA_NOL7_TARGETS_UP.html Genes up-regulated in SiHa cells (cervical carcinoma) by stable expression of NOL7 [GeneID=51406] off a plasmid vector. 16205646 10/17 Leona Saunders 3.25493270616513e-05 6.89539541640587e-05 375 1027.45454545455 949 2.95907351306902e-06 243 2.40339281374046 2.40339281374046 1 3.6558446441277 371 1805 1259 949 2619 491 243 988 304 1966 307 764 M19492 GUTIERREZ_CHRONIC_LYMPHOCYTIC_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_CHRONIC_LYMPHOCYTIC_LEUKEMIA_DN.html Genes exclusively down-regulated in B lymphocytes from CLL (chronic lymphocytic leukemia) patients but with a similiar expression pattern in the normal cells and in the cells from WM (Waldenstroem's macroblobulinemia) patients. 17252022 39/90 Arthur Liberzon 5.41879386238959e-07 3.27556613442881e-06 950 1129.09090909091 949 4.92617745189703e-08 371 1.61065127916304 1.82519224738194 1 3.22904969603913 949 1114 1736 2397 473 723 371 700 1283 1915 759 765 M3210 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_DN.html Genes down-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 3 days after transduction. 16818636 14/55 Arthur Liberzon 8.38735998628624e-07 4.23525526893721e-06 950 968.818181818182 950 7.62487562174142e-08 559 1.96297655589015 2.01471487535081 1 3.85532448218724 950 972 710 980 644 1493 1544 850 797 559 1158 766 M7363 ELVIDGE_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HYPOXIA_UP.html Genes up-regulated in MCF7 cells (breast cancer) under hypoxia conditions. 16565084 117/258 Arthur Liberzon 4.29458241716266e-07 2.83442439532736e-06 1345 913.545454545455 951 3.90416659590998e-08 273 1.71024801595737 1.80484233100557 1 3.46799454926649 951 816 535 647 395 1177 1345 1459 1343 273 1108 767 M12828 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_UP.html Genes up-regulated in reverted NIH3T3 cells (fibroblasts transformed by activated KRAS [GeneID=3845] which then reverted to normal cells upon stable over-expression of a dominant negative form of CDC25 [GeneID=5923]) vs normal fibroblasts. 16607279 94/214 Lauren Kazmierski 2.76048090699964e-06 9.19375517427172e-06 245 895.636363636364 951 2.50953124614357e-07 245 1.840358552349 1.82899433479946 1 3.38806038162197 245 1629 951 1174 1191 292 373 332 2020 1210 435 768 M10219 DAVIES_MULTIPLE_MYELOMA_VS_MGUS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAVIES_MULTIPLE_MYELOMA_VS_MGUS_DN.html Genes down-regulated in multiple myeloma (MM) compared to monoclonal gammopathy of uncertain significance (MGUS). 12947006 25/123 Arthur Liberzon 5.88991480511874e-05 0.000116051737875061 865 1432.09090909091 953 5.3546113616647e-06 480 1.81430214391534 1.96584356756278 1 2.60982895798057 863 2199 2032 1882 2531 815 511 498 480 2989 953 769 M2244 BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B.html Category B genes: p53-dependent genes whose expression in the absence of S389 phosphorylation is dissimilar to loss of TP53 [GeneID=7157] in MEF (embryonic fibroblast) cells in response to UV-C irradiation. 18195040 357/874 Arthur Liberzon 1.00610017828228e-07 1.2119756903421e-06 955 899.909090909091 954 9.14636567539165e-09 59 1.5368047357566 1.60420203512185 1 3.32355795706345 954 227 430 490 59 1155 1339 1771 1869 396 1209 770 M188 REACTOME_AMINO_ACID_TRANSPORT_ACROSS_THE_PLASMA_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINO_ACID_TRANSPORT_ACROSS_THE_PLASMA_MEMBRANE.html Genes involved in Amino acid transport across the plasma membrane 15/36 Reactome 3.11812162871623e-06 1.00838633210243e-05 960 1013.09090909091 956 2.83466004375103e-07 621 1.86085655025286 1.8150148177321 1 3.3984978774516 981 880 958 905 1240 1506 1520 868 956 621 709 771 M16586 LAIHO_COLORECTAL_CANCER_SERRATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/LAIHO_COLORECTAL_CANCER_SERRATED_UP.html Genes up-regulated in serrated vs conventional colorectal carcinoma (CRC) samples. 16819509 87/175 Arthur Liberzon 6.04774937579049e-07 3.47495592160468e-06 960 898.727272727273 957 5.49795548936683e-08 34 1.7502664707225 1.72271920714244 1 3.49253326578519 277 2065 957 959 2550 124 176 160 1294 1290 34 772 M362 LE_SKI_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LE_SKI_TARGETS_UP.html Selected genes implicated in metastasis and epithelial-to-mesenchymal transition (EMT) which were up-regulated in MDA-MB-231 cells (breast cancer) upon knockdown of SKI [GeneID=6497] by RNAi. 18451154 13/54 Jessica Robertson 6.04442092496732e-06 1.68411483876129e-05 315 719.545454545455 957 5.49494321078221e-07 66 2.13311762466206 2.13311762466206 1 3.72205386382413 311 1219 1004 995 1770 247 66 211 975 957 160 773 M8673 MARTINEZ_TP53_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_TP53_TARGETS_DN.html Genes down-regulated in mice with skin specific knockout of TP53 [GeneID=7157]. 18245467 404/997 Jessica Robertson 1.77284035382202e-10 4.56457686703846e-09 2005 1060.72727272727 958 1.61167304905899e-11 16 1.77828211797061 2.085680877609 1 5.42147148904012 2004 16 175 51 430 2882 2130 1471 958 227 1324 774 M9945 UDAYAKUMAR_MED1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/UDAYAKUMAR_MED1_TARGETS_DN.html Genes down-regulated in HeLa cells after knockdown of MED1 [GeneID=5469] by RNAi. 16574658 191/406 Leona Saunders 1.75416678584664e-06 6.77102599545088e-06 830 1056.81818181818 959 1.5946983495732e-07 415 1.80411361080856 1.97152851948948 1 3.40893479875556 829 808 718 415 959 1717 1689 1105 1328 846 1211 775 M14693 VANTVEER_BREAST_CANCER_POOR_PROGNOSIS http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_POOR_PROGNOSIS.html The optimal set of 70 prognostic markers predicting poor breast cancer clinical outcome (defined as developing metastases with 5 years). 11823860 45/129 Arthur Liberzon 2.27369979341287e-05 5.06877128065305e-05 660 1122.63636363636 959 2.06702117494373e-06 377 2.13891869857484 2.22413478027477 1 3.35804517810778 659 2047 606 1799 1961 959 1031 605 1499 806 377 776 M12717 LOPES_METHYLATED_IN_COLON_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/LOPES_METHYLATED_IN_COLON_CANCER_DN.html Genes un-methylated aberrantly in HCT116 and Colo320 (colon cancer) cells. 18794111 18/46 Jessica Robertson 2.08719098210289e-05 4.69092419287009e-05 960 1020.27272727273 960 1.89746434911857e-06 359 1.68498268000604 2.13192029492963 1 2.66609948974979 960 359 1529 1520 1941 836 388 500 430 1779 981 777 M11238 LINDGREN_BLADDER_CANCER_CLUSTER_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_3_DN.html Genes whose expression profile is specific to Cluster III of urothelial cell carcinoma (UCC) tumors. 16532037 152/375 Leona Saunders 6.05491221983841e-07 3.47495592160468e-06 975 990.636363636364 961 5.50446716935624e-08 476 1.87648804389299 2.26637942518965 1 3.74439951058763 973 920 660 571 518 1947 1676 961 1073 476 1122 778 M19439 DOANE_BREAST_CANCER_ESR1_UP http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_BREAST_CANCER_ESR1_UP.html Genes up-regulated in breast cancer samples positive for ESR1 [GeneID=2099] compared to the ESR1 negative tumors. 16491124 67/174 Arthur Liberzon 1.73898887024805e-09 3.46761780680101e-08 1095 895.454545454545 962 1.58089897420239e-10 94 1.87573628760139 -1.83735300434495 -1 5.11479274434305 1092 94 226 257 1015 1108 2766 962 807 232 1291 779 M4371 MARTINEZ_TP53_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_TP53_TARGETS_UP.html Genes up-regulated in mice with skin specific knockout of TP53 [GeneID=7157]. 18245467 442/969 Jessica Robertson 1.91019118388637e-08 3.01385720124294e-07 695 878.363636363636 962 1.7365374549745e-09 275 1.74070852693952 1.98654417390867 1 4.14907549803234 694 1159 275 655 1121 1029 962 613 1753 402 999 780 M277 PID_INTEGRIN_A4B1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN_A4B1_PATHWAY.html Alpha4 beta1 integrin signaling events 18832364 31/61 Pathway Interaction Database 8.17976865947387e-06 2.13604865885288e-05 670 916.727272727273 963 7.4361809751265e-07 289 2.04814906821101 2.13449355374175 1 3.49650258970522 670 1442 1018 659 1622 1008 874 289 452 1087 963 781 M1570 MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP.html Genes up-regulated in non-apoptotic tissues (fetal liver) after MDM4 [GeneID=4194] knockout. 15608685 163/354 Arthur Liberzon 5.41634201364162e-06 1.54291663683433e-05 480 1027.27272727273 964 4.92395940779897e-07 127 1.72617832641603 1.82992727630202 1 3.03598498477021 478 2219 1209 1352 1465 425 336 812 1913 964 127 782 M9556 BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_48HR_DN.html Genes down-regulated in T98G cells (glioma, express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 48 h. 15980968 102/308 John Newman 4.99450920910625e-07 3.09990333163866e-06 595 949.545454545455 964 4.54046394815982e-08 448 1.81951141640064 2.07842449408176 1 3.6636954134493 1149 1249 1054 964 448 591 592 900 1303 1461 734 783 M678 REACTOME_CHONDROITIN_SULFATE_DERMATAN_SULFATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHONDROITIN_SULFATE_DERMATAN_SULFATE_METABOLISM.html Genes involved in Chondroitin sulfate/dermatan sulfate metabolism 19/50 Reactome 2.49515317521132e-06 8.56577859270347e-06 320 870.545454545455 965 2.26832364101824e-07 54 1.67887561153066 1.67887561153066 1 3.10962957661081 317 965 1245 2024 1136 133 54 233 1890 1451 128 784 M18705 JAZAG_TGFB1_SIGNALING_VIA_SMAD4_DN http://www.broadinstitute.org/gsea/msigdb/cards/JAZAG_TGFB1_SIGNALING_VIA_SMAD4_DN.html Genes down-regulated in PANC-1-S4KD cells (pancreatic cancer; SMAD4 [GeneID=4089] knocked down by RNAi) after stimulation by TGF1B [GeneID=7040] for 2 h. 15592526 41/105 Leona Saunders 4.54612117627457e-07 2.92102274825625e-06 2555 1451.54545454545 965 4.1328382869944e-08 164 2.01722195307372 2.16984975647457 1 4.08083078136156 2552 320 561 164 415 3303 2762 3011 714 965 1200 785 M10668 DORN_ADENOVIRUS_INFECTION_12HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_12HR_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) 12 h after infection with adenovirus Ad12. 15681441 37/77 Arthur Liberzon 0.000137872704661439 0.000246780555402407 1220 1144.18181818182 965 1.25346678018929e-05 604 2.09683184374417 2.15892711069628 1 2.76510707586462 1219 604 861 965 2490 1247 893 1374 803 1194 936 786 M891 REACTOME_RECYCLING_PATHWAY_OF_L1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RECYCLING_PATHWAY_OF_L1.html Genes involved in Recycling pathway of L1 19/41 Reactome 9.99349702805938e-07 4.72749354697327e-06 765 1143.54545454545 966 9.08500142509723e-08 151 1.76274191300759 2.05923574115518 1 3.43129211029305 763 1736 1867 1286 719 1022 945 704 151 2420 966 787 M15887 IZADPANAH_STEM_CELL_ADIPOSE_VS_BONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/IZADPANAH_STEM_CELL_ADIPOSE_VS_BONE_UP.html Genes up-regulated in adipose tissue mesenchymal stem cells (ASC) vs bone marrow mesenchymal stem cells (rBMSC) 18519682 96/244 Leona Saunders 8.60083932628332e-06 2.22425679265804e-05 915 1051.27272727273 968 7.81897541019228e-07 164 1.61079985225392 1.80660597817398 1 2.7395335493878 915 1529 1032 835 1808 968 682 357 2170 1104 164 788 M1696 WOOD_EBV_EBNA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WOOD_EBV_EBNA1_TARGETS_UP.html Genes up-regulated in the Ad/AH cells (adenocarcinoma) engineered to stably express the Epstein-Barr virus (EBV) gene EBNA1. 17486072 85/175 Arthur Liberzon 8.48277545660939e-07 4.25749323161521e-06 650 1074.18181818182 969 7.71161702491426e-08 388 1.44833611508287 1.4945589290971 1 2.84335648839148 553 1720 1447 969 649 746 994 388 2290 1412 648 789 M12621 LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_UP.html Genes up-regulated in Wilm's tumor samples compared to fetal kidney. 12057921 125/342 Kevin Vogelsang 5.86198045405139e-11 1.69563212393116e-09 870 945 969 5.32907314018872e-12 125 1.8242799064353 1.91083379723967 1 5.84848546515869 870 265 155 383 1171 1920 1556 1284 969 125 1697 790 M4151 HINATA_NFKB_TARGETS_FIBROBLAST_UP http://www.broadinstitute.org/gsea/msigdb/cards/HINATA_NFKB_TARGETS_FIBROBLAST_UP.html Genes up-regulated in primary fibroblast cells by expression of p50 (NFKB1) and p65 (RELA) [GeneID=4790;5970] components of NFKB. 12673201 56/141 Arthur Liberzon 1.80216232886629e-06 6.89382259025915e-06 4140 2242.72727272727 973 1.63833073194158e-07 584 1.75592975021493 1.65115152830198 1 3.31287977903546 4138 584 848 618 973 3396 4656 3753 828 641 4235 791 M12110 KANG_FLUOROURACIL_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_FLUOROURACIL_RESISTANCE_DN.html Genes down-regulated in gastric cancer cell lines resistant to 5-fluorouracil [PubChem=3385]. 14734480 10/26 John Newman 1.21447965010541e-05 2.96254640312023e-05 1230 1062.18181818182 975 1.10407850411326e-06 563 1.59977403057892 1.75723189811936 1 2.64799051562402 1230 1063 1545 1354 1756 883 691 563 898 975 726 792 M2334 BILANGES_SERUM_SENSITIVE_VIA_TSC2 http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_SERUM_SENSITIVE_VIA_TSC2.html Genes translationally up-regulated by serum in MEF cells (embryonic fibroblast) lacking TSC2 [GeneID=7249]. 17562867 36/98 Arthur Liberzon 3.77353176577028e-06 1.17104436121851e-05 590 1006.27272727273 975 3.43048930754991e-07 586 1.77172582998082 1.93300708649846 1 3.19365754657435 586 1357 1071 664 1315 1269 1265 975 848 774 945 793 M18334 REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS.html Genes involved in Class A/1 (Rhodopsin-like receptors) 68/346 Reactome 1.24554536476005e-06 5.50106086641434e-06 730 1571.36363636364 976 1.13231460903165e-07 391 2.0841691067917 2.23164699362428 1 4.00683155939475 510 3113 391 3565 1631 729 728 1647 3187 976 808 794 M18928 BIOCARTA_IL5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL5_PATHWAY.html IL 5 Signaling Pathway 4/16 BioCarta 0.000116585761844151 0.000211998789290528 535 1338 978 1.16591878803757e-05 385 1.86585054134695 1.86585054134695 1 2.50550829709093 535 1325 3843 1513 2642 485 385 626 1611 978 775 795 M1801 GAUSSMANN_MLL_AF4_FUSION_TARGETS_D_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_D_UP.html Up-regulated genes from the set D (Fig. 5a): specific signature shared by cells expressing MLL-AF4 [GeneID=4297;4299] alone and those expressing both MLL-AF4 and AF4-MLL fusion proteins. 17130830 18/59 Arthur Liberzon 6.47359948956666e-07 3.6257472226713e-06 980 1374 978 5.88509217677578e-08 547 1.66934762280878 1.75858192510733 1 3.31980846762467 978 1967 1716 2913 547 791 591 849 2802 1035 925 796 M1464 VALK_AML_CLUSTER_2 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_2.html Top 40 genes from cluster 2 of acute myeloid leukemia (AML) expression profile; 71% of the samples are FAB M4 or M5 subtypes, and 82% bear internal tundem duplications in FLT3 [GeneID=2322]. 15084694 19/51 Jessica Robertson 8.08984704131345e-07 4.15669114425382e-06 945 1039.09090909091 983 7.35440910556011e-08 625 1.97231395974362 1.82470428345314 1 3.87952584029859 941 1380 787 739 625 1309 1280 1457 983 864 1065 797 M11733 GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_1_DN.html Genes exclusively down-regulated in B lymphocytes from WM (Waldenstroem's macroblobulinemia) patients but with a similiar expression pattern in the normal cells and in the cells from CLL (chronic lymphocytic leukemia) patients. 17252022 4/15 Arthur Liberzon 3.63819900384933e-06 1.13961233502928e-05 2110 1268.81818181818 983 3.63820496028445e-07 357 1.69725879360958 1.83884208352137 1 3.06675629535032 2108 525 4591 707 1340 1040 596 384 357 983 1326 798 M994 REACTOME_DSCAM_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DSCAM_INTERACTIONS.html Genes involved in DSCAM interactions 7/19 Reactome 2.20828607055341e-05 4.93939309146219e-05 630 1361.36363636364 984 2.20830801523349e-06 307 1.40208685143196 -1.40208685143196 -1 2.20699379505018 630 984 4068 1555 2465 467 307 363 2155 1497 484 799 M1488 HANSON_HRAS_SIGNALING_VIA_NFKB http://www.broadinstitute.org/gsea/msigdb/cards/HANSON_HRAS_SIGNALING_VIA_NFKB.html Genes changed by expression of activated form of HRas[GeneID=3265] in MEF cells (embryonic fibroblast) with or without p65/c-Rel complex [GeneID=5970;5966]. 15492243 10/36 Kevin Vogelsang 1.36696459424194e-06 5.83387621914185e-06 1520 1152.45454545455 984 1.2426958578207e-07 361 2.43025810073842 2.8901891968183 1 4.64952854882458 1520 979 984 863 838 1830 1745 1390 361 974 1193 800 M19469 ICHIBA_GRAFT_VERSUS_HOST_DISEASE_D7_DN http://www.broadinstitute.org/gsea/msigdb/cards/ICHIBA_GRAFT_VERSUS_HOST_DISEASE_D7_DN.html Hepatic graft versus host disease (GVHD), day 7: down-regulated in allogeneic vs syngeneic bone marrow transplant. 12663442 24/66 Arthur Liberzon 1.53014015197604e-07 1.61491818742336e-06 4685 2201.54545454545 986 1.39103659854554e-08 102 1.8930451680759 -1.40533685793109 -1 4.00772111924422 4682 162 889 858 102 3600 3419 4316 986 944 4259 801 M1974 MIKKELSEN_IPS_LCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_LCP_WITH_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV8.1 cells (induced pluripotent cells, iPS). 18509334 9/30 Jessica Robertson 6.02680398670614e-06 1.68104782629196e-05 770 1461.18181818182 987 6.02682033183335e-07 220 2.52157645309309 3.55389468427202 1 4.4006011221117 768 2130 4573 987 1666 1156 627 220 952 2584 410 802 M2446 PLASARI_TGFB1_TARGETS_10HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_TARGETS_10HR_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) upon stimulation with TGFB1 [GeneID=7040] for 10 h. 19752192 171/413 Arthur Liberzon 1.92449002260483e-07 1.8479836569521e-06 330 1031.36363636364 988 1.74953653723011e-08 327 1.69480283984978 1.77139791689869 1 3.55175697990495 327 1164 327 1690 1246 676 989 958 2425 555 988 803 M72 PID_NECTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NECTIN_PATHWAY.html Nectin adhesion pathway 18832364 29/55 Pathway Interaction Database 2.32531334501438e-08 3.60808554130376e-07 2750 1676.63636363636 989 2.11392124508365e-09 5 1.79749398879908 2.02456518000006 1 4.23307700087399 2750 619 989 235 5 3112 2351 3910 377 808 3287 804 M1829 MATZUK_SPERMATOGONIA http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_SPERMATOGONIA.html Genes important for spermatogonia, based on mouse models with male reproductive defects. 18989307 7/32 Jessica Robertson 9.11179681730342e-06 2.33577023445754e-05 620 1247.81818181818 989 9.11183417869759e-07 329 1.72757412924096 1.72757412924096 1 2.92471911232834 616 1754 4493 994 1695 496 422 329 989 1502 436 805 M9809 KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION.html Cytokine-cytokine receptor interaction 86/310 KEGG 1.07617568254966e-06 4.95128411507793e-06 870 1086.72727272727 990 9.78342008167001e-08 382 1.89930455390167 1.97327780092061 1 3.68317493104043 868 1530 382 2159 1288 990 938 1052 1939 393 415 806 M4508 ENK_UV_RESPONSE_EPIDERMIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ENK_UV_RESPONSE_EPIDERMIS_DN.html Genes down-regulated in epidermis after to UVB irradiation. 16434974 384/857 Lauren Kazmierski 2.74111212442021e-07 2.25744313093727e-06 990 900.818181818182 990 2.49192042359263e-08 234 1.65340319708257 1.76210669806159 1 3.41246629768686 990 399 363 288 234 1401 1686 1368 1518 452 1210 807 M1469 BIOCARTA_LYM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LYM_PATHWAY.html Adhesion and Diapedesis of Lymphocytes 6/14 BioCarta 2.06574354568763e-05 4.65388185340973e-05 365 1152.09090909091 992 2.06576274877265e-06 110 2.3143066101806 2.3143066101806 1 3.66477321854263 362 208 3812 992 2080 251 110 1129 2139 1318 272 808 M8696 VALK_AML_CLUSTER_7 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_7.html Top 40 genes from cluster 7 of acute myeloid leukemia (AML) expression profile; 61% of the samples are FAB M1 or M2 subtype. 15084694 16/47 Jessica Robertson 6.06508108891105e-07 3.47495592160468e-06 4375 1758.09090909091 992 5.51371160087875e-08 191 2.10891159877262 -1.5625869770491 -1 4.20818431773856 4372 504 992 874 519 2855 3293 1405 191 689 3645 809 M1613 MILI_PSEUDOPODIA_CHEMOTAXIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MILI_PSEUDOPODIA_CHEMOTAXIS_DN.html Transcripts depleted in pseudopodia of NIH/3T3 cells (fibroblast) in response to the chemotactic migration stimulus by lysophosphatidic acid (LPA) [PubChem=3988]. 18451862 367/764 Jessica Robertson 1.01988212950764e-06 4.79448552966058e-06 885 1017.90909090909 995 9.2716600209795e-08 478 1.57198016421226 1.75071752712943 1 3.05645049846724 885 1084 1204 708 727 1015 936 1304 1861 478 995 810 M12671 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN.html Genes down-regulated in nsopharyngeal carcinoma relative to the normal tissue. 16912175 172/528 Leona Saunders 2.70505015607719e-12 9.67623284837993e-11 125 897.272727272727 997 2.45913650552775e-13 123 1.84853394462194 -1.78220901918237 -1 6.7665454654314 677 997 125 673 1153 532 1790 1391 1312 123 1097 811 M2530 SHIRAISHI_PLZF_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHIRAISHI_PLZF_TARGETS_DN.html Genes down-regulated in A375 and 397 cells (melanoma) by forced expression of PLZF [GeneID=7704] off adenovirus vector. 16862184 7/12 Arthur Liberzon 2.31897605891948e-05 5.15499137196238e-05 975 1367.09090909091 997 2.31900025869973e-06 499 1.44274673620032 1.50584379743614 1 2.26121074505472 975 898 4185 1686 1993 768 499 997 1094 1005 938 812 M6434 FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_UP.html Top 100 genes positively associated with T-cell acute lymphoblastic leukemia MLL T-ALL) expressing MLL-ENL fusion [GeneID=4297;4298]. 12637319 85/194 Kevin Vogelsang 4.25833797158624e-05 8.70238627773795e-05 880 1174.27272727273 998 3.87129127141594e-06 461 1.49853952191702 1.57362420919935 1 2.22408903066028 877 568 1196 461 2159 905 1395 998 2052 1413 893 813 M1311 WONG_ENDMETRIUM_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WONG_ENDMETRIUM_CANCER_DN.html Genes down-regulated in cancer endometrium samples compared to the normal endometrium. 17043662 52/156 Arthur Liberzon 1.03917865714787e-09 2.30786312198811e-08 1340 982.909090909091 1000 9.44707870580665e-11 147 2.16560285596067 2.23931231138422 1 6.04517547316783 147 1018 203 951 2329 915 1000 1396 1339 176 1338 814 M11215 REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK.html Genes involved in NRAGE signals death through JNK 25/60 Reactome 1.22786531089323e-07 1.40336020654773e-06 4110 1950.81818181818 1002 1.11624125402084e-08 76 1.61963419477072 1.70542503233608 1 3.46499139237767 4107 618 1002 478 76 4040 3993 2979 203 464 3499 815 M1077 REACTOME_PLATELET_ACTIVATION_SIGNALING_AND_AGGREGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_ACTIVATION_SIGNALING_AND_AGGREGATION.html Genes involved in Platelet activation, signaling and aggregation 123/310 Reactome 5.30570997198991e-07 3.23731210009697e-06 785 1234.09090909091 1003 4.82337386505561e-08 468 1.65115610422439 1.6446321792936 1 3.31333332291476 785 1003 614 669 468 1315 1123 2525 2547 675 1851 816 M7804 ROSS_ACUTE_MYELOID_LEUKEMIA_CBF http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_ACUTE_MYELOID_LEUKEMIA_CBF.html Top 100 probe sets for core-binding factor (CBF) acute myeloid leukemia (AML): contains CBFB MYH11 [GeneID=865;4629] or AML1 ETO [GeneID=861;862] fusions. 15226186 57/176 Kate Stafford 2.29497062448361e-05 5.11132716080333e-05 740 1288.18181818182 1004 2.08635869567555e-06 738 1.9182428711265 2.0536593503627 1 3.00904409323262 738 1534 931 1915 1963 841 800 994 1980 1470 1004 817 M1823 HOEGERKORP_CD44_TARGETS_DIRECT_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOEGERKORP_CD44_TARGETS_DIRECT_DN.html Genes directly down-regulated by CD44 [GeneID=960] stimulation of B lymphocytes. 12411303 12/39 Kevin Vogelsang 1.40126334719244e-05 3.33146628358384e-05 890 1144.18181818182 1004 1.27388388404468e-06 457 1.67333364576987 1.81280456958787 1 2.73857256391642 887 1797 1801 1228 1813 1004 457 599 546 1598 856 818 M16701 HUANG_FOXA2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_FOXA2_TARGETS_DN.html Genes down-regulated in H358 cells (lung cancer) by inducible expression of FOXA2 [GeneID=3170] in a Tet-off system. 18593902 22/57 Leona Saunders 8.59165611814643e-07 4.283031975493e-06 1615 1282.72727272727 1006 7.81059952131474e-08 482 2.13318508938677 2.15130811546418 1 4.18581872137496 1615 961 722 1006 657 2179 2430 1739 550 482 1769 819 M1711 DASU_IL6_SIGNALING_SCAR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DASU_IL6_SIGNALING_SCAR_DN.html Genes down-regulated in hypertrophic scar fibroblasts in response to IL6 [GeneID=3569]. 15095275 18/34 John Newman 1.32423820255407e-06 5.72980629470763e-06 1160 1175.72727272727 1008 1.20385363604432e-07 426 2.35119075626686 2.19993494576214 1 4.50497659122375 1156 1838 898 1008 822 1360 1896 2096 618 815 426 820 M623 REACTOME_NGF_SIGNALLING_VIA_TRKA_FROM_THE_PLASMA_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NGF_SIGNALLING_VIA_TRKA_FROM_THE_PLASMA_MEMBRANE.html Genes involved in NGF signalling via TRKA from the plasma membrane 84/169 Reactome 9.82873135715268e-07 4.69016651116267e-06 990 1316.72727272727 1009 8.93521431658592e-08 467 1.37689410485781 1.4597272003593 1 2.68194685805122 989 1009 2343 467 710 772 731 2050 1793 2586 1034 821 M2121 VERHAAK_GLIOBLASTOMA_CLASSICAL http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_GLIOBLASTOMA_CLASSICAL.html Genes correlated with classical type of glioblastoma multiforme tumors. 20129251 138/331 Arthur Liberzon 5.4243263344361e-07 3.27556613442881e-06 870 1214.36363636364 1010 4.93120697441821e-08 475 1.53888784087162 1.76679001317628 1 3.08517764146815 867 1414 1010 877 475 1727 979 967 2275 1604 1163 822 M3134 HUMMEL_BURKITTS_LYMPHOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUMMEL_BURKITTS_LYMPHOMA_UP.html Up-regulated genes constituting the molecular signature of Burkitt 's lymphoma. 16760442 28/71 Arthur Liberzon 2.0151636287651e-06 7.40631903089667e-06 610 1048.63636363636 1011 1.83196861329457e-07 454 1.86672848754552 2.05532756633367 1 3.50067205724059 607 956 1214 454 1035 1183 1749 607 882 1837 1011 823 M5040 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_4NQO_IN_WS http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_4NQO_IN_WS.html Human environmental stress response genes not changed in primary fibroblasts from Wilmor syndrom (WS) patients in response to 4NQO treatment. 15897889 26/61 Jessica Robertson 1.05304591126653e-06 4.89540986130452e-06 2335 1765.27272727273 1011 9.57314923013555e-08 477 1.93682101359081 2.28974445696604 1 3.7594170956468 2334 477 1663 750 740 3995 3834 1011 966 3029 619 824 M1327 MANTOVANI_VIRAL_GPCR_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/MANTOVANI_VIRAL_GPCR_SIGNALING_UP.html Up-regulated genes in the expression signature of direct and paracrine viral GPCR signaling in endothelial cells. 17906691 63/156 Jessica Robertson 4.89233185168433e-08 6.96822706899476e-07 2880 1461.45454545455 1012 4.4475745095267e-09 286 2.18772812349175 2.51745053722109 1 4.92349076310105 2877 1012 293 598 299 3745 2924 1064 513 286 2465 825 M1431 NADLER_OBESITY_UP http://www.broadinstitute.org/gsea/msigdb/cards/NADLER_OBESITY_UP.html Genes up-regulated in adipose tissue from obese mouse strains compared to the lean ones. 11027337 49/125 Kevin Vogelsang 8.48424129528458e-06 2.20471593024812e-05 770 1070.45454545455 1012 7.71297637701036e-07 595 1.83244346792792 2.14820204195381 1 3.11905610196287 770 595 628 1296 1632 1077 1001 1012 1651 801 1312 826 M5355 CASTELLANO_HRAS_AND_NRAS_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_HRAS_AND_NRAS_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) isolated from HRAS and NRAS [GeneID=3265;4893] double knockout mice. 16909116 5/12 Leona Saunders 6.92963834930792e-06 1.87268081342889e-05 810 1257.54545454545 1013 6.92965995835221e-07 257 2.32415495716098 2.32415495716098 1 4.01623574618484 808 387 4160 1553 1596 851 1013 257 1492 1161 555 827 M2761 NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_UP.html Top 100 probe sets contrubuting to the positive side of the 2nd principal component; associated with adipocytic differentiation. 17464315 66/209 Nikolaos Papanikolaou 2.52727500275202e-09 4.85361092741637e-08 150 1059.27272727273 1015 2.29752273241387e-10 150 2.18967395962265 2.33009851664764 1 5.85396070500685 150 2447 235 1087 1422 1118 798 1015 1953 477 950 828 M2544 ROESSLER_LIVER_CANCER_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROESSLER_LIVER_CANCER_METASTASIS_UP.html Genes up-regulated in liver samples containing tumor thrombi in the major branches of the portal vein at surgery (PT) compared to those from metastasis-free HCC patients (PN) at the time of surgery and at follow-up. 21159642 83/214 Yujin Hoshida 5.88606779585167e-06 1.64472949859039e-05 385 963.090909090909 1015 5.35098503999899e-07 381 1.82917493302055 1.92784014925468 1 3.19857902774369 524 1908 1448 1018 1497 381 559 575 1287 1015 382 829 M1644 SAFFORD_T_LYMPHOCYTE_ANERGY http://www.broadinstitute.org/gsea/msigdb/cards/SAFFORD_T_LYMPHOCYTE_ANERGY.html Genes up-regulated in anergic mouse T helper cells (A.E7), versus non-anergic stimulated controls 15834410 59/156 John Newman 7.25996270037782e-07 3.88358278698293e-06 795 1012.18181818182 1017 6.59996826923119e-08 588 1.59301589041431 1.66970961048579 1 3.15063596070963 794 1017 1387 1353 588 1062 872 772 1227 985 1077 830 M25 ASTON_MAJOR_DEPRESSIVE_DISORDER_UP http://www.broadinstitute.org/gsea/msigdb/cards/ASTON_MAJOR_DEPRESSIVE_DISORDER_UP.html Genes up-regulated in the temporal cortex samples from patients with major depressive disorder. 15303102 28/77 Jean Junior 5.86588797729884e-05 0.000115639676321508 665 1085.45454545455 1018 5.33276762368587e-06 297 1.82807640289488 2.04267792433569 1 2.63067512994776 664 1834 1293 1786 2640 297 328 497 1018 1169 414 831 M1544 LEE_AGING_CEREBELLUM_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_CEREBELLUM_DN.html Downregulated in the cerebellum of aged adult mice (30-month) vs young adult (5-month) 10888876 65/167 John Newman 7.26578442261356e-06 1.94113260002093e-05 1020 1092.63636363636 1018 6.60528038083355e-07 405 2.1427509363801 2.42808622405416 1 3.69055037545574 1018 1425 590 405 1579 1431 1614 982 721 769 1485 832 M14181 YAMASHITA_METHYLATED_IN_PROSTATE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_METHYLATED_IN_PROSTATE_CANCER.html Genes up-regulated in prostate cancer cell lines after treatment with 5-aza-2'-deoxycytidine (decitabine) [PubChem=451668]. 18381416 45/104 Jessica Robertson 1.07038364175913e-09 2.35484401187009e-08 445 997.909090909091 1018 9.73076038436284e-11 205 2.1829333983855 2.13629194929768 1 6.08656936373292 445 597 205 1117 2105 1018 934 1501 1372 349 1334 833 M4013 KEGG_GAP_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GAP_JUNCTION.html Gap junction 39/107 KEGG 1.65457616414121e-07 1.69286984828946e-06 690 1283.45454545455 1019 1.50416026234418e-08 122 1.47903356062885 1.50589613839347 1 3.12015867493991 686 2156 1640 1019 122 426 412 1369 2884 2646 758 834 M1217 SMITH_TERT_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMITH_TERT_TARGETS_DN.html Genes consistently down-regulated in HMEC cells (primary mammary epithelium) upon expression of TERT [GeneID=7015] off a retroviral vector. 12717449 70/169 Broad Institute 8.17489749709351e-06 2.13604865885288e-05 1020 1157.72727272727 1019 7.43175261276961e-07 622 1.51107404433159 1.56188025912547 1 2.579633675244 1019 1011 1049 1005 1621 789 1246 622 1938 1591 844 835 M14365 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_UP.html All common up-regulated stress response genes (Human Environmental Stress Response, H-ESR). 15897889 51/114 Jessica Robertson 6.2608166006087e-06 1.72882655217751e-05 995 1077.36363636364 1019 5.69166765261149e-07 240 1.94895315978563 2.2125066455925 1 3.3926004286564 994 1723 1593 310 1516 1702 1769 404 581 1019 240 836 M3848 LINDSTEDT_DENDRITIC_CELL_MATURATION_D http://www.broadinstitute.org/gsea/msigdb/cards/LINDSTEDT_DENDRITIC_CELL_MATURATION_D.html Genes down-regulated during the course of maturation of monocyte-derived dendritic cells (DC) in response to inflammatory stimuli (cluster D). 12356685 45/129 Arthur Liberzon 1.97437686691255e-06 7.31956487211409e-06 530 1125 1019 1.79488967164319e-07 269 2.06901862541794 2.17259238042289 1 3.88389634146705 526 2110 831 1921 1019 393 269 1055 2192 1343 716 837 M15699 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_0 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_0.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 0. 12554760 49/110 Arthur Liberzon 6.10557964805595e-07 3.48486555795252e-06 1000 1218.18181818182 1025 5.55052849319621e-08 120 1.67634905528431 1.68270031452791 1 3.34427847207911 1000 120 771 1025 525 2410 2111 1324 1599 442 2073 838 M4281 REACTOME_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Neurotransmitter Release Cycle 17/61 Reactome 1.63718510877456e-07 1.68242311835912e-06 720 1039.27272727273 1027 1.48835020964528e-08 120 2.7438920279451 2.7438920279451 1 5.79119141501174 718 2368 1234 1250 120 1093 1027 467 787 1701 667 839 M19146 LY_AGING_MIDDLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LY_AGING_MIDDLE_UP.html Genes up-regulated in fibroblasts from middle-age individuals, compared to those from the young donors. 10741968 8/21 John Newman 0.00111388243369181 0.00171755613171432 300 1475 1027 0.000111444115822349 297 2.88100779945132 2.88100779945132 1 2.91187554062523 297 1983 4413 1027 3167 739 695 1031 786 1135 952 840 M5459 NEWMAN_ERCC6_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NEWMAN_ERCC6_TARGETS_UP.html Genes up-regulated in Cockayne syndrome fibroblasts rescued by expression of ERCC6 [GeneID=2074] off a plasmid vector. 16772382 12/44 Leona Saunders 1.05640532448872e-05 2.62895132796291e-05 1580 1158 1030 9.60373088376989e-07 494 1.86408723287929 -1.69141634557645 -1 3.12084054662645 1576 1220 1030 912 1712 803 1073 2452 494 626 840 841 M4420 LEE_LIVER_CANCER_MYC_E2F1_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_E2F1_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) from MYC and E2F1 [GeneID=4609;1869] double transgenic mice. 15565109 45/125 Yujin Hoshida 2.05299619170857e-10 5.20018386721426e-09 2320 1497 1030 1.86636017445469e-11 79 2.37245455360582 2.66763950364834 1 7.18383356915166 2320 313 178 79 1030 3660 3456 1709 397 220 3105 842 M9834 DORN_ADENOVIRUS_INFECTION_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_24HR_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) 24 h after infection with adenovirus Ad12. 15681441 11/21 Arthur Liberzon 2.35288706174585e-06 8.21581875658796e-06 1240 987.090909090909 1030 2.13899052558954e-07 402 2.75073968370172 3.14000227849443 1 5.11316160855207 1237 1390 529 682 1106 1411 1733 792 402 546 1030 843 M5236 ROSS_AML_WITH_CBFB_MYH11_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_AML_WITH_CBFB_MYH11_FUSION.html Top 63 probe sets for pediatric acute myeloid leukemia (AML) subtype inv(16); has a CBFB-MYH11 fusion [GeneID=865;4629]. 15226186 32/91 Kate Stafford 2.62817825035274e-05 5.73888316922318e-05 510 1148.81818181818 1032 2.38928149799192e-06 508 1.9726393640056 2.1252754927228 1 3.0581085308991 508 1032 794 1648 2003 1250 1017 1189 1030 947 1219 844 M1932 MEISSNER_NPC_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing the H3K27 tri-methylation (H3K27me3) mark in neural precursor cells (NPC). 18600261 24/125 Jessica Robertson 2.20172541023334e-07 2.02299711222616e-06 1035 1047.27272727273 1032 2.00156875507145e-08 178 2.28964582864531 2.48950770229599 1 4.76546609228265 1032 1963 676 2025 178 855 443 450 1579 1189 1130 845 M933 REACTOME_REGULATION_OF_WATER_BALANCE_BY_RENAL_AQUAPORINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_WATER_BALANCE_BY_RENAL_AQUAPORINS.html Genes involved in Regulation of Water Balance by Renal Aquaporins 19/48 Reactome 1.86673556661101e-05 4.26292537287485e-05 540 1322.72727272727 1033 1.6970467330475e-06 321 1.52715493922408 1.52302842184037 1 2.4395674688564 538 632 866 1206 1903 512 321 2674 3751 1114 1033 846 M19779 FARMER_BREAST_CANCER_CLUSTER_6 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_6.html Cluster 6: selected luminal genes clustered together across breast cancer samples. 15897907 14/26 Leona Saunders 1.33821640839042e-05 3.20925388419524e-05 1100 1015.09090909091 1035 1.21656777142272e-06 138 1.59662474384441 -1.79950671741599 -1 2.62250377983511 1099 1134 1304 635 1788 1035 2112 311 138 1024 586 847 M1263 WANG_RESPONSE_TO_BEXAROTENE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_BEXAROTENE_UP.html Genes up-regulated in the mouse lung cancer model and which reverted to normal levels upon treatment with bexarotene [PubChem=82146]. 16247446 18/53 Leona Saunders 9.1136568092427e-07 4.46254919624987e-06 2580 1681.09090909091 1036 8.28514598603836e-08 168 2.02066414506757 -1.96111147057095 -1 3.95185513188123 2577 168 741 983 681 2087 2574 4328 238 1036 3079 848 M12300 CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP.html Up-regulated genesin the left ventricle myocardium of patients with heart failure following implantation of LVAD (left ventricular assist device). 12824457 71/140 John Newman 2.18884681820749e-06 7.82972228253458e-06 630 1086.54545454545 1036 1.98986272360064e-07 629 1.85868545998498 1.9028172800696 1 3.4691856045602 629 1423 742 1431 1069 868 951 1206 1775 822 1036 849 M16801 SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON_BY_RHO_GTPASES http://www.broadinstitute.org/gsea/msigdb/cards/SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON_BY_RHO_GTPASES.html Genes related to regulation of the actin cytoskeleton 20/63 Signaling Gateway 4.35778299887521e-05 8.88623635018679e-05 785 1442.72727272727 1037 3.96169938244568e-06 188 3.48672413696935 3.48672413696935 1 5.16332340644918 784 2510 1408 2715 2167 662 636 659 188 3104 1037 850 M2067 ONGUSAHA_BRCA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONGUSAHA_BRCA1_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) lacking TP53 and BRCA1 [GeneID=7157;672] by expression of BRCA1. 12802282 14/20 Arthur Liberzon 5.37953477597887e-06 1.53429701523049e-05 1385 898.545454545455 1039 4.89049811844916e-07 202 1.92706297036613 2.11075316734276 1 3.39101266933395 473 1385 1155 1039 1767 469 465 202 1165 1383 381 851 M10775 REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS.html Genes involved in G alpha (z) signalling events 16/47 Reactome 7.71932966708042e-06 2.04135320654282e-05 865 1333.18181818182 1040 7.01759704790088e-07 502 1.70835230585384 1.76393715778277 1 2.9287149898263 862 761 1040 1251 1600 558 502 2215 3732 913 1231 852 M6998 FURUKAWA_DUSP6_TARGETS_PCI35_UP http://www.broadinstitute.org/gsea/msigdb/cards/FURUKAWA_DUSP6_TARGETS_PCI35_UP.html Genes up-regulated in PCI-35 cells (pancreatic cancer, lack endogenous DUSP6 [GeneID=1848]) upon expression of DUSP6 off an adenoviral vector. 16532023 62/159 Arthur Liberzon 2.11683129659793e-07 1.97206191965366e-06 2585 1819.63636363636 1040 1.92439227298057e-08 170 2.12946188436788 2.31002430004282 1 4.44069370070338 2581 935 330 170 641 4389 4074 3504 1040 268 2084 853 M1963 MIKKELSEN_MEF_ICP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_ICP_WITH_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MEF cells (embryonic fibroblasts). 18509334 84/379 Jessica Robertson 1.56516064990623e-11 4.9893488472521e-10 3670 2129.45454545455 1041 1.42287331810669e-12 115 1.74733700880109 1.83278868745473 1 5.94114583355179 3668 282 141 378 115 4218 4191 4559 1041 178 4653 854 M2322 KASLER_HDAC7_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/KASLER_HDAC7_TARGETS_2_DN.html Genes down-regulated in DO11.10 cells (hybridoma) by expression of transciptionally activating and by transcriptionally repressive forms of HDAC7 [GeneID=51564]. 17470548 29/62 Arthur Liberzon 5.50279704280192e-07 3.30167822568115e-06 915 1072.36363636364 1042 5.00254401745571e-08 360 1.34249815019056 1.29205610417756 1 2.68976145449863 914 1123 1898 1042 482 366 479 1357 2235 1540 360 855 M1047 YAGI_AML_WITH_INV_16_TRANSLOCATION http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_WITH_INV_16_TRANSLOCATION.html Genes specifically expressed in samples from patients with pediatric acute myeloid leukemia (AML) bearing inv(16) translocation. 12738660 297/770 Arthur Liberzon 1.68754751473563e-06 6.61744573560767e-06 1035 984.727272727273 1046 1.53413528109011e-07 470 1.67164687019636 1.96909001010841 1 3.16472270730585 1033 1162 1046 470 939 1076 1268 851 1455 1058 474 856 M18647 REACTOME_STRIATED_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_STRIATED_MUSCLE_CONTRACTION.html Genes involved in Striated Muscle Contraction 21/48 Reactome 7.81089003186256e-06 2.06091389016374e-05 310 927.818181818182 1048 7.10083433074544e-07 309 2.71249604459649 2.93166828659598 1 4.646063077688 309 1048 633 1381 1604 753 555 1203 409 1252 1059 857 M10761 PEREZ_TP63_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/PEREZ_TP63_TARGETS.html Genes up-regulated in the HMEC cells (primary mammary epithelium) upon expression of the transcriptionally active isoform of TP63 [GeneID=8626] off adenoviral vector. 17563751 235/644 Leona Saunders 3.17576586765081e-16 2.0668942855294e-14 40 804.363636363636 1049 2.88705987968255e-17 40 1.82577551553453 1.848303885407 1 9.13274498020749 1049 40 69 40 434 1464 1661 1485 1140 64 1402 858 M2206 CHYLA_CBFA2T3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHYLA_CBFA2T3_TARGETS_DN.html Genes down-regulated in immature bone marrow progenitor cells upon knock out of CBFA2T3 [GeneID=863]. 18710942 165/395 Arthur Liberzon 6.94865798846834e-14 3.28903144787501e-12 2085 1304.81818181818 1049 6.31696180769867e-15 51 1.70712453998471 1.70136042433266 1 7.16534734464575 2084 51 94 473 504 2847 1818 2867 1049 65 2501 859 M14801 HOOI_ST7_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOOI_ST7_TARGETS_DN.html Genes down-regulated in PC-3 cells (prostate cancer) stably expressing ST7 [GeneID=7982] off a plasmid vector. 16474848 71/228 Leona Saunders 4.07732790793917e-07 2.7892494272413e-06 1140 992.454545454545 1053 3.70666242145739e-08 346 1.87560456293077 2.17414090723167 1 3.80808374904877 1137 829 453 404 368 1927 1659 1053 1057 346 1684 860 M15535 KIM_WT1_TARGETS_12HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_12HR_UP.html Genes up-regulated in UB27 cells (osteosarcoma) at 12 hr after inducing the expression of a mutated form of WT1 [GeneID=7490]. 17430890 113/253 Arthur Liberzon 5.02809402158398e-06 1.45802280848654e-05 630 1217 1053 4.57100501210543e-07 555 1.42754232817302 1.43685817161775 1 2.52357200937754 628 1006 1385 1053 1432 555 809 1314 2599 1912 694 861 M6510 PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_UP http://www.broadinstitute.org/gsea/msigdb/cards/PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_UP.html Genes up-regulated in post-GC, BCL6 [GeneID=604] dependent B cell non-Hodgkin's lymphoma (B-NHL) vs MYC [GeneID=4609] driven pre-GC lymphoma. 18066064 184/414 Jessica Robertson 2.00565802518133e-07 1.91026697276417e-06 1060 1106.36363636364 1056 1.82332564366338e-08 162 1.4988781830737 1.55990978406027 1 3.13327520384201 1045 254 1767 338 162 1057 1056 3194 1472 676 1149 862 M1679 ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP.html Genes up-regulated in CD-1 compared to CD-2 cluster of multiple myeloma samples. 16728703 40/94 Kevin Vogelsang 2.63674072800112e-07 2.21827056578335e-06 730 876.909090909091 1056 2.39703731274494e-08 49 1.70607552023352 1.80853900557216 1 3.52591786232946 729 1434 1056 1338 1349 617 274 49 1097 1101 602 863 M116 BILD_SRC_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/BILD_SRC_ONCOGENIC_SIGNATURE.html Genes selected in supervised analyses to discriminate cells expressing c-Src (CSK) [GeneID=1445] from control cells expressing GFP. 16273092 46/109 Arthur Liberzon 6.9089684099764e-08 9.1456005562569e-07 725 1046.90909090909 1057 6.28088056995314e-09 26 1.62774992127567 1.87867791160293 1 3.59299572363523 723 126 1775 1057 26 1618 1411 738 754 2020 1268 864 M5314 MILI_PSEUDOPODIA_HAPTOTAXIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MILI_PSEUDOPODIA_HAPTOTAXIS_DN.html Transcripts depleted from pseudopodia of NIH/3T3 cells (fibroblast) in response to haptotactic migratory stimulus by fibronectin, FN1 [GeneID=2335]. 18451862 492/998 Jessica Robertson 1.96008833315662e-07 1.87448447534121e-06 1030 1139.09090909091 1057 1.78189864344597e-08 159 1.39086343036375 1.56716516493426 1 2.91165478026338 1030 222 1628 607 159 2061 1152 1057 2244 724 1646 865 M2288 BIOCARTA_NFAT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NFAT_PATHWAY.html NFAT and Hypertrophy of the heart (Transcription in the broken heart) 38/91 BioCarta 2.1176988105796e-06 7.65704986603088e-06 975 1119.81818181818 1058 1.92518259005348e-07 596 2.1902922386504 2.61090067549771 1 4.09587441223667 972 1540 910 900 1058 1085 1044 1110 596 1832 1271 866 M2668 KEGG_BETA_ALANINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BETA_ALANINE_METABOLISM.html beta-Alanine metabolism 11/30 KEGG 2.30252478756778e-05 5.12571551284686e-05 1580 1313.54545454545 1061 2.09322626017765e-06 144 2.58022839833436 3.07306613333625 1 4.0463136668592 1579 890 975 817 1964 1885 2877 665 144 1061 1592 867 M7528 KEGG_PANTOTHENATE_AND_COA_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PANTOTHENATE_AND_COA_BIOSYNTHESIS.html Pantothenate and CoA biosynthesis 11/20 KEGG 3.34927456615194e-06 1.06621607452364e-05 715 964.272727272727 1062 3.04479969553648e-07 108 2.34963583121296 2.34963583121296 1 4.27035958090542 711 1616 1400 615 1270 1294 1598 230 108 1062 703 868 M666 REACTOME_HYALURONAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HYALURONAN_METABOLISM.html Genes involved in Hyaluronan metabolism 11/23 Reactome 1.29314301905095e-07 1.4496433896277e-06 810 1102.63636363636 1063 1.17558463187355e-08 28 1.94771305067717 2.12945667658537 1 4.15683966457098 809 775 1198 1736 2275 850 606 28 1688 1063 1101 869 M8513 SMID_BREAST_CANCER_NORMAL_LIKE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_NORMAL_LIKE_UP.html Genes up-regulated in the normal-like subtype of breast cancer. 18451135 264/820 Jessica Robertson 7.24552803100291e-38 3.39525443532796e-35 110 960.181818181818 1063 6.58684366454812e-39 9 2.06224343752092 2.25620607074829 1 25.9830107815712 107 1409 9 803 1920 1063 1057 1146 1771 44 1233 870 M2351 TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_DN.html Genes down-regulated in leukemic progenitor cells expressing activated fusion of ESWR1 and FLI1 [GeneID=2130, 2313] compared to normal hematopoetic progenitors. 17875932 207/516 Arthur Liberzon 3.42805889413496e-07 2.53773838513687e-06 1460 1207.18181818182 1063 3.11641766208923e-08 308 1.42847419808158 1.52606805905459 1 2.92169364598116 1460 804 1015 1063 308 1229 1028 1715 2230 720 1707 871 M759 REACTOME_PKA_MEDIATED_PHOSPHORYLATION_OF_CREB http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PKA_MEDIATED_PHOSPHORYLATION_OF_CREB.html Genes involved in PKA-mediated phosphorylation of CREB 10/16 Reactome 2.63196064182383e-06 8.87682708082428e-06 305 1073.54545454545 1065 2.3926943550582e-07 43 1.4409912407175 1.4409912407175 1 2.66085846407722 302 1065 1454 748 1168 218 43 1629 2882 1963 337 872 M823 REACTOME_TRANSPORT_OF_INORGANIC_CATIONS_ANIONS_AND_AMINO_ACIDS_OLIGOPEPTIDES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_INORGANIC_CATIONS_ANIONS_AND_AMINO_ACIDS_OLIGOPEPTIDES.html Genes involved in Transport of inorganic cations/anions and amino acids/oligopeptides 33/101 Reactome 8.09900240998353e-07 4.15683738150962e-06 1105 1050.27272727273 1066 7.36273217411205e-08 145 1.70526278636718 1.71910633809941 1 3.35422878678972 1105 145 1066 985 626 1753 1711 1277 1191 655 1039 873 M2570 ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_UP.html Genes up-regulated during prostate cancer progression in the JOCK1 model due to inducible activation of FGFR1 [GeneID=2260] gene in prostate. 18068632 194/499 Yujin Hoshida 8.83055834081564e-11 2.40581374331756e-09 2655 1288.36363636364 1066 8.02778031015463e-12 114 1.7798451415339 -1.68750623833701 -1 5.607188376228 2652 917 165 515 695 1066 2712 2022 1342 114 1972 874 M347 WEIGEL_OXIDATIVE_STRESS_BY_HNE_AND_H2O2 http://www.broadinstitute.org/gsea/msigdb/cards/WEIGEL_OXIDATIVE_STRESS_BY_HNE_AND_H2O2.html Oxidative stress genes down-regulated in ARPE-19 cells (retinal pigmented epithelium) in response to HNE and H2O2 [PubChem=5283344;784]. 12419474 27/62 John Newman 2.63992899500463e-05 5.75381733515892e-05 820 1511.09090909091 1067 2.39996424893884e-06 357 2.38437981507812 2.38437981507812 1 3.69543053710291 819 3120 1770 2707 2892 760 607 372 1067 2151 357 875 M409 LOPEZ_EPITHELIOID_MESOTHELIOMA http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_EPITHELIOID_MESOTHELIOMA.html Top 20 genes expressed higher in epithelioid than in sarcomatoid mesothelioma samples. 16540645 17/30 Arthur Liberzon 3.27640023715717e-07 2.46734573623285e-06 3400 1630.09090909091 1068 2.97854611372969e-08 295 1.83955478654312 -2.12594862897009 -1 3.77070163607782 3400 757 769 1068 295 2509 3389 1756 945 751 2292 876 M15148 LE_EGR2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LE_EGR2_TARGETS_DN.html Genes down-regulated in P14 nerves of transgenic mice having hypomorhic (reduced function) allele of EGR2 [GeneID=1959]. 15695336 64/159 Kate Stafford 2.82397625245756e-07 2.29742234705141e-06 1165 983.818181818182 1069 2.56725146813676e-08 242 2.21718887507948 2.36751682421163 1 4.56988726757059 1163 837 775 612 242 1137 1069 1953 673 1153 1208 877 M5968 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREEN_UP.html Genes from the green module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 24/79 Arthur Liberzon 3.02244167939684e-07 2.35268466937768e-06 525 1118.27272727273 1070 2.7476746314829e-08 20 1.66616087075344 1.63020052333449 1 3.42786677783285 523 2238 1070 1468 2493 185 167 256 2389 1492 20 878 M651 REACTOME_CS_DS_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CS_DS_DEGRADATION.html Genes involved in CS/DS degradation 8/13 Reactome 9.93122428415536e-06 2.5074200967431e-05 585 1137.18181818182 1071 9.93126866758163e-07 102 1.79384952605659 1.79384952605659 1 3.01672732315506 582 1071 3946 1552 1720 146 102 1096 438 1658 198 879 M5652 FARMER_BREAST_CANCER_BASAL_VS_LULMINAL http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_BASAL_VS_LULMINAL.html Genes which best discriminated between two groups of breast cancer according to the status of ESR1 and AR [GeneID=2099;367]: basal (ESR1- AR-) and luminal (ESR1+ AR+). 15897907 235/582 Leona Saunders 1.22291491278739e-07 1.40111962868502e-06 3875 1948.81818181818 1071 1.11174089160511e-08 75 1.74569573368702 -1.60707929025631 -1 3.73512604792258 3873 243 322 208 75 3505 3663 3446 1071 373 4658 880 M13251 BROWNE_HCMV_INFECTION_14HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_14HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 14 h time point that were not down-regulated at the previous time point, 12 h. 11711622 218/510 John Newman 1.68268672287659e-07 1.71042732828626e-06 1865 1241.72727272727 1071 1.52971531961652e-08 127 1.58255257598789 1.83269870950165 1 3.33594951674766 1861 405 803 756 127 2757 1832 1071 1748 678 1621 881 M11350 KYNG_DNA_DAMAGE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_DN.html Genes with GO annotation and down-regulated after DNA damage in cell lines from young donors. 15897889 174/346 Jessica Robertson 1.24637968279613e-05 3.02148742554717e-05 1855 1105.72727272727 1071 1.13307885822225e-06 205 1.7606591948587 2.1157200883849 1 2.90878598817634 880 1855 1125 710 1855 957 1074 875 1556 1071 205 882 M256 PID_TAP63_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TAP63_PATHWAY.html Validated transcriptional targets of TAp63 isoforms 18832364 37/73 Pathway Interaction Database 2.2028985761062e-06 7.86797463996467e-06 1355 1190.36363636364 1072 2.00263707446388e-07 263 1.75293085543471 2.05358556308628 1 3.27044133292364 1351 953 2019 1475 1072 962 1127 815 534 2523 263 883 M1582 BURTON_ADIPOGENESIS_2 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_2.html Strongly up-regulated at 8 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 60/131 John Newman 6.5203601410236e-07 3.63831479011075e-06 1075 997.636363636364 1073 5.92760188502616e-08 521 2.03931698411029 2.1891747001448 1 4.05444121956299 1073 1262 689 1129 549 1510 1527 1166 866 521 682 884 M5369 POOLA_INVASIVE_BREAST_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/POOLA_INVASIVE_BREAST_CANCER_UP.html Genes up-regulated in atypical ductal hyperplastic tissues from patients with (ADHC) breast cancer vs those without the cancer (ADH). 15864312 142/518 Jessica Robertson 6.99682917936671e-16 4.25807032915746e-14 170 1170.90909090909 1074 6.36075379942426e-17 74 1.92880146470111 1.92840674511892 1 9.42678829012161 168 2104 74 1710 2002 874 482 1201 2919 272 1074 885 M7846 BROWNE_HCMV_INFECTION_8HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_8HR_DN.html Genes down-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 8 h time point that were not down-regulated at the previous time point, 6 h. 11711622 23/77 John Newman 7.15270534611913e-07 3.84756432956263e-06 935 1298.54545454545 1075 6.50246151966273e-08 81 1.41974471550155 1.66718257667371 1 2.81004363092434 934 2743 1750 1787 687 1010 1075 81 2706 1111 400 886 M940 REACTOME_TRAF6_MEDIATED_NFKB_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF6_MEDIATED_NFKB_ACTIVATION.html Genes involved in TRAF6 mediated NF-kB activation 12/29 Reactome 7.3091594967793e-06 1.950079641381e-05 745 1466.09090909091 1076 6.64471252767582e-07 488 1.05412997544726 -1.05412997544726 -1 1.8148030213019 745 1056 2701 2128 1581 547 721 1076 2843 2241 488 887 M13283 HSIAO_LIVER_SPECIFIC_GENES http://www.broadinstitute.org/gsea/msigdb/cards/HSIAO_LIVER_SPECIFIC_GENES.html Liver selective genes 11773596 122/467 Kevin Vogelsang 1.27311816820267e-08 2.0932742934027e-07 3325 1744.90909090909 1077 1.15738015960916e-09 64 1.83413572036338 -1.91406910259823 -1 4.47789048374696 3325 64 267 1023 515 2473 3912 3065 1077 131 3342 888 M15896 MARTINEZ_RB1_AND_TP53_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RB1_AND_TP53_TARGETS_UP.html Genes up-regulated in mice with skin specific double knockout of both RB1 and TP53 [GeneID=5925;7157] by Cre-lox. 18245467 427/970 Jessica Robertson 1.18037868025059e-09 2.54896520537062e-08 745 933 1077 1.07307152807628e-10 209 1.76706353227009 2.01828870117431 1 4.90479878411447 744 1234 209 545 1301 1173 1077 761 1783 324 1112 889 M5785 KEGG_TASTE_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TASTE_TRANSDUCTION.html Taste transduction 19/88 KEGG 0.000154124650276553 0.000273571254240881 635 1593.54545454545 1078 1.40123135267073e-05 635 1.80542601570777 1.46137295852033 1 2.35128991023823 635 1551 875 1078 2506 1003 647 4056 2601 859 1718 890 M4479 TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_LOBULAR_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_LOBULAR_NORMAL_UP.html Genes up-regulated in ductal carcinoma vs normal lobular breast cells. 17389037 50/146 Arthur Liberzon 2.21998219071258e-06 7.90489099215742e-06 900 1219.63636363636 1078 2.01816766441966e-07 351 2.00734732291615 2.08959072717423 1 3.74361423699559 896 2689 759 1797 1078 1237 1344 351 1628 832 805 891 M15008 PIEPOLI_LGI1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PIEPOLI_LGI1_TARGETS_UP.html Up-regulated genes in U87 cells (glioblastoma multiforme, GBM) engineered to stably express LGI1 [GeneID=9211]. 16533756 13/33 Arthur Liberzon 1.18026670662049e-06 5.29763389580804e-06 1255 1262.54545454545 1078 1.07297030892381e-07 518 1.87554886628778 1.82996383904522 1 3.61697640814192 1255 2084 1520 1411 785 889 518 2463 930 955 1078 892 M2356 KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3 http://www.broadinstitute.org/gsea/msigdb/cards/KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3.html Genes with promoters occupied by SMAD2 or SMAD3 [GeneID=4087, 4088] in HaCaT cells (keratinocyte) according to a ChIP-chip analysis. 18955504 596/1317 Arthur Liberzon 2.97649931972595e-07 2.33632760673967e-06 1195 1342.18181818182 1078 2.97649971840569e-08 294 1.58617881644713 1.79005204763525 1 3.26507290011983 1195 532 4653 401 294 1473 1593 1078 1580 920 1045 893 M14765 REACTOME_PLC_BETA_MEDIATED_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLC_BETA_MEDIATED_EVENTS.html Genes involved in PLC beta mediated events 19/48 Reactome 1.4689140405573e-07 1.57874568670906e-06 405 1054.90909090909 1081 1.33537648966815e-08 92 1.18740477902352 1.32138789895271 1 2.51809667424512 403 1297 1733 1081 92 115 99 1575 3027 1917 265 894 M7727 RICKMAN_HEAD_AND_NECK_CANCER_B http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_B.html Cluster b: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 32/167 Jessica Robertson 2.23208570784493e-06 7.93592839678404e-06 410 1298.18181818182 1081 2.02917088407956e-07 365 2.02314960486399 1.92630131080083 1 3.77182624774888 1848 465 523 406 1081 2422 2462 2081 410 365 2217 895 M6322 REACTOME_ACTIVATION_OF_RAC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_RAC.html Genes involved in Activation of Rac 4/20 Reactome 0.000116705178136008 0.000212133617046288 1085 1571.63636363636 1082 1.16711307633435e-05 343 1.23036719434994 -1.23036719434994 -1 1.65204202912985 1082 1402 4016 2085 2475 759 598 995 343 2665 868 896 M17600 NAGASHIMA_NRG1_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAGASHIMA_NRG1_SIGNALING_DN.html Genes down-regulated in MCF7 cells (breast cancer) after stimulation with NRG1 [GeneID=3084]. 17142811 31/84 Arthur Liberzon 2.24073209178789e-06 7.96062970592726e-06 1050 1216 1082 2.03703124909951e-07 328 1.7985043232487 1.76696556322451 1 3.35212516649249 1048 2231 1753 2165 1082 584 498 668 1340 1679 328 897 M270 PID_MAPK_TRK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MAPK_TRK_PATHWAY.html Trk receptor signaling mediated by the MAPK pathway 18832364 24/49 Pathway Interaction Database 1.74087124592565e-06 6.74979256763237e-06 1185 1107.63636363636 1083 1.58261147589772e-07 610 1.3884627693052 1.39146974773031 1 2.6242405044603 1185 958 1998 1083 951 751 610 1128 1112 1490 918 898 M1533 CUI_TCF21_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/CUI_TCF21_TARGETS_2_DN.html All significantly down-regulated genes in kidney glomeruli isolated from TCF21 [Gene ID=6943] knockout mice. 16207825 575/1393 John Newman 3.58011157716327e-06 1.12504417218126e-05 595 1465 1083 3.58011734491585e-07 593 1.58214283867973 1.79968686019129 1 2.86198605215082 593 1083 4403 1164 1331 839 1483 1032 2603 683 901 899 M1781 MCGOWAN_RSP6_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCGOWAN_RSP6_TARGETS_DN.html Genes down-regulated by hemizygotic cre-lox knockout of RSP6 [GeneID=81492] in keratinocytes. 18641651 3/7 Jessica Robertson 6.80529029247007e-05 0.000132212231801471 1150 1470.18181818182 1084 6.8054987053446e-06 77 2.54971056225001 -2.54971056225001 -1 3.61492673287055 1150 529 4450 1816 2934 639 109 916 77 2468 1084 900 M15514 REACTOME_TRANSMISSION_ACROSS_CHEMICAL_SYNAPSES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSMISSION_ACROSS_CHEMICAL_SYNAPSES.html Genes involved in Transmission across Chemical Synapses 74/243 Reactome 7.00597075516692e-07 3.81051980858506e-06 875 1221.72727272727 1085 6.36906635112894e-08 575 1.59658600490918 1.69563210786327 1 3.1625105563217 874 1339 1601 1085 575 716 847 1371 2295 1788 948 901 M3695 SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_UP.html Genes up-regulated in prostate cancer samples bearing the fusion of TMPRSS2 with ERG [GeneID=7113;2078]. 18505969 48/126 Jessica Robertson 7.99662986340086e-06 2.102817482598e-05 800 1169.18181818182 1085 7.26968993632086e-07 424 1.35699184997175 1.47087630071406 1 2.31996954603778 797 846 1877 1778 1610 632 424 1085 1626 1257 929 902 M2262 KIM_GLIS2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_GLIS2_TARGETS_DN.html Partial list of genes down-regulated in the kidney of GLIS2 [GeneID=84662] knockout mice compared to the wild type. 18227149 2/9 Arthur Liberzon 0.000491870871380793 0.000795343996994616 1135 1814.6 1085 5.4664270247632e-05 239 0.921065653530816 0.921065653530816 1 1.04350316532494 1133 1671 4635 NA 2802 631 474 1037 239 4669 855 903 M2504 PHONG_TNF_RESPONSE_NOT_VIA_P38 http://www.broadinstitute.org/gsea/msigdb/cards/PHONG_TNF_RESPONSE_NOT_VIA_P38.html Genes whose expression changes in Calu-6 cells (lung cancer) by TNF [GeneID=7124] were not affected by p38 inhibitor LY479754. 20516219 270/583 Arthur Liberzon 2.09445264904766e-06 7.59916453954163e-06 840 1145.72727272727 1085 1.90404967547214e-07 488 1.69632177743961 1.80103434338691 1 3.17418680867806 839 1085 641 583 1052 1570 1743 1438 2076 488 1088 904 M1386 KEGG_PENTOSE_PHOSPHATE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PENTOSE_PHOSPHATE_PATHWAY.html Pentose phosphate pathway 14/33 KEGG 6.97673618188886e-06 1.88215231711751e-05 1090 1224.18181818182 1086 6.34250755174354e-07 37 1.42249301243169 -1.25293337216662 -1 2.4569874352916 1086 767 2399 1783 2643 135 37 1305 663 2497 151 905 M187 PID_TRKR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TRKR_PATHWAY.html Neurotrophic factor-mediated Trk receptor signaling 18832364 48/98 Pathway Interaction Database 1.65961243583873e-06 6.54508119249709e-06 275 2211.45454545455 1088 1.50873971618246e-07 272 1.79901934806393 -1.5156969831417 -1 3.40900152144081 4137 938 1088 273 933 3883 3965 4627 272 512 3698 906 M1750 CALVET_IRINOTECAN_SENSITIVE_VS_REVERTED_UP http://www.broadinstitute.org/gsea/msigdb/cards/CALVET_IRINOTECAN_SENSITIVE_VS_REVERTED_UP.html Genes up-regulated in neuroblastoma xenografts: resistant vs those that reverted to be sensitive to the topoisomerase inhibitor irinotecan [PubChem=3750]. 16501609 3/7 Arthur Liberzon 3.659986030976e-06 1.14567097803297e-05 1650 1384.90909090909 1088 3.65999205896396e-07 13 2.40120121825145 2.75490610024131 1 4.33668016194238 1649 217 4288 211 1343 1775 3199 1088 13 778 673 907 M244 SMID_BREAST_CANCER_RELAPSE_IN_BRAIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_BRAIN_DN.html Genes down-regulated in brain relapse of breast cancer. 18451135 64/196 Jessica Robertson 2.28227786337557e-06 8.07151250398335e-06 4195 2015.36363636364 1088 2.07480021001077e-07 105 1.90135544634602 -1.81582402324493 -1 3.53964806189122 4194 105 714 183 1088 3017 4334 3261 1076 740 3457 908 M1233 OHM_METHYLATED_IN_ADULT_CANCERS http://www.broadinstitute.org/gsea/msigdb/cards/OHM_METHYLATED_IN_ADULT_CANCERS.html Genes showing frequent DNA methylation and which are silenced in adult cancers but remain unmethylated in embryonic carcinoma and embryonic stem (ES) cells. 17211412 19/42 Leona Saunders 6.97879863585319e-07 3.80263376832652e-06 1090 1280.72727272727 1089 6.34436440877777e-08 78 2.5719522489588 2.64366630572582 1 5.09535758137711 1089 2122 1288 2742 2657 769 475 78 154 1921 793 909 M393 VANTVEER_BREAST_CANCER_ESR1_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_ESR1_UP.html Up-regulated genes from the optimal set of 550 markers discriminating breast cancer samples by ESR1 [GeneID=2099] expression: ER(+) vs ER(-) tumors. 11823860 107/252 Arthur Liberzon 2.28753761793141e-06 8.07792108336594e-06 1545 1246.45454545455 1092 2.07958181499383e-07 68 1.47192259232342 -1.34150092649296 -1 2.74001126782461 1542 68 1318 722 1092 792 2005 2710 846 924 1692 910 M1676 SHEN_SMARCA2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHEN_SMARCA2_TARGETS_DN.html Genes whose expression negatively correlated with that of SMARCA2 [GeneID=6595] in prostate cancer samples. 19074882 147/664 Jessica Robertson 6.94985775177459e-10 1.56572276080845e-08 2185 1370.72727272727 1093 6.31805250360915e-11 58 1.85050407914418 1.9786786081896 1 5.27956413735822 2182 58 200 488 879 3209 1926 2355 1093 154 2534 911 M7054 SU_LIVER http://www.broadinstitute.org/gsea/msigdb/cards/SU_LIVER.html Genes up-regulated specifically in human liver tissue. 11904358 27/140 John Newman 5.24862762839674e-06 1.50919893779846e-05 1095 1132.36363636364 1095 4.77149104572596e-07 426 2.0776670947833 -2.36445726993518 -1 3.66146747010662 1095 1922 1116 1241 1446 837 1677 426 799 1093 804 912 M2621 ZWANG_EGF_PERSISTENTLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_EGF_PERSISTENTLY_DN.html Genes persistently repressed by EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 45/110 Yaara Zwang 1.17573858316253e-06 5.28743858032593e-06 1375 1030 1095 1.06885382864455e-07 658 1.84335955886032 2.26692290372376 1 3.55546336809351 1373 1110 1179 658 782 1377 1095 787 1003 1143 823 913 M12816 DOANE_RESPONSE_TO_ANDROGEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_RESPONSE_TO_ANDROGEN_DN.html Genes down-regulated in MDA-MB-453 cells (class A ER(-) [GeneID=2099] breast cancer) after exposure to the androgen R1881 [PubChem=13766]. 16491124 211/480 Arthur Liberzon 2.4208240208115e-06 8.39284483788818e-06 1100 1123.81818181818 1096 2.20075153148069e-07 249 1.56971334020454 1.60740354137083 1 2.91252044092602 1096 2383 1576 249 1118 807 675 1386 1962 514 596 914 M6311 ODONNELL_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_METASTASIS_DN.html Down-regulated genes in the signature set for lymph node metastasis in head and neck squamous cell carcinoma (HNSCC). 15558013 15/40 Leona Saunders 3.25275748341431e-07 2.45845509149669e-06 2050 1202.54545454545 1096 2.95705269485737e-08 178 1.55261664977712 1.9143510226684 1 3.1834283368535 2046 178 1334 773 292 1692 889 2930 364 1096 1634 915 M2296 BERGER_MBD2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BERGER_MBD2_TARGETS.html Genes strongly up-regulated in colon tissue upon MBD2 [GeneID=8932] knockout. 17353267 6/23 Arthur Liberzon 0.000164500465731569 0.000290557550854931 890 1645.27272727273 1096 1.64512644181835e-05 596 2.43190856626795 -2.43190856626795 -1 3.14393128234269 889 2255 4642 2506 2546 596 622 710 1096 1330 906 916 M1317 GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_UP.html Genes up-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of ELK3 [GeneID=2004] and HIF1A [GeneID=3091] by RNAi. 17704799 108/210 Jessica Robertson 3.67056806473296e-07 2.64619722328287e-06 880 1271.72727272727 1097 3.3368806155867e-08 327 1.62754387818484 1.86897016799911 1 3.31804307094922 878 1582 1097 695 327 1609 2099 2277 1982 567 876 917 M1638 ZAMORA_NOS2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZAMORA_NOS2_TARGETS_DN.html Down-regulated in hepatocytes upon expression of NOS2 [GeneID=4843]. 12381414 78/193 John Newman 6.079770655764e-07 3.4755305144353e-06 475 906.545454545455 1097 5.52706575993527e-08 312 1.80261985494944 1.87658706009481 1 3.59695343743245 474 1097 1357 1143 522 594 312 1177 1130 1315 851 918 M1921 REACTOME_REGULATION_OF_INSULIN_SECRETION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_INSULIN_SECRETION.html Genes involved in Regulation of Insulin Secretion 48/133 Reactome 4.25777316281834e-05 8.70238627773795e-05 625 1435.18181818182 1098 3.87077778902293e-06 202 1.53597823497926 1.53355389618516 1 2.27965448615425 624 1911 1098 1400 2158 202 222 3548 2753 925 946 919 M815 REACTOME_TRANSPORT_OF_GLUCOSE_AND_OTHER_SUGARS_BILE_SALTS_AND_ORGANIC_ACIDS_METAL_IONS_AND_AMINE_COMPOUNDS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_GLUCOSE_AND_OTHER_SUGARS_BILE_SALTS_AND_ORGANIC_ACIDS_METAL_IONS_AND_AMINE_COMPOUNDS.html Genes involved in Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds 32/102 Reactome 1.02955783893221e-06 4.82450803323633e-06 3145 1973.72727272727 1100 9.35962109768967e-08 364 1.95737396297622 1.97244895811163 1 3.80384412700686 3143 725 538 1100 734 3968 2647 4540 1023 364 2929 920 M3468 NABA_ECM_REGULATORS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_ECM_REGULATORS.html Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix 22159717 73/319 Alexandra Naba 8.3306392266235e-09 1.43519762558668e-07 1450 1088.81818181818 1101 7.57330841651707e-10 128 1.91836486486602 2.10129156188144 1 4.7984680298813 1448 424 259 1101 128 1936 1935 1081 1421 218 2026 921 M768 REN_ALVEOLAR_RHABDOMYOSARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/REN_ALVEOLAR_RHABDOMYOSARCOMA_UP.html Genes commonly up-regulated in human alveolar rhabdomyosarcoma (ARMS) and its mouse model overexpressing PAX3-FOXO1 [GeneID=5077;2308] fusion. 18701482 63/192 Jessica Robertson 5.48798369072704e-07 3.29701174035217e-06 1160 1089.18181818182 1102 4.98907732702357e-08 293 1.87994170671495 2.19232056811133 1 3.7669783019162 1160 1102 674 293 481 1445 1586 1383 1891 968 998 922 M1719 LEIN_CHOROID_PLEXUS_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_CHOROID_PLEXUS_MARKERS.html Genes enriched in choroid plexus cells in the brain identified through correlation-based searches seeded with the choroid plexus cell-type specific gene expression patterns. 17151600 59/154 Jessica Robertson 2.07933916062664e-07 1.9505763884193e-06 3415 1774.54545454545 1102 1.89030850650571e-08 187 1.9767042846625 -1.68444970957144 -1 4.12557671691451 3411 433 329 1102 187 2168 3203 4069 855 404 3359 923 M2049 REACTOME_SIGNALING_BY_PDGF http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_PDGF.html Genes involved in Signaling by PDGF 71/154 Reactome 1.1557837544753e-06 5.22276053372348e-06 565 1076.81818181818 1104 1.05071305606724e-07 562 1.51872832872256 1.71916672904199 1 2.93228348143584 562 934 1255 629 774 1032 1104 1407 1630 1235 1283 924 M1605 BURTON_ADIPOGENESIS_4 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_4.html Progressively up-regulated from 8-48 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 51/108 John Newman 0.000177522487110719 0.000311912401425133 410 1348.09090909091 1104 1.61397103073388e-05 410 1.90606247469531 2.18407216736167 1 2.44266691399691 410 2271 1104 1808 2539 951 834 855 1467 1696 894 925 M1714 LEIN_OLIGODENDROCYTE_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_OLIGODENDROCYTE_MARKERS.html Genes enriched in oligodendrocytes in the adult mouse brain identified through correlation-based searches seeded with the oligodendrocyte cell-type specific gene expression patterns. 17151600 49/114 Jessica Robertson 7.02518469276857e-07 3.81051980858506e-06 2950 1715.63636363636 1105 6.38653357827068e-08 312 1.94348938487554 2.09613371165363 1 3.84965525032332 2949 312 999 872 576 3626 1695 3378 390 1105 2970 926 M19231 EPPERT_HSC_R http://www.broadinstitute.org/gsea/msigdb/cards/EPPERT_HSC_R.html Genes up-regulated in human hematopoietic stem cell (HSC) enriched populations compared to committed progenitors and mature cells. 21873988 82/206 Kolja Eppert 8.46107947772285e-07 4.25414360864906e-06 505 1040.36363636364 1105 7.69189339255401e-08 43 1.78108769013888 1.84281751129153 1 3.49683301825034 503 2000 1105 1532 2049 487 1002 153 1281 1289 43 927 M16867 MULLIGHAN_MLL_SIGNATURE_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_MLL_SIGNATURE_2_DN.html The 'MLL signature 2': genes down-regulated in pediatric AML (acute myeloid leukemia) with rearranged MLL [GeneID=4297] compared to the AML cases with intact MLL and NPM1 [GeneID=4869]. 17597811 198/552 Arthur Liberzon 6.1428663677427e-06 1.70530046204042e-05 1245 1061.90909090909 1106 5.58443956363168e-07 480 1.64270661157525 1.79621178423172 1 2.86308100714475 1106 1241 584 1343 1508 544 817 1242 2004 812 480 928 M2603 VALK_AML_CLUSTER_13 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_13.html Top 40 genes from cluster 13 of acute myeloid leukemia (AML) expression profile; 91% of the samples are FAB M2 subtype, all bear the t(8;21) translocation producing the AML1-ETO fusion [GeneID=861;862]; indicate good survival. 15084694 23/50 Jessica Robertson 2.35763262533063e-06 8.22625948049093e-06 425 1078.27272727273 1107 2.14330468354022e-07 370 1.75334831379165 1.75334831379165 1 3.25882560971454 423 1453 1450 2039 1107 548 589 370 1952 1424 506 929 M2104 STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_DN http://www.broadinstitute.org/gsea/msigdb/cards/STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_DN.html Genes repressed in SKBR3 cells (breast cancer) by 25-hydroxyvitamin D3 [PubChem=1593]. 20227041 24/61 Arthur Liberzon 1.59508597150212e-05 3.72239684385405e-05 490 1113.09090909091 1107 1.45008866965103e-06 487 2.32810289915581 2.47519927922755 1 3.76915927787196 487 1041 702 1361 1859 1460 1449 1107 844 747 1187 930 M239 PID_A6B1_A6B4_INTEGRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_A6B1_A6B4_INTEGRIN_PATHWAY.html a6b1 and a6b4 Integrin signaling 18832364 30/64 Pathway Interaction Database 1.9044692633963e-06 7.14787130607259e-06 1110 1078.54545454545 1109 1.7313371927601e-07 104 2.32583062463281 2.77546226917675 1 4.37473954700745 1109 2159 1217 104 1000 1334 1522 138 501 1979 801 931 M12802 SNIJDERS_AMPLIFIED_IN_HEAD_AND_NECK_TUMORS http://www.broadinstitute.org/gsea/msigdb/cards/SNIJDERS_AMPLIFIED_IN_HEAD_AND_NECK_TUMORS.html Genes from the recurrent amplicons in 89 samples of oral squamous cell carcinoma (SCC). 15824737 23/61 Leona Saunders 1.01487482609843e-05 2.55134304458008e-05 815 1112.18181818182 1109 9.22617734376943e-07 271 1.61274357238763 1.74386590731654 1 2.70771450133051 814 1644 1187 1320 1698 877 523 345 2446 1109 271 932 M1294 GALIE_TUMOR_ANGIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/GALIE_TUMOR_ANGIOGENESIS.html Angiogenic genes up-regulated in A17 carcinomas (high vascularization) compared to the syngeneic BB1 and spontaneous tumors (little vascularization). 17998939 4/9 Jessica Robertson 3.64804236076186e-07 2.63401024692297e-06 685 1380.63636363636 1112 3.64804295963157e-08 26 2.37966725577642 2.37966725577642 1 4.8531266407365 682 2353 4303 1112 2606 474 156 1183 657 1635 26 933 M13766 NIKOLSKY_BREAST_CANCER_5P15_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_5P15_AMPLICON.html Genes within amplicon 5p15 identified in a copy number alterations study of 191 breast tumor samples. 19010930 14/36 Jessica Robertson 1.32707477245471e-06 5.73149528453711e-06 1180 1564.72727272727 1113 1.20643233906169e-07 531 1.57179085668049 1.81388795928733 1 3.01154131781288 1179 2623 2200 2957 823 1113 974 620 531 3149 1043 934 M2020 MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED.html Genes with high-CpG-density promoters (HCP) with unmethylated histone H3 in MEF cells (embryonic fibroblast). 17603471 98/480 Arthur Liberzon 4.48821641036638e-07 2.90609255474862e-06 1165 1143.18181818182 1114 4.08019756909722e-08 238 1.68300742120133 1.74949969217532 1 3.40608540342149 1162 819 424 1304 408 1009 1114 2804 1725 238 1568 935 M12701 MARTINEZ_RB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RB1_TARGETS_DN.html Genes down-regulated in mice with skin specific knockout of RB1 [GeneID=5925] by Cre-lox. 18245467 380/937 Jessica Robertson 3.42083770956359e-09 6.31104153819488e-08 2255 1322.90909090909 1115 3.10985246807523e-10 17 1.7854668143638 2.1836206825795 1 4.6989133325808 2254 17 244 72 465 3721 2239 1832 1115 554 2039 936 M6951 ELLWOOD_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ELLWOOD_MYC_TARGETS_DN.html Genes down-regulated in transgenic mice expressing human MYC [GeneID=4609] in prostate. 14522256 34/73 Arthur Liberzon 0.000432987578938731 0.000708690113484769 385 1220.72727272727 1115 3.93702563463757e-05 371 1.79439574374094 -1.59633894113612 -1 2.06578494964731 381 1115 1644 1658 2740 371 608 1219 670 1930 1092 937 M9488 KEGG_RETINOL_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RETINOL_METABOLISM.html Retinol metabolism 12/101 KEGG 1.31471933043816e-05 3.16261539139282e-05 1850 1223.36363636364 1117 1.1952065338751e-06 290 2.09393152843648 2.23923929425102 1 3.44421111668945 1849 889 1117 907 1833 2539 1634 290 386 1594 419 938 M1535 JIANG_AGING_HYPOTHALAMUS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_AGING_HYPOTHALAMUS_DN.html Down-regulated in the hypothalamus of aged (22 months) BALB/c mice, compared to young (2 months) controls 11172053 35/71 John Newman 3.35257928882994e-07 2.49812279321805e-06 935 1228.45454545455 1117 3.04779981793591e-08 304 1.46657622709341 1.72567037810835 1 3.00328769161813 931 1117 2221 1393 304 607 632 1643 1247 2776 642 939 M3941 HASLINGER_B_CLL_WITH_13Q14_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_13Q14_DELETION.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with deletions in the 13q14 region. 15459216 19/43 Kevin Vogelsang 3.92162578091425e-07 2.75100874391679e-06 1125 977.818181818182 1118 3.56511498178786e-08 224 1.58770979963911 1.76308169211622 1 3.22704370998057 1125 629 1249 295 348 1705 1393 1089 224 1118 1581 940 M4381 LUI_THYROID_CANCER_PAX8_PPARG_UP http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_PAX8_PPARG_UP.html Top up-regulated genes distinguishing between follicular thyroid carcinoma (FTC) samples by the presence or absence of the PAX8-PPARG [GeneID=7849;5468] fusion protein. 15608688 33/84 Leona Saunders 3.52156585385906e-06 1.10900924671933e-05 435 973.545454545455 1119 3.20142862807595e-07 135 1.4600290133317 1.4053926181181 1 2.64441783542538 431 1119 1485 1592 1287 190 135 666 1327 2226 251 941 M4562 LENAOUR_DENDRITIC_CELL_MATURATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/LENAOUR_DENDRITIC_CELL_MATURATION_UP.html Genes up-regulated during in vitro maturation of CD14+ [GeneID=929] monocytes (day 0) into immature (day 7) and mature dendritic cells (day 14). 11279020 85/177 Kevin Vogelsang 9.02975160974458e-07 4.43872831030423e-06 1120 1347.18181818182 1119 8.20886846904306e-08 416 1.85325595248941 1.95567148677652 1 3.62602604735496 1119 1096 416 1041 677 2439 2059 1660 2045 629 1638 942 M10102 NIELSEN_MALIGNAT_FIBROUS_HISTIOCYTOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_MALIGNAT_FIBROUS_HISTIOCYTOMA_UP.html Top 20 positive significant genes associated with malignant fibrous histiocytoma tumors. 11965276 18/44 John Newman 5.59965281678588e-05 0.000110904366438963 575 1219.18181818182 1119 5.09072304513205e-06 438 1.9596120542943 1.91836198304968 1 2.83296676531994 575 2205 843 1128 2240 1092 1347 1119 1351 438 1073 943 M6590 MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP.html The 'NPM1-mutated signature 2': genes up-regulated in pediatric AML (acute myeloid leukemia) samples with mutated NPM1 [GeneID=4869] compared to the AML cases with the intact gene and without recurring cytogenetic anomalities or M7 phenotype. 17597811 105/214 Arthur Liberzon 2.61238823043762e-07 2.20570292753706e-06 1665 1159.27272727273 1120 2.37489867331409e-08 223 1.88583659658828 2.30017549693384 1 3.89912798957196 1120 2387 867 1997 223 1255 1663 360 1664 758 458 944 M427 CHESLER_BRAIN_HIGHEST_GENETIC_VARIANCE http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_HIGHEST_GENETIC_VARIANCE.html Neurologically relevant transcripts with highest variance accounted for by mouse strain (genotype) differences. 15711545 30/64 Jean Junior 7.07134214300725e-06 1.90329174509661e-05 735 1167.54545454545 1120 6.42851352013251e-07 731 2.13498480812191 2.37891062187094 1 3.68384669010652 731 1120 817 1793 1561 942 774 1017 1373 1287 1428 945 M16859 SENESE_HDAC3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC3_TARGETS_DN.html Genes down-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC3 [GeneID=8841] by RNAi. 17470557 322/789 Leona Saunders 4.40397475958909e-07 2.87423756593795e-06 1155 831.636363636364 1121 4.00361421925451e-08 28 1.64001185685624 1.85894394595306 1 3.32194012075854 1154 28 356 159 491 1584 1321 1476 1315 143 1121 946 M9673 ZHOU_INFLAMMATORY_RESPONSE_LPS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_INFLAMMATORY_RESPONSE_LPS_UP.html Genes up-regulated in macrophages by P.gingivalis LPS (lipopolysaccharide). 18025224 204/673 Arthur Liberzon 1.87725904708951e-07 1.81926618188875e-06 1470 1086 1123 1.70659927934178e-08 152 1.65626045489439 1.85478306203002 1 3.4751025533864 1467 249 338 811 152 1919 2006 1680 1881 320 1123 947 M2195 LEE_LIVER_CANCER_CIPROFIBRATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_CIPROFIBRATE_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) induced by ciprofibrate [PubChem=2763]. 15565109 42/99 Yujin Hoshida 2.65154291490701e-11 8.12100006487206e-10 1500 1071.90909090909 1123 2.41049355903542e-12 121 2.29229046273458 2.59577174535423 1 7.61678044485269 1497 121 147 260 1217 2420 2616 1123 282 141 1967 948 M2137 GREGORY_SYNTHETIC_LETHAL_WITH_IMATINIB http://www.broadinstitute.org/gsea/msigdb/cards/GREGORY_SYNTHETIC_LETHAL_WITH_IMATINIB.html Genes identified as synthetic lethal with imatinib [PubChem=5291] in RNAi screen in K562 cells (CML, chronic myelogenous leukemia). 20609354 111/291 Arthur Liberzon 3.73396636612864e-07 2.6805936035782e-06 1615 1190.72727272727 1124 3.39451545443546e-08 330 2.14359681557886 2.44755570349391 1 4.36571577618744 1613 927 548 919 330 2288 2048 1562 598 1124 1141 949 M7047 MCCOLLUM_GELDANAMYCIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCCOLLUM_GELDANAMYCIN_RESISTANCE_UP.html Genes up-regulated in A549GARS cells (lung cancer) resistant to the geldanamycin and 17-AAG [PubChem=5476289;6440175]. 18794130 5/28 Jessica Robertson 0.00112402298640211 0.00173075713619206 1115 1905.54545454545 1125 0.000112459193392021 641 1.78822534533944 1.78822534533944 1 1.80521128535663 1112 2259 4429 2647 4161 1125 641 1072 780 1876 859 950 M10280 ZHAN_LATE_DIFFERENTIATION_GENES_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_LATE_DIFFERENTIATION_GENES_UP.html B lymphocyte late differentiation genes (LDG): top genes up-regulated in plasma cells from tonsils (TPC) compared to those from bone marrow (BPC). 12393520 27/48 Arthur Liberzon 0.00133003042854504 0.00202230017291397 1190 1536.09090909091 1125 0.000120985017455584 901 1.70143122154456 1.86796790083965 1 1.67554511600589 1188 1835 1068 2166 3234 955 1125 1051 2437 901 937 951 M594 REACTOME_SIGNALING_BY_NOTCH4 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH4.html Genes involved in Signaling by NOTCH4 8/16 Reactome 1.21823799057072e-05 2.96722441807461e-05 2395 1849.72727272727 1127 1.21824466908936e-06 67 2.62338261184033 3.0671270605586 1 4.34163885823315 2391 781 3934 280 2045 4323 4340 292 67 1127 767 952 M604 REACTOME_SIGNALING_BY_NOTCH2 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH2.html Genes involved in Signaling by NOTCH2 8/16 Reactome 1.21823799057072e-05 2.96722441807461e-05 2395 1850.90909090909 1128 1.21824466908936e-06 68 2.62338261184033 3.0671270605586 1 4.34163885823315 2392 782 3937 281 2046 4324 4341 293 68 1128 768 953 M15804 TURJANSKI_MAPK1_AND_MAPK2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TURJANSKI_MAPK1_AND_MAPK2_TARGETS.html Examples of transcription factors whose activities are regulated by MAPK1 and MAPK3 [GeneID=5594;5595] phosphorylation. 17496919 9/17 Arthur Liberzon 4.41998261165198e-06 1.31839837798862e-05 1130 1676.45454545455 1128 4.41999140298743e-07 55 3.42334574748382 3.42334574748382 1 6.10640610761098 1128 3032 4200 2150 2881 1016 413 195 55 2575 796 954 M596 HASINA_NOL7_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HASINA_NOL7_TARGETS_DN.html Genes down-regulated in SiHa cells (cervical carcinoma) by stable expression of NOL7 [GeneID=51406] off a plasmid vector. 16205646 9/25 Leona Saunders 4.13831835813522e-05 8.48315653249889e-05 920 1494 1128 4.13839542570986e-06 348 1.68796319272882 1.73511774775858 1 2.5120630203763 916 1618 4282 1738 3020 960 630 551 1128 1243 348 955 M13569 ZHAN_MULTIPLE_MYELOMA_LB_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_LB_DN.html Top 50 down-regulated genes in cluster LB of multiple myeloma samples belonging to the low bone disease group. 16728703 31/56 Arthur Liberzon 2.47696188123022e-06 8.53480041710536e-06 910 1328 1128 2.25178606365964e-07 471 1.3318270641857 1.33693446864206 1 2.46758891117354 909 471 1542 1943 1128 970 905 2445 1966 1684 645 956 M618 REACTOME_SIGNALING_BY_NOTCH3 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH3.html Genes involved in Signaling by NOTCH3 8/16 Reactome 1.25571935216769e-05 3.04098236912549e-05 2395 1852.18181818182 1129 1.25572644796404e-06 69 2.62338261184033 3.0671270605586 1 4.33141344227384 2393 783 3940 282 2047 4325 4342 295 69 1129 769 957 M100 PID_SHP2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SHP2_PATHWAY.html SHP2 signaling 18832364 38/91 Pathway Interaction Database 1.72441207092728e-06 6.71252655339338e-06 985 1209.63636363636 1131 1.56764856596705e-07 191 1.58431575001989 1.78362278735335 1 2.995801526129 984 1028 1443 1227 949 1131 1460 191 2387 1504 1002 958 M15762 RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_DN.html Neuroblastoma markers down-regulated in neuroblastoma cell lines expressing ESWR1-FLI1 [GeneID=2130;2313] fusion protein. 14973077 15/43 Kevin Vogelsang 0.000606138021593831 0.000967755628343678 705 1372.54545454545 1131 5.51186443217561e-05 451 2.19241968686264 2.52552514282279 1 2.41557179584402 705 1457 1131 2077 2908 882 451 897 1573 1992 1025 959 M979 REACTOME_N_GLYCAN_ANTENNAE_ELONGATION_IN_THE_MEDIAL_TRANS_GOLGI http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_N_GLYCAN_ANTENNAE_ELONGATION_IN_THE_MEDIAL_TRANS_GOLGI.html Genes involved in N-glycan antennae elongation in the medial/trans-Golgi 8/19 Reactome 1.854013821662e-07 1.81543270535505e-06 1000 1390.72727272727 1132 1.85401397634354e-08 42 1.32829986690275 1.32829986690275 1 2.78743293764112 997 1396 4067 1770 2192 514 263 42 2707 1132 218 960 M1309 GROSS_HYPOXIA_VIA_HIF1A_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_HIF1A_DN.html Genes down-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of HIF1A [GeneID=3091] by RNAi. 17704799 83/182 Jessica Robertson 4.85484693052195e-07 3.053666136433e-06 1135 1242.18181818182 1132 4.41349818351359e-08 437 1.74826832687542 2.08684186838832 1 3.52441392815001 1132 2735 929 1216 437 863 1514 1348 1912 784 794 961 M1129 MCBRYAN_TERMINAL_END_BUD_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_TERMINAL_END_BUD_UP.html The 'TEB profile genes': up-regulated during pubertal mammary gland development specifically in the TEB (terminal end bud) structures. 17486082 7/17 Arthur Liberzon 2.08309055975462e-05 4.68395506862292e-05 1140 1301.72727272727 1138 2.0831100867105e-06 81 3.75500722184762 3.86230560901065 1 5.94232586422272 1138 1661 4179 1276 1962 913 347 447 81 1500 815 962 M19523 HOFFMANN_LARGE_TO_SMALL_PRE_BII_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_LARGE_TO_SMALL_PRE_BII_LYMPHOCYTE_DN.html Genes down-regulated during differentiation from large pre-BII to small pre-BII lymphocyte. 11779835 60/133 Arthur Liberzon 1.51631969778604e-06 6.16259679429782e-06 950 1108.54545454545 1138 1.37847340262683e-07 301 1.71732319463593 1.87692993481051 1 3.27060956025479 948 301 760 1138 892 1395 1444 1349 1873 752 1342 963 M8342 CROONQUIST_IL6_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_IL6_DEPRIVATION_UP.html Genes up-regulated in the ANBL-6 cell line (multiple myeloma, MM) after withdrawal of IL6 [GeneID=3569]. 12791645 13/42 Arthur Liberzon 2.72804634837598e-06 9.11813494186151e-06 220 1139.63636363636 1139 2.48004521019709e-07 53 1.534254958843 1.534254958843 1 2.82654185614921 217 1139 1404 1946 2151 90 53 411 2682 2362 81 964 M2366 PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP http://www.broadinstitute.org/gsea/msigdb/cards/PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP.html Genes up-regulated in HEK-293 cells (fibroblast) upon knockdown of CTBP1 but not of SATB1 [GeneID=1487, 6304] by RNAi. 19103759 244/737 Arthur Liberzon 4.52310003122509e-07 2.91543971751317e-06 2605 1628.72727272727 1139 4.11190996468561e-08 413 1.69710085104275 1.92752317717345 1 3.43374267683844 2604 678 1126 794 413 4102 3062 1001 1660 1337 1139 965 M19580 KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS.html Pentose and glucuronate interconversions 8/32 KEGG 4.97318099274445e-07 3.09762857924374e-06 2515 1753.18181818182 1140 4.97318210570861e-08 20 2.51358994518971 -1.4732852061074 -1 5.06155709497505 2514 663 3785 321 480 3398 4268 1042 20 1654 1140 966 M18395 URS_ADIPOCYTE_DIFFERENTIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/URS_ADIPOCYTE_DIFFERENTIATION_DN.html Genes down-regulated in primary adipocytes compared to preadipocytes. 15051823 29/64 John Newman 4.0751884391792e-05 8.37870435421322e-05 780 1377.36363636364 1141 3.70478538930134e-06 500 2.20666747480846 2.23038447657694 1 3.28834983947369 780 1122 558 1141 2354 2062 1951 1985 868 500 1830 967 M11067 KENNY_CTNNB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KENNY_CTNNB1_TARGETS_UP.html Genes up-regulated in HC11 cells (mammary epithelium) by expression of constantly active CTNNB1 [GeneID=1499]. 15642117 32/72 Yujin Hoshida 1.87208050038435e-07 1.81926618188875e-06 1280 1326.81818181818 1143 1.7018915088075e-08 150 1.9019355458385 -1.81577143645841 -1 3.99056866486775 1278 3087 1143 2733 150 620 567 1270 2145 946 656 968 M5863 BOYLAN_MULTIPLE_MYELOMA_D_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_D_UP.html Genes up-regulated in group D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 52/121 Jessica Robertson 4.04457703891689e-07 2.7830966232547e-06 1145 1445.27272727273 1143 3.6768888931727e-08 363 1.35944097160545 1.51526614619541 1 2.76058132665694 1143 2189 2269 2869 363 389 452 1049 2561 2034 580 969 M15798 KEGG_MELANOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MELANOMA.html Melanoma 32/89 KEGG 9.44140709898002e-07 4.5792352259061e-06 1145 1289.27272727273 1144 8.58310104618934e-08 681 1.81052174842981 2.31842834187292 1 3.53345658002877 2049 1489 977 1144 697 2216 1311 681 741 1144 1733 970 M4974 REACTOME_BASIGIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BASIGIN_INTERACTIONS.html Genes involved in Basigin interactions 13/30 Reactome 1.00078395189874e-06 4.72749354697327e-06 1175 1292 1145 9.09804006506769e-08 511 1.55563612746441 1.3396895798842 1 3.02814718983786 1172 511 1441 956 721 1027 1145 3360 1767 953 1159 971 M2379 IKEDA_MIR30_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR30_TARGETS_UP.html Genes up-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-30 microRNA. 19188439 102/261 Arthur Liberzon 5.64455845270787e-06 1.59243834493613e-05 685 1376.63636363636 1145 5.13142994095533e-07 681 1.85675786255877 2.20982474298922 1 3.25633514819876 681 3442 1476 1669 1482 818 1113 1145 985 1462 870 972 M658 REACTOME_CHONDROITIN_SULFATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHONDROITIN_SULFATE_BIOSYNTHESIS.html Genes involved in Chondroitin sulfate biosynthesis 7/21 Reactome 1.23646735705007e-05 3.00211711665109e-05 275 1246 1149 1.2364742369358e-06 217 1.85606970191585 1.85606970191585 1 3.06830873844994 271 1149 3950 1239 1797 283 217 1413 1868 999 520 973 M9826 VANTVEER_BREAST_CANCER_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_METASTASIS_DN.html Genes whose expression is significantly and negatively correlated with poor breast cancer clinical outcome (defined as developing distant metastases in less than 5 years). 11823860 83/263 Jean Junior 5.79296935284678e-05 0.000114346480149284 2630 1519.27272727273 1150 5.26647445188999e-06 424 1.75805474637759 1.84718952398216 1 2.533049743169 424 2687 849 2626 2251 1231 1068 749 2627 1150 1050 974 M16026 VERRECCHIA_RESPONSE_TO_TGFB1_C1 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C1.html Cluster 1: ECM related genes up-regulated in dermal fibroblasts within 30 min after TGFB1 [GeneID=7040] addition, and which kept increasing with time. 11279127 35/82 John Newman 4.22061831704755e-07 2.82649481163302e-06 1155 976.727272727273 1153 3.83692647887066e-08 322 1.70591606772329 1.68950250458001 1 3.45996901563444 1153 858 1395 798 383 853 1174 1220 1277 1311 322 975 M13247 BIOCARTA_TCYTOTOXIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCYTOTOXIC_PATHWAY.html T Cytotoxic Cell Surface Molecules 4/15 BioCarta 6.47588793320326e-06 1.77047904638218e-05 705 1587.18181818182 1154 6.47590680498669e-07 38 1.30592893983013 1.30592893983013 1 2.26833362512657 702 1154 3875 2604 2347 374 38 287 3925 1624 529 976 M6427 BIOCARTA_THELPER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_THELPER_PATHWAY.html T Helper Cell Surface Molecules 4/15 BioCarta 6.47588793320326e-06 1.77047904638218e-05 705 1588.18181818182 1155 6.47590680498669e-07 39 1.30592893983013 1.30592893983013 1 2.26833362512657 703 1155 3876 2605 2348 375 39 288 3926 1625 530 977 M2005 MIKKELSEN_ES_ICP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_ICP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing bivalent histone H3 methylation mark (H3K4me3 and H3K27me3) in embryonic stem cells (ES). 17603471 78/277 Arthur Liberzon 1.24658165979573e-09 2.667343222741e-08 1155 1316.27272727273 1155 1.13325605500189e-10 186 1.76309975129328 1.73635593476693 1 4.88109107496967 1155 288 211 567 777 2159 2086 3131 1550 186 2369 978 M2303 VANDESLUIS_NORMAL_EMBRYOS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_NORMAL_EMBRYOS_UP.html Genes up-regulated in normal 9.5 days post coitus (dpc) embryos compared to normal 8.5 dpc and 9.5 dpc embryos. 17371845 4/13 Arthur Liberzon 6.48438823274239e-05 0.000126713274639828 945 1406.45454545455 1156 6.4845774533217e-06 49 5.02790383837703 5.02790383837703 1 7.16236489636363 945 1156 4645 311 2305 898 887 1389 49 1645 1241 979 M13479 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP.html Genes up-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 10 days after transduction. 16818636 96/350 Arthur Liberzon 2.10199475551984e-08 3.283315808122e-07 280 1233.81818181818 1158 1.91090434145763e-09 182 1.73073692737204 -1.37440610623329 -1 4.10178010668561 1793 278 278 268 356 3220 2601 1158 1375 182 2063 980 M12143 CHESLER_BRAIN_D6MIT150_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_D6MIT150_QTL_CIS.html Cis-regulatory QTLs (quantitative trait loci) found at the D6Mit150 region. 15711545 3/16 Jean Junior 8.1822606543767e-06 2.13604865885288e-05 1080 1682.72727272727 1158 8.18229078175807e-07 170 1.25416119826726 1.25416119826726 1 2.14104429422852 1077 1158 4365 2135 2495 642 432 1112 2459 2465 170 981 M215 LIU_VAV3_PROSTATE_CARCINOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_VAV3_PROSTATE_CARCINOGENESIS_UP.html Selected genes up-regulated in prostate tumors developed by transgenic mice overexpressing VAV3 [GeneID=10451] in prostate epithelium. 18676865 80/208 Jessica Robertson 1.0744928218213e-11 3.52103032381441e-10 1130 1316.36363636364 1159 9.76811656205948e-13 137 2.27235721700839 2.31342959423803 1 7.85200710547187 1130 694 137 952 1174 2222 1731 2424 1159 318 2539 982 M19675 FARMER_BREAST_CANCER_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_3.html Cluster 3: selected apocrine, basal and hypoxia genes clustered together across breast cancer samples. 15897907 13/23 Arthur Liberzon 2.82423278292998e-06 9.36613929285908e-06 1845 1097 1159 2.56748764411202e-07 185 1.9232236663634 -2.0971182540387 -1 3.53494177295814 1841 185 1159 1122 1198 593 1323 1657 941 1285 763 983 M15193 GRUETZMANN_PANCREATIC_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRUETZMANN_PANCREATIC_CANCER_UP.html Genes up-regulated in pancreatic ductal adenocarcinoma (PDAC) identified in a meta analysis across four independent studies. 15897887 318/686 Leona Saunders 5.74155143045232e-06 1.6168816107632e-05 980 1192.09090909091 1160 5.2196058316233e-07 630 1.61406911854623 1.72295989986037 1 2.82681063901365 980 1160 735 630 1485 1465 931 774 2226 1434 1293 984 M17778 DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_DN.html Genes down-regulated in CD34+ [GeneID=947] cells isolated from bone marrow of CML (chronic myelogenous leukemia) patients, compared to those from normal donors. 17252012 84/301 Leona Saunders 2.59941416558282e-06 8.78849551220857e-06 1200 1100.81818181818 1162 2.36310657902784e-07 248 1.89063528784692 2.17111641691811 1 3.49414896596654 1200 2188 658 759 1162 1471 1513 248 1231 706 973 985 M5754 SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_2FC_DN http://www.broadinstitute.org/gsea/msigdb/cards/SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_2FC_DN.html Genes down-regulated more than two-fold in lymphoblastoid cell lines from European population compared to those from Asian population. 17206142 12/30 Leona Saunders 3.83231516126361e-06 1.18301902804225e-05 735 1208.63636363636 1162 3.48392894275011e-07 361 1.748858995861 1.67352085228892 1 3.14961403411541 732 1058 1722 2029 1321 710 361 482 2122 1596 1162 986 M11513 SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_DN http://www.broadinstitute.org/gsea/msigdb/cards/SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_DN.html Genes down-regulated in MCF10A cells (breast cancer) grown at low (mesenchymal phenotype) compared to those grown at high (epithelial, basal-like phenotype) confluency. 18281472 143/351 Jessica Robertson 7.62194187317529e-09 1.32774794117842e-07 2300 1652.27272727273 1162 6.92903809052876e-10 256 2.08177698621697 2.47664952797948 1 5.23293301185887 2296 1089 256 301 1405 4204 3334 798 1162 697 2633 987 M10487 HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_DN.html Genes down-regulated during differentiation from small pre-BII to immature B lymphocyte. 11779835 49/114 Arthur Liberzon 0.00012293215370551 0.000222588899638339 835 1494.18181818182 1163 1.11762748615237e-05 612 2.05603975020354 2.18880276116576 1 2.74498872713169 832 2857 1163 1968 2844 993 1038 612 1433 1885 811 988 M1285 SCHMAHL_PDGF_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/SCHMAHL_PDGF_SIGNALING.html These genes form a a network that controls specific processes downstream of PDGF signaling. 17143286 5/11 Leona Saunders 3.41033236937426e-05 7.18561937180206e-05 1045 1450.54545454545 1164 3.4103847071556e-06 420 1.72792655443274 1.96915691307358 1 2.61707171549472 1041 1513 4291 1727 2219 718 1043 420 1174 1164 646 989 M19208 RADAEVA_RESPONSE_TO_IFNA1_DN http://www.broadinstitute.org/gsea/msigdb/cards/RADAEVA_RESPONSE_TO_IFNA1_DN.html Genes down-regulated in primary hepatocytes and Hep3B (hepatocyte) cells in response to IFNA [GeneID=3439]. 11910354 6/16 Yujin Hoshida 1.10990938254172e-06 5.06923525008821e-06 1425 1427.72727272727 1164 1.10990993689658e-07 586 1.12520053805534 -1.26648621854556 -1 2.17780939196922 1425 899 4382 1427 791 1164 1094 586 1768 1323 846 990 M13883 BIOCARTA_MPR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MPR_PATHWAY.html How Progesterone Initiates Oocyte Membrane 26/66 BioCarta 1.5653635914742e-05 3.66581398783014e-05 780 1317 1165 1.42306793599962e-06 431 1.73521946443198 1.95249571941105 1 2.81351032483892 777 1198 1949 848 1853 825 688 1254 431 3499 1165 991 M13944 GOZGIT_ESR1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GOZGIT_ESR1_TARGETS_UP.html Genes up-regulated in TMX2-28 cells (breast cancer) which do not express ESR1 [GeneID=2099]) compared to the parental MCF7 cells which do. 17726467 82/244 Arthur Liberzon 1.37960413470234e-09 2.89570442442327e-08 1670 1198.09090909091 1166 1.25418557778862e-10 163 1.88769858888829 2.15653205912573 1 5.2014232469246 1668 564 214 316 163 2873 1532 1901 1166 461 2321 992 M12227 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_5 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_5.html Amplification hot spot 5: colocolized fragile sites and cancer genes in the 17q22-q25 region. 16751803 3/7 Arthur Liberzon 6.77302489734975e-06 1.83990693733223e-05 1270 1542 1166 6.77304554067813e-07 8 1.48962880236821 1.48962880236821 1 2.57831525502249 1266 910 4233 1166 1588 857 760 2834 8 2458 882 993 M14215 HOFMANN_MYELODYSPLASTIC_SYNDROM_HIGH_RISK_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_HIGH_RISK_UP.html Genes up-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with high risk of myelodysplastic syndrome (MDS) compared with healthy controls. 12411319 5/15 Arthur Liberzon 1.60003435489152e-07 1.65513487572223e-06 3385 1832.45454545455 1167 1.60003447009648e-08 57 1.65552969502753 -1.87520134505815 -1 3.49841809883266 3383 210 4541 603 135 2660 4025 1075 57 1167 2301 994 M17966 VALK_AML_WITH_T_8_21_TRANSLOCATION http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_WITH_T_8_21_TRANSLOCATION.html Genes that best predicted acute myeloid leukemia (AML) with the t(8;21) translocation producing the AML1-ETO fusion [GeneID=861;862]. 15084694 5/9 Jessica Robertson 1.47046918231504e-06 6.06035056141449e-06 1350 1313.09090909091 1168 1.47047015534177e-07 129 3.10729465707181 4.13225032466414 1 5.92603666359682 1346 988 4560 1509 2517 657 1231 129 136 1168 203 995 M2520 RAO_BOUND_BY_SALL4_ISOFORM_B http://www.broadinstitute.org/gsea/msigdb/cards/RAO_BOUND_BY_SALL4_ISOFORM_B.html Loci bound exclusively by SALL4 [GeneID=57167] isoform b in ES cells (embryonic stem). 20837710 357/939 Arthur Liberzon 1.84476862670012e-06 6.9883474411615e-06 1170 1189.81818181818 1168 1.67706379417998e-07 197 1.61741670479777 1.88943931724781 1 3.04805317052649 1168 1992 1244 1140 985 930 1381 514 1766 1771 197 996 M13380 KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION.html Neuroactive ligand-receptor interaction 55/344 KEGG 1.13791739548851e-05 2.80498733048877e-05 795 1660.63636363636 1170 1.03447571021838e-06 587 2.30591544660841 2.39553558396285 1 3.83682043560797 793 3310 587 3688 1734 995 1170 1540 2465 852 1133 997 M521 BROWNE_HCMV_INFECTION_2HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_2HR_DN.html Genes down-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 2 h time point that were not down-regulated at the previous time point, 1 h. 11711622 33/89 Arthur Liberzon 1.02054641014917e-05 2.55965683695145e-05 440 1315.54545454545 1171 9.27773767580812e-07 180 1.94029391254813 2.04381412666648 1 3.25665281491306 439 2891 1171 2520 2274 535 402 484 2103 1472 180 998 M950 ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN.html Genes up-regulated in A549 cells (lung carcinoma) upon infection with RSV (respiratory syncytial virus) and down-regulated by further treatment with ribavirin [PubChem=5064]. 12719586 37/97 John Newman 1.38491203794334e-06 5.85372787868602e-06 1075 1382.27272727273 1172 1.25901173613983e-07 566 1.5348433791276 1.58316339313686 1 2.93560860776148 1075 2502 1776 1403 846 688 653 1172 2390 2134 566 999 M9379 REACTOME_SIGNAL_AMPLIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_AMPLIFICATION.html Genes involved in Signal amplification 13/36 Reactome 1.19892017688291e-07 1.38377831253038e-06 2650 1741.90909090909 1173 1.08992749292701e-08 72 1.69732343340848 1.59933417088086 1 3.63498334090058 2650 183 1048 826 72 2540 2300 3581 1173 954 3834 1000 M8583 STEIN_ESTROGEN_RESPONSE_NOT_VIA_ESRRA http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESTROGEN_RESPONSE_NOT_VIA_ESRRA.html Genes up-regulated by estradiol [PubChem=5757] and not modulated by ESRRA [GeneID=2101] in MCF-7 cells (breast cancer). 18974123 12/24 Arthur Liberzon 0.00039297261250879 0.000647720598739427 715 1326.54545454545 1173 3.57311658521809e-05 401 1.59289760136544 1.77440000492565 1 1.85655929515437 715 1935 1919 1865 2722 899 777 1007 401 1179 1173 1001 M2012 DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP.html Genes up-regulated in mARMS (molecular ARMS) compared to the mERMS (molecular ERMS) class of rhabdomyosarcoma tumors. 16849537 207/551 Arthur Liberzon 6.44452142693005e-07 3.62335367154678e-06 1175 1246.09090909091 1174 5.85865755885679e-08 356 1.76396049092448 1.92532746356299 1 3.50814868526197 1174 3411 1720 1480 543 576 1087 356 1395 1586 379 1002 M5409 MOROSETTI_FACIOSCAPULOHUMERAL_MUSCULAR_DISTROPHY_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOROSETTI_FACIOSCAPULOHUMERAL_MUSCULAR_DISTROPHY_UP.html Genes up-regulated in FSHD (facioscapulohumeral muscular dystrophy) mesoangioblasts. 17761758 15/36 Arthur Liberzon 0.000342212914725307 0.000570033202349028 320 1263.27272727273 1174 3.11151052720753e-05 224 1.8566462280732 1.8566462280732 1 2.20162132126987 316 2058 1174 1659 2951 298 224 1253 2169 1095 699 1003 M3278 DE_YY1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DE_YY1_TARGETS_DN.html Genes down-regulated in SaOS-2 cells (osteosarcoma) upon knockdown of YY1 [GeneID=7528] by RNAi. 18339860 74/162 Jessica Robertson 1.26077003686045e-06 5.54746019276978e-06 815 1512.72727272727 1175 1.14615523579973e-07 804 1.83281578735608 1.85355069210444 1 3.52115903651681 812 3764 1175 2111 804 893 844 1363 2359 1564 951 1004 M17837 DASU_IL6_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/DASU_IL6_SIGNALING_DN.html Genes down-regulated in normal fibroblasts in response to IL6 [GeneID=3569]. 15095275 9/15 Arthur Liberzon 1.58536308279459e-05 3.70894228955339e-05 1175 1789.18181818182 1175 1.58537439310062e-06 306 2.60184155098283 2.60184155098283 1 4.21383313832772 1175 2486 4614 2474 3757 1053 975 322 306 1827 692 1005 M10183 BIOCARTA_RELA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RELA_PATHWAY.html Acetylation and Deacetylation of RelA in The Nucleus 10/19 BioCarta 3.94456640575445e-06 1.2084566496517e-05 1190 1115.63636363636 1179 3.58597588938139e-07 274 1.36845135814058 -1.45475883273982 -1 2.45989592770162 1187 660 2278 1350 1332 694 1179 725 274 1957 636 1006 M12490 ONKEN_UVEAL_MELANOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONKEN_UVEAL_MELANOMA_UP.html Genes up-regulated in uveal melanoma: class 2 vs class 1 tumors. 16651410 534/1255 Arthur Liberzon 1.81242602935743e-06 6.92742934222589e-06 1005 1544.09090909091 1180 1.81242750755878e-07 584 1.48978753693842 1.72684702038046 1 2.80960414252324 1005 2261 4109 1332 1024 1070 1180 824 2190 1406 584 1007 M16842 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_DN.html Genes down-regulated in reverted NIH3T3 cells (fibroblasts transformed by activated KRAS [GeneID=3845] which then reverted to normal cells upon stable over-expression of a dominant negative form of CDC25 [GeneID=5923]) vs normal fibroblasts. 16607279 140/271 Lauren Kazmierski 2.55210860981623e-06 8.66528384925486e-06 530 1114.90909090909 1180 2.32010142763001e-07 56 1.58310560691405 1.79359004696152 1 2.92934088470489 1180 56 530 528 1149 2114 1754 1507 1357 428 1661 1008 M14601 CAIRO_HEPATOBLASTOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_HEPATOBLASTOMA_UP.html Genes up-regulated in hepatoblastoma samples compared to normal liver tissue. 19061838 130/338 Arthur Liberzon 2.59311291831199e-06 8.77986064682803e-06 1010 1302 1181 2.35737815889756e-07 496 1.96215226117681 2.26185371818884 1 3.62662816669821 1007 3176 1181 1256 1160 1204 1154 496 1456 1544 688 1009 M15615 DER_IFN_GAMMA_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_GAMMA_RESPONSE_UP.html Genes up-regulated in HT1080 (fibrosarcoma) cells by treatment with interferon gamma for 6 h. 9861020 80/230 Yujin Hoshida 2.51854726255152e-06 8.58945594782853e-06 750 1161.81818181818 1182 2.28959104161315e-07 303 1.70625109885674 1.842987528605 1 3.1595870421457 747 571 1695 936 1143 1648 1404 303 1740 1411 1182 1010 M4342 BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G6, defined by unsupervised clustering. 17187432 53/123 Yujin Hoshida 2.72653444125688e-06 9.11813494186151e-06 1515 1109.45454545455 1182 2.47867074577194e-07 441 1.73551801819876 2.27423435788933 1 3.19732668460843 1512 441 1289 1048 1182 1347 1216 987 902 941 1339 1011 M4872 TARTE_PLASMA_CELL_VS_PLASMABLAST_UP http://www.broadinstitute.org/gsea/msigdb/cards/TARTE_PLASMA_CELL_VS_PLASMABLAST_UP.html Genes up-regulated in mature plasma cells compared with plasmablastic B lymphocytes. 12663452 289/952 Kate Stafford 3.69197341696963e-15 2.03536322728467e-13 1030 1133.72727272727 1183 3.3563394699724e-16 80 1.87431719551277 1.96538944873616 1 8.69501704349051 1028 401 80 339 1183 2157 2214 1868 1334 128 1739 1012 M16794 KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450.html Metabolism of xenobiotics by cytochrome P450 24/110 KEGG 1.78312522821991e-06 6.84895477003156e-06 3595 2169.45454545455 1186 1.62102424860454e-07 865 1.93425625398138 -1.51277703176257 -1 3.65133003242916 3591 1044 1119 865 965 2949 3118 3568 940 1186 4519 1013 M8475 WANG_ESOPHAGUS_CANCER_VS_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_ESOPHAGUS_CANCER_VS_NORMAL_UP.html Up-regulated genes specific to esophageal adenocarcinoma (EAC) relative to normal tissue. 16449976 112/224 Arthur Liberzon 2.53876373359408e-06 8.6395402001611e-06 520 1012.90909090909 1188 2.30796969390028e-07 421 1.55746394163187 1.75573867110511 1 2.88262978050856 518 557 421 574 1249 1463 1379 1188 1820 718 1255 1014 M11542 YE_METASTATIC_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/YE_METASTATIC_LIVER_CANCER.html Genes up-regulated in hepatocellular carcinoma (HCC) with intra-hepatic metastasis compared to the non-metastatic tumors. 12640447 24/71 Yujin Hoshida 0.000126514192746292 0.000228193035877261 740 1532.27272727273 1188 1.15019517013034e-05 620 1.61325662113679 1.55095017787207 1 2.14746744141715 736 2948 1519 2101 2653 1054 928 621 2487 1188 620 1015 M2242 BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A.html Category A genes: p53-dependent genes whose expression in the absence of S389 phosphorylation is similar to loss of TP53 [GeneID=7157] in MEF (embryonic fibroblast) cells in response to UV-C irradiation. 18195040 488/1481 Arthur Liberzon 5.47810094645565e-20 4.75377426575763e-18 1310 886.818181818182 1188 4.98009176950513e-21 10 1.91717251302029 2.10225782812995 1 12.1395498578877 1310 10 53 32 69 2110 1670 1809 1188 80 1424 1016 M2414 PEDERSEN_TARGETS_OF_611CTF_ISOFORM_OF_ERBB2 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_TARGETS_OF_611CTF_ISOFORM_OF_ERBB2.html Genes up-regulated in MCF7 cells (breast cancer) more than three-fold by the truncated form 611-CTF of ERBB2 [GeneID=2064] and less than two-fold by the full-length ERBB2 [GeneID=2064]. 19364815 62/133 Arthur Liberzon 1.21062619072713e-06 5.41833269316841e-06 855 1106 1188 1.10056986992421e-07 663 1.98192619521814 2.22013517345569 1 3.81503618403307 854 1683 663 751 788 1374 1188 1549 1293 692 1331 1017 M811 REACTOME_ADP_SIGNALLING_THROUGH_P2RY1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADP_SIGNALLING_THROUGH_P2RY1.html Genes involved in ADP signalling through P2Y purinoceptor 1 12/29 Reactome 2.33867467341624e-07 2.09141784725735e-06 3335 2012.45454545455 1190 2.12606811093212e-08 186 1.85886164317123 1.85752872233376 1 3.8590548057855 3333 186 987 1120 195 3459 2958 3411 1190 854 4444 1018 M2122 VERHAAK_GLIOBLASTOMA_MESENCHYMAL http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_GLIOBLASTOMA_MESENCHYMAL.html Genes correlated with mesenchymal type of glioblastoma multiforme tumors. 20129251 156/399 Arthur Liberzon 1.64313470510051e-08 2.63689357126746e-07 1090 1074.18181818182 1190 1.49375883397523e-09 55 1.6407097289237 1.92114898290638 1 3.94552479789621 1088 55 273 1190 617 1804 1672 1367 1812 207 1731 1019 M17427 DOANE_BREAST_CANCER_CLASSES_UP http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_BREAST_CANCER_CLASSES_UP.html Genes up-regulated in ER(-) / PR(-) breast tumors (do not express ESR1 and PGR [GeneID=2099;5241]) with molecular similarity to ER(+) (class A) relative to the rest of the ER(-) / PR(-) samples (class B). 16491124 42/126 Arthur Liberzon 2.77142948314672e-06 9.22366374859769e-06 1800 1328.45454545455 1192 2.51948452221393e-07 411 2.04946103083864 -1.96031071965311 -1 3.77195685963454 1800 1106 823 851 1192 1482 2390 1933 411 707 1918 1020 M1936 MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED.html Genes with high-CpG-density promoters (HCP) that have no histone H3 methylation marks in neural precursor cells (NPC). 18600261 276/913 Jessica Robertson 1.00292053400962e-31 2.13622073744048e-29 3290 1806.90909090909 1192 9.11745940008744e-33 9 1.8833369995477 -1.82404052018728 -1 19.7369637066413 3286 29 21 367 293 4236 3531 3424 1192 9 3488 1021 M8215 IVANOVA_HEMATOPOIESIS_STEM_CELL_AND_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_STEM_CELL_AND_PROGENITOR.html Genes in the expression cluster 'HSC and Progenitors Shared': up-regulated in hematopoietic stem cells (HSC) and progenitors from adult bone marrow and fetal liver. 12228721 393/1015 John Newman 2.39910056171179e-07 2.12517679247286e-06 1015 1180.09090909091 1194 2.18100074848528e-08 199 1.55394363563112 1.74187560376224 1 3.22208542920388 1222 1576 964 1512 199 1194 1481 1013 2036 1014 770 1022 M1369 SCHAEFFER_SOX9_TARGETS_IN_PROSTATE_DEVELOPMENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_SOX9_TARGETS_IN_PROSTATE_DEVELOPMENT_DN.html Predicted targets of SOX9 [GeneID=6662] that are down-regulated during early prostate development. 18794802 38/77 Jessica Robertson 1.85105479362007e-05 4.23124037214812e-05 595 1331.81818181818 1195 1.68279124396953e-06 281 1.7045020374308 1.88719113623175 1 2.72489086850024 591 2501 1195 2170 2936 281 305 330 1846 2198 297 1023 M769 REACTOME_ELEVATION_OF_CYTOSOLIC_CA2_LEVELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ELEVATION_OF_CYTOSOLIC_CA2_LEVELS.html Genes involved in Elevation of cytosolic Ca2+ levels 4/9 Reactome 8.34079512086142e-07 4.22997466843686e-06 1770 1443.54545454545 1196 8.3407982514619e-08 213 1.65477661893236 1.77348772697233 1 3.25034148783975 1767 213 3999 1196 686 1358 733 2320 615 980 2012 1024 M10172 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_DN.html Genes from the yellow module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 20/32 Arthur Liberzon 4.58977332003296e-06 1.35952451186311e-05 1115 1340.90909090909 1196 4.17252990502197e-07 748 1.29492545853059 1.42736060224476 1 2.30351384941074 1111 748 2089 1905 1392 823 781 1248 2353 1196 1104 1025 M2378 IKEDA_MIR133_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR133_TARGETS_DN.html Genes down-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-133 microRNA. 19188439 3/11 Arthur Liberzon 4.56902620585272e-06 1.35423509175369e-05 1200 1810 1197 4.56903560008012e-07 198 1.88142245296776 1.88142245296776 1 3.34798447602103 1197 2032 4659 2547 3105 1011 955 198 812 2475 919 1026 M13061 BILD_E2F3_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/BILD_E2F3_ONCOGENIC_SIGNATURE.html Genes selected in supervised analyses to discriminate cells expressing E2F3 [GeneID=1871] from control cells expressing GFP. 16273092 147/390 Arthur Liberzon 6.00223768619106e-07 3.4681240194194e-06 1925 1471.09090909091 1200 5.45658120343283e-08 517 1.56763579378075 1.54702510888238 1 3.12859637697753 1923 921 1120 1033 517 1820 1200 2588 2132 691 2237 1027 M812 REACTOME_GPCR_DOWNSTREAM_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GPCR_DOWNSTREAM_SIGNALING.html Genes involved in GPCR downstream signaling 161/1312 Reactome 1.02007848771958e-07 1.22252884743068e-06 875 1325.72727272727 1204 9.27344122743428e-09 309 1.68896260229975 1.79157789851492 1 3.65029640716149 875 812 309 1859 441 1428 1204 2251 2979 539 1886 1028 M1581 RUAN_RESPONSE_TO_TNF_TROGLITAZONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TNF_TROGLITAZONE_UP.html Adipocyte abundant genes up-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to troglitazone [PubChem=5591] and TNF [GeneID=7124]. 12732648 16/42 John Newman 8.63421032213707e-07 4.29055244639812e-06 2530 1728.36363636364 1205 7.84928519159686e-08 175 2.28120512319156 -1.93732900618427 -1 4.47563408432919 2530 175 930 997 661 3250 2776 2817 1059 1205 2612 1029 M19976 HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_UP.html Genes up-regulated during differentiation of immature to mature B lymphocyte. 11779835 25/72 Arthur Liberzon 1.40296099282805e-06 5.88565372640309e-06 1215 1140.36363636364 1210 1.27541989773679e-07 221 1.51824387304177 1.49695927842582 1 2.90254875452089 1211 742 1422 1210 854 1007 899 221 2047 1570 1361 1030 M600 REACTOME_G_ALPHA_I_SIGNALLING_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_ALPHA_I_SIGNALLING_EVENTS.html Genes involved in G alpha (i) signalling events 46/229 Reactome 3.03655342002988e-06 9.89519424635606e-06 795 1347.18181818182 1212 2.76050691931414e-07 518 1.75914187848746 1.88654654992505 1 3.2180099217366 791 714 518 1817 1229 1212 937 1973 3295 577 1756 1031 M927 REACTOME_GABA_SYNTHESIS_RELEASE_REUPTAKE_AND_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GABA_SYNTHESIS_RELEASE_REUPTAKE_AND_DEGRADATION.html Genes involved in GABA synthesis, release, reuptake and degradation 11/36 Reactome 0.0002233104623692 0.000384294097195031 920 1570.72727272727 1212 2.03030120604342e-05 778 2.28299031984629 2.28299031984629 1 2.8500783078305 918 3295 1847 1434 2594 1073 1184 778 1212 2102 841 1032 M8516 BIOCARTA_PITX2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PITX2_PATHWAY.html Multi-step Regulation of Transcription by Pitx2 9/25 BioCarta 2.69631319628521e-06 9.03785667939379e-06 960 1788.36363636364 1213 2.69631646783798e-07 439 1.64178232586904 1.64178232586904 1 3.02694318191022 957 2645 3849 2886 1213 975 976 439 3409 1801 522 1033 M9118 IWANAGA_CARCINOGENESIS_BY_KRAS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_CARCINOGENESIS_BY_KRAS_UP.html Cluster 3: genes up-regulated in lung tissue samples from mice with tumor-bearing genotypes (activated KRAS [GeneID=3845] alone or together with inactivated PTEN [GeneID=5728]). 18281487 106/309 Jessica Robertson 1.34132534908909e-06 5.75590712988232e-06 1245 1252.54545454545 1214 1.21938742444266e-07 653 2.01403348410818 2.14004726863094 1 3.85751651357919 1322 2064 948 653 832 1241 875 2265 1214 1122 1242 1034 M13333 RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN.html Genes down-regulated in peripheral blood mononucleocytes by HGF [GeneID=3082] compared to those regulated by CSF2RB (GM-CSF) and IL4 [GeneID=1437;3565]. 16527888 163/368 Arthur Liberzon 2.45994941102562e-06 8.50724940226278e-06 1430 1274.90909090909 1214 2.23632014694915e-07 481 1.51947514088612 1.8414009916907 1 2.81604031939369 943 2037 1429 1135 1125 1079 1264 1214 1887 1430 481 1035 M10654 REACTOME_PYRIMIDINE_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRIMIDINE_CATABOLISM.html Genes involved in Pyrimidine catabolism 10/16 Reactome 1.37454609704359e-05 3.28293731434569e-05 900 1207.36363636364 1215 1.24959516835987e-06 745 2.03440730764281 2.43519131822848 1 3.33424361175304 900 1940 1251 1240 1802 978 984 1215 745 1361 865 1036 M692 REACTOME_HEPARAN_SULFATE_HEPARIN_HS_GAG_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HEPARAN_SULFATE_HEPARIN_HS_GAG_METABOLISM.html Genes involved in Heparan sulfate/heparin (HS-GAG) metabolism 21/53 Reactome 4.50512252956568e-05 9.13500829664421e-05 800 1566.63636363636 1217 4.09564980667497e-06 787 1.27092327335965 1.36305368577283 1 1.8764790951748 796 1206 2523 2204 2181 897 787 1440 1217 3162 820 1037 M1885 YOSHIMURA_MAPK8_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/YOSHIMURA_MAPK8_TARGETS_DN.html Genes down-regulated in vascular smooth muscle cells (VSMC) by MAPK8 (JNK1) [GeneID=5599]. 16311603 270/619 Jessica Robertson 4.71586283459758e-06 1.38375286430334e-05 1220 1275.63636363636 1217 4.28715722129905e-07 543 1.78911228322465 2.05161957188771 1 3.17759479312238 1217 2329 1313 1098 1409 969 1206 840 1662 1446 543 1038 M1097 GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP.html Genes up-regulated in ME-A cells (breast cancer) undergoing apoptosis upon serum starvation (5% to 0% FCS) for 22 hr. 17160024 419/1097 Arthur Liberzon 1.76713290152939e-06 6.80479964415993e-06 1605 1464.90909090909 1219 1.60648574633341e-07 568 1.6312185214558 1.90367542933255 1 3.08095515040655 1603 1624 568 1219 961 2913 2526 763 1984 789 1164 1039 M1796 ZHENG_GLIOBLASTOMA_PLASTICITY_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_GLIOBLASTOMA_PLASTICITY_UP.html The glioblastoma multiforme (GBM) plasticity signature: genes up-regulated in neural stem cells (NSC) with double knockout of TP53 and PTEN [GeneID=7157;5728] vs those with knockout of TP53 alone. 18948956 195/447 Jessica Robertson 1.48401098337699e-14 7.6418411737413e-13 350 1151.90909090909 1222 1.34910089397909e-15 86 1.8509930126801 1.93138099578469 1 8.19807790021839 348 1995 86 1202 705 1581 1222 2036 1907 243 1346 1040 M3464 VANTVEER_BREAST_CANCER_BRCA1_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_BRCA1_DN.html Down-regulated genes from the optimal set of 100 markers discriminating ER(-) breast cancer tumors by BRCA1 [GeneID=672] mutation status. 11823860 29/71 Arthur Liberzon 6.94582899777846e-07 3.80235451911096e-06 2030 1471.72727272727 1222 6.31439199155734e-08 383 1.88029163683876 2.22363920879735 1 3.72511372569449 2027 621 1031 1372 569 3075 2836 1874 383 1222 1179 1041 M12676 FOSTER_TOLERANT_MACROPHAGE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FOSTER_TOLERANT_MACROPHAGE_DN.html Class NT (non-tolerizeable) genes: induced during the first LPS stimulation and induced at equal or greater degree in tolerant macrophages. 17538624 288/651 Jessica Robertson 4.17310278979726e-07 2.81825276987931e-06 1175 1283.36363636364 1224 3.79373052852608e-08 377 1.43535022856564 1.50561238558245 1 2.91186801360074 1171 1329 778 1387 377 1224 1827 1607 2551 945 921 1042 M1987 GYORFFY_DOXORUBICIN_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/GYORFFY_DOXORUBICIN_RESISTANCE.html Genes associated with resistance to doxorubicin [PubChem=31703]. 16044152 29/77 Arthur Liberzon 1.60243083398465e-06 6.4234310419607e-06 1380 1371.90909090909 1224 1.4567563646915e-07 416 2.44521785466414 2.29023946720554 1 4.64077995159296 1379 863 828 1154 914 2220 2313 2402 416 1224 1378 1043 M2145 DEMAGALHAES_AGING_DN http://www.broadinstitute.org/gsea/msigdb/cards/DEMAGALHAES_AGING_DN.html Genes consistently underexpressed with age, based on meta-analysis of microarray data. 19189975 18/35 Joao Pedro de Magalhaes 0.0022690209265783 0.00335202776227804 605 1298.27272727273 1224 0.000206487683499908 605 2.12898520545241 2.55986121885254 1 1.92580857909239 605 1604 852 1224 3104 963 1266 1316 1336 1040 971 1044 M6327 BIOCARTA_CSK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CSK_PATHWAY.html Activation of Csk by cAMP-dependent Protein Kinase Inhibits Signaling through the T Cell Receptor 12/36 BioCarta 5.70530316170649e-05 0.00011275854329716 545 1367.45454545455 1225 5.18677374893156e-06 541 1.41851811736495 1.41851811736495 1 2.04698584799151 541 1225 1795 1564 2246 794 694 705 2264 2235 979 1045 M2450 PLASARI_TGFB1_SIGNALING_VIA_NFIC_1HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_SIGNALING_VIA_NFIC_1HR_UP.html Genes up-regulated after 1 h of TGFB1 [GeneID=7040] stimulation in MEF cells (embryonic fibroblast) with NFIC [GeneID=4782] knockout vs wild type MEFs. 19752192 20/57 Arthur Liberzon 4.29218211714702e-06 1.29013248242148e-05 680 1358 1225 3.90199135562028e-07 314 2.04998654190821 2.13346142373882 1 3.66372426623236 679 2659 1225 2848 1366 507 314 1280 1946 1202 912 1046 M16021 KORKOLA_TERATOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_TERATOMA_UP.html Genes from the 12p region that up-regulated in teratoma cells compared to normal testis. 16424014 10/25 Arthur Liberzon 2.26044569724381e-06 8.0072637846423e-06 1385 1428.45454545455 1228 2.0549527452721e-07 611 1.6985101019485 2.12871730335705 1 3.16417696793381 1385 1069 2114 2333 1084 1295 1021 611 872 2701 1228 1047 M19948 HOQUE_METHYLATED_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/HOQUE_METHYLATED_IN_CANCER.html Genes whose DNA was methylated both in primary tumors and across a panel of cancer cell lines. 18413733 25/73 Jessica Robertson 4.23707330372037e-07 2.82649481163302e-06 1230 1461.09090909091 1229 3.851885563415e-08 385 1.76996154072271 1.93621902529517 1 3.58986717210146 1229 1691 1042 2469 385 954 965 3132 1653 1569 983 1048 M1910 VANASSE_BCL2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANASSE_BCL2_TARGETS_DN.html Genes down-regulated in primary B lymphocytes engineered to overexpress BCL2 [GeneID=12043]. 15561778 46/141 Arthur Liberzon 1.67654897877568e-06 6.58533823515745e-06 2080 1758.27272727273 1229 1.52413659674627e-07 124 1.65827827809773 1.93726068854408 1 3.14069396388892 2079 124 653 698 937 4098 4469 1990 1229 369 2695 1049 M1451 NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN.html Top 100 probe sets contrubuting to the negative side of the 2nd principal component; associated with adipocytic differentiation. 17464315 43/131 Nikolaos Papanikolaou 1.15540777548782e-09 2.50659297959997e-08 570 1388.72727272727 1230 1.05037070554057e-10 208 2.00094017101308 2.34396619661785 1 5.55928958440046 566 942 208 1024 2683 1517 1230 2097 2793 486 1730 1050 M2742 LEE_LIVER_CANCER_MYC_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) induced by overexpression of MYC [GeneID=4609]. 15565109 37/99 Yujin Hoshida 6.39071890237602e-07 3.60371946769363e-06 4565 2319 1232 5.80974614436268e-08 540 2.14571114611565 -1.78837947824052 -1 4.26922172743956 4565 1189 1232 795 540 3930 3300 3688 597 1193 4480 1051 M8276 REACTOME_NUCLEAR_RECEPTOR_TRANSCRIPTION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEAR_RECEPTOR_TRANSCRIPTION_PATHWAY.html Genes involved in Nuclear Receptor transcription pathway 18/50 Reactome 1.35476536287568e-06 5.80295291630298e-06 1235 1312.36363636364 1235 1.23160563376747e-07 753 1.55142256421138 -1.72628129630618 -1 2.96946424485991 1235 753 1659 1766 834 1207 2088 1068 1083 1348 1395 1052 M1304 GROSS_HYPOXIA_VIA_ELK3_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_DN.html Genes down-regulated in SEND cells (skin endothelium) at hypoxia with ELK3 [GeneID=2004] knockdown by RNAi. 17704799 126/258 Jessica Robertson 2.46374451733272e-07 2.14593063349835e-06 1130 1446.18181818182 1235 2.23976799385776e-08 207 1.62733803230733 1.90177677096918 1 3.37175734972528 1127 2222 960 1221 207 2024 2069 1479 2443 921 1235 1053 M16384 XU_GH1_AUTOCRINE_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_GH1_AUTOCRINE_TARGETS_DN.html Genes down-regulated in MFCF-7 cells (breast cancer) upon stable autocrine expression of HG1 [GeneID=2688]. 15845533 102/237 John Newman 1.24999543000736e-07 1.41484989976195e-06 2060 1475.09090909091 1235 1.13635954639052e-08 78 1.58773388746269 1.91237146884531 1 3.39468976385876 2057 279 1235 616 78 3831 3035 1404 1506 1017 1168 1054 M2776 IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP.html Cluster 1: genes up-regulated in lung tissue samples from mice with oncogenic form of KRAS [GeneID=3845] and inactivated PTEN [GeneID=5728]. 18281487 119/300 Jessica Robertson 0.000110407937847623 0.000201782994053807 1210 1472.72727272727 1235 1.0037589009671e-05 600 1.99868097169931 2.26739156346495 1 2.69954604089376 1207 2833 809 2449 2538 1210 1235 600 1257 1341 721 1055 M6318 GRANDVAUX_IFN_RESPONSE_NOT_VIA_IRF3 http://www.broadinstitute.org/gsea/msigdb/cards/GRANDVAUX_IFN_RESPONSE_NOT_VIA_IRF3.html Genes up-regulated in Jurkat cells (T lymphocyte) by IFN1@, and IFNB1 [GeneID=3438;3456] but not by overexpression of a constitutively active form of IRF3 [GeneID=3661]. 11991981 15/27 Yujin Hoshida 1.17498059963664e-06 5.28743858032593e-06 855 1523.90909090909 1236 1.06816475197564e-07 727 1.04986479142245 1.16248508526267 1 2.0249743399143 852 879 2637 2211 781 907 727 1545 2375 2613 1236 1056 M17026 RIZKI_TUMOR_INVASIVENESS_3D_UP http://www.broadinstitute.org/gsea/msigdb/cards/RIZKI_TUMOR_INVASIVENESS_3D_UP.html Genes up-regulated in three-dimentional (3D) cultures of preinvasive (S3-C) vs invasive (T4-2) breast cancer cells. 18316601 148/374 Jessica Robertson 1.52727582949627e-07 1.61491818742336e-06 1270 1180.45454545455 1236 1.38843266865659e-08 101 1.578244562637 1.90482657551672 1 3.34126420812026 1267 1579 1236 967 101 1622 1112 662 1856 1770 813 1057 M19097 SWEET_LUNG_CANCER_KRAS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SWEET_LUNG_CANCER_KRAS_UP.html Genes up-regulated in the Kras2LA mouse lung cancer model with mutated KRAS [GeneID=3845]. 15608639 334/808 Arthur Liberzon 9.29901298030296e-07 4.52518701432489e-06 2625 1455.27272727273 1236 8.45365173712227e-08 668 1.65492677882065 -1.67333845683049 -1 3.2329130215563 2623 1236 739 1047 690 668 2690 1803 2204 997 1311 1058 M1610 CUI_TCF21_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/CUI_TCF21_TARGETS_2_UP.html All significantly up-regulated genes in kidney glomeruli isolated from TCF21 [Gene ID=6943] knockout mice. 16207825 290/664 John Newman 2.20307468125157e-11 6.92859594385561e-10 1050 1291.18181818182 1237 2.0027951647942e-12 143 1.91141769313802 2.11854504707154 1 6.39940701329428 1047 1237 143 852 607 2784 1816 1840 1310 219 2348 1059 M896 ZHAN_MULTIPLE_MYELOMA_SPIKED http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_SPIKED.html 'Spiked' genes: genes most highly up-regulated in multiple myeloma samples; were not differentially expressed as compared to the normal plasma cells. 11861292 9/30 Kevin Vogelsang 9.24996533560292e-05 0.000172005307788235 695 1578.81818181818 1238 9.2503503865248e-06 691 2.33404221192715 2.26930372965794 1 3.21166641371547 691 980 4386 946 2421 1068 766 1993 1632 1246 1238 1060 M267 PID_ANTHRAX_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ANTHRAX_PATHWAY.html Cellular roles of Anthrax toxin 18832364 9/18 Pathway Interaction Database 2.76176504134766e-07 2.26714713690475e-06 1505 1290.18181818182 1239 2.76176538457829e-08 50 2.48815506126795 2.37298337282834 1 5.13362015363476 1502 1942 3907 776 1977 1363 961 50 91 1239 384 1061 M9524 RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_DN.html Down-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: well vs moderately differentiated tumors. 18679425 99/229 Jessica Robertson 1.2469769500437e-06 5.50219772872391e-06 1815 1433.45454545455 1242 1.1336160516731e-07 337 1.90721757430274 2.10836405359829 1 3.66657827784756 1813 690 419 337 803 2766 2104 2908 1242 468 2218 1062 M2372 IKEDA_MIR1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR1_TARGETS_UP.html Genes up-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-1 microRNA. 19188439 40/76 Arthur Liberzon 1.52340580700196e-07 1.61491818742336e-06 230 901.181818181818 1243 1.38491446590118e-08 15 1.76909341248233 1.93095072211245 1 3.74530579114753 229 2193 1243 1292 1789 82 73 35 1627 1335 15 1063 M15672 RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP.html Up-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: moderately vs poorly differentiated tumors. 18679425 78/186 Jessica Robertson 8.98857482137082e-07 4.42441823665375e-06 1125 1341.45454545455 1244 8.17143499440833e-08 676 1.68885951000344 1.86545886581606 1 3.30523853458862 1121 1680 1101 2049 676 1381 948 1244 1941 871 1744 1064 M8689 CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_DN.html Top 200 marker genes down-regulated in the 'CTNNB1' subclass of hepatocellular carcinoma (HCC); characterized by activated CTNNB1 [GeneID=1499]. 18701503 113/315 Yujin Hoshida 2.14352172257245e-13 9.21517687337112e-12 655 1164.63636363636 1244 1.9486561114297e-14 104 1.97187275066112 2.32683540492533 1 7.95408094902012 652 1244 104 943 2399 1828 2025 436 1641 163 1376 1065 M15902 KEGG_GLYCEROLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCEROLIPID_METABOLISM.html Glycerolipid metabolism 22/70 KEGG 0.000259614375088724 0.000441740363713057 1600 1487.63636363636 1246 2.36040923948794e-05 626 2.04049214880247 -1.96952448862631 -1 2.50221759598481 1596 1125 1241 1902 2623 1230 2199 1246 626 830 1746 1066 M1298 GROSS_ELK3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_ELK3_TARGETS_UP.html Genes up-regulated in SEND cells (skin endothelium) at normal oxygen (normoxia) conditions after knockdown of ELK3 [GeneID=2004] by RNAi. 17704799 18/43 Jessica Robertson 6.06582012799108e-07 3.47495592160468e-06 1250 1306.45454545455 1246 5.51438345495834e-08 313 1.7043000001627 1.7043000001627 1 3.40081041654547 1246 1653 1489 2518 520 795 354 1033 2674 1776 313 1067 M453 MURAKAMI_UV_RESPONSE_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/MURAKAMI_UV_RESPONSE_6HR_UP.html Genes up-regulated in primary keratinocytes at 6 h after UVB irradiation. 11532376 39/71 John Newman 7.15468231374224e-08 9.33895301453931e-07 1195 1226.27272727273 1246 6.50425686038338e-09 30 1.70710309638214 1.8695428660113 1 3.76248550727366 1192 1594 1855 920 30 1246 1517 2140 502 1914 579 1068 M2292 ITO_PTTG1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ITO_PTTG1_TARGETS_DN.html Genes down-regulated in HSA/c and KYSE140 cells (esophageal squamous cell carcinoma, ESCC) after knockdown of PTTG1 [GeneID=9232] by RNAi. 18451147 12/17 Jessica Robertson 2.13069965953945e-06 7.68035277277066e-06 970 1376.36363636364 1247 1.93700156647685e-07 141 1.42964619073715 1.42964619073715 1 2.67276696657232 966 1614 2510 2218 1247 621 429 141 1862 2974 558 1069 M15066 LIU_CMYB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_CMYB_TARGETS_UP.html Genes up-regulated in MCF-7 cells (breast cancer) by overexpression of CMYB [GeneID=4602] off adenovirus vector. 16205643 124/304 Arthur Liberzon 2.64594573178584e-07 2.21828405955824e-06 1475 1227.18181818182 1253 2.40540550001316e-08 226 1.53389547760124 1.66312914352614 1 3.17007475455306 1118 1416 1474 1472 226 1043 1024 956 2179 1338 1253 1070 M1461 PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP http://www.broadinstitute.org/gsea/msigdb/cards/PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP.html Genes up-regulated in LEC (lymphatic endothelial cells) compared to BEC (blood endothelial cells). 12198161 96/224 Kevin Vogelsang 8.03570400917989e-12 2.72864557876935e-10 1215 1239.45454545455 1254 7.30518546291747e-13 132 1.91114245481479 2.14621507673297 1 6.68119702328729 563 1254 132 1502 1868 1442 1211 1211 2309 763 1379 1071 M12051 CHANG_IMMORTALIZED_BY_HPV31_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_IMMORTALIZED_BY_HPV31_DN.html Genes down-regulated in normal keratinocytes immortalized by infection with the high risk HPV31 (human papilloma virus) strain. 10756030 46/164 John Newman 1.20551220916742e-07 1.38796811109546e-06 2250 1427.27272727273 1255 1.09592025020426e-08 73 1.6740324477507 1.20229144667705 1 3.58430001774816 2249 128 1085 1255 73 1663 744 2392 2247 1192 2672 1072 M19768 LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT http://www.broadinstitute.org/gsea/msigdb/cards/LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT.html Genes downregulated in MCF10A cells (breast cancer) co-cultured with cancer-associated fibroblasts (CAF). 19074894 67/209 Jessica Robertson 1.75884942653516e-09 3.49235949692533e-08 4235 2308.27272727273 1257 1.59895402540121e-10 227 2.13312087899485 -2.11262903850176 -1 5.8142263220704 4235 1257 227 724 986 3545 4530 4644 1092 409 3742 1073 M1759 WANG_LSD1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_LSD1_TARGETS_UP.html Genes up-regulated after Cre-lox knockout of LSD1 [GeneID=23028] in pituitary. 17392792 14/34 Jessica Robertson 0.000208603092610364 0.00036123950183746 1485 1333.90909090909 1257 1.89657158996058e-05 537 2.16810872239261 2.46407707346558 1 2.72795378445553 1484 2244 1099 1036 2706 1342 1489 712 537 767 1257 1074 M1102 GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN.html Genes down-regulated in ME-A cells (breast cancer, sensitive to apoptotic stimuli) upon serum deprivation for 22 hr in the presence of medium concentrate (MC) from ME-C cells (breast cancer, resistant to apoptotic stimuli). 17160024 68/129 Arthur Liberzon 4.30833825567749e-06 1.29250147670325e-05 1260 1292.09090909091 1258 3.91667881170243e-07 426 2.03626026476194 2.05791441635961 1 3.63859972358612 1258 2333 592 1195 1368 1419 1131 2076 988 426 1427 1075 M1685 ZHONG_SECRETOME_OF_LUNG_CANCER_AND_MACROPHAGE http://www.broadinstitute.org/gsea/msigdb/cards/ZHONG_SECRETOME_OF_LUNG_CANCER_AND_MACROPHAGE.html Proteins secreted in co-culture of LKR-13 tumor cells (non-small cell lung cancer, NSCLC) and MHS stroma cells (macrophages). 18757440 67/143 Jessica Robertson 1.85572399885845e-07 1.81543270535505e-06 3420 2042.63636363636 1258 1.68702195944619e-08 147 2.32888494176634 -1.70142955896796 -1 4.88715745458177 3416 1424 818 1014 147 4645 4244 861 749 1258 3893 1076 M4034 YEGNASUBRAMANIAN_PROSTATE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/YEGNASUBRAMANIAN_PROSTATE_CANCER.html Genes expressed in at least one prostate cancer cell line but not in normal prostate epithelial cells or stromal cells 18974140 70/278 Leona Saunders 1.89767271337845e-06 7.13683333458381e-06 1405 1185.81818181818 1258 1.72515850024739e-07 629 1.89008379578261 -2.10932327243572 -1 3.55559115825523 1402 1258 1374 1741 997 675 1758 754 1423 1033 629 1077 M7343 LUI_THYROID_CANCER_CLUSTER_2 http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_CLUSTER_2.html Cluster 2: genes with similar expression profiles across follicular thyroid carcinoma (FTC) samples. 15608688 31/74 Leona Saunders 2.3438597550453e-06 8.20876443358915e-06 1260 1361.81818181818 1259 2.13078386561422e-07 332 1.79174895942324 1.70253194427371 1 3.33080375596296 1259 332 781 1066 1102 1578 1378 3071 1291 908 2214 1078 M16496 CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP.html Top 200 marker genes up-regulated in the 'CTNNB1' subclass of hepatocellular carcinoma (HCC); characterized by activated CTNNB1 [GeneID=1499]. 18701503 119/302 Yujin Hoshida 4.47174460270463e-07 2.90229850530109e-06 3170 1579.27272727273 1261 4.065223192397e-08 272 1.61799345761118 -1.39926284384254 -1 3.27484511520974 3167 272 586 638 407 3434 1971 1261 1517 446 3673 1079 M16587 SASSON_RESPONSE_TO_GONADOTROPHINS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SASSON_RESPONSE_TO_GONADOTROPHINS_UP.html Genes up-regulated in primary granulosa cells after stimulation with LH or FSH gonadotrophic hormones for 24 h. 15026540 75/157 Arthur Liberzon 5.65046932993843e-07 3.34613067568844e-06 1935 1407.45454545455 1263 5.13679161927523e-08 492 1.69446258461654 2.11120746573753 1 3.39134220648517 1934 1174 1558 971 492 3037 1541 819 1263 1052 1641 1080 M2098 MARTENS_TRETINOIN_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTENS_TRETINOIN_RESPONSE_UP.html Genes up-regulated in NB4 cells (acute promyelocytic leukemia, APL) in response to tretinoin [PubChem=444795]; based on Chip-seq data. 20159609 366/1518 Arthur Liberzon 1.53613109183323e-27 2.24947196760328e-25 1265 1139.18181818182 1265 1.39648281075747e-28 26 1.93297467880063 1.9239027229354 1 17.4150883062051 1265 225 31 514 241 2387 1537 2782 1348 26 2175 1081 M9611 MASRI_RESISTANCE_TO_TAMOXIFEN_AND_AROMATASE_INHIBITORS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MASRI_RESISTANCE_TO_TAMOXIFEN_AND_AROMATASE_INHIBITORS_UP.html Genes up-regulated in derivatives of MCF-7aro cells (breast cancer) that developed resistance to tamoxifen [PubChem=5376] or inhibitors of aromatase (CYP19A1) [GeneID=1588]. 18559539 6/31 Leona Saunders 1.63176470234273e-06 6.49104362918338e-06 3220 1878.45454545455 1266 1.63176590053919e-07 76 2.70598474331661 2.58310052450197 1 5.13119159460654 3217 787 4463 204 971 3633 2500 1266 76 549 2997 1082 M2397 SERVITJA_LIVER_HNF1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SERVITJA_LIVER_HNF1A_TARGETS_UP.html Genes up-regulated in liver tissue upon knockout of HNF1A [GeneID=6927]. 19289501 83/232 Arthur Liberzon 3.31854771507662e-06 1.05859187153499e-05 3325 2093 1267 3.016866109897e-07 307 1.69983727034891 1.8941165357031 1 3.09131583112747 3322 1171 435 1160 1267 4624 3446 1194 2267 307 3830 1083 M1828 MATZUK_MALE_REPRODUCTION_SERTOLI http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_MALE_REPRODUCTION_SERTOLI.html Genes important for Sertoli, peritubular, Leydig and interstitial cells, based on mouse models with male reproductive defects. 18989307 17/40 Jessica Robertson 1.29668847744989e-05 3.12565957064309e-05 760 1819.36363636364 1268 1.178814654768e-06 195 1.45522753329491 1.45522753329491 1 2.3963517762408 757 3778 2566 3573 3607 430 195 941 2689 1268 209 1084 M5149 MARTINELLI_IMMATURE_NEUTROPHIL_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINELLI_IMMATURE_NEUTROPHIL_DN.html Neutrophil-specific genes down-regulated in comparison of immature with mature neutrophils. 15302890 4/19 Arthur Liberzon 1.06079447380771e-05 2.63707315876017e-05 1220 1457.54545454545 1268 1.06079953762385e-06 339 1.77744672569667 2.08446168906865 1 2.9749173087223 1220 526 4531 1587 1743 1268 1448 1841 339 982 548 1085 M2588 SMIRNOV_RESPONSE_TO_IR_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_RESPONSE_TO_IR_6HR_UP.html Genes up-regulated in B lymphocytes at 6 h after exprosure to 10 Gy dose of ionizing radiation. 21844125 101/276 Itai Pashtan 2.25229449717767e-06 7.99432925967499e-06 1270 1372 1268 2.04754254819366e-07 451 2.02898133370672 2.30035239515693 1 3.780336917109 1268 1419 1112 1436 1083 1948 2074 1048 939 2314 451 1086 M17941 BIOCARTA_VIP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VIP_PATHWAY.html Neuropeptides VIP and PACAP inhibit the apoptosis of activated T cells 13/34 BioCarta 9.49029515842208e-07 4.5941656107816e-06 4675 2090.72727272727 1270 8.62754477483646e-08 153 1.66597625158812 1.30667909172303 1 3.25049732680342 4671 768 1683 654 699 3926 4376 1010 153 1270 3788 1087 M86 PID_ARF6_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF6_PATHWAY.html Arf6 signaling events 18832364 33/66 Pathway Interaction Database 1.02916071595088e-05 2.57482494124177e-05 680 1266.63636363636 1270 9.35605027635992e-07 201 1.74812509991443 1.62068365825178 1 2.93247077379138 676 1688 1270 2107 1705 468 201 1333 2540 1213 732 1088 M1980 SEKI_INFLAMMATORY_RESPONSE_LPS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SEKI_INFLAMMATORY_RESPONSE_LPS_DN.html Genes down-regulated in hepatic stellar cells after stimulation with bacterial lipopolysacharide (LPS). 17952090 16/30 Jessica Robertson 1.85816106425222e-06 7.01074295256513e-06 2630 1796 1270 1.68923875790145e-07 176 1.86137908547576 -2.09070182295206 -1 3.50685958074672 2626 176 609 1234 992 3275 4394 2018 1270 494 2668 1089 M6386 CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_4 http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_4.html The 'group 4 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 but not ERBB2 [GeneID=2099;2064]. 18794137 191/488 Jessica Robertson 2.00120937177673e-06 7.37818026447343e-06 1315 1330.54545454545 1272 1.81928290196399e-07 937 1.69425459586022 2.01311171021899 1 3.17825591678281 1315 1713 1272 1213 1027 1934 1387 1000 1701 937 1137 1090 M5516 VALK_AML_CLUSTER_12 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_12.html Top 40 genes from cluster 12 of acute myeloid leukemia (AML) expression profile; 89% of the samples are FAB M3 subtype, 95% bear the t(15;17) translocation, all have the PML-RARA fusion [GeneID=5371;5914]; indicate good survival. 15084694 16/47 Jessica Robertson 1.79614255421884e-07 1.78699023547123e-06 4095 1949.36363636364 1273 1.63285700078276e-08 140 1.62807978589381 -1.04320563019435 -1 3.42060134828538 4094 971 1246 1273 140 4385 4072 1416 681 916 2249 1091 M18117 XU_AKT1_TARGETS_48HR http://www.broadinstitute.org/gsea/msigdb/cards/XU_AKT1_TARGETS_48HR.html Genes up-regulated in DU-145 cells (prostate cancer) expressing a dominant negative form of AKT1 [GeneID=207] upon sham-treatment for 48 h (as a control for the HGF [GeneID=3082] experiments). 17099727 8/13 Arthur Liberzon 3.10693075460548e-06 1.00615601355088e-05 1285 1507.09090909091 1274 3.10693509847244e-07 479 1.52118463983174 1.54714219907657 1 2.77868692197213 1281 1753 4246 2241 1274 1214 1022 479 1321 787 960 1092 M8845 CHIN_BREAST_CANCER_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIN_BREAST_CANCER_COPY_NUMBER_DN.html Genes from common regions of losses observed in more than 15% of 148 primary breast cancer tumors. 17001317 10/23 Arthur Liberzon 2.28032462218729e-07 2.06580091022617e-06 3940 1990.45454545455 1276 2.07302259867776e-08 147 2.68135875239669 -1.74406924037379 -1 5.57183036348171 3939 892 1267 498 186 4652 4082 1276 147 1364 3592 1093 M19053 KYNG_DNA_DAMAGE_BY_4NQO_OR_GAMMA_RADIATION http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_4NQO_OR_GAMMA_RADIATION.html Genes responding to 4NQO treatment and gamma irradiation. 15897889 13/30 Jessica Robertson 3.16994775565068e-05 6.75615025590082e-05 685 1245.36363636364 1276 2.88181221080426e-06 162 2.0717761746358 2.0717761746358 1 3.15812601934475 685 2719 1787 2346 2065 352 162 548 1396 1276 363 1094 M856 REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE.html Genes involved in Phospholipase C-mediated cascade 21/61 Reactome 6.27241810780689e-07 3.55411744294838e-06 1280 1436.09090909091 1277 5.70219990557836e-08 472 1.43229539352462 1.43137476820838 1 2.85292287288749 1277 872 1399 1249 534 752 472 3617 2538 1613 1474 1095 M17340 DEBOSSCHER_NFKB_TARGETS_REPRESSED_BY_GLUCOCORTICOIDS http://www.broadinstitute.org/gsea/msigdb/cards/DEBOSSCHER_NFKB_TARGETS_REPRESSED_BY_GLUCOCORTICOIDS.html NF-kB-driven pro-inflammatory genes that are negatively regulated by glucocorticoids. 17072333 13/29 Arthur Liberzon 2.01432507325889e-05 4.55996487598607e-05 1045 1347.18181818182 1277 1.83122137882012e-06 603 1.91604541428686 1.76310796223687 1 3.04031573184136 1044 1387 746 2281 1924 1277 603 1298 2507 700 1052 1096 M11120 HASLINGER_B_CLL_WITH_MUTATED_VH_GENES http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_MUTATED_VH_GENES.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with mutations in the variable immunoglobulin veriable heavy chain (VH) genes. 15459216 15/44 Kevin Vogelsang 6.7428992266432e-05 0.000131272230062526 1290 1476.81818181818 1277 6.13009627480383e-06 735 2.13138470558526 2.3801156056305 1 3.02424719948987 1287 2056 1253 2435 2286 1257 1277 884 735 1991 784 1097 M7284 SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_UP http://www.broadinstitute.org/gsea/msigdb/cards/SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_UP.html Genes up-regulated in CT60/4 cells (breast cancer reverted to normal by transfer of chromosome 8p region) vs parental MDA-MB-231 cells (deleted chromosome 8p). 15580292 51/147 Arthur Liberzon 9.02922643478451e-06 2.31840849717262e-05 745 1213.18181818182 1279 8.20842135699355e-07 647 1.8114545739719 1.96607062216372 1 3.06887102735146 743 1268 647 1753 1651 1560 1324 768 1629 723 1279 1098 M9150 GRESHOCK_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRESHOCK_CANCER_COPY_NUMBER_UP.html Genes from common genomic gains observed in a meta analyis of copy number alterations across a panel of different cancer cell lines and tumor samples. 17440070 185/483 Jessica Robertson 3.9197263393341e-07 2.75100874391679e-06 1280 1599.90909090909 1279 3.56338821609953e-08 347 1.78446095930665 2.10955630055908 1 3.62694335961072 1279 3304 1202 1853 347 1953 1984 1208 1151 2290 1028 1099 M8604 HALMOS_CEBPA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HALMOS_CEBPA_TARGETS_DN.html Genes down-regulated in H358 cells (lung cancer) by inducible expression of CEBPA [GeneID=1050] off plasmid vector. 15205324 32/78 Kevin Vogelsang 2.0571578738182e-06 7.5193773765305e-06 1280 1263.36363636364 1280 1.8701452703736e-07 602 1.91114037445066 1.8125599288415 1 3.57936133896653 1280 1545 681 602 1043 2096 1806 1883 920 618 1423 1100 M1238 DAWSON_METHYLATED_IN_LYMPHOMA_TCL1 http://www.broadinstitute.org/gsea/msigdb/cards/DAWSON_METHYLATED_IN_LYMPHOMA_TCL1.html Genes hypermethylated in at least one of the lymphoma tumors of transgenic mice overexpressing TCL1 [GeneID=8115] in germinal center B lymphocytes. 17260020 36/94 Arthur Liberzon 4.26462444691763e-06 1.28514663397145e-05 1305 1285.81818181818 1289 3.87693883069827e-07 772 1.87713148814211 1.77143950134 1 3.35595253358455 1304 1541 1000 1289 1363 981 970 1965 1735 772 1224 1101 M16289 REACTOME_CYTOSOLIC_SULFONATION_OF_SMALL_MOLECULES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYTOSOLIC_SULFONATION_OF_SMALL_MOLECULES.html Genes involved in Cytosolic sulfonation of small molecules 2/18 Reactome 3.85031850405063e-06 1.18623224917694e-05 1460 1577.2 1289.5 4.27813899214935e-07 46 2.41144211048533 -2.41144211048533 -1 4.34185718812363 1459 1762 4087 NA 3136 1041 1120 192 46 2158 771 1102 M1966 MIKKELSEN_MEF_LCP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_LCP_WITH_H3K4ME3.html Genes with low-CpG-density promoters (LCP) bearing tri-methylation mark at H3K4 (H3K4me3) in MEF cells (embryonic fibroblasts). 18509334 101/230 Jessica Robertson 5.69929919436332e-06 1.60691432158764e-05 575 1197.27272727273 1290 5.18119450815224e-07 460 1.84310963719848 2.128098132011 1 3.22975150599152 571 817 460 1394 1873 1477 1195 1290 1603 589 1901 1103 M12892 SMID_BREAST_CANCER_LUMINAL_B_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_LUMINAL_B_UP.html Genes up-regulated in the luminal B subtype of breast cancer. 18451135 91/288 Jessica Robertson 3.55915944752635e-06 1.12009544466813e-05 3380 2203.54545454545 1291 3.23560473231514e-07 470 1.85635253428413 1.93741776240595 1 3.35931137461153 3378 1094 470 1107 1291 4651 2671 4292 1070 485 3730 1104 M19511 WANG_CISPLATIN_RESPONSE_AND_XPC_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_CISPLATIN_RESPONSE_AND_XPC_UP.html Genes up-regulated in fibroblasts with defective XPC [GeneID=7508] in response to cisplatin [PubChem=2767]. 15107491 140/404 John Newman 2.16825376771275e-08 3.37556051677805e-07 1295 2099.45454545455 1292 1.97113980825673e-09 279 2.0206304576068 2.34689476831298 1 4.77992896298237 3032 1166 279 1291 778 4543 3750 2702 1292 570 3691 1105 M1737 GAVIN_PDE3B_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_PDE3B_TARGETS.html Genes changed in peripheral regulatory T lymphocytes that depend on PDE3B [GeneID=5140]. 17220874 15/35 Jessica Robertson 8.28061942669672e-05 0.000156843098761119 730 1497.45454545455 1292 7.52811919894546e-06 550 2.28762105970354 2.28762105970354 1 3.18130181216786 728 2482 1292 1949 2798 1270 953 550 1409 1993 1048 1106 M5103 YAGI_AML_FAB_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_FAB_MARKERS.html Genes specifically expressed in FAB subtypes M2, M4, M5 and M7 of pediatric AML (acute myeloid leukemia). 12738660 140/403 Kevin Vogelsang 6.35060374227166e-06 1.74641602912471e-05 1295 1100.27272727273 1293 5.77329279476385e-07 217 1.88771810488302 2.25947881123151 1 3.28297326929289 1293 1581 543 660 1719 1344 1812 217 1410 653 871 1107 M707 WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_DN.html Genes down-regulated in mucinous ovarian carcinoma tumors of grades 1 and 2 compared to the normal ovarian survace epithelium tissue. 16467078 44/119 Arthur Liberzon 5.3748127546509e-06 1.53388383485348e-05 240 1122.45454545455 1294 4.88620535080287e-07 237 1.5501006838776 1.46268018877088 1 2.72774624117197 237 716 1515 1771 1463 351 249 2413 1769 1294 569 1108 M6467 REACTOME_OPIOID_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OPIOID_SIGNALLING.html Genes involved in Opioid Signalling 35/93 Reactome 2.73260307605619e-07 2.25439753774636e-06 1295 1439.09090909091 1295 2.48418492315526e-08 233 1.37701873417856 1.30624896767031 1 2.84233027607225 1295 607 1588 879 233 1203 903 3563 2289 1308 1962 1109 M2311 AZARE_NEOPLASTIC_TRANSFORMATION_BY_STAT3_DN http://www.broadinstitute.org/gsea/msigdb/cards/AZARE_NEOPLASTIC_TRANSFORMATION_BY_STAT3_DN.html Genes down-regulated in RWPE-1 cells (prostate cancer) upon expression of constitutively active form of STAT3 [GeneID=6774]. 17438134 7/19 Arthur Liberzon 4.50521909234431e-07 2.91061642551722e-06 1635 1529.63636363636 1295 4.50522000570953e-08 199 1.32788606235506 -1.49176358973772 -1 2.68705974589074 1631 199 4646 1105 443 1147 1701 1295 2217 1011 1431 1110 M1208 YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_DN http://www.broadinstitute.org/gsea/msigdb/cards/YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_DN.html Genes down-regulated in HUVEC cells (endothelium) by ETS1 [GeneID=2113] which were up-regulated by SP100 [GeneID=6672]. 15592518 64/206 Arthur Liberzon 3.36732341496052e-06 1.07050729460685e-05 1655 1454.27272727273 1296 3.06120779000183e-07 706 2.00106341839372 1.99848658065565 1 3.63556864915401 1655 706 908 933 1272 1984 2620 1296 1995 1339 1289 1111 M9065 KUNINGER_IGF1_VS_PDGFB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KUNINGER_IGF1_VS_PDGFB_TARGETS_UP.html Genes up-regulated in C2AS12 cells (myoblast) by IGF1 [GeneID=3479] vs PDGFB [GeneID=5155]. 15475267 55/160 John Newman 3.60124907033138e-06 1.12954840318426e-05 565 1294 1296 3.27386815031141e-07 564 1.94188986559314 2.13688239913428 1 3.51151161641989 564 1632 743 1876 1296 953 1046 1862 1381 1608 1273 1112 M16644 PARENT_MTOR_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/PARENT_MTOR_SIGNALING_DN.html Genes down-regulated in HepaRG cells (liver cancer) expressing constituvely active form of MTOR [GeneID=2475]. 17483347 33/81 Arthur Liberzon 5.86656594814115e-07 3.4235028683673e-06 3115 1541.54545454545 1297 5.33324319321133e-08 507 1.73772606116813 -1.9054280954774 -1 3.47162487844455 3113 609 1106 1382 507 2042 3546 1251 1448 656 1297 1113 M5624 KIM_MYCL1_AMPLIFICATION_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYCL1_AMPLIFICATION_TARGETS_DN.html Genes negatively correlated with amplifications of MYCL1 [GeneID=4610] in SCLC (small cell lung cancer) cell lines. 16116477 20/37 Arthur Liberzon 1.88293661591132e-07 1.81926618188875e-06 1605 1271 1298 1.71176070642561e-08 154 1.75950805218004 1.43593361905096 1 3.69173272654763 1604 1298 1999 609 154 1312 890 2131 856 2013 1115 1114 M1699 BAFNA_MUC4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BAFNA_MUC4_TARGETS_UP.html Genes up-regulated in NIH3T3 cells (fibroblast) engineered to stably express MUC4 [GeneID=4585]. 19010895 5/10 Leona Saunders 0.00132993998035564 0.00202230017291397 1140 1956.36363636364 1298 0.00013307365845716 534 1.5272062795912 -1.5272062795912 -1 1.50397088650256 1136 2181 4434 2643 3296 534 947 1077 1298 2910 1064 1115 M2155 MCBRYAN_PUBERTAL_BREAST_6_7WK_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_6_7WK_UP.html Genes up-regulated during pubertal mammary gland development between week 6 and 7. 17486082 138/343 Arthur Liberzon 3.19777186617126e-06 1.02846664137807e-05 910 1361.81818181818 1299 2.90706955840598e-07 910 1.60365210583937 1.60154158255928 1 2.92374365675627 910 1332 1480 1623 1250 1013 1259 1955 1770 1299 1089 1116 M5601 BROWNE_HCMV_INFECTION_20HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_20HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 20 h time point that were not down-regulated at the previous time point, 18 h. 11711622 78/203 John Newman 9.81552337296868e-05 0.00018151358534227 1150 1384.36363636364 1299 8.92360120896916e-06 581 1.61899231936728 1.91836229916605 1 2.21392189488553 1299 1585 1148 1258 2535 1424 1693 581 1645 1149 911 1117 M15657 SAGIV_CD24_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SAGIV_CD24_TARGETS_DN.html Genes down-regulated in HT29 cells (colon cancer) after knockdown of CD24 [GeneID=100133941] by both RNAi and monoclonal antibodies. 18413748 32/67 Jessica Robertson 2.3783957409204e-05 5.26958035080521e-05 855 1357.18181818182 1299 2.16220132171243e-06 596 1.33764308112829 1.46546267589963 1 2.09181375451694 853 729 1764 1518 1972 1616 925 596 2510 1147 1299 1118 M8825 DORN_ADENOVIRUS_INFECTION_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_24HR_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) 24 h after infection with adenovirus Ad12. 15681441 52/104 Arthur Liberzon 3.17045975516985e-05 6.75615025590082e-05 705 1291.81818181818 1299 2.88227767832741e-06 306 1.91077015670655 1.97469408084246 1 2.91269540719277 704 1771 1299 1580 2858 796 996 453 1709 1738 306 1119 M14127 HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP.html Genes up-regulated in multiple myeloma (MM) cell lines treated with both decitabine [PubChem=451668] TSA [PubChem=5562]. 18172295 310/881 Jessica Robertson 3.80351114757841e-07 2.69640744894893e-06 1665 1126.90909090909 1301 3.457738004687e-08 353 1.67467273281902 1.88281691025356 1 3.40912670995813 1301 1161 353 453 1324 1694 1665 1400 1665 370 1010 1120 M9032 MOHANKUMAR_TLX1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOHANKUMAR_TLX1_TARGETS_DN.html Down-regulated in MCF7 cells (breast cancer) by TLX1 (HOX11) [GeneID=3195]. 17213808 114/353 Arthur Liberzon 5.0153764562966e-11 1.45975491144136e-09 2030 1405.72727272727 1302 4.55943314219176e-12 154 2.20131484023441 2.42179191622076 1 7.10957040688269 2028 1245 154 266 1302 3272 2747 1466 763 200 2020 1121 M17434 LIN_APC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LIN_APC_TARGETS.html Genes up-regulated by forced expression of APC [GeneID=324] in the APC-deficient SW480 cell line (colon cancer). 11522623 69/156 Yujin Hoshida 4.2933402878491e-08 6.22866643617984e-07 2550 1400.09090909091 1303 3.90303670148583e-09 8 1.62033479136354 1.5719014880292 1 3.67542978761391 2549 576 1651 831 8 2218 1303 1986 1221 1012 2046 1122 M2164 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION.html Leukocyte transendothelial migration 64/141 KEGG 4.45160895780634e-09 8.08536417685292e-08 4075 1884.09090909091 1305 4.04691724255819e-10 104 2.18617063508895 -2.21459814596256 -1 5.66748566164069 4074 104 248 125 397 3675 2420 4215 1305 638 3524 1123 M28 PID_IL4_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL4_2PATHWAY.html IL4-mediated signaling events 18832364 49/106 Pathway Interaction Database 3.68244521010875e-06 1.14830687329376e-05 835 1240.72727272727 1305 3.34768306722055e-07 772 1.90467063781119 2.0426478090711 1 3.43922817710065 834 1022 772 1225 1305 1338 1436 1720 1537 950 1509 1124 M1325 MANTOVANI_NFKB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MANTOVANI_NFKB_TARGETS_UP.html NF-kB-controlled genes up-regulated in endothelial cells in response to viral GPCR protein. 17906691 36/77 Jessica Robertson 7.75031985981088e-06 2.04658167221209e-05 1305 1309.09090909091 1305 7.04577014848683e-07 497 1.6769976194363 1.47555609208378 1 2.87428107743578 1305 603 833 1201 1602 1706 1640 1962 1102 497 1949 1125 M2978 CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_LD_MTX_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_LD_MTX_DN.html Genes specifically down-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490] and low-dose methotrexate (LDMTX) [PubChem=4112]. 12704389 14/38 Jean Junior 0.000461294612530178 0.000750564775804311 855 1407.09090909091 1305 4.19446695360515e-05 439 2.51203892685887 -2.68349601925171 -1 2.86907358354157 851 1556 1305 2402 2749 439 485 1144 1634 1898 1015 1126 M1557 DELASERNA_MYOD_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DELASERNA_MYOD_TARGETS_UP.html Genes up-regulated in NIH 3T3 cells (fibroblasts) 24 h after inducing MyoD [GeneID=4654] differentiation program. 15870273 68/146 John Newman 2.52656668410195e-07 2.17979909250208e-06 2175 1513.54545454545 1306 2.2968790675117e-08 213 1.78997152763675 2.33979678016652 1 3.70427561498321 2173 579 1023 793 213 2503 1811 2065 1163 1306 3020 1127 M2230 BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP http://www.broadinstitute.org/gsea/msigdb/cards/BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP.html Genes bound by ESR1 [GeneID=2099] and up-regulated by estradiol [PubChem=5757] in MCF-7 cells (breast cancer). 18838536 130/310 Arthur Liberzon 3.76987516326775e-07 2.69293216693181e-06 4100 1905.27272727273 1306 3.42715982660548e-08 333 1.71438273496657 -1.5243513308791 -1 3.49031524389258 4099 1001 709 940 333 1561 3317 4026 1306 483 3183 1128 M11893 RAY_ALZHEIMERS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/RAY_ALZHEIMERS_DISEASE.html A biomarker of plasma signaling proteins that predicts clinical Alzheimer's diagnosis. 17934472 9/20 Jessica Robertson 6.53150273697823e-06 1.78360267048252e-05 1025 1628.45454545455 1307 6.53152193429524e-07 888 2.25142947233863 2.10586930877658 1 3.9079815406039 1024 2211 4528 1646 1566 1413 1307 1297 978 888 1055 1129 M12176 CAIRO_HEPATOBLASTOMA_CLASSES_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_HEPATOBLASTOMA_CLASSES_DN.html Genes down-regulated in robust Cluster 2 (rC2) of hepatoblastoma samples compared to those in the robust Cluster 1 (rC1). 19061838 125/372 Arthur Liberzon 4.00006046165224e-07 2.76872722648484e-06 845 1267.90909090909 1307 3.63641926267921e-08 360 1.55489336664721 1.70792780754731 1 3.15875913488309 843 414 704 1307 360 1736 1925 1437 2325 989 1907 1130 M5740 JAEGER_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JAEGER_METASTASIS_UP.html Genes up-regulated in metastases from malignant melanoma compared to the primary tumors. 17289871 26/79 Leona Saunders 5.44527071606911e-06 1.54927374471766e-05 1390 1294.54545454545 1308 4.95025835802808e-07 238 1.92865237947382 2.22754833070151 1 3.39083543027128 1388 1493 1037 760 1469 2466 2106 238 1308 1044 931 1131 M1717 ZHAN_VARIABLE_EARLY_DIFFERENTIATION_GENES_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_VARIABLE_EARLY_DIFFERENTIATION_GENES_UP.html The vEDG up-regulated set: most variable early differentiation genes (EDG) with similar expression patterns in tonsil B lymphocytes (TBC) and multiple myeloma (MM) cells compared to the plasma cells from tonsil (TPC) and bone marrow (BPC). 12393520 14/35 Arthur Liberzon 8.99946512105806e-05 0.000168080883050132 1310 1430.09090909091 1310 8.18166661836284e-06 799 1.68188979752782 1.55544281675028 1 2.3204601154953 799 1306 970 2124 2379 1095 831 1364 2174 1379 1310 1132 M1394 BIOCARTA_GATA3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GATA3_PATHWAY.html GATA3 participate in activating the Th2 cytokine genes expression 11/17 BioCarta 2.4891152631285e-06 8.55131533945759e-06 1050 1422.09090909091 1312 2.26283461759806e-07 284 1.12240317535159 1.1748842378175 1 2.07922707581585 1050 1312 2376 1871 1135 570 284 2104 1519 2813 609 1133 M873 REACTOME_ROLE_OF_SECOND_MESSENGERS_IN_NETRIN1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ROLE_OF_SECOND_MESSENGERS_IN_NETRIN1_SIGNALING.html Genes involved in Role of second messengers in netrin-1 signaling 4/13 Reactome 1.92579385054201e-05 4.38284117709561e-05 1315 1538.72727272727 1312 1.92581053981436e-06 105 2.00674952560799 -2.00674952560799 -1 3.19686271802653 1312 990 4043 2026 2215 1052 2373 349 105 1627 834 1134 M76 PID_P38_ALPHA_BETA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_ALPHA_BETA_PATHWAY.html Regulation of p38-alpha and p38-beta 18832364 21/37 Pathway Interaction Database 1.05100634917999e-07 1.25000399803488e-06 3055 1723.81818181818 1313 9.55460363081579e-09 63 1.44469810885192 -1.2711288101849 -1 3.11727887281897 3054 627 1536 448 63 2593 1313 4468 620 590 3650 1135 M1634 WENG_POR_DOSAGE http://www.broadinstitute.org/gsea/msigdb/cards/WENG_POR_DOSAGE.html Genes up-regulated in liver from mice with liver specific knockout of POR [GeneID=5447] vs mice with reduced expression of POR in all tissues. 16006652 17/69 John Newman 8.84333164884792e-07 4.3730726529055e-06 1490 1094.54545454545 1313 8.03939563963689e-08 320 1.83720900606848 2.19021424452947 1 3.59897524356692 1490 639 1380 1321 670 1313 1253 320 330 1705 1619 1136 M670 REACTOME_KERATAN_SULFATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KERATAN_SULFATE_BIOSYNTHESIS.html Genes involved in Keratan sulfate biosynthesis 13/27 Reactome 7.71435472567544e-06 2.04118951126567e-05 1330 1291.18181818182 1314 7.01307434216816e-07 515 2.01753568635484 2.27799317038786 1 3.45878942213307 1326 515 869 1608 1599 1554 1281 1636 1314 1272 1229 1137 M8236 KANG_CISPLATIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_CISPLATIN_RESISTANCE_DN.html Genes down-regulated in gastric cancer cell lines resistant to cisplatin [PubChem=2767]. 14734480 7/15 Arthur Liberzon 0.000107082631262863 0.000196011410194444 1315 1558.90909090909 1314 1.070877916233e-05 190 1.52406266961084 1.77762851966871 1 2.06551734826093 1314 986 4451 1821 2453 1318 593 1004 190 2274 744 1138 M14233 MARSON_FOXP3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_FOXP3_TARGETS_UP.html Genes up-regulated by FOXP3 [GeneID=50943] in both ex vivo and hybridoma cells. 17237765 49/108 Arthur Liberzon 1.81426256090068e-07 1.78961007243281e-06 2270 1534 1314 1.64932973683322e-08 141 1.61181036247354 1.89760592229097 1 3.38604438776871 2266 592 1472 926 141 2839 2090 1191 1009 1314 3034 1139 M2843 REACTOME_ACTIVATION_OF_NMDA_RECEPTOR_UPON_GLUTAMATE_BINDING_AND_POSTSYNAPTIC_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_NMDA_RECEPTOR_UPON_GLUTAMATE_BINDING_AND_POSTSYNAPTIC_EVENTS.html Genes involved in Activation of NMDA receptor upon glutamate binding and postsynaptic events 22/49 Reactome 1.8178710936364e-07 1.78961007243281e-06 1435 1563 1315 1.65261022168002e-08 143 1.17981774705976 1.05610298296211 1 2.47852684984274 1433 1202 3012 840 143 1082 1110 1858 1958 3240 1315 1140 M74 REACTOME_POST_NMDA_RECEPTOR_ACTIVATION_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POST_NMDA_RECEPTOR_ACTIVATION_EVENTS.html Genes involved in Post NMDA receptor activation events 22/45 Reactome 1.8178710936364e-07 1.78961007243281e-06 1435 1564 1316 1.65261022168002e-08 144 1.17981774705976 1.05610298296211 1 2.47852684984274 1434 1203 3013 841 144 1083 1111 1859 1959 3241 1316 1141 M1928 MIKKELSEN_PARTIALLY_REPROGRAMMED_TO_PLURIPOTENCY http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_PARTIALLY_REPROGRAMMED_TO_PLURIPOTENCY.html Genes up-regulated in cells that have been partially reprogrammed to pluripotency: comparison with the parental lineage-committed cell lines, fully reprogrammed stem cells, and embryonic stem cells. 18509334 4/12 Jessica Robertson 6.22235180863259e-06 1.72040678779681e-05 1135 1446.09090909091 1316 6.22236923164916e-07 11 2.11508332192064 2.75059800001026 1 3.68342734493238 1134 989 4551 327 1544 1316 1735 2070 11 1643 587 1142 M7988 BORCZUK_MALIGNANT_MESOTHELIOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/BORCZUK_MALIGNANT_MESOTHELIOMA_DN.html Genes down-regulated in biphasic (mixed) vs epithelial subtypes of malignant peritoneal mesothelioma. 16862182 60/198 Arthur Liberzon 6.80865201858819e-07 3.75356980695344e-06 885 1331.36363636364 1320 6.18968556887201e-08 112 1.47997598611226 1.50468164493729 1 2.93506774425417 882 112 902 1422 562 1320 1149 2177 2963 1404 1752 1143 M15844 DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_UP.html Genes exclusively up-regulated in fibroblasts expressing the TTD mutant form of ERCC3 [GeneID=2071], after UVC irradiation. 15608684 54/131 Arthur Liberzon 3.82927569482878e-06 1.18285998061751e-05 860 1298.27272727273 1320 3.48116578182289e-07 308 2.15264727648342 2.22563160108179 1 3.87686396732616 857 308 1062 1627 1320 2022 2322 639 1388 1566 1170 1144 M5718 NIKOLSKY_BREAST_CANCER_21Q22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_21Q22_AMPLICON.html Genes within amplicon 21q22 identified in a copy alterations study of 191 breast tumor samples. 19010930 6/21 Jessica Robertson 0.00239151428300081 0.00352520790504617 505 1629.81818181818 1321 0.000239409189122405 502 2.24176606477238 2.24176606477238 1 2.00989968054114 502 1809 4358 1951 3094 637 581 1193 1413 1321 1069 1145 M4270 KAYO_CALORIE_RESTRICTION_MUSCLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAYO_CALORIE_RESTRICTION_MUSCLE_DN.html Downregulated in the vastus lateralis muscle of middle aged rhesus monkeys subjected to caloric restriction since young adulthood vs age matched controls 11309484 70/169 John Newman 3.42305908214003e-07 2.53773838513687e-06 1325 1578.36363636364 1324 3.11187237704201e-08 307 1.69008984582886 1.76643326254854 1 3.45678260818227 1562 832 842 1324 307 2781 2865 2664 1940 922 1323 1146 M2276 KIM_PTEN_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_PTEN_TARGETS_UP.html Genes up-regulated in HCT116 cells (colorectal carcinoma) upon knockout of PTEN [GeneID=5728]. 17060456 12/23 Arthur Liberzon 1.53271777787453e-05 3.60015814893235e-05 1115 1485.72727272727 1326 1.39338950569875e-06 515 1.46971777946209 1.62083350722845 1 2.38723855961192 1113 2721 2320 2000 1844 679 527 1047 1326 2251 515 1147 M9257 KEGG_DRUG_METABOLISM_CYTOCHROME_P450 http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DRUG_METABOLISM_CYTOCHROME_P450.html Drug metabolism - cytochrome P450 24/122 KEGG 3.89469938260768e-06 1.19754339284118e-05 2730 1689.90909090909 1327 3.54064207043709e-07 163 1.99069789382421 -1.60394215728378 -1 3.58129846552638 2727 163 755 596 1327 2355 2467 3147 642 744 3666 1148 M14973 SENESE_HDAC1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC1_TARGETS_UP.html Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC1 [GeneID=3065] by RNAi. 17470557 286/714 Leona Saunders 1.74434460081152e-06 6.74979256763237e-06 1330 1341.63636363636 1327 1.58576907625075e-07 861 1.57349431530747 1.63006068221733 1 2.97395623950843 861 1523 1328 1408 953 1179 1328 1327 2630 1054 1167 1149 M6139 STARK_BRAIN_22Q11_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/STARK_BRAIN_22Q11_DELETION.html Genes located outside the microdeletion region in 22q11 which were differentially expressed in the same manner both in hyppocampus and prefrontal cortex. 18469815 6/17 Jessica Robertson 1.61007466987252e-05 3.7499055184009e-05 965 1603 1328 1.61008633552347e-06 716 1.13155685476341 1.21376501938688 1 1.83064884199602 965 1471 4340 1730 1893 979 873 1328 716 2061 1277 1150 M17359 XU_HGF_TARGETS_INDUCED_BY_AKT1_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_TARGETS_INDUCED_BY_AKT1_48HR_UP.html Genes up-regulated in DU-145 cells (prostate cancer) in the absence but not in the presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 19/37 Arthur Liberzon 1.1618765437464e-06 5.2401862213625e-06 595 1193.18181818182 1330 1.05625196123974e-07 17 1.85606830307508 1.70017744437143 1 3.58262092189975 595 2313 1330 2263 1690 236 17 502 2149 1452 578 1151 M12498 UEDA_PERIFERAL_CLOCK http://www.broadinstitute.org/gsea/msigdb/cards/UEDA_PERIFERAL_CLOCK.html Molecular timetable composed of 162 time-indicating genes (182 probes) in the peripheral (liver) clock. 15273285 124/267 Kate Stafford 2.05176486009894e-07 1.93870664292301e-06 1525 1284 1330 1.86524095586431e-08 166 1.67816095287086 1.88952028481306 1 3.50411342534678 1524 1718 1072 1330 166 1632 2114 1198 1972 776 622 1152 M7429 BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_24HR_DN.html Genes down-regulated in T98G cells (glioma, express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 24 h. 15980968 24/64 Arthur Liberzon 1.63644462608782e-06 6.49115128016012e-06 1330 1465.18181818182 1330 1.48767803939958e-07 632 1.41306414449825 1.588233462741 1 2.67950246567103 1330 1547 2238 2207 926 776 897 690 1996 2878 632 1153 M9874 OUYANG_PROSTATE_CANCER_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/OUYANG_PROSTATE_CANCER_MARKERS.html Mouse orthologs of human prostate cancer tumor markers which were deregulated in mice heterozygotic for both NKX3.1 and PTEN [GeneID=4824;5728]. 18381418 13/27 Jessica Robertson 1.62516722475413e-05 3.77340608904535e-05 2060 1504.63636363636 1331 1.47743566380881e-06 607 1.82645935321157 -1.30001592937067 -1 2.95306063068506 2056 885 1331 1954 1865 722 1166 3055 607 1277 1633 1154 M16932 CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_DN.html Top 200 marker genes down-regulated in the 'proliferation' subclass of hepatocellular carcinoma (HCC); characterized by increased proliferation, high levels of serum AFP [GeneID=174], and chromosomal instability. 18701503 87/313 Yujin Hoshida 8.29563499235811e-07 4.21381153484506e-06 3380 1994.27272727273 1332 7.54148920039151e-08 287 1.83311749648151 -1.55098280970182 -1 3.60175586303186 3377 287 920 1237 637 2105 3226 4587 1332 996 3233 1155 M14262 LU_TUMOR_VASCULATURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LU_TUMOR_VASCULATURE_DN.html Genes down-regulated in endothelial cells derived from invasive ovarian cancer tissue. 17308118 2/17 Arthur Liberzon 0.00393640266086246 0.00564788207862875 1065 1671.2 1333.5 0.000438145173679402 492 3.06908479856712 3.06908479856712 1 2.52200847649049 1062 1573 4107 NA 3133 934 584 1359 492 2160 1308 1156 M11773 REACTOME_PECAM1_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PECAM1_INTERACTIONS.html Genes involved in PECAM1 interactions 8/17 Reactome 1.45417869215264e-07 1.56650146009823e-06 1335 1347.18181818182 1334 1.45417878731125e-08 46 1.81060666875718 1.54876067555504 1 3.84194166973408 1334 665 3966 1399 111 427 46 2051 2545 1659 616 1157 M1598 CHEN_PDGF_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_PDGF_TARGETS.html Up-regulated PDGF targets identified by a gene-trap screen. 14981515 24/37 John Newman 5.27359826689078e-05 0.000105068373633717 1100 1495.54545454545 1334 4.79429516730578e-06 807 1.75475372936967 2.00149601360144 1 2.5518658626771 1097 2452 1885 1714 2222 1152 1334 807 1017 1493 1278 1158 M18559 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_UP.html Genes up-rgulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 6h. 16818636 32/135 Arthur Liberzon 3.73869739817418e-06 1.16177294481726e-05 1105 1458.36363636364 1335 3.3988215925102e-07 612 1.43835154348928 1.6023878208532 1 2.59454244477738 1102 2006 1401 2076 1313 1375 612 1202 2474 1146 1335 1159 M1733 GAVIN_FOXP3_TARGETS_CLUSTER_P3 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_P3.html Cluster P3 of genes with similar expression profiles in peripheral T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 107/250 Jessica Robertson 1.7422020887008e-06 6.74979256763237e-06 3025 2169.18181818182 1335 1.58382133488151e-07 748 1.75979210727873 -1.478532705229 -1 3.3260652212724 3021 1335 748 1199 952 4347 3889 3049 1232 814 3275 1160 M2890 KEGG_CALCIUM_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CALCIUM_SIGNALING_PATHWAY.html Calcium signaling pathway 59/193 KEGG 8.34033252909926e-05 0.000157846519512759 520 1667.90909090909 1336 7.58240793901118e-06 349 1.93756448602439 1.88394847718101 1 2.69253081863609 516 3667 811 2651 2349 349 672 2338 2965 1336 693 1161 M17074 AIYAR_COBRA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/AIYAR_COBRA1_TARGETS_UP.html Genes up-regulated in T47D cells (breast cancer) after COBRA1 [GeneID=25920] knockdown by RNAi. 17043641 26/63 Arthur Liberzon 1.53772399680329e-06 6.22798154625776e-06 1805 1628.72727272727 1337 1.39793188329118e-07 649 1.85042301629902 1.37529068140229 1 3.52099542752395 1801 2545 1514 2164 899 1310 649 3669 725 1303 1337 1162 M2817 STARK_PREFRONTAL_CORTEX_22Q11_DELETION_UP http://www.broadinstitute.org/gsea/msigdb/cards/STARK_PREFRONTAL_CORTEX_22Q11_DELETION_UP.html Genes up-regulated in prefrontal cortex (PFC) of mice carrying a hemizygotic microdeletion in the 22q11.2 region. 18469815 127/347 Jessica Robertson 5.04288693890812e-08 7.13926531592854e-07 760 1088 1340 4.58444277682023e-09 12 1.41072057705632 1.68613575113131 1 3.16940172434534 758 65 1340 738 12 1292 1588 1616 1695 1445 1419 1163 M14666 TIAN_TNF_SIGNALING_NOT_VIA_NFKB http://www.broadinstitute.org/gsea/msigdb/cards/TIAN_TNF_SIGNALING_NOT_VIA_NFKB.html Genes modulated in HeLa cells (cervical carcinoma) by TNF [GeneID=7124] not via NFKB pathway. 15722553 18/31 Arthur Liberzon 7.69841510031486e-05 0.000147123870962787 470 1528.09090909091 1340 6.99880409325581e-06 404 1.4555995261074 1.41116257068589 1 2.0390250687603 466 2663 1193 2266 2322 404 444 1340 3790 1351 570 1164 M625 REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES.html Genes involved in Chemokine receptors bind chemokines 17/74 Reactome 0.000129292555566209 0.000232577702642325 750 1732.45454545455 1341 1.17545595118225e-05 750 2.0524708989869 2.07629926680637 1 2.72592113032617 750 2699 956 2966 2478 1071 848 1341 3308 1260 1380 1165 M12289 REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS.html Genes involved in Peptide ligand-binding receptors 45/226 Reactome 6.11169732194108e-05 0.000119930542925527 680 1881.90909090909 1342 5.55624283109094e-06 575 2.00722501677491 2.05472958620014 1 2.87686795790818 680 3568 575 3760 2357 895 676 2142 3474 1342 1232 1166 M16992 ZHANG_PROLIFERATING_VS_QUIESCENT http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_PROLIFERATING_VS_QUIESCENT.html Genes up-regulated in HDMEC cells (microvascular endothelium): proliferating vs quiescent cells. 14517420 47/97 John Newman 1.50823326442548e-05 3.55396060881347e-05 750 1447.36363636364 1342 1.37113054943396e-06 591 2.3480502008617 2.39413032763639 1 3.81871359203896 748 2190 1706 977 1835 1435 1342 591 1179 3139 779 1167 M7825 BIOCARTA_ACTINY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ACTINY_PATHWAY.html Y branching of actin filaments 18/36 BioCarta 2.45022248340228e-05 5.40826309807965e-05 1160 1302.90909090909 1343 2.22749979352203e-06 87 2.72014980853257 3.28345229317577 1 4.24256819764997 1159 2123 1343 847 1980 1427 1552 836 87 1774 1204 1168 M1106 GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP.html Genes up-regulated in ME-A cells (breast cancer, sensitive to apoptotic stimuli) exposed to doxorubicin [PubChem=31703] in the presence of medium concentrate (MC) from ME-C cells (breast cancer, resistant to apoptotic stimuli). 17160024 468/970 Arthur Liberzon 1.14978278323559e-07 1.34361150180598e-06 1520 1167.27272727273 1343 1.04525713029684e-08 68 1.47657604708669 1.47324227083614 1 3.16913596449167 1517 397 679 564 68 2028 1343 2169 2033 313 1729 1169 M2332 BILANGES_SERUM_SENSITIVE_VIA_TSC1 http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_SERUM_SENSITIVE_VIA_TSC1.html Genes translationally up-regulated by serum in MEF cells (embryonic fibroblast) lacking TSC1 [GeneID=7248]. 17562867 13/35 Arthur Liberzon 3.01772919951578e-07 2.35268466937768e-06 1345 1407.54545454545 1343 2.74339055768754e-08 262 1.37609424017628 1.36849464545434 1 2.83109981235676 1343 1222 2208 1798 271 561 262 2038 2229 2367 1184 1170 M1281 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5.html Cluster PAM5: genes changed exclusively in hepatocellular carcinoma (HCC) samples from 27 month old mice deficient for TXNIP [GeneID=10628]. 16607285 49/185 Leona Saunders 4.64295144731153e-06 1.36855026979256e-05 2215 1461 1346 4.22087385997818e-07 800 1.92777121864767 2.18743218821117 1 3.42724400903396 2212 1346 1137 859 1397 2937 1660 1589 816 800 1318 1171 M11840 SHEPARD_BMYB_MORPHOLINO_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHEPARD_BMYB_MORPHOLINO_DN.html Human orthologs of genes down-regulated in zebra fish after knockdown of BMYB [GeneID=4605] by morpholino. 16150706 129/360 Jennifer Shepard 2.63255425186597e-11 8.11588764752892e-10 1150 1457.27272727273 1346 2.39323113808862e-12 146 1.98477876264678 2.25762245984372 1 6.5951846553283 1148 1415 146 1280 1163 2644 2295 1346 2048 460 2085 1172 M103 PID_S1P_S1P1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P1_PATHWAY.html S1P1 pathway 18832364 15/45 Pathway Interaction Database 5.13570743132587e-06 1.48371917528934e-05 1520 1401.09090909091 1348 4.66883583656774e-07 834 1.52354476038828 1.31640366341182 1 2.68905720788936 1518 1214 1348 1058 1441 1055 840 2101 1949 834 2054 1173 M3518 WU_HBX_TARGETS_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_3_DN.html Genes down-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] both in SK-Hep-1 cells (hepatocellular carcinoma) and normal primary hepatocytes. 11439330 9/23 John Newman 2.63768993439383e-06 8.87946482224819e-06 1350 1685.90909090909 1348 2.63769306523275e-07 161 2.70574474593936 2.70574474593936 1 4.99615800304731 1348 2791 4408 3014 2198 812 244 161 197 2580 792 1174 M19548 STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_UP.html Genes up-regulated by estradiol [PubChem=5757] and up-regulated by ESRRA [GeneID=2101] in MCF-7 cells (breast cancer). 18974123 18/42 Leona Saunders 7.3379742969207e-06 1.95484636471691e-05 1615 1415.45454545455 1350 6.67090797493544e-07 555 1.95322353573401 2.4004344099028 1 3.36193646632454 1614 1694 1111 913 1584 2516 2337 753 555 1350 1143 1175 M18153 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 9. 12554760 44/91 Arthur Liberzon 8.49766628032794e-06 2.20609773903694e-05 1515 1315.63636363636 1350 7.72518100307611e-07 770 1.90728654885872 -2.07327226800498 -1 3.24625901370875 1514 1350 1262 1542 1634 1185 1623 895 1176 770 1521 1176 M15456 MCCABE_HOXC6_TARGETS_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCCABE_HOXC6_TARGETS_CANCER_UP.html Genes whose promoters were bound by HOXC6 [GeneID=3223] in LNCaP cells (prostate cancer) and which were up-regulated in comparison of tumor vs normal prostate tissue samples. 18339881 16/50 Jessica Robertson 4.30760381902177e-05 8.79539498733595e-05 1160 1525.81818181818 1351 3.91608014935582e-06 741 2.04174864114852 2.22352835688455 1 3.02685857552657 1070 2514 1320 2319 2163 1351 1157 741 1417 1576 1156 1177 M685 REACTOME_HS_GAG_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HS_GAG_BIOSYNTHESIS.html Genes involved in HS-GAG biosynthesis 10/30 Reactome 0.000402466614049602 0.000662437145569525 1200 1922.72727272727 1352 3.65945690819035e-05 804 0.938628615298907 1.03981577561008 1 1.0906459792009 1196 1067 2707 2685 4170 1352 804 829 1797 3482 1061 1178 M5014 TSUNODA_CISPLATIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TSUNODA_CISPLATIN_RESISTANCE_DN.html Genes down-regulated in bladder cancer cells resistant to cisplatin [PubChem=2767] compared to the parental cells sensitive to the drug. 15608674 32/80 Leona Saunders 1.72612010889387e-06 6.71252655339338e-06 765 2234.36363636364 1352 1.56920133019025e-07 136 1.66580173433635 1.34092636190876 1 3.14988434473174 4465 136 762 1104 950 3544 4448 2779 1352 762 4276 1179 M3340 PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP.html Genes up-regulated in CD38+ [GeneID=952] CLL (chronic lymphocytic leukemia) cells. 17287849 26/87 Arthur Liberzon 4.15560517254672e-06 1.25795644951899e-05 1870 1379.90909090909 1353 3.77783002012513e-07 671 1.73282055720149 1.77290056952068 1 3.10383451891172 1868 1038 1001 1113 1353 1781 1371 1163 2013 671 1807 1180 M45 PID_CD40_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CD40_PATHWAY.html CD40/CD40L signaling 18832364 19/44 Pathway Interaction Database 9.76657501420175e-05 0.000180679709895576 1015 1734 1354 8.87909873983737e-06 663 1.02692169673023 -1.07166209388992 -1 1.40503428144085 1011 1299 2730 1406 2407 663 779 1354 3370 3001 1054 1181 M15913 KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY.html RIG-I-like receptor signaling pathway 36/79 KEGG 1.30636074697238e-05 3.14434395514642e-05 680 1378.27272727273 1355 1.18760773110129e-06 194 1.21696294553867 -1.20906104607628 -1 2.00284540506748 678 2048 2384 2326 1780 194 670 522 2692 1355 512 1182 M10082 BIOCARTA_TNFR2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TNFR2_PATHWAY.html TNFR2 Signaling Pathway 11/22 BioCarta 0.000194061259083845 0.000338307686036793 1310 1639.45454545455 1355 1.76434890251294e-05 773 1.12783448733479 -1.15398774423258 -1 1.43080421774242 1309 773 2687 1050 2555 1114 1891 2055 1148 2097 1355 1183 M15476 URS_ADIPOCYTE_DIFFERENTIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/URS_ADIPOCYTE_DIFFERENTIATION_UP.html Genes up-regulated in primary adipocytes compared to preadipocytes. 15051823 52/149 John Newman 3.56704028580022e-07 2.60766782827767e-06 1195 1255.72727272727 1355 3.24276442195803e-08 348 1.9608017427453 2.23467165655657 1 4.00201510678694 1194 442 348 1355 655 2215 2046 1725 1501 516 1816 1184 M17123 YAGI_AML_WITH_11Q23_REARRANGED http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_WITH_11Q23_REARRANGED.html Genes specifically expressed in samples from patients with pediatric acute myeloid leukemia (AML) bearing 11q23 rearrangements. 12738660 254/627 Arthur Liberzon 2.69930958069032e-07 2.24693882174369e-06 1625 1241 1356 2.45391810171325e-08 228 1.6664985626109 1.91581285968326 1 3.44072775770127 1625 240 675 743 228 2673 1924 1356 1497 906 1784 1185 M15025 LIAO_HAVE_SOX4_BINDING_SITES http://www.broadinstitute.org/gsea/msigdb/cards/LIAO_HAVE_SOX4_BINDING_SITES.html Genes up-regulated in the samples with intrahepatic metastatic hepatocellular carcinoma (HCC) vs primary HCC that also have putative binding sites for SOX4 [GeneID=6659]. 18504433 31/66 Jessica Robertson 1.66071308960287e-06 6.54508119249709e-06 1360 1483.27272727273 1357 1.50974031202363e-07 934 1.73086041856589 1.848117949284 1 3.27984565953688 1357 1775 1309 2134 934 1653 1249 1155 1785 1680 1285 1186 M16673 VALK_AML_CLUSTER_16 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_16.html Top 40 genes from cluster 16 of acute myeloid leukemia (AML) expression profile; 81% of the samples are FAB M5 subtype, 45% have 11q23 abnormalities. 15084694 14/39 Jessica Robertson 9.697724517456e-06 2.45773591610594e-05 740 1326.27272727273 1357 8.81615205985306e-07 516 1.85386849292874 2.35720848022691 1 3.12355153179569 1511 1142 1906 1158 1681 1944 1357 516 737 1900 737 1187 M18496 LEE_LIVER_CANCER_MYC_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) induced by overexpression of MYC [GeneID=4609]. 15565109 36/119 Yujin Hoshida 1.88075025538964e-07 1.81926618188875e-06 3675 1848.36363636364 1358 1.70977310561132e-08 153 1.70362555153267 -1.30186939725835 -1 3.57448219374898 3675 466 981 1214 153 2630 4032 1287 2130 1358 2406 1188 M2196 GABRIELY_MIR21_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/GABRIELY_MIR21_TARGETS.html Genes significantly de-regulated (p < 0.05) by MIR21 [GeneID=406991] in A172 cells (glioma). 18591254 184/461 Arthur Liberzon 3.03641363741974e-05 6.50579567626207e-05 1360 1397.63636363636 1359 2.76041413313337e-06 644 1.65251199479105 1.7891486256184 1 2.52892336960431 644 1997 1359 1402 2053 1129 1369 1245 1757 1060 1359 1189 M6868 HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_UP.html Genes up-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with low risk of myelodysplastic syndrome (MDS) compared with healthy controls. 12411319 12/55 Arthur Liberzon 6.87807563894925e-07 3.77408225340939e-06 4485 2021.18181818182 1364 6.25279799028218e-08 566 1.84146302150766 -1.75140352307685 -1 3.65037064809991 4482 655 1521 606 566 4097 2730 4333 701 1178 1364 1190 M2387 KATSANOU_ELAVL1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KATSANOU_ELAVL1_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) with ELAVL1 [GeneID=1994] knocked out. 19307312 86/232 Arthur Liberzon 3.42031429747124e-06 1.08312511900384e-05 465 1274.90909090909 1364 3.10938146818681e-07 462 2.12826411938696 2.19849281702602 1 3.86271028926962 462 1422 524 2289 1275 1612 1364 1116 1710 849 1401 1191 M19629 MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_DN.html The 'NPM1-mutated signature 1': genes down-regulated in pediatric AML (acute myeloid leukemia) samples with mutated NPM1 [GeneID=4869] compared to all AML cases with the intact gene. 17597811 92/259 Arthur Liberzon 3.87151900196862e-07 2.72401472120494e-06 1365 1184 1365 3.51956334842862e-08 346 1.74602213877381 1.86056171173254 1 3.55154906821065 1365 822 750 617 346 2021 1748 1704 1513 682 1456 1192 M15940 NAKAMURA_METASTASIS_MODEL_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_METASTASIS_MODEL_DN.html Bottom genes down-regulated in subcutaneous tumors from highly metastatic pancreatic cancer cells. 17210693 26/63 Jessica Robertson 4.29146053953886e-06 1.29013248242148e-05 2455 1648.09090909091 1365 3.90133537341709e-07 625 1.61244494816144 1.89861796979071 1 2.8817524227538 2451 625 1183 1731 1365 3497 2504 892 1215 1653 1013 1193 M18306 KEGG_REGULATION_OF_ACTIN_CYTOSKELETON http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_REGULATION_OF_ACTIN_CYTOSKELETON.html Regulation of actin cytoskeleton 94/251 KEGG 4.89820096765795e-07 3.07268671143844e-06 1715 1286.63636363636 1366 4.4529109620188e-08 438 1.85145103692581 2.23240826950625 1 3.73059963870375 1713 693 1280 764 438 1943 1366 1484 871 1765 1836 1194 M7068 BONOME_OVARIAN_CANCER_SURVIVAL_OPTIMAL_DEBULKING http://www.broadinstitute.org/gsea/msigdb/cards/BONOME_OVARIAN_CANCER_SURVIVAL_OPTIMAL_DEBULKING.html Genes whose expression in optimally debulked ovarian tumors is associated with survival prognosis. 18593951 157/433 Jessica Robertson 1.91289388379498e-06 7.1687063813697e-06 2630 1610.18181818182 1367 1.73899595186629e-07 259 1.44090823965777 -1.13611711212046 -1 2.70959102375487 2629 259 2014 749 1004 854 2175 3440 1367 1255 1966 1195 M722 REACTOME_TRANSLOCATION_OF_ZAP_70_TO_IMMUNOLOGICAL_SYNAPSE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSLOCATION_OF_ZAP_70_TO_IMMUNOLOGICAL_SYNAPSE.html Genes involved in Translocation of ZAP-70 to Immunological synapse 4/16 Reactome 3.93820128593537e-06 1.20774942577835e-05 2070 1621.27272727273 1369 3.93820826519599e-07 781 1.93886965713515 1.71597743607958 1 3.48544660599025 2067 793 3971 813 1369 1751 1365 1850 781 979 2095 1196 M1914 ZHANG_TLX_TARGETS_60HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_60HR_UP.html Genes up-regulated in neural stem cells (NSC) at 60 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 247/528 Jessica Robertson 2.94300342082972e-07 2.32954628885271e-06 1370 1250 1369 2.6754580132035e-08 259 1.53815130839063 1.71754461195354 1 3.16692034587601 1369 538 712 645 259 2667 1888 1686 1596 400 1990 1197 M18887 YAGI_AML_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_SURVIVAL.html Genes differentially expressed in pediatric AML (acute myeloid leukemia) samples from patients with good survival (>3 years without relapse) compared to those with poor survival (relapsed within one year after treatment). 12738660 100/221 Kevin Vogelsang 4.33403930028678e-06 1.29854911516265e-05 1675 1399.63636363636 1370 3.94004348949561e-07 530 1.72200697949462 1.90043111804751 1 3.07578347855241 1674 2041 1647 1092 1370 2182 2158 530 873 1232 597 1198 M1267 HOWLIN_PUBERTAL_MAMMARY_GLAND http://www.broadinstitute.org/gsea/msigdb/cards/HOWLIN_PUBERTAL_MAMMARY_GLAND.html Genes up-regulated in pubertal mammary glands compared to mammary glands from other developmental stages. 16278680 35/115 Arthur Liberzon 9.88342682784174e-07 4.70668070277098e-06 585 1402.45454545455 1371 8.98493751631016e-08 378 2.00406342621247 1.80368503218044 1 3.90244387308481 583 1030 378 1106 2409 1681 1920 2156 1371 455 2338 1199 M2324 LEE_BMP2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_BMP2_TARGETS_UP.html Genes up-regulated in uterus upon knockout of BMP2 [GeneID=650]. 17515606 510/1167 Arthur Liberzon 1.11014482953844e-18 8.8171841885036e-17 1375 1749.90909090909 1372 1.11014482953844e-19 6 1.78319732554896 1.86039676531584 1 10.4645375374628 1372 6 4648 369 323 3313 2607 2633 1265 13 2700 1200 M2733 NOJIMA_SFRP2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NOJIMA_SFRP2_TARGETS_DN.html Cellular proliferation, growth, apoptosis and Wnt signaling genes down-regulated in SNU638 cells (gastric cancer) by overexpression of SFRP2 [GeneID=6423] off a plasmid vector. 17297461 14/40 Arthur Liberzon 1.36498685824323e-06 5.83074605080017e-06 645 1581.54545454545 1373 1.24089791377101e-07 642 1.27505487479237 1.17225637651353 1 2.43952197612652 1671 644 1920 1785 837 1039 642 3703 2839 1373 944 1201 M2840 CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_UP.html Genes up-regulated in luminal-like breast cancer cell lines compared to the basal-like ones. 16288205 247/589 Arthur Liberzon 4.46824385776651e-07 2.90229850530109e-06 1800 1265.81818181818 1374 4.06204069570545e-08 37 1.38173080842052 -1.26725287236324 -1 2.7966456642828 1797 37 1585 381 406 809 3249 1961 1598 727 1374 1202 M2412 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_6 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_6.html Genes regulated in MCF7 cells (breast cancer) by expression of the full-length form of ERBB2 [GeneID=2064] at 60 h time point. 19364815 15/65 Arthur Liberzon 3.2600799870092e-06 1.04420607102701e-05 1875 1424.81818181818 1374 2.96371347089413e-07 367 2.03958029950524 1.95936709667342 1 3.71360100149503 1872 367 1081 1374 1259 1961 1873 1772 815 1098 2201 1203 M12027 RODRIGUES_NTN1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_NTN1_TARGETS_UP.html Genes up-regulated in HCT8/S11 cells (colon cancer) engineered to stably express NTN1 [GeneID=1630] off a plasmid vector. 17334389 15/43 Arthur Liberzon 8.48763879250452e-06 2.20471593024812e-05 1375 1338.72727272727 1375 7.7160650346741e-07 711 1.82209874141908 1.98000446493684 1 3.10144803769029 1375 1609 1622 2065 1633 1138 1052 983 711 1094 1444 1204 M1549 LINDVALL_IMMORTALIZED_BY_TERT_UP http://www.broadinstitute.org/gsea/msigdb/cards/LINDVALL_IMMORTALIZED_BY_TERT_UP.html Genes up-regulated in BJ cells (foreskin fibroblasts) immortalized by expression of TERT [GeneID=7015]. 12702554 53/119 John Newman 1.96338812197969e-06 7.29614333037022e-06 1095 1362.18181818182 1376 1.78489988564176e-07 667 1.67008355066752 1.76858305486668 1 3.13587773724531 1091 1264 918 1987 1016 1664 1376 1518 2097 667 1386 1205 M9206 YAMASHITA_LIVER_CANCER_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_LIVER_CANCER_STEM_CELL_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) cells with hepatic stem cell properties. 19150350 41/175 Yujin Hoshida 1.43570849666966e-06 5.96429965903727e-06 4045 2306.45454545455 1376 1.30519039418761e-07 562 1.78138938656509 1.96973595826942 1 3.40187147823531 4045 1277 1376 945 870 4199 3267 3584 562 967 4279 1206 M69 PID_REELIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_REELIN_PATHWAY.html Reelin signaling pathway 18832364 20/47 Pathway Interaction Database 7.94589485699565e-06 2.09299962337727e-05 950 1590.72727272727 1377 7.22356686898956e-07 440 0.901271914601021 1.01488108797828 1 1.54152140502894 947 1377 2821 1715 1606 742 440 952 2985 3106 807 1207 M579 REACTOME_PPARA_ACTIVATES_GENE_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PPARA_ACTIVATES_GENE_EXPRESSION.html Genes involved in PPARA Activates Gene Expression 56/156 Reactome 1.38369167749451e-06 5.85372787868602e-06 2420 1388.18181818182 1377 1.25790231615383e-07 566 1.55278133039486 -1.38336981539769 -1 2.96991751829536 2416 1020 1844 1377 845 566 1503 1265 1279 1692 1463 1208 M13910 CLIMENT_BREAST_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/CLIMENT_BREAST_CANCER_COPY_NUMBER_UP.html Genes from the most frequent genomic gains and amplifications in a panel of patients with lymph node negative breast cancer (NNBC). 17234794 14/41 Jessica Robertson 1.61332401924172e-06 6.4579543144717e-06 2545 1623.81818181818 1377 1.4666592748549e-07 427 2.01118600703782 1.93492615672306 1 3.81531939310563 2542 769 1074 744 915 2938 1717 2754 427 1377 2605 1209 M2051 ZEMBUTSU_SENSITIVITY_TO_CYCLOPHOSPHAMIDE http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_CYCLOPHOSPHAMIDE.html Top genes associated with chemosensitivity to cyclophosphamide [PubChem=2907] across 85 tumor xenografts. 11809704 14/29 Arthur Liberzon 5.04778514140739e-07 3.12605187497923e-06 965 1398.27272727273 1382 4.5888966359961e-08 449 2.00241573227001 -2.00241573227001 -1 4.02931410178417 961 1463 1025 2068 449 1161 2081 1630 1896 1382 1265 1210 M1023 REACTOME_LIPID_DIGESTION_MOBILIZATION_AND_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LIPID_DIGESTION_MOBILIZATION_AND_TRANSPORT.html Genes involved in Lipid digestion, mobilization, and transport 22/63 Reactome 0.000144708840398167 0.00025852292264804 420 1233.54545454545 1383 1.31562145228525e-05 418 1.615041050973 1.615041050973 1 2.11784825681502 418 2053 1383 1456 2529 603 570 645 1658 1713 541 1211 M10728 BASSO_HAIRY_CELL_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/BASSO_HAIRY_CELL_LEUKEMIA_DN.html Genes down-regulated in hairy cell leukemia (HCL) compared with normal and other neoplastic B cell populations. 14707115 55/147 Arthur Liberzon 0.00129771315487123 0.00197823156920188 455 1677.18181818182 1384 0.000118043569925149 453 1.82702519204503 1.98753339863881 1 1.80561835453949 453 2804 1215 2523 3122 1126 904 1046 1930 1942 1384 1212 M2204 TURASHVILI_BREAST_NORMAL_DUCTAL_VS_LOBULAR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_NORMAL_DUCTAL_VS_LOBULAR_UP.html Genes up-regulated in normal ductal and normal lobular breast cells. 17389037 34/102 Arthur Liberzon 2.95705457865636e-05 6.36507016793004e-05 1125 1888.81818181818 1385 2.68826756876334e-06 1058 1.78247894400007 1.82715957018738 1 2.73400627727042 1123 3270 2108 3180 2039 1349 1335 1174 1385 2756 1058 1213 M3462 REACTOME_LIPOPROTEIN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LIPOPROTEIN_METABOLISM.html Genes involved in Lipoprotein metabolism 14/44 Reactome 1.02036617672468e-05 2.55965683695145e-05 645 1197.81818181818 1386 9.27609917493077e-07 361 1.42421119573931 1.42421119573931 1 2.39044268948753 642 1386 1637 1860 1700 554 382 361 2312 1889 453 1214 M1734 GAVIN_FOXP3_TARGETS_CLUSTER_P4 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_P4.html Cluster P4 of genes with similar expression profiles in peripheral T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 54/154 Jessica Robertson 7.5973294020472e-07 4.00913125878301e-06 1400 1274.45454545455 1386 6.90666547787108e-08 440 1.35048448799331 1.38629996175444 1 2.66414110237402 1400 440 1386 960 601 1791 1551 595 2464 1331 1500 1215 M7600 DOANE_RESPONSE_TO_ANDROGEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_RESPONSE_TO_ANDROGEN_UP.html Genes up-regulated in MDA-MB-453 cells (class A ER(-) [GeneID=2099] breast cancer) after exposure to the androgen R1881 [PubChem=13766]. 16491124 123/341 Arthur Liberzon 2.36983585679237e-06 8.26268662569124e-06 2590 1780.18181818182 1388 2.15439855416267e-07 815 1.48121239194139 -1.32135795704091 -1 2.75198672274382 2589 815 1205 1004 1108 1388 4284 2763 1976 952 1498 1216 M2987 ROZANOV_MMP14_CORRELATED http://www.broadinstitute.org/gsea/msigdb/cards/ROZANOV_MMP14_CORRELATED.html Genes whose expression most uniformly correlated with that of MMP14 [GeneID=4323] both in HT1080 cells (fibrosarcoma) and in 190 human tumors. 18519667 14/23 Jessica Robertson 2.79010488489985e-05 6.03899837904882e-05 1095 1340 1388 2.5364911549647e-06 462 1.90570585275282 2.5973306207061 1 2.9389233220966 1093 2517 1388 1312 2024 1406 1470 520 653 1895 462 1217 M1586 CHEN_ETV5_TARGETS_SERTOLI http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_ETV5_TARGETS_SERTOLI.html Genes down-regulated in Sertoli cells from both 4 and 10 week old ETV5 [GeneID=2119] knockout mice. 16107850 11/29 John Newman 0.00209604248643786 0.00310333494200563 480 1654.36363636364 1388 0.0001907311046828 477 2.00426259868755 2.00426259868755 1 1.83751576974974 477 1938 978 2917 3230 828 623 1147 3153 1519 1388 1218 M1857 MALONEY_RESPONSE_TO_17AAG_UP http://www.broadinstitute.org/gsea/msigdb/cards/MALONEY_RESPONSE_TO_17AAG_UP.html Up-regulated genes in A2780 cells (ovarian cancer) treated with 17AAG [PubChem=6440175], a chemical with anticancer properties. 17409432 44/107 Jessica Robertson 6.30373674340358e-06 1.73760649291701e-05 1375 1249.45454545455 1388 5.73068618708439e-07 552 1.637065874487 1.93626729603359 1 2.84837253779999 1374 1686 1398 552 1520 1455 1616 1388 1098 1075 582 1219 M11420 BIOCARTA_CTCF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CTCF_PATHWAY.html CTCF: First Multivalent Nuclear Factor 17/34 BioCarta 3.95829365780514e-06 1.21153259833278e-05 1390 1318 1389 3.59845525425597e-07 166 1.9923245947168 2.60451587441106 1 3.58055175688081 1389 1654 1925 465 2302 1529 1063 178 166 2798 1029 1220 M1596 HAN_JNK_SINGALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAN_JNK_SINGALING_UP.html Genes up-regulated in 3T3 cells (fibroblast) upon activation of JNK pathway. 12354774 27/58 John Newman 4.72810418583782e-06 1.38647660918874e-05 660 1477.81818181818 1390 4.2982857701982e-07 660 1.43108055549601 1.46959855382195 1 2.54125741988852 660 1599 1987 1791 1410 941 854 1209 3059 1390 1356 1221 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 4.81623351054506e-05 9.69036935612458e-05 1395 1778.09090909091 1391 4.81633789620265e-06 372 1.95952492470059 1.95952492470059 1 2.87481953188058 1391 2180 4580 2691 3200 935 533 652 1143 1882 372 1222 M16229 KANNAN_TP53_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANNAN_TP53_TARGETS_UP.html Primary up-regulated targets of TP53 [GeneID=7157] in the H1299 (lung cancer) cell line. 11402317 52/111 Broad Institute 2.02052280506641e-06 7.4143851719195e-06 2290 1770.90909090909 1393 1.8368406006875e-07 865 1.5797804148467 2.01307255441673 1 2.96228595417609 2287 1724 1375 1326 1038 3546 2713 865 1393 1236 1977 1223 M1194 NAISHIRO_CTNNB1_TARGETS_WITH_LEF1_MOTIF http://www.broadinstitute.org/gsea/msigdb/cards/NAISHIRO_CTNNB1_TARGETS_WITH_LEF1_MOTIF.html Genes regulated by CTNNB1 [GeneID=1499] and whose promoters contain binding sites for LEF1 [GeneID=51176]. 15735679 3/11 Leona Saunders 2.95626252727755e-07 2.33605272916533e-06 55 1951.27272727273 1394 2.95626292055459e-08 51 3.69636223202461 -2.38236779657299 -1 7.60885314024297 2914 1157 4251 914 2252 3513 3699 53 51 1394 1266 1224 M1084 REACTOME_TRYPTOPHAN_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRYPTOPHAN_CATABOLISM.html Genes involved in Tryptophan catabolism 5/11 Reactome 0.00220660936302885 0.00326394301614685 940 1887.90909090909 1399 0.000220880353624561 811 2.17344675209166 -2.17344675209166 -1 1.97521488316181 937 1399 4097 1901 3032 811 954 1573 3712 1159 1192 1225 M11584 HEIDENBLAD_AMPLICON_8Q24_DN http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLICON_8Q24_DN.html Down-regulated genes whose expression is associated with amplification of the 8q24 chromosome region in pancreatic cancer cell lines. 15688027 36/76 Arthur Liberzon 0.000436313768197715 0.000713386712412594 1105 1619.27272727273 1399 3.96727567195463e-05 674 2.25071121693409 2.50488226522594 1 2.58875477641809 1101 1868 1082 2262 3069 1657 2057 1399 1286 1357 674 1226 M3698 SEIKE_LUNG_CANCER_POOR_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/SEIKE_LUNG_CANCER_POOR_SURVIVAL.html The 'CLASS-11' set of pro- and anti-inflammatory cytokines whose expression identifies stage I lung adenocarcinoma patients with poor prognosis. 17686824 3/10 Jessica Robertson 0.000265219222893576 0.000450786100282661 1405 1649.18181818182 1401 2.65250881767801e-05 97 1.91984168325261 -1.91984168325261 -1 2.34808833215199 1590 1405 4578 1775 2921 1140 1158 775 97 1401 1301 1227 M2254 CERIBELLI_GENES_INACTIVE_AND_BOUND_BY_NFY http://www.broadinstitute.org/gsea/msigdb/cards/CERIBELLI_GENES_INACTIVE_AND_BOUND_BY_NFY.html Transcriptionally inactive genes which where bound by NF-Y transcription factor. 18212061 14/65 Arthur Liberzon 0.000462661814084817 0.000752266919084474 1120 1569.45454545455 1402 4.2069012809282e-05 848 1.70604303664878 1.92372792804486 1 1.94790846478759 1117 2348 2433 1464 2803 1017 1009 848 1402 1903 920 1228 M281 PID_FAK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FAK_PATHWAY.html Signaling events mediated by focal adhesion kinase 18832364 60/118 Pathway Interaction Database 2.24318846106105e-07 2.04904115565928e-06 2310 1616.72727272727 1403 2.03926244525778e-08 147 1.7339248037316 -1.41948899219617 -1 3.60531655439023 2310 1260 1064 147 181 2700 2217 2547 1042 1403 2913 1229 M1218 BORLAK_LIVER_CANCER_EGF_UP http://www.broadinstitute.org/gsea/msigdb/cards/BORLAK_LIVER_CANCER_EGF_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) developed by transgenic mice overexpressing a secretable form of EGF [GeneID=1950] in liver. 15674348 50/134 Leona Saunders 1.12506914338745e-09 2.46358598407177e-08 4400 1973.45454545455 1404 1.02279013087528e-10 206 2.17292110887388 -2.05481725806125 -1 6.04308062619192 4398 436 206 333 1404 2287 3642 4437 740 248 3577 1230 M14590 AIGNER_ZEB1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/AIGNER_ZEB1_TARGETS.html Genes up-regulated in MDA-MB-231 cells (breast cancer) after knockdown of ZEB1 [GeneID=6935] by RNAi. 17486063 23/55 Leona Saunders 2.6930453253137e-08 4.09727610208441e-07 1970 1375.27272727273 1407 2.44822305298143e-09 284 2.40457419442205 -2.42228946430612 -1 5.61421021313776 1966 478 284 903 1740 1518 3511 2507 426 388 1407 1231 M4196 NUYTTEN_EZH2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NUYTTEN_EZH2_TARGETS_UP.html Genes up-regulated in PC3 cells (prostate cancer) after knockdown of EZH2 [GeneID=2146] by RNAi. 17724462 676/1657 Jessica Robertson 2.48413287276308e-06 8.54295206713065e-06 1005 1743.63636363636 1407 2.4841356496797e-07 820 1.49096009479779 1.64774789634352 1 2.76220221707015 1003 1407 4308 1267 1185 1580 2155 1692 2476 820 1287 1232 M1684 DURCHDEWALD_SKIN_CARCINOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DURCHDEWALD_SKIN_CARCINOGENESIS_DN.html Genes down-regulated upon skin specific knockout of FOS [GeneID=2353] by cre-lox in the K5-SOS-F mice (express a constitutively active form of SOS1 [GeneID=6654] in the skin). 18757399 188/460 Jessica Robertson 2.36167747424968e-05 5.2424541185855e-05 970 1465.36363636364 1407 2.14700256999689e-06 679 1.62719765320589 1.77947527332576 1 2.54595396457209 968 2217 728 2369 1969 827 1276 1434 2245 1407 679 1233 M15409 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_3 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_3.html Amplification hot spot 3: colocolized fragile sites and cancer genes in the 15q21-q26 region. 16751803 5/7 Arthur Liberzon 1.01432979581499e-05 2.55134161201774e-05 1410 1474.54545454545 1409 1.01433442573694e-06 190 1.81565133489634 2.25304539964923 1 3.04838648524171 1409 1078 4230 1550 2196 1116 1708 679 194 1870 190 1234 M988 RUIZ_TNC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUIZ_TNC_TARGETS_UP.html Genes up-regulated in T98G cells (glioblastoma) by TNC [GeneID=3371]. 15492259 126/287 Arthur Liberzon 4.35402004460085e-05 8.88242835393973e-05 470 1322.18181818182 1410 3.9582783794546e-06 449 1.89953499611491 2.08960008426523 1 2.81305998681864 470 2266 563 1261 2580 1439 1684 449 1774 648 1410 1235 M1252 CEBALLOS_TARGETS_OF_TP53_AND_MYC_DN http://www.broadinstitute.org/gsea/msigdb/cards/CEBALLOS_TARGETS_OF_TP53_AND_MYC_DN.html Genes down-regulated in K562 cells (chronic myelogenous leukemia, CML) expressing TP53 and MYC [GeneID=7157;4609]. 15856024 31/62 Arthur Liberzon 4.76331532988465e-06 1.39365569125892e-05 1330 1856.90909090909 1413 4.33029603925121e-07 613 1.59597569918699 1.78163684917139 1 2.83276335786619 1329 3511 1771 4057 1413 1139 726 1063 2287 2517 613 1236 M1508 JIANG_AGING_CEREBRAL_CORTEX_UP http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_AGING_CEREBRAL_CORTEX_UP.html Up-regulated in the cerebral cortex of aged (22 months) BALB/c mice, compared to young (2 months) controls 11172053 45/99 John Newman 4.64247297930812e-06 1.36855026979256e-05 1355 1577.09090909091 1413 4.22043888723013e-07 451 2.06474519972753 2.17287103286713 1 3.67076007139376 1354 2943 2101 1413 1396 1592 1976 451 589 2310 1223 1237 M2613 ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF.html Class III of genes transiently induced by EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 153/365 Yaara Zwang 2.29931406928001e-07 2.07203571704733e-06 2620 1963.72727272727 1413 2.09028573599199e-08 190 1.73852942748717 1.797449127445 1 3.61181097499073 2618 1413 455 689 190 4239 2949 3947 1392 304 3405 1238 M3001 CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP.html Genes up-regulated in type 1 (soleus) vs type 2B (EDL) myofibers. 21364395 38/85 Emmanuelle Fouilloux-Meugnier 0.000182913587268145 0.000320543406858087 515 1364.81818181818 1414 1.66298906307962e-05 512 2.35912372489344 2.78939003571709 1 3.01305412633541 512 2337 648 1717 2547 1308 689 1414 884 1508 1449 1239 M16975 NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP.html Up-regulated genes in peripheral zone of human pancreatic cancer growing in the pancreas of nude mice compared to that of the tumor from the central zone. 17699763 199/439 Arthur Liberzon 3.75786512170836e-06 1.16695533202951e-05 835 1470.27272727273 1415 3.41624685510018e-07 816 1.65897225396841 1.92872835548594 1 2.99133266752224 833 1994 816 1054 1314 2316 2036 920 1867 1415 1608 1240 M4965 VALK_AML_CLUSTER_6 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_6.html Top 40 genes from cluster 6 of acute myeloid leukemia (AML) expression profile; all samples are FAB M1 or M2 subtypes and all samples have internal tundem duplication of FLT3 [GeneID=2322]. 15084694 24/55 Jessica Robertson 0.00281116613740532 0.00411146208485685 1025 1810.72727272727 1415 0.000255887699320636 710 1.98969184918753 2.45410070222295 1 1.73530646874967 710 2694 1022 2877 3345 989 852 1415 3054 1938 1022 1241 M6122 BROWNE_HCMV_INFECTION_20HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_20HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 20 h time point that were not up-regulated at the previous time point, 18 h. 11711622 199/539 John Newman 2.72268824664987e-05 5.91219514541303e-05 1055 1620.36363636364 1416 2.47520176620952e-06 866 1.65405210676664 1.79919174252586 1 2.55640243158317 1054 3012 1817 2237 2015 1301 1384 926 1796 1416 866 1242 M6905 JAATINEN_HEMATOPOIETIC_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/JAATINEN_HEMATOPOIETIC_STEM_CELL_DN.html Genes down-regulated in CD133+ [GeneID=8842] cells (hematopoietic stem cells, HSC) compared to the CD133- cells. 16210406 112/410 Arthur Liberzon 2.43500912521742e-11 7.55659123229723e-10 1035 1439.54545454545 1417 2.21364465931307e-12 145 1.8529326961334 1.93492102923023 1 6.17807883110809 1035 1417 145 989 458 2718 2232 2434 2057 317 2033 1243 M1073 REACTOME_POTASSIUM_CHANNELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POTASSIUM_CHANNELS.html Genes involved in Potassium Channels 25/106 Reactome 1.02038299763311e-05 2.55965683695145e-05 1515 1386.81818181818 1418 9.27625209369863e-07 465 1.82557392768812 1.82795764009787 1 3.06410303706181 1513 1043 928 1418 1701 1812 1173 2329 1218 465 1655 1244 M2007 MIKKELSEN_ES_LCP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_LCP_WITH_H3K4ME3.html Genes with low-CpG-density promoters (LCP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in embryonic stem cells (ES). 17603471 78/229 Arthur Liberzon 1.06168248001445e-06 4.91916777462895e-06 3700 1887.81818181818 1418 9.65166356695144e-08 466 1.96154943994514 -2.0100044475391 -1 3.8059080325826 3700 699 466 723 744 3058 4198 1929 1418 873 2958 1245 M8315 MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_DN.html The 'NPM1-mutated signature 2': genes down-regulated in pediatric AML (acute myeloid leukemia) samples with mutated NPM1 [GeneID=4869] compared to the AML cases with the intact gene and without recurring cytogenetic anomalities or M7 phenotype. 17597811 58/115 Arthur Liberzon 1.49856304567019e-07 1.59596964363875e-06 2615 2024.18181818182 1420 1.36233013431552e-08 98 1.84099498770016 1.86495663925385 1 3.90097630119424 2613 585 730 1161 98 4150 3442 4400 1420 471 3196 1246 M10575 DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_DN.html Genes exclusively down-regulated in fibroblasts expressing the XP/CS mutant form of ERCC3 [GeneID=2071] after high dose UVC irradiation. 15608684 55/142 Arthur Liberzon 4.85226671437576e-06 1.41324160485981e-05 1610 1219.09090909091 1420 4.41116128768249e-07 236 1.42653535006042 1.74227105153709 1 2.52885627710139 719 1428 1608 2129 1420 500 678 236 2320 1607 765 1247 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 0.000149279039273568 0.000265674735296596 1055 1740.54545454545 1420 1.49289068125947e-05 923 1.73211177130746 1.73211177130746 1 2.26386295998002 1051 2325 4283 1952 2522 1610 1420 953 944 1163 923 1248 M8637 STREICHER_LSM1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/STREICHER_LSM1_TARGETS_DN.html Genes down-regulated in MCF10A cells (breast cancer) by expression of LSM1 [GeneID=27257] off a letiviral vector. 17001308 15/29 Arthur Liberzon 4.85255173328943e-06 1.41324160485981e-05 805 1354.72727272727 1421 4.41142039692884e-07 295 1.3329872878288 1.397768831048 1 2.36302119664356 805 1968 1944 2003 1421 844 906 758 1971 1987 295 1249 M8617 WEI_MIR34A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WEI_MIR34A_TARGETS.html Potential direct target genes for MIR34A [GeneID=407040] microRNA in IMR32 cells (neuroblastoma). 18504438 98/211 Jessica Robertson 2.56391967792518e-07 2.19144534472488e-06 1865 1338.54545454545 1422 2.33083634248096e-08 216 1.47311218800296 1.77739498579059 1 3.04730158831133 1864 821 1837 1517 216 2115 1260 747 1422 1709 1216 1250 M8776 HELLER_SILENCED_BY_METHYLATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_SILENCED_BY_METHYLATION_UP.html Genes up-regulated in at least one of three multiple myeloma (MM) cell lines treated with the DNA hypomethylating agent decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 18172295 170/565 Jessica Robertson 2.55578428093943e-08 3.92228168327994e-07 1635 1323.90909090909 1422 2.32344028239135e-09 136 1.75290020244374 1.90050860319438 1 4.10482496737111 1635 1087 282 503 136 2653 2266 1422 2051 534 1994 1251 M1496 KIM_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/KIM_HYPOXIA.html Genes up-regulated in normal fibroblasts under hypoxia conditions. 14499499 23/42 John Newman 7.20348239466684e-06 1.92998962272206e-05 795 1302.54545454545 1423 6.54864180110064e-07 119 1.39514076534349 1.41006516648561 1 2.40418484378777 795 2010 1973 1840 1570 538 119 1131 2184 1423 745 1252 M9780 CUI_GLUCOSE_DEPRIVATION http://www.broadinstitute.org/gsea/msigdb/cards/CUI_GLUCOSE_DEPRIVATION.html Representative genes up-regulated in MiaPaCa2 cells (pancreatic cancer) under glucose-deprived conditions. 17409444 49/162 Jessica Robertson 2.7960045836087e-05 6.04897390525871e-05 930 1509 1424 2.54185465361424e-06 843 1.30781739041387 -1.30330943553727 -1 2.01653472091235 929 843 1811 1424 2025 945 1775 2029 2157 1313 1348 1253 M8759 ROPERO_HDAC2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ROPERO_HDAC2_TARGETS.html Genes up-regulated genes in cell lines with HDAC2 [GeneID=3066] loss of function (LOS). 18264134 80/222 Jessica Robertson 1.02493440530602e-05 2.56836503917863e-05 1580 1381.27272727273 1425 9.31762891176497e-07 713 1.64780447941924 -1.36966805365907 -1 2.76484055602737 1580 1255 1052 1045 1703 1545 1567 1910 1399 713 1425 1254 M15841 FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN.html Genes down-regulated in kidney biopsies from patients with well functioning kidneys more than 1-year post transplant compared to the biopsies from normal living kidney donors. 15307835 16/42 Jean Junior 4.40038017657495e-06 1.31422444279351e-05 2320 1945.09090909091 1426 4.00035361647306e-07 783 1.44940654634472 -1.62393928507732 -1 2.5861140792397 2318 2924 3361 2659 1378 1065 783 1108 1024 3350 1426 1255 M4655 HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_DN.html Genes down-regulated during differentiation of immature to mature B lymphocyte. 11779835 26/64 Arthur Liberzon 1.58344192462491e-06 6.37457805738172e-06 1430 1947.63636363636 1426 1.43949369482052e-07 301 1.33553732738421 -1.07229518541458 -1 2.53633543410288 1426 3185 2438 4346 907 629 301 1165 2708 3031 1288 1256 M8857 KIM_WT1_TARGETS_8HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_8HR_UP.html Genes up-regulated in UB27 cells (osteosarcoma) at 8 hr after inducing the expression of a mutant form of WT1 [GeneID=7490]. 17430890 125/284 Arthur Liberzon 4.9386851591442e-06 1.43387104434633e-05 615 1568.81818181818 1427 4.48972385983678e-07 611 1.61322543321117 1.69920301889157 1 2.85609539841604 611 3140 1516 1407 1427 1000 1319 1921 2311 1552 1053 1257 M13537 KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_UP.html Genes up-regulated in MEWO cells (melanoma) after 48h of methionine [PubChem=876] deprivation. 16908595 95/209 Arthur Liberzon 2.55769799692526e-05 5.60588064246576e-05 930 1431.18181818182 1427 2.32520702995488e-06 369 1.89674269457518 2.14161172846737 1 2.94750913319673 930 3111 1051 1537 2103 1519 1531 369 1427 1231 934 1258 M980 KEGG_TRYPTOPHAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TRYPTOPHAN_METABOLISM.html Tryptophan metabolism 16/53 KEGG 0.0023731388376341 0.00349922233894066 1430 1625.90909090909 1430 0.000215972964894765 620 2.19551204673629 -2.02079749637012 -1 1.97100837653602 1430 1384 1194 2442 3029 740 620 2306 1923 1572 1245 1259 M2024 NAKAMURA_ADIPOGENESIS_EARLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_ADIPOGENESIS_EARLY_UP.html Genes up-regulated in mesenchymal stem cells during early phase of adipogenesis, defined as days 1 to 5 of culturing with adipogenic hormones. 12646203 36/96 Arthur Liberzon 4.76448232479043e-06 1.39365569125892e-05 1415 1486.36363636364 1430 4.33135694830562e-07 813 1.34152851800884 1.51822658942341 1 2.38113451904478 1087 1830 2134 1430 1414 1563 1414 813 2093 1691 881 1260 M153 PID_P75_NTR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P75_NTR_PATHWAY.html p75(NTR)-mediated signaling 18832364 56/106 Pathway Interaction Database 9.57150044190195e-07 4.60984738132019e-06 2825 1816.45454545455 1431 8.70136782378179e-08 186 1.81540839767388 2.29547579015681 1 3.54107334620058 2824 1685 1346 186 700 3946 3816 1332 684 1431 2031 1261 M12353 FONTAINE_PAPILLARY_THYROID_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_PAPILLARY_THYROID_CARCINOMA_UP.html Genes up-regulated in papillary thyroid carcinoma (PTC) compared to other thyroid tumors. 17968324 44/119 Arthur Liberzon 1.04769806344037e-06 4.87830942267135e-06 4215 2089.45454545455 1431 9.52453238529249e-08 536 2.50156183422922 -2.12321458467348 -1 4.85698249059763 4213 1431 536 577 739 4575 2353 2688 693 642 4537 1262 M706 REACTOME_GLYCEROPHOSPHOLIPID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCEROPHOSPHOLIPID_BIOSYNTHESIS.html Genes involved in Glycerophospholipid biosynthesis 34/85 Reactome 9.7494732829901e-06 2.46818108071808e-05 1915 1422.09090909091 1432 8.86319680801539e-07 784 1.73757984195183 -1.57797492317207 -1 2.92644897102345 1221 1915 1912 1858 1683 785 1377 784 1122 1554 1432 1263 M1584 LIU_VMYB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_VMYB_TARGETS_UP.html Genes up-regulated in MCF-7 cells (breast cancer) by overexpression of v-MYB oncogenic varian of CMYB [GeneID=4602] off adenovirus vector. 16205643 101/224 Arthur Liberzon 1.12979697330858e-07 1.32355715423101e-06 1275 1343.36363636364 1432 1.02708821029877e-08 67 1.50653382562973 1.56892067225941 1 3.23703003779077 1272 1420 1555 931 67 1476 1500 1492 2336 1432 1296 1264 M8 PID_ENDOTHELIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ENDOTHELIN_PATHWAY.html Endothelins 18832364 46/104 Pathway Interaction Database 5.06728037770644e-06 1.46798824174025e-05 1010 1366.81818181818 1433 4.60662913568901e-07 313 1.73737551219248 1.8831727426304 1 3.06940834873174 1010 1024 927 313 1433 1817 1642 1767 2038 1417 1647 1265 M1773 JEPSEN_SMRT_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/JEPSEN_SMRT_TARGETS.html Genes up-regulated in neural progenitor cells (NPC) isolated from E13 cortical tissue of SMRT [GeneID=9612] knockout mice. 17928865 20/47 Jessica Robertson 0.000245615446277306 0.000420056197538488 1085 2026.09090909091 1433 2.23311701730725e-05 742 2.3267375509437 2.3267375509437 1 2.87182634864728 1081 4332 1433 4124 2942 1087 782 742 2650 2015 1099 1266 M89 BIOCARTA_CDK5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CDK5_PATHWAY.html Phosphorylation of MEK1 by cdk5/p35 down regulates the MAP kinase pathway 7/15 BioCarta 3.18345943443746e-05 6.7715346844185e-05 1490 1526.45454545455 1434 3.18350504021983e-06 335 1.39318318133908 1.57223599295109 1 2.12320516445767 1488 985 3855 1168 2102 2177 1434 993 335 1494 760 1267 M18834 FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_DN http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_DN.html Genes down-regulated in thyroid tumors of uncertain malignancy (T-UM) compared to other thyroid tumors. 17968324 16/65 Arthur Liberzon 5.11422679047385e-06 1.47842484516721e-05 1595 1619.45454545455 1438 4.64930789026581e-07 791 1.81424224536243 1.84627452341355 1 3.20316792235271 1595 1381 791 1499 1438 1731 1309 3932 2018 918 1202 1268 M500 VANTVEER_BREAST_CANCER_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_METASTASIS_UP.html Genes whose expression is significantly and positively correlated with poor breast cancer clinical outcome (defined as developing distant metastases in less than 5 years). 11823860 37/109 Jean Junior 1.86230661741325e-07 1.81807683524969e-06 3945 2206.63636363636 1439 1.69300615914372e-08 148 1.79448428731522 1.93180320474374 1 3.76530482330827 3944 1113 1266 910 148 4489 4088 2653 485 1439 3738 1269 M6489 ZHANG_BREAST_CANCER_PROGENITORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_BREAST_CANCER_PROGENITORS_DN.html Genes down-regulated in cancer stem cells isolated from mammary tumors compared to the non-tumorigenic cells. 18559513 105/242 Leona Saunders 1.37908839205554e-06 5.84912142521847e-06 2490 1749.45454545455 1439 1.25371750595399e-07 790 1.68514383046135 -1.35006177158524 -1 3.22329042174769 2487 1248 934 790 843 3464 2243 1821 1439 1079 2896 1270 M12695 ROSS_LEUKEMIA_WITH_MLL_FUSIONS http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_LEUKEMIA_WITH_MLL_FUSIONS.html Top 100 probe sets associated with MLL fusions [GeneID=4297] irrespective of the lineage of the pediatric acute leukemia. 15226186 53/157 Arthur Liberzon 4.28391923263461e-06 1.29013146041939e-05 1440 1538.54545454545 1440 3.89447961314469e-07 608 1.62917097342444 2.04290891001628 1 2.91164528468285 1440 2417 1832 2332 1364 1030 1025 608 1567 2442 867 1271 M2354 VANLOO_SP3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANLOO_SP3_TARGETS_DN.html Genes down-regulated in E12.5 hearts from mice with SP3 [GeneID=6670] knockout compared to the wild type organ. 17923686 48/134 Arthur Liberzon 2.62235952379473e-06 8.8532973548286e-06 3960 2327.63636363636 1441 2.38396604509477e-07 719 1.82361093472028 1.52069584117414 1 3.36815219313512 3956 1182 719 1415 1166 3908 3506 2912 1441 760 4639 1272 M16518 ST_WNT_CA2_CYCLIC_GMP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_WNT_CA2_CYCLIC_GMP_PATHWAY.html Wnt/Ca2+/cyclic GMP signaling. 13/28 Signaling Transduction KE 1.41052673634721e-05 3.35009036316422e-05 1295 1483.72727272727 1443 1.28230525454512e-06 491 1.43640646950844 1.17496769944081 1 2.34954710840788 1292 1055 2277 1913 1816 1046 491 1443 1661 2349 978 1273 M4960 SMID_BREAST_CANCER_BASAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_BASAL_DN.html Genes down-regulated in basal subtype of breast cancer samles. 18451135 447/1156 Jessica Robertson 1.00542222031944e-22 1.02421924443845e-20 45 1923.45454545455 1445 9.14020200290399e-24 12 1.76625197161677 -1.62599153240893 -1 12.905539594427 3358 12 45 30 287 4485 3274 3850 1445 43 4329 1274 M19993 HUTTMANN_B_CLL_POOR_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUTTMANN_B_CLL_POOR_SURVIVAL_UP.html Up-regulated genes in B-CLL (B-cell chronic leukemia) patients expressing high levels of ZAP70 and CD38 [GeneID=7535;952], which are associated with poor survival. 16932341 190/551 Leona Saunders 5.34579483288647e-07 3.25018412907834e-06 1450 1680 1447 4.859814665332e-08 471 1.54587059610349 1.71028165958769 1 3.1010857317129 1867 544 782 588 471 3821 3091 1446 1893 1447 2530 1275 M14744 ZHAN_MULTIPLE_MYELOMA_LB_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_LB_UP.html Top 50 up-regulated genes in cluster LB of multiple myeloma samples belonging to the low bone disease group. 16728703 22/68 Kevin Vogelsang 0.000405360020370113 0.000666965258235376 1080 2251.18181818182 1448 3.68577026429511e-05 663 1.75893733554221 1.75893733554221 1 2.04190718659303 1080 3573 1427 4414 2984 1102 995 1448 3416 3661 663 1276 M2246 BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_D http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_D.html Category D genes: p53-independent genes whose expression in the absence of S389 phosphorylation is similar to loss of TP53 [GeneID=7157] in MEF (embryonic fibroblast) cells in response to UV-C irradiation. 18195040 160/496 Arthur Liberzon 9.01686079873833e-08 1.11485513727936e-06 2225 1373.54545454545 1449 8.19714651663727e-09 48 1.54450634359549 1.73771248511942 1 3.36069339955467 2223 257 747 906 48 3128 2393 1449 1604 741 1613 1277 M10792 KEGG_MAPK_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MAPK_SIGNALING_PATHWAY.html MAPK signaling pathway 120/294 KEGG 4.0747038329899e-07 2.7892494272413e-06 1750 1428.27272727273 1450 3.7042768978923e-08 367 1.65760129743529 1.81181713914585 1 3.36546662741659 1749 1719 1095 460 367 1633 1358 2496 1450 881 2503 1278 M16407 IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM.html Genes in the expression cluster 'LT-HSC Shared': up-regulated in long term hematopoietic stem cells (LT-HSC) from adult bone marrow and fetal liver. 12228721 173/476 John Newman 1.32653827786555e-07 1.46954098583404e-06 1450 1347.45454545455 1450 1.20594396168372e-08 280 1.81183045680025 1.83717031481825 1 3.86291590595908 1450 1163 314 804 546 2305 1823 2711 1546 280 1880 1279 M1568 APRELIKOVA_BRCA1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/APRELIKOVA_BRCA1_TARGETS.html Genes down-regulated in embryonic stem cells with BRCA1 [GeneID=672] loss of function (LOF). 11384963 41/85 John Newman 2.80226102950081e-05 6.05971166785455e-05 1290 1706.63636363636 1450 2.54754247643427e-06 661 2.25039080736391 2.71152456092066 1 3.46926307404531 1288 3083 1530 2235 2026 1450 1359 791 661 3173 1177 1280 M1969 MIKKELSEN_IPS_ICP_WITH_H3K4ME3_AND_H327ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_ICP_WITH_H3K4ME3_AND_H327ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the bivalent tri-methylation marks at H3K4 (H3K4me3) and H3K27 (H3K27me3) in MCV8.1 cells (induced pluripotent cells, iPS). 18509334 76/250 Jessica Robertson 1.56598833066893e-07 1.63071584833658e-06 1080 1303.45454545455 1450 1.42362585648909e-08 255 1.85037033482312 1.79017638846303 1 3.91451574780342 1079 700 320 818 1450 1924 1784 2430 1685 255 1893 1281 M3029 ALONSO_METASTASIS_EMT_DN http://www.broadinstitute.org/gsea/msigdb/cards/ALONSO_METASTASIS_EMT_DN.html EMT (epithelial-mesenchymal transition) genes down-regulated genes in melanoma tumous that developed metastatic disease compared to primary melanoma that did not. 17409456 2/19 Jessica Robertson 6.60451605047532e-07 3.66257540976655e-06 1330 1853.8 1451 7.3383533212516e-08 87 2.54802914711823 2.54802914711823 1 5.06314238597313 1327 1575 4506 NA 2641 777 1042 87 3711 2172 700 1282 M3506 MOREIRA_RESPONSE_TO_TSA_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOREIRA_RESPONSE_TO_TSA_DN.html Down-regulated in CD4+ [GeneID=920] T lymphocytes after 4 h treatment with 100 nM TSA [PubChem=5562]. 14606959 10/24 John Newman 1.98086873946803e-05 4.49508518796475e-05 4350 2192.27272727273 1452 1.800805977576e-06 456 1.72468566361443 1.31445400614126 1 2.74059604061202 4349 1392 949 1452 1918 4302 3412 1384 743 456 3758 1283 M2348 TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP.html Genes up-regulated in leukemic progenitor cells expressing activated fusion of ESWR1 and FLI1 [GeneID=2130, 2313] compared to normal hematopoetic progenitors. 17875932 179/424 Arthur Liberzon 5.87516000603948e-07 3.42421053989756e-06 1045 1387.09090909091 1452 5.34105597728869e-08 366 1.70709672069981 1.79327306577926 1 3.41037764529399 1043 810 366 2438 508 1795 1452 1819 2501 825 1701 1284 M265 ODONNELL_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_METASTASIS_UP.html Up-regulated genes in the signature set for lymph node metastasis in head and neck squamous cell carcinoma (HNSCC). 15558013 55/204 Leona Saunders 1.32879710342777e-06 5.73364937998389e-06 1065 1400.81818181818 1453 1.20799809638195e-07 608 2.1046251196057 2.03565247351236 1 4.03232284519786 1061 2069 668 1661 824 1491 1713 2425 1453 608 1436 1285 M1787 WORSCHECH_TUMOR_REJECTION_UP http://www.broadinstitute.org/gsea/msigdb/cards/WORSCHECH_TUMOR_REJECTION_UP.html Up-regulated genes defining rejection of mammary carcinoma (MMC) tumors. 18381452 29/115 Jessica Robertson 1.6988888219314e-06 6.64677658017817e-06 1060 1563.81818181818 1453 1.54444557622952e-07 811 1.4160315242855 1.48115871252795 1 2.6798035747347 1059 1918 1531 2086 942 1168 1081 2345 2808 811 1453 1286 M7327 LIN_NPAS4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIN_NPAS4_TARGETS_DN.html Genes down-regulated in neurons after NPAS4 [GeneID=266743] knockdown by RNAi. 18815592 41/113 Jessica Robertson 6.32601598194979e-06 1.7416986422689e-05 1510 1365.18181818182 1454 5.75094015658217e-07 588 1.65559982453173 1.72487922705364 1 2.88000200156357 1510 1538 1184 1454 1522 749 601 3314 1591 966 588 1287 M1959 HINATA_NFKB_TARGETS_KERATINOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HINATA_NFKB_TARGETS_KERATINOCYTE_DN.html Genes down-regulated in primary keratinocytes by expression of p50 (NFKB1) and p65 (RELA) [GeneID=4790;5970] components of NFKB. 12673201 16/44 Arthur Liberzon 4.37736522801038e-05 8.92228510589675e-05 2230 1380.36363636364 1454 3.97950211579503e-06 477 2.23299822486561 -2.23648133090234 -1 3.3053054145383 2227 1454 807 1029 2170 1530 1915 1227 477 688 1660 1288 M19422 BIOCARTA_IL17_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL17_PATHWAY.html IL 17 Signaling Pathway 5/14 BioCarta 0.00148026669093975 0.00222753041546039 1235 1954.36363636364 1455 0.000148125365160757 420 1.55548206728826 1.55548206728826 1 1.50794901510447 1234 1515 3842 3899 3018 702 420 1455 3344 1156 913 1289 M1662 REACTOME_SIGNALING_BY_BMP http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_BMP.html Genes involved in Signaling by BMP 13/27 Reactome 5.2918937196241e-06 1.51761407406111e-05 885 1639 1455 4.81082404438284e-07 517 1.39484681472726 1.5458644511245 1 2.45690379262035 884 3097 2543 2820 1455 661 517 1065 2207 1748 1032 1290 M1436 GUO_HEX_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUO_HEX_TARGETS_UP.html Genes up-regulated in day 6 embryoid bodies derived from embryonic stem cells (ES) with HEX [GeneID=3087] knockout. 12791650 63/141 Kevin Vogelsang 5.3044591250448e-05 0.000105593438657434 1015 1671.54545454545 1456 4.82235184192684e-06 761 1.84490067421252 1.79696895678514 1 2.68150290180198 1012 3389 1456 2337 2224 961 761 1678 2251 1298 1020 1291 M2013 MIKKELSEN_NPC_ICP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_ICP_WITH_H3K4ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in neural progenitor cells (NPC). 17603471 312/901 Arthur Liberzon 2.80070915369738e-07 2.29042287857346e-06 1435 1687.81818181818 1456 2.5460995547651e-08 238 1.33348156155245 1.47576255471026 1 2.74910838595213 1432 673 2700 3055 238 1456 1283 1673 2522 2320 1214 1292 M17843 NIELSEN_SCHWANNOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_SCHWANNOMA_UP.html Top 20 positive significant genes associated with schwannoma tumors. 11965276 7/25 John Newman 8.8709304738193e-06 2.28276662275218e-05 1380 1605.81818181818 1457 8.8709658860516e-07 269 1.4193442292439 1.69986403857664 1 2.40806908645322 2251 383 4418 1380 1684 1718 1457 1376 269 1008 1720 1293 M12037 SHAFFER_IRF4_TARGETS_IN_PLASMA_CELL_VS_MATURE_B_LYMPHOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/SHAFFER_IRF4_TARGETS_IN_PLASMA_CELL_VS_MATURE_B_LYMPHOCYTE.html IRF4 [GeneID=3662] target genes up-regulated in plasma cells compared to mature B lymphocytes. 18568025 44/93 Jessica Robertson 9.03659156643243e-07 4.43872831030423e-06 1145 1707.81818181818 1458 8.21508661659287e-08 678 1.30162283413998 1.33074294338795 1 2.5467169243906 1142 1725 2137 1708 678 1367 1349 3154 2992 1076 1458 1294 M1377 HE_PTEN_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HE_PTEN_TARGETS_UP.html Genes up-regulated in the intestine after the tissue specific knockout of PTEN [GeneID=5728] by Cre-lox. 17237784 10/26 Jessica Robertson 4.32310088205579e-06 1.29610049477373e-05 1825 1381.54545454545 1459 3.93009943379148e-07 132 2.13299487802225 2.58694171408784 1 3.81051355346905 1825 2024 1477 1365 2689 1459 915 187 132 1366 1758 1295 M19164 RICKMAN_HEAD_AND_NECK_CANCER_D http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_D.html Cluster d: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 13/70 Jessica Robertson 0.000795253594904175 0.00125010343700804 905 1567.81818181818 1461 7.23219279879294e-05 726 2.42024790587164 -2.42024790587164 -1 2.56823183590864 901 1461 726 1984 2932 1322 2031 1695 1424 956 1814 1296 M18536 FALVELLA_SMOKERS_WITH_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/FALVELLA_SMOKERS_WITH_LUNG_CANCER.html Genes that distinguish normal from cancer (lung adenocarcinoma) samples and smokers from non-smoking subjects. 17724461 52/126 Jessica Robertson 8.78559538142948e-07 4.35193445638251e-06 2380 1738.63636363636 1463 7.98690808174288e-08 457 1.71097353023499 1.70919196079312 1 3.35300407168197 2380 1265 1690 457 668 2238 1380 3447 802 1463 3335 1297 M2116 VERHAAK_GLIOBLASTOMA_NEURAL http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_GLIOBLASTOMA_NEURAL.html Genes correlated with neural type of glioblastoma multiforme tumors. 20129251 79/198 Arthur Liberzon 9.55710940584774e-06 2.42407166832711e-05 1475 1494.45454545455 1464 8.68831902138873e-07 1114 1.54185718163601 1.73989236955682 1 2.60122474325729 1472 1172 1464 1379 1678 1902 1774 1114 1262 1782 1440 1298 M5487 ICHIBA_GRAFT_VERSUS_HOST_DISEASE_D7_UP http://www.broadinstitute.org/gsea/msigdb/cards/ICHIBA_GRAFT_VERSUS_HOST_DISEASE_D7_UP.html Hepatic graft versus host disease (GVHD), day 7: up-regulated in allogeneic vs syngeneic bone marrow transplant. 12663442 78/204 Arthur Liberzon 2.47824810499015e-06 8.53480041710536e-06 1465 1551 1465 2.25295536062053e-07 570 1.69722987174144 1.96807080200201 1 3.14460167126793 1465 570 821 924 1129 3069 2598 1499 1520 661 2805 1299 M1754 ZHENG_FOXP3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_DN.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are down-regulated both in developing (located in the thymus) and mature (from peripheral blood) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 2/11 Jessica Robertson 0.000136557403863797 0.000244613147746847 1790 1820.2 1466 1.51739658381042e-05 116 2.28071318215885 -2.28071318215885 -1 3.01078658179156 1787 2648 4443 NA 3270 1145 967 671 116 2166 989 1300 M13669 TSAI_DNAJB4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TSAI_DNAJB4_TARGETS_UP.html Genes up-regulated in CL1-5 cells (lung cancer) overexpressing DNAJB4 [GeneID=11080] off a plasmid vector. 16788156 14/34 Jessica Robertson 9.75280466852769e-07 4.65867917193892e-06 1470 1624 1466 8.8661899927631e-08 709 1.05714331508346 1.03423673396864 1 2.06025915593482 1466 1138 2220 2653 709 1372 909 1783 2941 1901 772 1301 M2215 WIERENGA_STAT5A_TARGETS_GROUP1 http://www.broadinstitute.org/gsea/msigdb/cards/WIERENGA_STAT5A_TARGETS_GROUP1.html Genes up-regulated to their maximal levels in CD34+ [GeneID=947] cells by intermediate activity levels of STAT5A [GeneID=6776]; predominant long-term growth and self-renewal phenotype. 18779318 112/243 Arthur Liberzon 8.31601073063306e-06 2.16854904194471e-05 1315 1438.09090909091 1466 7.56003833214594e-07 777 1.83006571801742 1.88498975062492 1 3.11981410825178 1311 1905 777 1466 1625 1132 1778 1289 1747 1292 1497 1302 M12313 KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_UP.html Genes up-regulated in MEWO cells (melanoma) after 96 h of methionine [PubChem=876] deprivation. 16908595 87/191 Arthur Liberzon 2.31138010954908e-05 5.14298537195963e-05 895 1569.27272727273 1467 2.10127672172476e-06 635 1.73580518693304 1.92524071978426 1 2.72116250480131 894 3265 1486 1934 1965 1451 1403 635 1788 1467 974 1303 M19261 YAGI_AML_WITH_T_8_21_TRANSLOCATION http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_WITH_T_8_21_TRANSLOCATION.html Genes specifically expressed in samples from patients with pediatric AML (acute myeloid leukemia ) bearing t(8;21) translocation. 12738660 244/708 Arthur Liberzon 2.06034124664033e-07 1.93870664292301e-06 1470 1307.90909090909 1469 1.87303767235925e-08 168 1.55571017560906 1.56310122501688 1 3.24842793103637 1469 677 922 1121 168 1849 1538 1942 2066 827 1808 1304 M2535 PECE_MAMMARY_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/PECE_MAMMARY_STEM_CELL_DN.html The '3/3 signature': genes consistently down-regulated in all three pools of normal mammary stem cells (defined by their ability to retain the dye PKH26). 20074520 87/217 Arthur Liberzon 4.5468439628542e-09 8.20959209284467e-08 375 1267.45454545455 1469 4.13349452022851e-10 1 1.84425811975229 1.84110444499184 1 4.77663869999408 373 2802 1980 2375 2411 32 272 206 2021 1469 1 1305 M2 PID_SMAD2_3NUCLEAR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SMAD2_3NUCLEAR_PATHWAY.html Regulation of nuclear SMAD2/3 signaling 18832364 55/130 Pathway Interaction Database 4.48484125884087e-06 1.33350038952591e-05 1470 1437.54545454545 1470 4.07713672863984e-07 189 1.93312531849777 2.19726348568178 1 3.44472446787286 1470 2980 1381 670 1800 2069 2009 189 810 1605 830 1306 M14487 HOEGERKORP_CD44_TARGETS_DIRECT_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOEGERKORP_CD44_TARGETS_DIRECT_UP.html Genes directly up-regulated by CD44 [GeneID=960] stimulation of B lymphocytes. 12411303 19/48 Kevin Vogelsang 1.38308244428782e-06 5.85372787868602e-06 1200 1804.72727272727 1470 1.25734846708757e-07 720 1.39679312848089 1.31393869992173 1 2.67156765748517 1198 1966 2297 3348 844 720 780 1470 3439 2428 1362 1307 M8273 CROONQUIST_NRAS_VS_STROMAL_STIMULATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_NRAS_VS_STROMAL_STIMULATION_UP.html Genes up-regulated in ANBL-6 cell line (multiple myeloma, MM) expressing an activated form of NRAS [GeneID=4893] off a plasmid vector compared to those co-cultured with bone marrow stromal cells. 12791645 29/67 Arthur Liberzon 4.54522564746084e-06 1.34803337873427e-05 1610 1610.45454545455 1471 4.13203185270652e-07 1149 1.86424963406296 1.51807915873228 1 3.31878388751415 1609 1364 1149 1471 1388 1722 1273 2946 1557 1223 2013 1308 M19096 KEGG_BLADDER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BLADDER_CANCER.html Bladder cancer 27/58 KEGG 9.48783460480549e-06 2.41143902706839e-05 1645 1330.09090909091 1472 8.62534138434756e-07 255 2.01898988237954 2.37268252015095 1 3.4078568053453 1643 1450 1286 1598 1673 2219 1472 255 301 1726 1008 1309 M2096 ABDULRAHMAN_KIDNEY_CANCER_VHL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ABDULRAHMAN_KIDNEY_CANCER_VHL_DN.html Genes down-regulated in the RCC4 cells (renal cell carcinoma, RCC) expressing VHL [GeneID=7428] mutants Type 1 and 2B (associated with RCC) but not those of Type 2A and 2C (not associated with RCC). 17001320 14/40 Arthur Liberzon 3.4937834000327e-05 7.3219449966696e-05 2220 1415.36363636364 1473 3.17621716859932e-06 99 2.99271641113637 3.54889245679116 1 4.52376004041989 2220 1969 870 697 2099 2193 1557 1370 99 1022 1473 1310 M11896 LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN.html Genes whose expression profile is specific to Cluster IIa of urothelial cell carcinoma (UCC) tumors. 16532037 107/246 Leona Saunders 5.78423602148747e-07 3.4051419593832e-06 1930 1594.54545454545 1476 5.25839776570756e-08 499 1.59287744620306 1.57428729328221 1 3.18360647424846 1929 1476 1282 1428 499 1396 1459 2716 1877 1852 1626 1311 M222 PID_CXCR3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CXCR3_PATHWAY.html CXCR3-mediated signaling events 18832364 26/62 Pathway Interaction Database 8.93796424989779e-06 2.297254422068e-05 1105 1780.90909090909 1477 8.1254550567911e-07 767 1.14241438376466 1.26377974594328 1 1.93708068018542 1103 1451 2565 1723 1649 1280 1239 767 3312 3024 1477 1312 M13616 SUH_COEXPRESSED_WITH_ID1_AND_ID2_UP http://www.broadinstitute.org/gsea/msigdb/cards/SUH_COEXPRESSED_WITH_ID1_AND_ID2_UP.html Genes whose expression positively correlates with that of both ID1 and ID2 [GeneID=3397;3398] genes in a cohort of 285 patients with primaly AML (acule myelogenous leukemia) [PMID=15084694]. 18542061 14/22 Jessica Robertson 7.93594904274558e-05 0.000151108724966704 545 1573.63636363636 1477 7.21475938790069e-06 268 1.34550673213389 1.34550673213389 1 1.87909723066523 544 2638 2946 2141 2496 457 268 543 1477 3148 652 1313 M2002 MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED.html Genes with high-CpG-density promoters (HCP) without H3 methylation marks at K4 and K27 in embryonic stem cells (ES). 17603471 38/135 Arthur Liberzon 0.00234856992454062 0.00346517590251805 1480 2085.45454545455 1477 0.000213734622825035 980 1.36109494841272 1.40309286234553 1 1.22402778228907 1477 2771 1402 3566 3027 1225 980 2423 3502 1234 1333 1314 M9197 ELVIDGE_HYPOXIA_BY_DMOG_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HYPOXIA_BY_DMOG_UP.html Genes up-regulated in MCF7 cells (breast cancer) treated with hypoxia mimetic DMOG [PubChem=3080614]. 16565084 96/201 Arthur Liberzon 4.98868257817191e-07 3.09990333163866e-06 1245 1348.72727272727 1478 4.53516700854312e-08 447 1.6357241506221 1.74129036735355 1 3.29362872579671 1241 1478 844 1173 447 1696 1688 2217 1934 584 1534 1315 M14265 APPIERTO_RESPONSE_TO_FENRETINIDE_DN http://www.broadinstitute.org/gsea/msigdb/cards/APPIERTO_RESPONSE_TO_FENRETINIDE_DN.html Genes down-regulated in A2780 cells (ovarian carcinoma) exposed to fenretinide [PubChem=1744]. 17213814 51/108 Arthur Liberzon 5.96563282572637e-05 0.000117408464600394 760 1609.18181818182 1479 5.42344963547906e-06 558 1.76986970528782 2.02975490662413 1 2.54264841708588 756 2652 2408 2313 2258 1479 884 558 1150 2003 1240 1316 M17844 KEGG_OTHER_GLYCAN_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OTHER_GLYCAN_DEGRADATION.html Other glycan degradation 7/17 KEGG 0.000191544665871676 0.000334418146153009 820 1900.36363636364 1480 1.91561178086396e-05 715 1.58480737927467 -1.58480737927467 -1 2.01344276644441 817 1896 3791 2769 3140 1189 1382 715 1480 2254 1471 1317 M653 REACTOME_SYNTHESIS_OF_PA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PA.html Genes involved in Synthesis of PA 9/29 Reactome 2.72640109479226e-06 9.11813494186151e-06 1860 1689.90909090909 1481 2.72640443976636e-07 542 1.79729076654428 -1.43827533164073 -1 3.31112997256433 1857 1147 3947 2499 1224 824 542 2058 1203 1807 1481 1318 M1363 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX5_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX5_DN.html Early prostate development genes (down-regulated at 12 hr dihydrotestosterone [PubChem=10635]) which are also down-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 10/20 Jessica Robertson 0.000355484700869563 0.000590081937043845 2110 1611.72727272727 1481 3.23220140446261e-05 712 1.38138370375652 -1.80917822290983 -1 1.63047226628253 2106 1068 2038 712 2700 996 1916 866 1481 2711 1135 1319 M2777 AMIT_SERUM_RESPONSE_240_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_240_MCF10A.html Genes whose expression peaked at 240 min after stimulation of MCF10A cells with serum. 17322878 57/123 Leona Saunders 5.58136267702738e-07 3.33207606048012e-06 1875 1399.72727272727 1483 5.07396735728193e-08 399 2.10808721332593 -1.76345941277399 -1 4.22059005329273 1873 1483 480 399 486 3019 2710 2060 552 792 1543 1320 M18219 BREUHAHN_GROWTH_FACTOR_SIGNALING_IN_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/BREUHAHN_GROWTH_FACTOR_SIGNALING_IN_LIVER_CANCER.html Growth factor signaling components up-regulated in hepatocellular carcinoma (HCC). 16799620 15/31 Arthur Liberzon 6.82168125992197e-05 0.000132475749622853 650 1542.18181818182 1484 6.20172072123255e-06 404 1.57483075073397 1.58992790635881 1 2.23226457578577 650 2346 1754 2377 2823 475 480 1301 2870 1484 404 1321 M2778 TAVAZOIE_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/TAVAZOIE_METASTASIS.html Putative metastasis genes: up-regulated in metastatic cell lines LM2 (lung) and BoM2 (bone) relative to the parental MDA-MB-231 line (breast adenocarcinoma). 18185580 70/262 Jessica Robertson 1.28720204342021e-05 3.10438948814571e-05 1420 1399.36363636364 1484 1.17019052254181e-06 511 1.97303919812846 2.26926901039009 1 3.25118111512689 1417 2576 511 890 1776 1973 1726 564 1484 923 1553 1322 M16812 KERLEY_RESPONSE_TO_CISPLATIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/KERLEY_RESPONSE_TO_CISPLATIN_UP.html Genes genes up-regulated in NT2/D1 cells (embryonal carcinoma) in response to treatment with cisplatin [PubChem=2767]. 15940259 38/77 Leona Saunders 5.78616735051798e-06 1.62651350956972e-05 2045 1621.09090909091 1486 5.26016597148572e-07 496 1.84186012578561 2.32081406891788 1 3.22401731327291 2042 949 1607 1056 1486 3252 2538 740 496 2196 1470 1323 M1139 DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP.html Genes up-regulated in squamous cell carcinoma (SCC) compared to normal skin. 17525749 103/272 Arthur Liberzon 3.79261389166352e-07 2.69640744894893e-06 1820 1440.81818181818 1486 3.4478314049802e-08 336 1.60748631767584 1.74287800489268 1 3.27235550801342 1819 1008 883 1322 336 2275 1486 1510 2256 1171 1783 1324 M3395 MARTORIATI_MDM4_TARGETS_FETAL_LIVER_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTORIATI_MDM4_TARGETS_FETAL_LIVER_DN.html Genes down-regulated in non-apoptotic tissues (fetal liver) after MDM4 [GeneID=4194] knockout. 15608685 334/902 Arthur Liberzon 1.22996165645244e-06 5.46742391794822e-06 815 1459.18181818182 1486 1.11814758553811e-07 488 1.60159841605617 1.76315233173151 1 3.08064500031385 815 2729 2152 1805 796 488 750 1486 1730 2753 547 1325 M1276 XU_RESPONSE_TO_TRETINOIN_AND_NSC682994_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_RESPONSE_TO_TRETINOIN_AND_NSC682994_UP.html Genes up-regulated synergistically in NB4 cells (acute promyelocytic leukemia, APL) by tretinoin and NSC682994 [PubChem=444795;388304]. 16140955 15/48 Kevin Vogelsang 1.23408365071303e-06 5.47519563194705e-06 1720 1182.27272727273 1486 1.12189485724476e-07 307 1.69490200718885 1.94967950792783 1 3.25973055122311 1718 362 1508 704 798 1982 1599 904 307 1486 1637 1326 M13976 GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_1_UP.html Genes exclusively up-regulated in B lymphocytes from WM (Waldenstroem's macroblobulinemia) patients but with a similiar expression pattern in the normal cells and in the cells from CLL (chronic lymphocytic leukemia) patients. 17252022 6/16 Arthur Liberzon 0.000170110654306659 0.000299563519759866 970 1854.63636363636 1486 1.70123677645392e-05 165 1.79666364302021 1.79666364302021 1 2.31399102835573 969 2407 4590 2552 3355 747 165 1073 991 2066 1486 1327 M223 PID_BETA_CATENIN_NUC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BETA_CATENIN_NUC_PATHWAY.html Regulation of nuclear beta catenin signaling and target gene transcription 18832364 43/123 Pathway Interaction Database 5.48216221141542e-07 3.29701174035217e-06 255 1217.36363636364 1487 4.98378507046497e-08 31 1.92128595885372 2.04657023821213 1 3.84982283918758 469 3019 1487 1572 2077 167 255 253 1521 2540 31 1328 M11218 TURJANSKI_MAPK7_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TURJANSKI_MAPK7_TARGETS.html Examples of transcription factors whose activities are regulated by MAPK7 [GeneID=5598] phosphorylation. 17496919 5/9 Arthur Liberzon 2.47071467863475e-05 5.44323882655499e-05 1415 1833.54545454545 1487 2.47074214900421e-06 376 2.09180949897451 2.09180949897451 1 3.26041664807986 1411 2676 4202 2044 2782 1487 1261 376 710 1869 1351 1329 M9343 BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G5, defined by unsupervised clustering. 17187432 16/56 Yujin Hoshida 0.000115080730535317 0.000209505945333527 1580 1626.18181818182 1487 1.04624318893467e-05 875 1.38665835143966 1.63854130438198 1 1.86464143367004 1431 875 1419 1314 2447 1593 1482 1487 2683 1577 1580 1330 M6110 BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_DN.html Genes down-regulated in patients at the incipient stage of Alzheimer's disease. 14769913 134/311 John Newman 3.28395471512877e-05 6.95059250004219e-05 1105 1392.09090909091 1488 2.98545794178626e-06 308 1.89880313129631 2.18633107452337 1 2.88590077467164 1104 2606 1336 1488 2272 1144 1495 487 1564 1509 308 1331 M19832 REACTOME_CELL_DEATH_SIGNALLING_VIA_NRAGE_NRIF_AND_NADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_DEATH_SIGNALLING_VIA_NRAGE_NRIF_AND_NADE.html Genes involved in Cell death signalling via NRAGE, NRIF and NADE 37/83 Reactome 5.54176180640256e-07 3.31656396229916e-06 3295 1914.36363636364 1492 5.03796654760294e-08 485 1.59054818520709 -1.4756713380781 -1 3.18560615237937 3291 1027 1492 569 485 1779 2923 4664 907 818 3103 1332 M17312 ZIRN_TRETINOIN_RESPONSE_WT1_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZIRN_TRETINOIN_RESPONSE_WT1_UP.html Genes up-regulated in MZ128 cells (Wilms tumor with mutated WT1 [GeneID=7490]) after treatment with 10 microM tretinoin (ATRA) [PubChem=444795] for 24 h. 15897880 20/34 Leona Saunders 1.63071215889758e-05 3.78292929534358e-05 1495 1316.45454545455 1492 1.48247658763309e-06 541 1.64399388511081 1.78291449324915 1 2.65738853260309 827 1603 1096 1157 1867 1492 1493 1543 1616 541 1246 1333 M9400 REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING.html Genes involved in p75 NTR receptor-mediated signalling 51/116 Reactome 3.31574475980348e-07 2.47808292574787e-06 3605 1964.54545454545 1493 3.01431387230753e-08 301 1.70074652207362 1.85282335175868 1 3.48500143726978 3604 937 1493 529 301 1832 2982 4516 929 853 3634 1334 M1202 TERAMOTO_OPN_TARGETS_CLUSTER_6 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_6.html Cluster 6: genes exhibiting prolonged up-regulation (>72 h) after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 19/44 Arthur Liberzon 4.00917058082223e-07 2.7690972138105e-06 1515 1412.27272727273 1493 3.64470119221248e-08 361 1.39535944392811 1.79028931160841 1 2.83463706383414 1515 964 2151 1591 361 1387 806 1493 2210 1453 1604 1335 M4956 BIOCARTA_MONOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MONOCYTE_PATHWAY.html Monocyte and its Surface Molecules 6/16 BioCarta 9.18730460418643e-07 4.4892293404815e-06 525 1536.90909090909 1494 9.18730840248409e-08 48 2.34804051426731 2.34804051426731 1 4.58989007147035 525 1664 3848 1391 1494 272 59 1641 3920 2044 48 1336 M2194 OHGUCHI_LIVER_HNF4A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OHGUCHI_LIVER_HNF4A_TARGETS_DN.html Genes down-regulated in liver samples of liver-specific knockout of HNF4A [GeneID=3172]. 18426912 55/243 Arthur Liberzon 1.54085998036891e-07 1.6225173848247e-06 2575 1604.72727272727 1494 1.40078189844486e-08 274 1.92863910707277 -2.1093299103048 -1 4.08163889020249 2575 1261 318 1494 1798 1481 3167 1751 1337 274 2196 1337 M2291 PASINI_SUZ12_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PASINI_SUZ12_TARGETS_UP.html Genes up-regulated in ES (embryonic stem cells) with defficient SUZ12 [GeneID=23512]. 17339329 69/167 Arthur Liberzon 2.12558778409041e-07 1.97452507215338e-06 3745 2033.18181818182 1495 1.93235271769062e-08 101 1.86568514973312 -1.74513110246099 -1 3.8902546715891 3744 101 576 331 173 4296 2473 3609 1495 1013 4554 1338 M209 PID_P38_GAMMA_DELTA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_GAMMA_DELTA_PATHWAY.html Signaling mediated by p38-gamma and p38-delta 18832364 8/12 Pathway Interaction Database 0.000179772606076267 0.000315392898567349 1600 1743.54545454545 1498 1.79787150917765e-05 785 1.60172166785481 -1.62486655615178 -1 2.04982498145905 1597 1984 3905 1498 2560 1195 1445 1240 2134 785 836 1339 M2604 ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_2HR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_2HR.html Cell cycle genes significantly (p =< 0.05) changed in fibroblast cells at 2 h after exposure to ionizing radiation. 17404513 5/9 Itai Pashtan 0.00209329414409654 0.00310024537270429 1040 2131.27272727273 1499 0.000209526860841946 1039 1.71555212686476 1.71555212686476 1 1.57309614712267 1039 1400 4684 2444 3023 1264 1227 2612 1329 2923 1499 1340 M15285 BIOCARTA_NFKB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NFKB_PATHWAY.html NF-kB Signaling Pathway 17/37 BioCarta 1.29992300735034e-05 3.13184535344148e-05 1505 1466.09090909091 1501 1.18175517120197e-06 454 1.30948194645153 -1.35719202756951 -1 2.15593866843912 1504 1501 2622 1254 1779 949 2178 454 819 2209 858 1341 M1919 COLINA_TARGETS_OF_4EBP1_AND_4EBP2 http://www.broadinstitute.org/gsea/msigdb/cards/COLINA_TARGETS_OF_4EBP1_AND_4EBP2.html Genes up-regulated in MEF cells (embryonic fibroblast) with double knockout of the translation repressors 4EBP1 [GeneID=1978] and 4EBP2 [GeneID=1979]. 18272964 273/630 Jessica Robertson 1.35863668908933e-06 5.81422057084255e-06 1505 1717.36363636364 1501 1.23512502557511e-07 835 1.49388422955504 1.64365922486511 1 2.85887430734342 1501 1410 980 1368 835 2819 1997 1906 2602 951 2522 1342 M1595 BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_UP.html Up-regulated genes in non-neoplastic mucosa samples from colon cancer patients who developed recurrence of the disease. 16091735 16/38 Leona Saunders 9.24716453061159e-05 0.000172005307788235 1380 1875.54545454545 1502 8.40686657776296e-06 567 1.10037549206207 1.10272133061532 1 1.51412814646433 1378 1502 2463 2741 2739 974 811 567 3756 2730 970 1343 M17552 MAINA_VHL_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAINA_VHL_TARGETS_DN.html Genes down-regulated in RCC4 cells (renal cell carcinoma) engineered to stably express VHL [GeneID=7428] off a plasmid vector. 15824735 14/27 Leona Saunders 2.56713653084281e-05 5.62130924463991e-05 3375 1960 1503 2.3337877152192e-06 560 2.36094127033118 -2.83245364730076 -1 3.6678365311149 3371 1503 695 820 1995 4162 3425 1488 608 560 2933 1344 M12746 KOYAMA_SEMA3B_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOYAMA_SEMA3B_TARGETS_UP.html Genes up-regulated in NCI-H1299 cells (large cell neuroendocrine carcinoma) stably expressing SEMA3B [GeneID=7869]. 18985860 170/474 Jessica Robertson 1.2631771040124e-07 1.42632479744629e-06 2215 1457.27272727273 1503 1.14834288776402e-08 79 1.55282195928117 1.75986370874731 1 3.31805436843053 2214 256 841 855 79 3444 2960 1899 1503 469 1510 1345 M2313 DELPUECH_FOXO3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DELPUECH_FOXO3_TARGETS_UP.html Genes up-regulated in DL23 cells (colon cancer) upon expression of an activated form of FOXO3 [GeneID=2309]. 17452451 59/143 Arthur Liberzon 6.38178504802873e-07 3.60301743795935e-06 3945 1971.09090909091 1504 5.80162445387722e-08 539 1.75533808809978 -1.74011105840855 -1 3.49256888836885 3945 1103 819 923 539 2623 3563 2344 1504 841 3478 1346 M853 REACTOME_MYOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MYOGENESIS.html Genes involved in Myogenesis 17/38 Reactome 1.07337724696779e-06 4.95063560953846e-06 1525 1224.72727272727 1507 9.75797973334151e-08 103 1.84255499811144 2.32339645522844 1 3.57316320464732 1523 1607 1507 2330 1645 991 830 103 580 1702 654 1347 M1683 DURCHDEWALD_SKIN_CARCINOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DURCHDEWALD_SKIN_CARCINOGENESIS_UP.html Genes up-regulated upon skin specific knockout of FOS [GeneID=2353] by cre-lox in the K5-SOS-F mice (express a constitutively active form of SOS1 [GeneID=6654] in the skin). 18757399 68/170 Jessica Robertson 6.15808595096947e-06 1.70773313354014e-05 4095 2232.81818181818 1509 5.59827562574546e-07 578 1.92257905416946 -1.45479010794693 -1 3.35043692004578 4091 578 925 1294 1509 2999 4257 2608 1110 1140 4050 1348 M2300 VANDESLUIS_COMMD1_TARGETS_GROUP_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_COMMD1_TARGETS_GROUP_3_DN.html Genes down-regulated in 9.5 days post coitus (dpc) embryos with COMMD1 [GeneID=150684] knockout compared to normal 9.5 dpc embryos. 17371845 21/54 Arthur Liberzon 0.000100773499993793 0.000185768930358345 905 1718.54545454545 1509 9.16164693950154e-06 660 1.49900302962101 1.6574275883405 1 2.04432595887986 905 1735 1509 2831 2419 860 660 1103 3850 2089 943 1349 M12524 KEGG_HISTIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HISTIDINE_METABOLISM.html Histidine metabolism 11/36 KEGG 0.000154958043213298 0.000274842312830247 1240 1766.54545454545 1510 1.40880871666319e-05 903 1.88037161051609 -1.58319331350333 -1 2.4475113500295 1236 1061 903 2066 2509 1127 1221 3180 2849 1510 1770 1350 M15410 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN.html Genes down-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 16 days after transduction. 16818636 86/287 Arthur Liberzon 6.97508973549206e-07 3.80263376832652e-06 2605 1611.18181818182 1510 6.34099267903817e-08 419 1.77406082761659 -1.84513151512329 -1 3.51463534754433 2601 419 556 947 573 2002 3414 2558 1510 654 2489 1351 M18325 OLSSON_E2F3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OLSSON_E2F3_TARGETS_UP.html Genes up-regulated in the 5637 cell line (bladder cancer) after knockdown of E2F3 [GeneID=1871] by RNAi. 16909110 17/42 Arthur Liberzon 7.53139302179357e-08 9.74920102213389e-07 4620 2163.90909090909 1510 6.84672116329118e-09 34 1.83313580564353 1.59222864517035 1 4.02775324899501 4617 505 1510 864 34 2854 3068 3519 973 1263 4596 1352 M1038 BOYLAN_MULTIPLE_MYELOMA_PCA1_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_PCA1_DN.html Top down-regulated genes from principal component 1 (PCA1) which captures variation between normal plasma cells and tumors arising from aberrant expression of BCL2L1 and MYC [GeneID=598;4609]. 17483317 4/9 Arthur Liberzon 7.86961170588904e-05 0.000150089541936492 1910 1781.27272727273 1511 7.86989040832771e-06 19 1.22440359670567 1.52901427215919 1 1.71128336932051 1908 1153 4588 1455 2445 1818 1456 554 19 2687 1511 1353 M10319 WALLACE_PROSTATE_CANCER_RACE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WALLACE_PROSTATE_CANCER_RACE_UP.html Genes up-regulated in prostate cancer samples from African-American patients compared to those from the European-American patients. 18245496 164/525 Jessica Robertson 1.2425381550383e-08 2.05743243622243e-07 1435 1550.45454545455 1513 1.12958014732366e-09 265 1.72956083736247 1.86649302069063 1 4.22732142539496 556 2036 265 1433 2336 1774 1431 1857 2956 898 1513 1354 M1121 JOHANSSON_GLIOMAGENESIS_BY_PDGFB_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOHANSSON_GLIOMAGENESIS_BY_PDGFB_DN.html Genes down-regulated in brain tumors induced by retroviral delivery of PDGFB [GeneID=5155]. 15750623 11/35 Arthur Liberzon 3.12766059978176e-06 1.01077362555706e-05 1245 1623.45454545455 1514 2.84333186024801e-07 127 2.06410956365085 -2.26364496566585 -1 3.76892573416917 2544 1394 1650 1244 1241 1275 2123 2697 127 1514 2049 1355 M740 SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_DN http://www.broadinstitute.org/gsea/msigdb/cards/SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_DN.html Genes down-regulated in CT60/4 cells (breast cancer reverted to normal by transfer of chromosome 8p region) vs parental MDA-MB-231 cells (deleted chromosome 8p). 15580292 18/43 Arthur Liberzon 1.42213195028623e-06 5.92922905861225e-06 810 1632.72727272727 1514 1.29284806326067e-07 352 1.29388805503873 1.42527887900462 1 2.47211460940115 806 1787 2159 1514 862 973 352 2583 2905 2936 1083 1356 M14573 BENPORATH_NOS_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_NOS_TARGETS.html Set 'NOS targets': genes upregulated and identified by ChIP on chip as targets of the transcription factors NANOG , OCT4, and Sox2 [GeneID=79923;5460;6657] (NOS) in human embryonic stem cells. 18443585 137/323 Jessica Robertson 4.25753699916795e-06 1.28466312801681e-05 1020 1435.36363636364 1514 3.87049567142145e-07 185 1.69901384317919 1.88381240412954 1 3.0376136999093 1016 3175 1321 1716 1726 1514 863 185 1595 1768 910 1357 M1551 ULE_SPLICING_VIA_NOVA2 http://www.broadinstitute.org/gsea/msigdb/cards/ULE_SPLICING_VIA_NOVA2.html Genes whose splicing in neocortex was most affected by knock out of NOVA2 [GeneID=4858]. 16041372 49/102 John Newman 0.000362036064310076 0.000599894270635437 360 1745.45454545455 1514 3.29177868511892e-05 356 1.80422016535713 1.80422016535713 1 2.1248302865159 356 3958 2328 2458 2797 696 838 805 1514 2555 895 1358 M5672 SU_KIDNEY http://www.broadinstitute.org/gsea/msigdb/cards/SU_KIDNEY.html Genes up-regulated specifically in human kidney tissue. 11904358 6/32 John Newman 6.58012306912232e-06 1.79374384536982e-05 1055 1859.54545454545 1514 6.58014255331235e-07 643 1.41796419516409 1.41796419516409 1 2.45999469932595 1053 1514 4409 2282 1574 1112 643 2250 3347 1324 947 1359 M935 REACTOME_IRAK1_RECRUITS_IKK_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IRAK1_RECRUITS_IKK_COMPLEX.html Genes involved in IRAK1 recruits IKK complex 4/11 Reactome 2.18836533860569e-07 2.0192398324547e-06 970 1422.54545454545 1516 2.18836555410814e-08 16 1.01599998521963 -1.01599998521963 -1 2.11491223987152 970 1623 4058 2202 1950 180 166 299 1516 2668 16 1360 M8472 REACTOME_FACILITATIVE_NA_INDEPENDENT_GLUCOSE_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FACILITATIVE_NA_INDEPENDENT_GLUCOSE_TRANSPORTERS.html Genes involved in Facilitative Na+-independent glucose transporters 5/11 Reactome 0.000776608087469435 0.00122202333709932 1225 1762.18181818182 1517 7.76879625089897e-05 579 2.417537483675 2.417537483675 1 2.57407442002589 1224 1517 4022 1909 2859 1110 579 1693 1255 1863 1353 1361 M19632 ZHAN_MULTIPLE_MYELOMA_MS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_MS_UP.html Top 50 up-regulated genes in cluster MS of multiple myeloma samples with characteristic expression spike of WHSC1 [GeneID=7468]. 16728703 33/75 Kevin Vogelsang 6.86449264075399e-07 3.77104484344352e-06 1120 1497.72727272727 1517 6.24044980239121e-08 565 1.52667066162478 1.50124132394084 1 3.02654629753864 1116 1774 1230 1815 565 1511 1809 1795 2128 1215 1517 1362 M19727 NIELSEN_LIPOSARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LIPOSARCOMA_DN.html Top 20 negative significant genes associated with liposarcomas, versus other soft-tissue tumors. 11965276 17/28 John Newman 0.000629892899063589 0.00100363078035089 1860 1820.72727272727 1518 5.72793926494527e-05 905 1.41898199702103 1.36961156515629 1 1.55521155637383 1860 1608 1518 3000 3036 1475 914 905 3329 1267 1116 1363 M7371 LOPES_METHYLATED_IN_COLON_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/LOPES_METHYLATED_IN_COLON_CANCER_UP.html Genes methylated aberrantly in HCT116 and Colo320 (colon cancer) cells. 18794111 11/42 Jessica Robertson 2.71959526262332e-05 5.90821669014968e-05 1520 1632.90909090909 1519 2.47238989298978e-06 223 2.40394138096548 2.46746118624608 1 3.71564261465772 1367 2953 1444 1037 2014 1858 1519 3051 223 1520 976 1364 M2140 LU_EZH2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LU_EZH2_TARGETS_DN.html Genes down-regulated in SKOV3ip1 cells (ovarian cancer) upon knockdown of EZH2 [GeneID=2146] by RNAi. 20708159 252/670 Arthur Liberzon 6.30246096313686e-06 1.73760649291701e-05 1295 1340.72727272727 1519 5.72952638019611e-07 549 1.51250471362497 1.75587192305131 1 2.63164540688299 1294 1577 1568 549 1519 2113 2211 853 1654 799 611 1365 M6786 REACTOME_NUCLEOTIDE_LIKE_PURINERGIC_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEOTIDE_LIKE_PURINERGIC_RECEPTORS.html Genes involved in Nucleotide-like (purinergic) receptors 7/18 Reactome 1.08175081814636e-07 1.27363927985775e-06 1230 1629.63636363636 1521 1.08175087080468e-08 71 2.76662387112246 2.76662387112246 1 5.96142051923994 1226 901 4007 2862 71 1587 1033 1521 1526 2259 933 1366 M17211 YEMELYANOV_GR_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/YEMELYANOV_GR_TARGETS_DN.html Transcription factors down-regulated in LNCaP cells (prostate cancer) by expression of GR [GeneID=2908] off a lentiviral vector. 17016446 16/26 Aravind Subramanian 0.00198520915278102 0.00294973945229014 1260 2030.72727272727 1526 0.000180636618904631 908 1.71626465060101 1.71626465060101 1 1.58730785081818 1260 3370 2621 2640 3008 1407 908 1523 1346 2729 1526 1367 M16108 CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN.html Genes down-regulated in SH-SY5Y cells (neuroblastoma) after treatment with epoxomicin [PubChem=3035402], a protease inhibitor causing apoptosis. 16983338 116/279 Leona Saunders 2.97278353116237e-07 2.33632760673967e-06 1035 1247.09090909091 1527 2.7025308480585e-08 265 1.69093255553448 1.94402595114612 1 3.48070344020903 1031 1527 508 1193 265 2254 1582 1531 1649 547 1631 1368 M1708 HOWLIN_CITED1_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOWLIN_CITED1_TARGETS_2_DN.html Genes down-regulated in mammary glands from the CITED1 [GeneID=4435] knockout mice: homozygotic vs wild type (WT) animals. 16278680 11/26 Arthur Liberzon 0.00021489905111857 0.000371045303442011 2205 1621.45454545455 1530 1.95381859660962e-05 703 1.86864873214486 -2.07675145754286 -1 2.34322285040604 2204 1803 1960 1862 2584 1402 1461 806 703 1521 1530 1369 M8268 AMBROSINI_FLAVOPIRIDOL_TREATMENT_TP53 http://www.broadinstitute.org/gsea/msigdb/cards/AMBROSINI_FLAVOPIRIDOL_TREATMENT_TP53.html Genes down-regulated by flavopiridol [PubChem=5287969] in the HCT116 cells (colon cancer) depending on their TP53 [GeneID=7157] status: wild-type vs loss of the gene's function (LOF). 18381438 83/209 Jessica Robertson 2.84062181917492e-07 2.29907642774426e-06 1870 1484.45454545455 1530 2.58238380541248e-08 245 1.93002826734841 2.24877196044735 1 3.97779494250073 1870 1819 909 993 245 1988 1691 2973 1347 1530 964 1370 M11333 WEIGEL_OXIDATIVE_STRESS_BY_TBH_AND_H2O2 http://www.broadinstitute.org/gsea/msigdb/cards/WEIGEL_OXIDATIVE_STRESS_BY_TBH_AND_H2O2.html Oxidative stress genes down-regulated in ARPE-19 cells (retinal pigmented epithelium) in response to tert-butyl hydroperoxide (tBH) and H2O2 [PubChem=6410;784]. 12419474 48/118 John Newman 8.76206620341602e-05 0.000164829555315967 1535 1553.09090909091 1532 7.96583199519318e-06 557 2.19970659045547 2.57398100274977 1 3.04169959247598 1532 2301 1277 978 3118 1582 1258 557 796 1785 1900 1371 M674 REACTOME_ALPHA_LINOLENIC_ACID_ALA_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ALPHA_LINOLENIC_ACID_ALA_METABOLISM.html Genes involved in alpha-linolenic acid (ALA) metabolism 8/17 Reactome 0.000810367774045186 0.00127300817605623 1345 2006.81818181818 1533 8.10663438969581e-05 381 0.696190991208641 -0.696190991208641 -1 0.736752366833723 1345 381 3954 2297 3002 677 895 1533 2844 4341 806 1372 M9126 BEIER_GLIOMA_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/BEIER_GLIOMA_STEM_CELL_UP.html Genes up-regulated in cancer stem cells derived from glyoblastoma tumors: CD133+ [GeneID=8842] vs. CD133- cells. 17483311 29/71 Jessica Robertson 1.38199642660508e-05 3.29569224176661e-05 770 1533.63636363636 1533 1.25636828009933e-06 209 1.47868522947121 1.49992749073043 1 2.42254585733447 767 2544 1533 3706 1909 419 209 838 3183 1538 224 1373 M177 PID_EPHA_FWDPATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHA_FWDPATHWAY.html EPHA forward signaling 18832364 23/45 Pathway Interaction Database 3.71322115631155e-06 1.15538873429455e-05 1535 1465.54545454545 1535 3.37566129418568e-07 823 1.59555569699586 1.40969421073215 1 2.87950781583598 1535 1780 1730 1059 1308 1420 823 1731 1109 1791 1835 1374 M16956 YAMASHITA_LIVER_CANCER_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_LIVER_CANCER_STEM_CELL_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) cells with hepatic stem cell properties. 19150350 47/95 Yujin Hoshida 1.41411719613178e-06 5.91656534024421e-06 2660 1630.72727272727 1535 1.28556191372692e-07 504 1.83335400921678 -1.89828212660012 -1 3.50344557102239 2659 1535 1129 504 859 1979 3942 1597 937 606 2191 1375 M9802 BROWNE_HCMV_INFECTION_1HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_1HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 1 h time point that were not down-regulated at the previous time point, 30 min. 11711622 161/402 Arthur Liberzon 3.09378167749892e-06 1.00397928952631e-05 3075 1835.90909090909 1535 2.81253275289319e-07 408 1.58194488562246 -1.70874186236406 -1 2.890219104227 3072 408 1416 1535 1236 1150 3318 2683 2112 1354 1911 1376 M16848 KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION.html Epithelial cell signaling in Helicobacter pylori infection 45/91 KEGG 2.56320680679449e-05 5.61532823592285e-05 555 1549.09090909091 1536 2.33021515550037e-06 551 1.56981532682983 -1.59852571713073 -1 2.4390493770278 551 1536 2018 1792 1994 917 1425 1236 2296 1950 1325 1377 M255 PID_HIF1_TFPATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HIF1_TFPATHWAY.html HIF-1-alpha transcription factor network 18832364 61/113 Pathway Interaction Database 0.000195755234142715 0.000341007073305859 1310 1869.18181818182 1537 1.77975140495843e-05 1226 1.72704952785481 2.04290784520604 1 2.18880727020517 1308 3078 1226 2268 2556 1537 1771 1529 2434 1436 1418 1378 M2128 CHICAS_RB1_TARGETS_GROWING http://www.broadinstitute.org/gsea/msigdb/cards/CHICAS_RB1_TARGETS_GROWING.html Genes up-regulated in growing IMR90 cells (fibroblast) after knockdown of RB1 [GeneID=5925] by RNAi. 20385362 149/431 Arthur Liberzon 1.38983284754275e-09 2.89570442442327e-08 510 1393.09090909091 1537 1.26348440765524e-10 215 1.95137406410042 2.12867095536897 1 5.37687662655381 506 2497 215 1248 1524 1883 2042 1537 1813 382 1677 1379 M912 MUELLER_METHYLATED_IN_GLIOBLASTOMA http://www.broadinstitute.org/gsea/msigdb/cards/MUELLER_METHYLATED_IN_GLIOBLASTOMA.html Genes up-regulated in short-term cultured glioblastomas after azacitidine [PubChem=9444] treatment. 16909125 30/104 Leona Saunders 6.66677340059449e-06 1.81314568515298e-05 2140 1831.54545454545 1538 6.06072145758843e-07 407 1.94907470416794 1.99963869232574 1 3.37807785471936 2140 1491 700 1378 1538 2395 1903 4395 1438 407 2362 1380 M16826 ZUCCHI_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZUCCHI_METASTASIS_DN.html The 50 most down-regulated genes in primary invasive breast dutcal carcinoma (IDC) or lymph node metastases, compared to normal mammary epithelium. 15608061 33/65 Kate Stafford 4.13839006258909e-05 8.48315653249889e-05 1145 1487.09090909091 1538 3.76224355575598e-06 831 1.88444925630421 -2.21453506435387 -1 2.80447779387745 1141 1914 1674 1563 2148 831 1256 1538 1127 1471 1695 1381 M5056 REACTOME_HDL_MEDIATED_LIPID_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HDL_MEDIATED_LIPID_TRANSPORT.html Genes involved in HDL-mediated lipid transport 9/27 Reactome 6.07239198792847e-06 1.68773599379791e-05 825 1732.81818181818 1539 6.07240858126729e-07 825 1.73542356141243 1.73542356141243 1 3.02753007305135 825 1466 3981 1903 1539 1232 1446 1631 2321 1809 908 1382 M659 KOBAYASHI_EGFR_SIGNALING_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOBAYASHI_EGFR_SIGNALING_6HR_DN.html Genes down-regulated in H1975 cells (non-small cell lung cancer, NSCLC) resistant to gefitinib [PubChem=123631] after treatment with EGFR inhibitor CL-387785 [PubChem=2776] for 6h. 17145885 17/34 Leona Saunders 7.15934397868054e-05 0.000138003644113933 990 1454.81818181818 1540 6.5087063382283e-06 372 1.44650022731862 1.45190156290739 1 2.04097354221416 987 2206 1935 1540 2306 736 372 1839 1765 1261 1056 1383 M1173 HESSON_TUMOR_SUPPRESSOR_CLUSTER_3P21_3 http://www.broadinstitute.org/gsea/msigdb/cards/HESSON_TUMOR_SUPPRESSOR_CLUSTER_3P21_3.html Genes in the tumor suppressor cluster of the 3p21.3 region. 17533367 4/8 Leona Saunders 8.70355213717589e-06 2.24709891541632e-05 1540 1768.63636363636 1540 8.70358622568271e-07 56 2.52640359049412 2.52640359049412 1 4.29262943887011 1540 1852 4213 2642 2895 1376 1080 247 56 2671 883 1384 M6319 KIM_MYC_AMPLIFICATION_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYC_AMPLIFICATION_TARGETS_DN.html Genes negatively correlated with amplifications of MYC [GeneID=4609] in SCLC (small cell lung cancer) cell lines. 16116477 63/196 Arthur Liberzon 5.63752303712227e-07 3.34397885467784e-06 3725 2007.45454545455 1542 5.12502225613087e-08 431 1.79687850652653 -1.2819276698169 -1 3.59650363526737 3724 431 1451 816 490 1958 3089 4484 574 1542 3523 1385 M14298 PETRETTO_BLOOD_PRESSURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_BLOOD_PRESSURE_UP.html Genes that are most strongly positively correlated with systolic blood pressure (SBP). 18443592 7/17 Jessica Robertson 8.24898196731548e-05 0.000156433547142211 1650 1768.63636363636 1545 8.24928818897945e-06 62 3.10327796151063 2.88851526527842 1 4.31689083674546 1647 1948 4342 1545 2382 1326 1232 2446 62 1501 1024 1386 M4519 CHESLER_BRAIN_HIGHEST_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_HIGHEST_EXPRESSION.html Neurologically relevant transcripts with highest abundance fold range in brain tissue among mouse strains. 15711545 33/83 Jean Junior 0.000338592620090213 0.00056464235506859 1465 2108.18181818182 1546 3.07858856970768e-05 639 2.14439689529619 2.77297871963091 1 2.54607229751576 1463 3510 2076 3543 3279 999 1202 1546 1466 3467 639 1387 M10544 BOYAULT_LIVER_CANCER_SUBCLASS_G56_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G56_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G56, defined by unsupervised clustering. 17187432 11/27 Yujin Hoshida 3.90913566810025e-05 8.0930887564301e-05 1550 1614.90909090909 1548 3.55382284588381e-06 430 1.7472096087821 1.91142191261692 1 2.61329088296424 1548 2457 1714 1958 2786 1329 1534 430 1697 1523 788 1388 M14899 BIOCARTA_AT1R_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AT1R_PATHWAY.html Angiotensin II mediated activation of JNK Pathway via Pyk2 dependent signaling 21/56 BioCarta 0.000375690827922662 0.000621640967388982 1535 1621.45454545455 1549 3.41595454041863e-05 628 1.5038811156956 -1.41020728967664 -1 1.76261975418414 1531 1549 2034 628 2709 1075 2171 1561 1087 2078 1413 1389 M1293 YANG_BREAST_CANCER_ESR1_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_DN.html Genes down-regulated in early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative ones. 16261164 18/54 Leona Saunders 2.45546544575277e-07 2.14593063349835e-06 2695 1645.45454545455 1549 2.2322415634658e-08 204 1.87909918710799 2.01565274734143 1 3.89339299497792 2691 758 1549 705 204 3693 3197 939 398 2326 1640 1390 M2205 CHYLA_CBFA2T3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHYLA_CBFA2T3_TARGETS_UP.html Genes up-regulated in immature bone marrow progenitor cells upon knock out of CBFA2T3 [GeneID=863]. 18710942 243/721 Arthur Liberzon 6.61012569099066e-08 8.85001399656635e-07 1550 1631.72727272727 1549 6.00920535418059e-09 41 1.594806446919 1.59855570405085 1 3.52859592203004 1549 41 300 1983 1187 2325 1340 2933 2754 821 2716 1391 M14636 OUYANG_PROSTATE_CANCER_PROGRESSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/OUYANG_PROSTATE_CANCER_PROGRESSION_DN.html Genes down-regulated during prostate cancer progression in mice heterozygotic for both NKX3.1 and PTEN [GeneID=4824;5728]. 18381418 12/28 Jessica Robertson 6.90416331048005e-06 1.86795088180771e-05 910 1404.81818181818 1551 6.27653179782502e-07 424 1.83561929988823 1.62753225593414 1 3.17276288520695 908 1615 1721 1864 1551 1298 1143 1445 424 1599 1885 1392 M2594 GHANDHI_DIRECT_IRRADIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GHANDHI_DIRECT_IRRADIATION_DN.html Genes significantly (FDR < 10%) down-regulated in IMR-90 cells (fibroblast) in response to direct irradiation. 19108712 20/45 Itai Pashtan 9.54184746918545e-06 2.42216128063938e-05 1125 1591.63636363636 1551 8.67444441306362e-07 784 1.53710224783738 1.31638471498027 1 2.59339520271369 1124 1208 1606 2075 1676 856 784 2624 2569 1551 1435 1393 M16650 KEGG_PHENYLALANINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PHENYLALANINE_METABOLISM.html Phenylalanine metabolism 12/27 KEGG 6.92269634243877e-06 1.87188430817473e-05 1855 1511.81818181818 1552 6.29338011458721e-07 265 1.82483483471097 -1.5265523173871 -1 3.15351319179851 1855 651 1016 1155 1552 1689 2505 3559 265 624 1759 1394 M9841 TURJANSKI_MAPK8_AND_MAPK9_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TURJANSKI_MAPK8_AND_MAPK9_TARGETS.html Examples of transcription factors whose activities are regulated by MAPK8 and MAPK9 [GeneID=5599;5601]. 17496919 6/11 Arthur Liberzon 2.63716664575952e-05 5.7504713364491e-05 1555 1627.72727272727 1552 2.63719794219786e-06 63 2.55775703152597 3.50117291424572 1 3.96437536694377 1552 1622 4201 1886 2034 1538 946 460 63 2056 1547 1395 M71 PID_ILK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ILK_PATHWAY.html Integrin-linked kinase signaling 18832364 34/68 Pathway Interaction Database 2.86389695852899e-06 9.47554064677048e-06 1710 1546.36363636364 1553 2.60354607879526e-07 681 1.81067311413455 1.96682465614747 1 3.32473257781649 1706 2113 1813 1318 1202 1291 720 2880 1733 1553 681 1396 M16864 REACTOME_METABOLISM_OF_CARBOHYDRATES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_CARBOHYDRATES.html Genes involved in Metabolism of carbohydrates 114/287 Reactome 6.9642019046198e-06 1.88036683852214e-05 1110 1743.09090909091 1554 6.33111268201928e-07 938 1.56883725262775 1.80777077477346 1 2.70999549041237 1110 1998 1914 3053 1554 1254 1162 938 2288 2623 1280 1397 M2018 MIKKELSEN_NPC_LCP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_LCP_WITH_H3K4ME3.html Genes with low-CpG-density promoters (LCP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in neural progenitor cells (NPC). 17603471 35/107 Arthur Liberzon 5.31742973326456e-07 3.24024391808553e-06 1445 1506.09090909091 1554 4.83402819863178e-08 469 1.40720196164501 1.69330184470302 1 2.82359447951989 1445 950 1554 1242 469 2300 1836 1922 1189 1588 2072 1398 M19062 DODD_NASOPHARYNGEAL_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/DODD_NASOPHARYNGEAL_CARCINOMA_UP.html Genes up-regulated in nasopharyngeal carcinoma (NPC) compared to the normal tissue. 17119049 916/2621 Arthur Liberzon 4.67055315847213e-17 3.21856060302947e-15 1925 1592.09090909091 1555 4.67055315847213e-18 22 1.68770819272232 -1.6259866977072 -1 8.94036135843811 1924 219 4149 593 558 1171 3395 2095 1555 22 1832 1399 M17183 BENPORATH_OCT4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_OCT4_TARGETS.html Set 'Oct4 targets': genes upregulated and identified by ChIP on chip as OCT4 [GeneID=5460] transcription factor targets in human embryonic stem cells. 18443585 216/499 Jessica Robertson 1.85914248761856e-05 4.24765562992714e-05 1485 1785.18181818182 1555 1.69014381705688e-06 331 1.61086731456275 1.91342454536349 1 2.5742121872789 1485 3045 1459 1536 1902 2583 1555 331 1836 2539 1366 1400 M4210 CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_3 http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_3.html The 'group 3 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 and ERBB2 [GeneID=2099;2064]. 18794137 451/1090 Jessica Robertson 8.36035112198384e-07 4.23525526893721e-06 3185 1628.72727272727 1556 7.60032209004763e-08 11 1.52030273603458 -1.51131697580729 -1 2.98590441143452 3185 11 443 631 640 1556 3574 3656 1608 135 2477 1401 M2339 DUAN_PRDM5_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/DUAN_PRDM5_TARGETS.html Direct targets of PRDM5 [GeneID=11107]. 17636019 57/174 Arthur Liberzon 1.84289189475893e-06 6.98688626119769e-06 1990 1444.27272727273 1556 1.67535767137362e-07 710 1.72944807711318 1.77765096095911 1 3.2592358758084 1988 710 761 1556 984 2080 1656 1785 1338 793 2236 1402 M18658 WIKMAN_ASBESTOS_LUNG_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WIKMAN_ASBESTOS_LUNG_CANCER_UP.html Genes positively correlated with the asbestos exposure of lung cancer patients. 17297452 10/26 Arthur Liberzon 1.14503540275761e-06 5.17948050359521e-06 2630 1740.27272727273 1557 1.04094181701396e-07 164 1.68424206162777 -2.09539889391506 -1 3.25407383883288 2630 977 2020 781 773 2536 4570 1557 164 1363 1772 1403 M714 REACTOME_PI3K_AKT_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_AKT_ACTIVATION.html Genes involved in PI3K/AKT activation 26/47 Reactome 0.00570813590462793 0.00804219027332726 1180 2099 1558 0.000520272754325609 998 1.59449304764954 1.78600487013759 1 1.22081062002615 1178 3089 2868 2060 3836 1286 998 1558 1533 3502 1181 1404 M6195 HWANG_PROSTATE_CANCER_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/HWANG_PROSTATE_CANCER_MARKERS.html Proteins implicated in prostate carcinogenesis. 16799640 20/47 Arthur Liberzon 3.3391291383082e-05 7.0546254022147e-05 1560 1671.90909090909 1558 3.03561801838072e-06 846 1.64680323821896 -1.68680906618509 -1 2.4990142304021 1558 3397 1932 1632 2084 846 1122 1186 2067 1198 1369 1405 M15842 NIELSEN_LIPOSARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LIPOSARCOMA_UP.html Top 20 positive significant genes associated with liposarcomas, versus other soft-tissue tumors. 11965276 10/21 John Newman 0.00399622053833364 0.00572494327197537 945 1755.63636363636 1558 0.00036395436749023 851 2.56596369758832 2.62376503709906 1 2.10305043012512 944 2371 851 2119 3348 1558 1886 1464 2005 1368 1398 1406 M1957 MIKKELSEN_MCV6_LCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MCV6_LCP_WITH_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state). 18509334 14/57 Jessica Robertson 3.2007696809422e-05 6.80526620911757e-05 1030 1470.09090909091 1558 2.9098329543079e-06 493 1.49881518923143 1.39472642808983 1 2.28300560745013 1026 1558 1679 2597 2069 704 493 1601 2006 1381 1057 1407 M2619 ZWANG_EGF_INTERVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_EGF_INTERVAL_UP.html Genes induced in the time interval between two pulses of EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 40/171 Yaara Zwang 1.5890850274152e-05 3.71394136581927e-05 1260 1992.54545454545 1558 1.44463318697564e-06 437 2.19259840911551 2.88643084729132 1 3.55057133491208 1257 4140 1979 4159 1857 1044 1051 437 1558 3446 990 1408 M1122 HUMMERICH_BENIGN_SKIN_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_BENIGN_SKIN_TUMOR_UP.html Genes up-regulated in benign skin tumors (papilloma) induced by treatment with DMBA and TPA [PubChem=6001;4792] chemicals in the two stage skin carcinogenesis model. 16247483 13/33 Leona Saunders 0.0105684575662372 0.0144258060458454 1350 2198.27272727273 1559 0.000965415534552347 1317 2.89119312762698 2.89119312762698 1 1.94543664976961 1349 3610 1559 3759 3752 1379 1363 1506 2233 2354 1317 1409 M2033 TRACEY_RESISTANCE_TO_IFNA2_UP http://www.broadinstitute.org/gsea/msigdb/cards/TRACEY_RESISTANCE_TO_IFNA2_UP.html Genes up-regulated in huT78R cells (cutaneous T-cell lymphoma, CTCL) resistant to IFNA2 [GeneID=3440] compared to the IFN2A sensitive parental cell line. 12414529 3/7 Arthur Liberzon 6.41927524963189e-06 1.75952983570706e-05 1980 2049.81818181818 1560 6.4192937928999e-07 263 2.42309093462525 -1.49934497260978 -1 4.21117468214422 1980 1082 4606 812 1560 2564 4377 2644 263 1402 1258 1410 M2534 PECE_MAMMARY_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/PECE_MAMMARY_STEM_CELL_UP.html The '3/3 signature': genes consistently up-regulated in all three pools of normal mammary stem cells (defined by their ability to retain the dye PKH26). 20074520 110/297 Arthur Liberzon 4.40876209199806e-06 1.31588911866898e-05 1905 1806.72727272727 1562 4.00797357009647e-07 451 1.92608695741057 2.40870432243555 1 3.43624749183569 1903 3262 1766 553 1379 3486 3290 1171 451 1562 1051 1411 M16519 BIOCARTA_TCAPOPTOSIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCAPOPTOSIS_PATHWAY.html HIV Induced T Cell Apoptosis 2/10 BioCarta 0.000192922795736132 0.00033669877870373 1225 1992.3 1562.5 2.14377044016324e-05 184 1.08740129226664 1.08740129226664 1 1.38033236997222 1225 1672 3841 NA 3111 1061 184 1453 3916 2155 1305 1412 M2152 IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_UP http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_UP.html Genes up-regulated during transition from L0 (non-tumor, not infected with HCV) to L1 (non-tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 13/37 Yujin Hoshida 1.28376225310109e-05 3.09768790835823e-05 2930 1765.90909090909 1564 1.16706340388936e-06 435 1.86207150359208 -1.54928920731353 -1 3.06896695490056 2928 1307 1564 1211 1775 1453 2498 1344 435 2357 2553 1413 M1337 RANKIN_ANGIOGENIC_TARGETS_OF_VHL_HIF2A_DN http://www.broadinstitute.org/gsea/msigdb/cards/RANKIN_ANGIOGENIC_TARGETS_OF_VHL_HIF2A_DN.html Angiogenic genes down-regulated in hepatocytes after knockout of VHL and HIF2A [GeneID=7428;2034]. 18490920 10/22 Jessica Robertson 0.000967996010241602 0.00150348999137957 1085 2066.81818181818 1567 8.80383808435401e-05 408 1.45322789604227 1.45322789604227 1 1.4995066168201 1085 2874 1567 3108 4306 623 408 980 4246 2710 828 1414 M5190 MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP.html Genes up-regulated in at least 8 of 11 sarcoma cell lines by trabectedin [PubChem=3199]. 15897246 47/105 John Newman 2.36696331513242e-07 2.10466605212724e-06 2435 1576.63636363636 1567 2.1517850634475e-08 197 1.34113990492477 1.6204037249641 1 2.78290393342525 1764 939 2449 1567 197 2435 1524 1173 993 2434 1868 1415 M18895 SA_TRKA_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/SA_TRKA_RECEPTOR.html The TrkA receptor binds nerve growth factor to activate MAP kinase pathways and promote cell growth. 16/28 SigmaAldrich 7.18872499417159e-06 1.92870586612568e-05 1185 1377.18181818182 1568 6.53522589470287e-07 363 1.91453252674716 2.17005224505474 1 3.29943209584501 1181 1840 1833 363 1568 1933 2089 760 382 2119 1081 1416 M834 CHIANG_LIVER_CANCER_SUBCLASS_POLYSOMY7_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_POLYSOMY7_UP.html Marker genes up-regulated in the 'chromosome 7 polysomy' subclass of hepatocellular carcinoma (HCC); characterized by polysomy of chromosome 7 and by a lack of gains of chromosome 8q. 18701503 52/144 Yujin Hoshida 3.15059827940951e-07 2.41631809121325e-06 4155 1886.36363636364 1568 2.86418066418516e-08 279 1.66621172519914 -1.73924200499216 -1 3.42091233725024 4154 1185 1007 1521 279 2692 3378 2017 1568 911 2038 1417 M3471 AMIT_EGF_RESPONSE_120_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_120_MCF10A.html Genes whose expression peaked at 120 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 37/73 Leona Saunders 4.44909474217159e-06 1.32421697199992e-05 1445 1609.54545454545 1569 4.04463976333783e-07 1295 1.72181309539471 1.69545660025652 1 3.07008705068269 1441 1687 1677 1569 1383 2212 1668 1905 1295 1438 1430 1418 M1741 ZHENG_BOUND_BY_FOXP3 http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_BOUND_BY_FOXP3.html Genes whose promoters are bound by FOXP3 [GeneID=50943] based an a ChIP-chip analysis. 17237761 296/805 Jessica Robertson 1.8212842059971e-06 6.94994933982281e-06 1355 1682.18181818182 1570 1.65571428523704e-07 976 1.34880625160011 1.50613829577889 1 2.54303129253762 1355 994 2232 1570 976 2352 2107 1070 2629 1943 1276 1419 M18367 PYEON_HPV_POSITIVE_TUMORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PYEON_HPV_POSITIVE_TUMORS_DN.html Down-regulated genes in cervical carcinoma and head and neck tumors positive for human papilloma virus (HPV) compared to those negative for HPV. 17510386 4/17 Arthur Liberzon 1.47209198514896e-06 6.06170741863622e-06 1610 1616.90909090909 1571 1.47209296032453e-07 262 2.45399704668797 2.45399704668797 1 4.68002139744111 1608 1571 4106 1543 918 1807 1798 1482 262 1629 1062 1420 M2004 MIKKELSEN_ES_ICP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_ICP_WITH_H3K4ME3.html Genes with intermediate-CpG-density (ICP) promoters bearing histone H3 K4 trimethylation mark (H3K4me3) in embryonic stem cells (ES). 17603471 437/1213 Arthur Liberzon 1.54426537266713e-07 1.6225173848247e-06 4090 1955.72727272727 1571 1.4038777100592e-08 14 1.59963661901306 1.74416360261311 1 3.38536069802832 4089 14 428 633 104 2917 3584 3501 1571 245 4427 1421 M5202 BIOCARTA_P53HYPOXIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P53HYPOXIA_PATHWAY.html Hypoxia and p53 in the Cardiovascular system 24/44 BioCarta 0.00153057593866398 0.00229954435671029 1185 2089.18181818182 1574 0.000139240165787931 996 2.43057553781764 2.91205075714085 1 2.34402442180697 1183 4276 2127 2279 2977 1574 1515 1142 996 3363 1549 1422 M241 PID_RAC1_REG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RAC1_REG_PATHWAY.html Regulation of RAC1 activity 18832364 26/51 Pathway Interaction Database 8.44382313277777e-07 4.25034540022798e-06 2960 1808.63636363636 1574 7.67620579418589e-08 155 1.42295403323248 1.16993350509181 1 2.79390624197379 2959 155 1574 731 648 3060 2034 2010 870 1301 4553 1423 M4095 SHI_SPARC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHI_SPARC_TARGETS_UP.html Genes up-regulated in glioma cell lines after knockdown of SPARC [GeneID=6678] by RNAi. 17213807 16/35 Arthur Liberzon 2.49876142254799e-05 5.49254679397744e-05 450 1423.81818181818 1574 2.27162709449789e-06 281 1.7790189936064 1.7790189936064 1 2.77033633149163 447 3343 1744 1832 2694 411 748 402 2186 1574 281 1424 M2041 GERHOLD_RESPONSE_TO_TZD_DN http://www.broadinstitute.org/gsea/msigdb/cards/GERHOLD_RESPONSE_TO_TZD_DN.html Genes down-regulated in 3T3-L1 cells (fibroblast) induced to differentiate to mature adipocytes and then treated with a TZD derivative AD-5075 [PubChem=128440], a PPARG [GeneID=5468] activator. 12021175 10/13 Arthur Liberzon 0.00427894853958873 0.00611315635869292 1015 2124.09090909091 1576 0.000389753975176383 1015 2.76464486032807 2.76464486032807 1 2.23709348825371 1015 1980 1411 2867 3723 1440 1490 1307 3839 2717 1576 1425 M2461 DELACROIX_RARG_BOUND_MEF http://www.broadinstitute.org/gsea/msigdb/cards/DELACROIX_RARG_BOUND_MEF.html Genes with DNA sequences bound by RARG [GeneID=5916] in MEF cells (embryonic fibroblast). 19884340 273/602 Arthur Liberzon 1.10283165259408e-06 5.04674719146081e-06 2855 1806.72727272727 1576 1.00257473220888e-07 237 1.54226766726775 1.74410725553803 1 2.98612532199477 2853 237 640 575 757 4500 3144 1982 1576 380 3230 1426 M12391 DAUER_STAT3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAUER_STAT3_TARGETS_UP.html Top 50 genes up-regulated in A549 cells (lung cancer) expressing STAT3 [GeneID=6774] off an adenovirus vector. 15735721 29/84 Arthur Liberzon 6.46987312833883e-06 1.77047904638218e-05 1245 1610.90909090909 1577 5.88172014122978e-07 154 1.2800062739101 1.29762536206205 1 2.22330724351231 1243 154 1692 1662 1530 1898 1577 2165 2797 1535 1467 1427 M2068 ONGUSAHA_BRCA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONGUSAHA_BRCA1_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) lacking TP53 and BRCA1 [GeneID=7157;672] by expression of BRCA1. 12802282 16/28 Arthur Liberzon 1.9762324074143e-05 4.48673694822839e-05 1585 1487.09090909091 1579 1.79659105444128e-06 611 1.85118519497118 2.17930962260283 1 2.94215524692215 1585 1879 1341 1611 1917 1531 1594 1520 611 1579 1190 1428 M1839 LABBE_TGFB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_TGFB1_TARGETS_DN.html Down-regulated genes in NMuMG cells (mammary epithelium) after stimulation with TGFB1 [GeneID=7040]. 17210685 83/235 Jessica Robertson 2.81838019675557e-07 2.29742234705141e-06 2985 1991.09090909091 1582 2.56216414346656e-08 239 1.6454568620167 1.51092314932802 1 3.39148028684293 2984 1095 814 1076 239 3334 2777 3985 1582 348 3668 1429 M145 PID_P53_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P53_DOWNSTREAM_PATHWAY.html Direct p53 effectors 18832364 85/185 Pathway Interaction Database 2.02938853881114e-06 7.43527341115637e-06 1690 1651.72727272727 1583 1.84490037347424e-07 1039 1.58278306700508 1.86629105608999 1 2.96720943098081 1689 2067 1462 1329 1039 2235 2018 1761 1415 1583 1571 1430 M12383 OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_UP http://www.broadinstitute.org/gsea/msigdb/cards/OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_UP.html Genes up-regulated in hematopoietic stem cells (HSC, CD34+ [GeneID=947]) cultured in a three-dimentional collagen gel compared to the cells grown in suspension. 16166251 157/392 Leona Saunders 7.32693584820022e-06 1.95301600595371e-05 2345 1905.36363636364 1583 6.66087295466104e-07 904 1.58214567963817 1.75405896237746 1 2.7234633944377 2345 999 904 1447 1583 3561 3163 959 2494 1031 2473 1431 M14027 NING_CHRONIC_OBSTRUCTIVE_PULMONARY_DISEASE_DN http://www.broadinstitute.org/gsea/msigdb/cards/NING_CHRONIC_OBSTRUCTIVE_PULMONARY_DISEASE_DN.html Down-regulated genes in lung tissue of smokers with chronic obstructive pulmonary disease (COPD) vs smokers without disease (GOLD-2 vs GOLD-0). 15469929 108/270 Kate Stafford 6.96540127764909e-07 3.80263376832652e-06 1590 1694.27272727273 1583 6.33218498450895e-08 571 1.54885737212573 1.79257705509626 1 3.06847926701955 1589 1583 1127 1268 571 2968 2201 1491 2263 1172 2404 1432 M1800 ZHENG_IL22_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_IL22_SIGNALING_UP.html Genes up-regulated in ex-vivo colonic tissue after treatment with IL22 [GeneID=50616]. 18264109 40/114 Jessica Robertson 2.16753787615938e-10 5.46079703638863e-09 3745 2286.27272727273 1584 1.97048897852085e-11 179 2.05695221670897 -2.1445428235163 -1 6.21251927516413 3745 1025 179 1153 1167 3914 4348 4025 1584 398 3611 1433 M1988 GYORFFY_MITOXANTRONE_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/GYORFFY_MITOXANTRONE_RESISTANCE.html Genes associated with resistance to mitoxantrone [PubChem=4212]. 16044152 35/111 Arthur Liberzon 7.25143916492667e-06 1.93840524397298e-05 1910 1834.45454545455 1587 6.59223915142615e-07 1171 1.65562802235954 2.12943996209772 1 2.85192755780896 1909 1359 1591 1458 1578 2018 1251 4594 1171 1587 1663 1434 M2238 JOHNSTONE_PARVB_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_2_UP.html Genes up-regulated upon overexpression of PARVB [GeneID=29780] in MDA-MB-231 cells (breast cancer) cultured in 3D collagen I and 3D Matrigel only. 17998334 104/250 Arthur Liberzon 5.92593300720319e-07 3.43674778115769e-06 2355 1776.18181818182 1587 5.38721327583328e-08 514 1.63288451992452 2.07723004167466 1 3.26117178500973 2351 1999 1223 797 514 3384 2202 1587 1261 1344 2876 1435 M7281 KONDO_PROSTATE_CANCER_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_PROSTATE_CANCER_WITH_H3K27ME3.html Top 200 genes with high histone H3 trimethylation mark at K27 (H3K27me3) in PC3 cells (prostate cancer), by ChIP-chip assay on an 88K microarray (all promoters). 18488029 49/442 Jessica Robertson 9.77607949513445e-08 1.18068836376804e-06 4140 2352.72727272727 1589 8.88734539050133e-09 57 2.01576584019456 -1.75642272302194 -1 4.36774842211408 4136 1589 591 1451 57 3590 4011 4127 1194 669 4465 1436 M14162 REACTOME_CHYLOMICRON_MEDIATED_LIPID_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHYLOMICRON_MEDIATED_LIPID_TRANSPORT.html Genes involved in Chylomicron-mediated lipid transport 7/19 Reactome 6.2662796181481e-05 0.000122604535660301 1285 1632.54545454545 1590 6.26645632333208e-06 82 1.57112129291097 1.57112129291097 1 2.24631974004904 1285 1150 4086 1693 2294 1615 1091 809 82 2263 1590 1437 M1904 SCHRAETS_MLL_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHRAETS_MLL_TARGETS_DN.html Genes down-regulated in fibroblasts from MLL [GeneID=4297] knockout mice. 12789274 17/47 Arthur Liberzon 0.000160861285773151 0.000284666157527562 1255 1511.18181818182 1590 1.46248226323706e-05 558 1.76556076190907 1.61283544744983 1 2.28822916306993 1252 631 616 944 2880 2000 1796 1793 1590 558 2563 1438 M7566 CHEN_LVAD_SUPPORT_OF_FAILING_HEART_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_LVAD_SUPPORT_OF_FAILING_HEART_DN.html Down-regulated genesin the left ventricle myocardium of patients with heart failure following implantation of LVAD (left ventricular assist device). 12824457 25/80 John Newman 1.13046127594807e-05 2.79395650796026e-05 1065 1840.90909090909 1591 1.02769734983663e-06 492 1.84705516473864 1.80536016465081 1 3.07447663109042 1065 1287 492 1342 3277 1879 1591 2740 3224 797 2556 1439 M3576 MCCLUNG_CREB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_CREB1_TARGETS_DN.html Genes down-regulated in the nucleus accumbens (a major reward center in the brain) 8 weeks after induction of CREB1 [GeneID=1385] expression in a transgenic Tet-Off system. 14566342 46/118 John Newman 9.05840943238817e-07 4.44478603143151e-06 3225 1979.90909090909 1591 8.23492105650282e-08 679 2.25795142663479 2.52073104934685 1 4.41735245383269 3225 1591 871 1218 679 4155 2732 1970 1088 994 3256 1440 M8202 AMIT_SERUM_RESPONSE_480_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_480_MCF10A.html Genes whose expression peaked at 480 min after stimulation of MCF10A cells with serum. 17322878 31/67 Leona Saunders 4.61325084466372e-06 1.36389233174096e-05 1490 1750.18181818182 1592 4.19387319851489e-07 905 2.08878677824834 2.78508130659068 1 3.71463234288205 1489 2506 1467 2070 1394 2052 1592 2578 905 1681 1518 1441 M13408 REACTOME_ERK_MAPK_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ERK_MAPK_TARGETS.html Genes involved in ERK/MAPK targets 15/26 Reactome 4.83371474026135e-06 1.40950760876569e-05 1905 1726.81818181818 1593 4.3942957824153e-07 509 1.25855425700096 1.2196697678047 1 2.23160040484823 1902 509 2841 2180 1418 1571 911 1588 1876 2606 1593 1442 M6175 CAIRO_LIVER_DEVELOPMENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_LIVER_DEVELOPMENT_DN.html Genes down-regulated at early fetal liver stage (embryonic days E11.5 - E12.5) compared to the late fetal liver stage (embryonic days E14.5 - E16.5). 19061838 131/344 Arthur Liberzon 1.472721679602e-13 6.57254646725234e-12 2155 1320.27272727273 1593 1.33883789054736e-14 60 1.8412115467478 -1.83008100927921 -1 7.52580172562262 2152 60 100 902 156 1773 2627 2533 1593 155 2472 1443 M501 REACTOME_SIGNALING_BY_RHO_GTPASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_RHO_GTPASES.html Genes involved in Signaling by Rho GTPases 58/130 Reactome 6.97322440795135e-08 9.17880044260113e-07 3915 2133.54545454545 1594 6.33929511725273e-09 27 1.55988846174731 1.43325906094193 1 3.44230519078585 3914 109 1077 323 27 4010 4019 3348 1594 694 4354 1444 M16050 KAYO_AGING_MUSCLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAYO_AGING_MUSCLE_UP.html Upregulated in the vastus lateralis muscle of aged vs young adult rhesus monkeys 11309484 144/538 John Newman 1.97321701454868e-07 1.88319652345726e-06 2275 1705.36363636364 1595 1.79383381048169e-08 160 1.84464026440061 -1.23135164209299 -1 3.86024031330005 2275 2854 699 1595 160 3180 2780 873 1511 1649 1183 1445 M1149 MOTAMED_RESPONSE_TO_ANDROGEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOTAMED_RESPONSE_TO_ANDROGEN_DN.html Genes down-regulated in ovarian epithelial cells in response to dihydrotestosterone (DHT) [PubChem=10635]. 16832351 2/6 Arthur Liberzon 0.00135327896356068 0.00205358329768308 1495 1826.6 1596.5 0.000150454844144777 345 1.40892272289947 1.40892272289947 1 1.38405358619618 1493 2099 4187 NA 3424 927 345 1360 570 2161 1700 1446 M142 PID_AJDISS_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AJDISS_2PATHWAY.html Posttranslational regulation of adherens junction stability and dissassembly 18832364 33/87 Pathway Interaction Database 7.74458331349357e-07 4.06395491680077e-06 1195 1854.54545454545 1600 7.04053276344871e-08 511 1.78119481776585 2.12461676056227 1 3.50997580826678 2543 1191 1600 709 606 3808 3644 1195 511 1843 2750 1447 M6753 ODONNELL_TFRC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_TFRC_TARGETS_UP.html Genes up-regulated in P493-6 cells (B lymphocyte, Burkitt's lymphoma model) upon knockdown of TFRC [GeneID=7037] by RNAi. 16508012 285/822 Leona Saunders 5.10689241331258e-07 3.14880234852405e-06 1740 1412.54545454545 1600 4.64263054434856e-08 314 1.73698214496972 1.90278335109682 1 3.49320210722919 1736 1408 418 922 456 2856 2149 1947 1732 314 1600 1448 M232 PID_ECADHERIN_STABILIZATION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ECADHERIN_STABILIZATION_PATHWAY.html Stabilization and expansion of the E-cadherin adherens junction 18832364 42/82 Pathway Interaction Database 4.17986699758028e-07 2.81825276987931e-06 1055 1635.09090909091 1601 3.79987981066359e-08 379 2.14205111504448 2.17764401725225 1 4.34553881173565 1055 2858 1620 2720 379 1014 1018 2300 1601 2091 1330 1449 M14414 BOYAULT_LIVER_CANCER_SUBCLASS_G6_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G6_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G6, defined by unsupervised clustering. 17187432 12/30 Yujin Hoshida 9.61682725585296e-07 4.61725947960317e-06 1685 1559.72727272727 1601 8.74257405422264e-08 98 2.03960311942925 2.27893141610086 1 3.97785969854219 1684 2059 1598 1920 3053 2385 1435 98 298 1601 1026 1450 M19358 BIOCARTA_MET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MET_PATHWAY.html Signaling of Hepatocyte Growth Factor Receptor 29/65 BioCarta 2.34324569174973e-05 5.20400441305176e-05 1640 1511.63636363636 1602 2.13024604573219e-06 314 2.03740361992836 2.8426851160081 1 3.19015330909309 1638 1365 1602 314 1968 1896 1934 1226 403 2779 1503 1451 M15377 CREIGHTON_AKT1_SIGNALING_VIA_MTOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_AKT1_SIGNALING_VIA_MTOR_DN.html Genes in the AKT1 [GeneID=207] pathway which depend on MTOR [GeneID=2475], sensitive to RAD001 (everolimus) [PubChem=6442177]. 17213801 22/43 Arthur Liberzon 1.14510068325323e-06 5.17948050359521e-06 750 1294.63636363636 1602 1.04100116298084e-07 108 1.29543159346455 -1.34466853876164 -1 2.502864732827 746 1602 2667 2047 2028 303 520 108 1910 2187 123 1452 M2187 TSUTSUMI_FBXW8_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TSUTSUMI_FBXW8_TARGETS.html Genes differentially expressed in E18.5 whole embryos upon knockout of FBXW8 [GeneID=26259]. 17998335 7/15 Arthur Liberzon 0.00184543335278901 0.00275229175403224 1345 2043.81818181818 1602 0.000184696767728876 1139 2.23766025958304 2.23766025958304 1 2.09413749902104 1342 1847 4625 1501 3492 1787 1388 1139 1602 2280 1479 1453 M12836 BIOCARTA_EPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPO_PATHWAY.html EPO Signaling Pathway 15/36 BioCarta 0.000150253611797994 0.000267206233353093 930 1783.27272727273 1603 1.36603522422447e-05 599 0.992164487484569 -0.992164487484569 -1 1.29584957773215 928 2316 3311 1603 2662 599 1030 654 1786 3765 962 1454 M10394 FARMER_BREAST_CANCER_CLUSTER_7 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_7.html Cluster 7: selected apocrine and luminal genes clustered together across breast cancer samples. 15897907 14/31 Leona Saunders 4.29322964682448e-05 8.76986666304252e-05 1405 1665.36363636364 1603 3.9030122091974e-06 149 1.54491771120971 -0.959950999345555 -1 2.29102780691196 1401 1557 1900 1957 2161 944 959 3182 149 2506 1603 1455 M724 REACTOME_RESPONSE_TO_ELEVATED_PLATELET_CYTOSOLIC_CA2_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESPONSE_TO_ELEVATED_PLATELET_CYTOSOLIC_CA2_.html Genes involved in Response to elevated platelet cytosolic Ca2+ 55/153 Reactome 3.47694418234839e-07 2.56178623246612e-06 1725 1695 1606 3.16085884714083e-08 312 1.498537517541 1.35750016795464 1 3.06275225980162 1078 2334 1264 1722 312 1213 1050 2903 3441 1606 1722 1456 M10311 BROWNE_HCMV_INFECTION_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_6HR_DN.html Genes down-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 6 h time point that were not down-regulated at the previous time point, 4 h. 11711622 102/254 John Newman 1.49396260557412e-07 1.59469448057411e-06 1245 1886 1606 1.35814791547749e-08 97 1.5937660322375 1.70620232266178 1 3.37731273823121 1242 3633 2190 2978 97 1258 1606 1262 2747 2599 1134 1457 M2109 KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN.html Genes whose expression significantly and negatively correlated with oligodendrocyte density in layer VI of BA9 brain region in patients with bipolar disorder. 18762803 47/174 Jessica Robertson 1.62870122553735e-06 6.48828316484466e-06 3465 2293.27272727273 1606 1.48063857390604e-07 732 1.73958431023353 1.58416726416123 1 3.298783657218 3464 1348 801 1284 922 3685 2566 4615 1606 732 4203 1458 M2323 DORMOY_ELAVL1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/DORMOY_ELAVL1_TARGETS.html Genes down-regulated in HeLa cells upon knockdown of ELAVL1 [GeneID=1994] by RNAi. 17548472 12/31 Arthur Liberzon 0.0019520104496408 0.00290569281036111 1335 1875 1606 0.000177613143549641 332 3.91143648379791 3.91143648379791 1 3.62688055709563 1333 3856 1494 2579 3215 1863 969 1126 332 2252 1606 1459 M1450 WANG_IMMORTALIZED_BY_HOXA9_AND_MEIS1_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_IMMORTALIZED_BY_HOXA9_AND_MEIS1_UP.html Up-regulated genes in myeloid progenitors immortalized by HOXA9 [GeneID=3205] vs those immortalized by HOXA9 and MEIS1 [GeneID=4211]. 15755900 16/63 Kevin Vogelsang 8.74261567993452e-05 0.000164529707133226 2260 1885.09090909091 1607 7.94814829407913e-06 1204 1.4936861111299 -1.34987746592418 -1 2.0658637657647 2260 1382 1403 1246 2365 1339 2665 3166 1607 1204 2099 1460 M2466 DELACROIX_RAR_BOUND_ES http://www.broadinstitute.org/gsea/msigdb/cards/DELACROIX_RAR_BOUND_ES.html Genes with DNA sequences bound by RARA and RARG [GeneID=5914, 5916] in ES cells. 19884340 298/658 Arthur Liberzon 2.83698006551563e-07 2.29907642774426e-06 1865 1385 1607 2.57907311941327e-08 244 1.61142951766271 1.77580231920159 1 3.32116181582615 1862 675 505 869 244 2689 1607 2465 1706 473 2140 1461 M636 REACTOME_HS_GAG_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HS_GAG_DEGRADATION.html Genes involved in HS-GAG degradation 8/21 Reactome 1.58997053185327e-05 3.71415848069014e-05 1075 1880.54545454545 1610 1.58998190799614e-06 323 1.20181691588537 1.20181691588537 1 1.94614399893513 1072 1660 3941 2771 3684 875 445 323 1610 3300 1005 1462 M4242 RIZKI_TUMOR_INVASIVENESS_2D_UP http://www.broadinstitute.org/gsea/msigdb/cards/RIZKI_TUMOR_INVASIVENESS_2D_UP.html Genes up-regulated in monolayer (2D) cultures of preinvasive (S3-C) vs invasive (T4-2) breast cancer cells. 18316601 50/114 Jessica Robertson 6.17890920008966e-07 3.51387967374031e-06 1365 1954 1610 5.61719175954158e-08 316 1.68710865188175 2.10977098186143 1 3.36352303473192 2576 316 1363 1363 529 4560 3247 2178 1125 1610 2627 1463 M1920 CHEN_METABOLIC_SYNDROM_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_METABOLIC_SYNDROM_NETWORK.html Genes forming the macrophage-enriched metabolic network (MEMN) claimed to have a causal relationship with the metabolic syndrom traits. 18344982 728/1952 Jessica Robertson 3.19392214989774e-15 1.8252096578562e-13 915 1434.72727272727 1610 3.19392214989775e-16 29 1.6780146903421 1.86143711752931 1 7.81339327015472 911 220 4547 513 548 2100 1610 1675 1714 29 1915 1464 M2491 BRIDEAU_IMPRINTED_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BRIDEAU_IMPRINTED_GENES.html List of genomically imprinted genes. 20421412 23/85 Arthur Liberzon 0.000490456138987251 0.000793604097822604 1610 1866.18181818182 1610 4.45968647975139e-05 959 1.862990380336 -1.83143888575988 -1 2.11128588549221 1610 2162 959 2470 2766 1227 2384 1503 2771 1426 1250 1465 M16393 BIOCARTA_NUCLEARRS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NUCLEARRS_PATHWAY.html Nuclear Receptors in Lipid Metabolism and Toxicity 3/24 BioCarta 0.0132350068883529 0.0178729804838103 920 2021.63636363636 1611 0.00133144984475568 699 2.2098433553673 2.2098433553673 1 1.41180015437141 917 1670 3852 2001 3447 1169 699 1567 3914 1391 1611 1466 M19202 CHENG_IMPRINTED_BY_ESTRADIOL http://www.broadinstitute.org/gsea/msigdb/cards/CHENG_IMPRINTED_BY_ESTRADIOL.html Genes whose CpG islands became hypermethylated in breast progenitor cells pre-exposed to estradiol [PubChem=5757]. 18339859 69/198 Jessica Robertson 1.48217758063782e-06 6.07122739761261e-06 2720 1982.72727272727 1611 1.34743507200647e-07 858 1.59402862106337 -1.14433140497372 -1 3.0395772403255 2716 1480 2341 1317 883 1222 1611 3702 858 2656 3024 1467 M2091 NOUSHMEHR_GBM_SILENCED_BY_METHYLATION http://www.broadinstitute.org/gsea/msigdb/cards/NOUSHMEHR_GBM_SILENCED_BY_METHYLATION.html Top 50 most differentially hypermethylated and down-regulated genes in proneural G-CIMP (a CpG island methylator phenotype) GBM (glyoblastoma multiforme) tumors. 20399149 27/75 Arthur Liberzon 8.03866131649643e-06 2.1126846286653e-05 1200 2371 1612 7.3079006267349e-07 652 2.50963976108604 -2.29216483415365 -1 4.28871918157276 4198 1196 652 1197 1612 3568 4298 3189 954 902 4315 1468 M5636 LEE_LIVER_CANCER_MYC_E2F1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_E2F1_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) from MYC and E2F1 [GeneID=4609;1869] double transgenic mice. 15565109 31/107 Yujin Hoshida 2.51360122487779e-06 8.5863063599357e-06 3535 2297.63636363636 1613 2.28509463344313e-07 614 1.7577800744845 -1.53193650962515 -1 3.25510926496923 3535 614 1017 1549 1141 3126 4615 3633 1613 1340 3091 1469 M2235 BHAT_ESR1_TARGETS_VIA_AKT1_DN http://www.broadinstitute.org/gsea/msigdb/cards/BHAT_ESR1_TARGETS_VIA_AKT1_DN.html Genes bound by ESR1 [GeneID=2099] and down-regulated by estradiol [PubChem=5757] in MCF-7 cells (breast cancer) expressing constitutevly active form of AKT1 [GeneID=207]. 18838536 52/125 Arthur Liberzon 1.36944888300009e-06 5.83638198535578e-06 2520 1907.72727272727 1613 1.2449543049554e-07 839 1.6228197199974 1.51766509262129 1 3.1046405153799 2519 1105 860 1613 839 3104 2325 3152 1153 1051 3264 1470 M16743 KEGG_TYROSINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TYROSINE_METABOLISM.html Tyrosine metabolism 18/53 KEGG 9.99975857081102e-07 4.72749354697327e-06 2755 1848.81818181818 1614 9.09069374186272e-08 499 1.72126393037088 -1.50385484167245 -1 3.35055251160506 2754 499 1339 1614 720 2404 3064 3526 697 1034 2686 1471 M3574 REACTOME_SIGNALLING_BY_NGF http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALLING_BY_NGF.html Genes involved in Signalling by NGF 130/279 Reactome 4.14686761282598e-07 2.81825276987931e-06 2240 1641.54545454545 1614 3.76988035862343e-08 232 1.4918805586156 1.5958539926705 1 3.02655003105988 2238 685 1614 232 373 3026 2208 3111 1386 1091 2093 1472 M10961 GOZGIT_ESR1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GOZGIT_ESR1_TARGETS_DN.html Genes down-regulated in TMX2-28 cells (breast cancer) which do not express ESR1 [GeneID=2099]) compared to the parental MCF7 cells which do. 17726467 502/1368 Arthur Liberzon 3.36082632132888e-13 1.40614572694171e-11 1670 1576.27272727273 1615 3.36082632132938e-14 8 1.63439143127024 1.65998783879233 1 6.48311758416605 1670 8 4152 425 629 2174 1615 2957 1500 42 2167 1473 M10791 ENK_UV_RESPONSE_KERATINOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ENK_UV_RESPONSE_KERATINOCYTE_UP.html Genes up-regulated in NHEK cells (normal epidermal keratinocytes) after UVB irradiation. 16434974 398/936 Lauren Kazmierski 1.2920056745071e-06 5.62148429966598e-06 2415 1488.81818181818 1617 1.17455130297341e-07 554 1.60088423537731 -1.52610513011687 -1 3.0722093536568 2415 1235 1670 554 816 715 2364 2049 1794 1148 1617 1474 M1973 HORIUCHI_WTAP_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HORIUCHI_WTAP_TARGETS_UP.html Genes up-regulated in primary endothelial cells (HUVEC) after knockdown of WTAP [GeneID=9589] by RNAi. 17088532 204/531 Leona Saunders 3.98578283746116e-06 1.2167673209344e-05 755 2036.45454545455 1618 3.62344550781804e-07 624 1.64491473038563 2.05009711195949 1 2.95507034540195 3087 918 753 624 1338 4086 4269 1618 1880 753 3075 1475 M13879 VANHARANTA_UTERINE_FIBROID_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANHARANTA_UTERINE_FIBROID_DN.html Genes down-regulated in uterine fibroids vs normal myometrium samples. 15940248 48/122 Leona Saunders 0.000100136706106902 0.000184813156682529 850 2201.54545454545 1619 9.10375129893048e-06 848 1.79196855677357 1.76075475867194 1 2.445336892302 848 3885 1584 3831 2416 1425 1619 933 3058 3219 1399 1476 M1925 BOYAULT_LIVER_CANCER_SUBCLASS_G56_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G56_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G56, defined by unsupervised clustering. 17187432 16/34 Yujin Hoshida 0.0162534017136508 0.0216373410312977 590 1744.09090909091 1620 0.00148861247574763 590 1.6257348121278 -1.51499768766898 -1 0.989304552705634 590 1053 1727 1620 3325 986 1316 2589 2731 1578 1670 1477 M18899 BIOCARTA_DREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DREAM_PATHWAY.html Repression of Pain Sensation by the Transcriptional Regulator DREAM 9/17 BioCarta 0.000190291723258896 0.000332354459631453 750 1695 1621 1.90308020145973e-05 504 1.63364034530899 1.63364034530899 1 2.07708865916409 749 3003 3860 1621 2573 711 504 1889 569 2562 604 1478 M11792 BIOCARTA_SHH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SHH_PATHWAY.html Sonic Hedgehog (Shh) Pathway 7/19 BioCarta 0.00147222030004562 0.00221613373787786 740 2033.27272727273 1621 0.000147319655511017 740 1.22021190488854 1.22021190488854 1 1.18391776304482 740 1621 3871 2169 2986 886 756 3281 1612 3192 1252 1479 M1539 MCCLUNG_COCAINE_REWARD_5D http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_COCAINE_REWARD_5D.html Genes up-regulated in the nucleus accumbens (a major reward center in the brain) after 5 days of cocaine [PubChem=5760] treatment. 14566342 77/143 John Newman 5.14143341306935e-08 7.23506215424714e-07 1075 1595.45454545455 1622 4.67403048475039e-09 13 1.65455455755211 1.90751340539692 1 3.71371149231954 1074 3015 1782 2219 13 1197 1128 1622 2236 2521 743 1480 M954 REACTOME_GABA_B_RECEPTOR_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GABA_B_RECEPTOR_ACTIVATION.html Genes involved in GABA B receptor activation 12/42 Reactome 8.89899559392203e-08 1.10906099343401e-06 1320 1770.63636363636 1624 8.08999632171476e-09 44 1.5389200905359 1.37029215133039 1 3.34981124381216 1317 1059 1624 2287 44 1096 971 2983 3929 2242 1925 1481 M1387 SHIN_B_CELL_LYMPHOMA_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_3.html Cluster 3 of genes distinguishing among different B lymphocyte neoplasms. 19010892 18/44 Jessica Robertson 3.33639919507042e-05 7.05203727023005e-05 1400 1795.81818181818 1624 3.03313617649351e-06 988 1.44903149680207 1.54087486599384 1 2.19898118157136 1396 2636 1423 2258 2083 1624 988 1712 3064 1349 1221 1482 M976 REACTOME_GABA_RECEPTOR_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GABA_RECEPTOR_ACTIVATION.html Genes involved in GABA receptor activation 12/59 Reactome 8.89899559392203e-08 1.10906099343401e-06 1320 1770.36363636364 1625 8.08999632171476e-09 45 1.5389200905359 1.37029215133039 1 3.34981124381216 1318 1060 1625 2288 45 1097 972 2970 3930 2243 1926 1483 M5125 KHETCHOUMIAN_TRIM24_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KHETCHOUMIAN_TRIM24_TARGETS_DN.html Retinoic acid-responsive genes down-regulated in hepatocellular carcinoma (HCC) samples of TRIM24 [GeneID=8805] knockout mice. 18026104 3/13 Leona Saunders 0.00128727495033436 0.00196359714103737 1070 1863.72727272727 1625 0.000128802124339862 864 2.75772412063544 -2.75772412063544 -1 2.72866310330399 1067 2031 4299 2038 2961 965 864 1766 1625 1396 1489 1484 M5792 LI_AMPLIFIED_IN_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LI_AMPLIFIED_IN_LUNG_CANCER.html Genes with increased copy number that correlates with increased expression across six different lung adenocarcinoma cell lines. 16369491 150/356 Arthur Liberzon 1.2912683060337e-06 5.62148429966598e-06 3015 2040.09090909091 1626 1.17388096721047e-07 98 2.11960865514416 2.22972429050916 1 4.06767797037059 3013 1626 602 98 815 4352 4203 3306 507 390 3529 1485 M18702 MARSON_FOXP3_TARGETS_STIMULATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_FOXP3_TARGETS_STIMULATED_DN.html Genes with promoters bound by FOXP3 [GeneID=50943], dependent on it, and down-regulated in hybridoma cells stimulated by PMA [PubChem=4792] and ionomycin [PubChem=3733]. 17237765 7/21 Arthur Liberzon 2.6462244756574e-07 2.21828405955824e-06 255 1906.54545454545 1629 2.64622479077013e-08 251 1.18269418921418 0.765019866440332 1 2.44425324000343 2123 894 4441 1310 254 1444 1629 2538 251 3208 2880 1486 M18077 ABRAHAM_ALPC_VS_MULTIPLE_MYELOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ABRAHAM_ALPC_VS_MULTIPLE_MYELOMA_UP.html Genes up-regulated in immunoglobulin light chain amyloidosis plasma cells (ALPC) compared to multiple myeloma (MM) cells. 15388584 19/42 Kevin Vogelsang 6.00982406880598e-05 0.000118129343902789 1170 1698.36363636364 1630 5.46362567976869e-06 855 1.98212757574269 2.03865902622696 1 2.84565844805107 1170 2281 1420 2095 2261 1289 855 1528 2231 1922 1630 1487 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 0.00197449362958158 0.00293729433276803 1000 2116.81818181818 1631 0.000197625020789491 386 1.5182933605918 1.5182933605918 1 1.40523078250952 996 1570 4215 2999 3401 833 386 1768 4114 1631 1372 1488 M2521 RAO_BOUND_BY_SALL4 http://www.broadinstitute.org/gsea/msigdb/cards/RAO_BOUND_BY_SALL4.html Loci bound by both isoforms (a and b) of SALL4 [GeneID=57167] in ES cells (embryonic stem). 20837710 181/435 Arthur Liberzon 1.28096852429239e-06 5.59423905389947e-06 2305 1774.45454545455 1631 1.1645175183161e-07 659 1.78277997559292 2.09130987392374 1 3.4226550400217 2304 2035 1354 765 812 3439 3048 1498 1631 1974 659 1489 M124 PID_CXCR4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CXCR4_PATHWAY.html CXCR4-mediated signaling events 18832364 65/141 Pathway Interaction Database 1.45366296428605e-06 6.01223711442581e-06 1635 1489.36363636364 1634 1.3215126589121e-07 581 1.31133743373496 1.52565498528573 1 2.50255942832072 1634 581 1905 763 875 1756 1620 924 2181 2496 1648 1490 M1552 MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN.html Cluster 10: genes down-regulated in SW260 cells (colon cancer) by sodium butyrate and TSA [PubChem=5222465;5562] with the same kinetics with which each alters the level of histone H4 acetylation. 10969808 42/101 John Newman 7.33157744792325e-05 0.00014097567468596 3205 2226.36363636364 1634 6.66529253338409e-06 1169 1.65223510662119 -1.13112458350979 -1 2.32567141192719 3201 1634 1351 1566 2309 4394 3396 1169 1234 1218 3018 1491 M2125 CHICAS_RB1_TARGETS_SENESCENT http://www.broadinstitute.org/gsea/msigdb/cards/CHICAS_RB1_TARGETS_SENESCENT.html Genes up-regulated in senescent IMR90 cells (fibroblast) after knockdown of RB1 [GeneID=5925] by RNAi. 20385362 376/946 Arthur Liberzon 7.43002813998691e-07 3.95193762681502e-06 1215 1620.81818181818 1634 6.75457331756431e-08 370 1.70988829182099 1.81790044865426 1 3.3770479094609 1213 1673 370 1634 1571 2738 2076 1489 2228 1059 1778 1492 M14663 REACTOME_ETHANOL_OXIDATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ETHANOL_OXIDATION.html Genes involved in Ethanol oxidation 4/13 Reactome 0.000248768741911087 0.000424674070890838 1085 1910.18181818182 1636 2.4879659494866e-05 940 1.68472822102034 -1.68472822102034 -1 2.07648829463478 1407 1081 4073 2508 2634 1081 940 1872 2152 1628 1636 1493 M346 LIN_MELANOMA_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIN_MELANOMA_COPY_NUMBER_UP.html Candidate genes in significant regions of chromosomal copy number gains in a panel of melanoma samples. 18245465 41/112 Jessica Robertson 8.9651394807184e-05 0.000167506553455528 1350 1967.90909090909 1636 8.15045894243656e-06 722 1.04231198483059 -0.990161504199733 -1 1.43861740196246 1350 1636 3398 2482 2378 943 1389 722 2401 3934 1014 1494 M2210 WIERENGA_STAT5A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WIERENGA_STAT5A_TARGETS_UP.html Genes up-regulated in CD34+ [GeneID=947] cells by intermediate activity levels of STAT5A [GeneID=6776]; predominant long-term growth and self-renewal phenotype. 18779318 153/369 Arthur Liberzon 8.90394504026224e-07 4.39198804828093e-06 1375 1354.54545454545 1638 8.09449876719221e-08 425 1.84057897161478 1.86327123874168 1 3.60431569209311 1371 1715 425 998 674 1638 1907 1698 1787 711 1976 1495 M126 KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP.html Genes up-regulated in glioma cell lines treated with both decitabine [PubChem=451668] and TSA [PubChem=5562]. 16885346 93/241 Arthur Liberzon 1.67232479023939e-09 3.37780774442318e-08 2920 1870.81818181818 1639 1.52029526500965e-10 223 2.10412925576402 2.23685695507531 1 5.74634402711543 2916 820 223 325 1639 4310 3128 2735 1202 228 3053 1496 M5958 VARELA_ZMPSTE24_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VARELA_ZMPSTE24_TARGETS_DN.html Top genes down-regulated in liver tissue from mice with knockout of ZMPSTE24 [GeneID=10269]. 16079796 28/80 John Newman 6.86505996728691e-05 0.000133152611782725 940 1902.90909090909 1639 6.24115836326649e-06 939 1.61363962098554 -1.71901246405637 -1 2.28596924994879 939 3184 1639 2747 2293 977 1228 1137 2580 2751 1457 1497 M1723 LEIN_CEREBELLUM_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_CEREBELLUM_MARKERS.html Top 100 ranked genes most specific to the cerebellum region of adult mouse brain. 17151600 42/121 Jessica Robertson 3.34660238753838e-06 1.06608965248164e-05 1840 1614.54545454545 1639 3.04237043485778e-07 598 1.71013883177615 1.96763357840386 1 3.10813415618583 1838 598 827 1453 1269 2458 1639 2926 1947 840 1965 1498 M2363 TERAO_AOX4_TARGETS_SKIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/TERAO_AOX4_TARGETS_SKIN_DN.html Genes down-regulated in skin upon knockout of AOX4 [GeneID=71872]. 18981221 17/39 Arthur Liberzon 1.27358066948644e-05 3.0794628571793e-05 1240 1474.18181818182 1639 1.15780731118961e-06 641 1.51389230198235 -1.50551765305488 -1 2.49653467298569 1238 641 1710 1906 1769 830 1059 1811 1639 2223 1390 1499 M15687 LE_SKI_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LE_SKI_TARGETS_DN.html Selected genes implicated in metastasis and epithelial-to-mesenchymal transition (EMT) which were down-regulated in MDA-MB-231 cells (breast cancer) upon knockdown of SKI [GeneID=6497] by RNAi. 18451154 4/11 Jessica Robertson 0.00753381951134919 0.0104540948268233 860 1903.72727272727 1640 0.000755948334555241 722 2.54039267615147 2.54039267615147 1 1.83925429153541 859 2030 4475 2283 3217 1088 722 1570 1680 1640 1377 1500 M10158 LEE_SP4_THYMOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/LEE_SP4_THYMOCYTE.html Genes enriched in the single positive 4 (SP4) thymocytes compared to all other T lymphocyte differentiation stages. 15210650 11/31 Arthur Liberzon 1.44330939746511e-05 3.41583224066743e-05 1640 1533.18181818182 1640 1.31210806034494e-06 545 2.00270819872169 -2.04826066079702 -1 3.26967511175632 1640 774 669 1505 1821 1915 2941 1691 1406 545 1958 1501 M305 CHIARETTI_ACUTE_LYMPHOBLASTIC_LEUKEMIA_ZAP70 http://www.broadinstitute.org/gsea/msigdb/cards/CHIARETTI_ACUTE_LYMPHOBLASTIC_LEUKEMIA_ZAP70.html Differentially expressed genes between high vs low ZAP70 [GeneID=7535] acute lymphoblastic leukemia (ALL) cases with no known molecular aberrations. 16160012 40/90 Kevin Vogelsang 9.91770300258434e-07 4.71342355680631e-06 1920 1553.81818181818 1641 9.01609770321282e-08 581 1.7389622599579 2.0450833761649 1 3.38582628229371 1641 2582 1355 1916 713 1811 1255 2216 1920 1102 581 1502 M1927 MIKKELSEN_DEDIFFERENTIATED_STATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_DEDIFFERENTIATED_STATE_DN.html Genes down-regulated in partially reprogrammed and pluripotent cell populations (induced, iPS; and embryonic stem cells, ES) compared to parental lineage-commited cell lines. 18509334 4/9 Jessica Robertson 8.93673058882084e-05 0.000167042359550117 985 1673.63636363636 1642 8.93709000235485e-06 359 1.63751198971188 1.63751198971188 1 2.26084432721197 983 2213 4550 1947 2783 728 359 582 1870 1642 753 1503 M10855 XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN.html Genes down-regulated in DU-145 cells (prostate cancer) in the presence but not in the absence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 46/188 Arthur Liberzon 2.50073397031918e-06 8.57525404595596e-06 1140 1897.09090909091 1645 2.27339710263741e-07 670 2.14474468521895 -1.82035456288202 -1 3.97214034250508 2760 2153 670 1612 1137 2958 1645 3030 1136 1190 2577 1504 M1512 RUAN_RESPONSE_TO_TNF_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TNF_UP.html Adipocyte abundant genes up-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to TNF [GeneID=7124]. 12732648 12/34 John Newman 4.81713281633725e-06 1.40554697243813e-05 4150 2636.27272727273 1648 4.37922123999242e-07 187 2.0540606863533 -1.93732900618427 -1 3.64306696332274 4150 187 1069 1311 1417 4669 4390 4442 1648 1177 4539 1505 M2130 KEGG_ETHER_LIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ETHER_LIPID_METABOLISM.html Ether lipid metabolism 15/37 KEGG 7.67546730171669e-07 4.03220176859242e-06 4630 2319.63636363636 1649 6.97769998142952e-08 179 1.53170463275013 -1.13524042386525 -1 3.02024428922035 4627 179 1327 1649 605 3056 3789 3265 1635 833 4551 1506 M7739 BIOCARTA_PYK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PYK2_PATHWAY.html Links between Pyk2 and Map Kinases 20/47 BioCarta 0.000465000971445125 0.000755022367356845 1340 1671.36363636364 1649 4.22817531854425e-05 906 1.37542709979707 -1.55175924065206 -1 1.56962286093922 1338 1649 2199 1146 2754 1026 1868 906 1744 2530 1225 1507 M8108 FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP.html Genes up-regulated in MCF-7 cells (breast cancer) by selective estrogen receptor modulators (SERM) 4-hydroxytamoxifen, raloxifene, or ICI 182780 but not by estradiol [PubChem=44959;5035;3478439;5757]. 14973112 10/33 Arthur Liberzon 5.20505132465291e-06 1.50005353673576e-05 1205 1634.18181818182 1650 4.73187603590307e-07 198 2.77354208665728 3.40860228918682 1 4.89048238068913 1204 2754 1237 2245 3549 1650 2026 201 198 1970 942 1508 M2053 ZEMBUTSU_SENSITIVITY_TO_VINBLASTINE http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_VINBLASTINE.html Top genes associated with chemosensitivity to vinblastine [PubChem=13342] across 85 tumor xenografts. 11809704 14/47 Arthur Liberzon 0.000387691772297856 0.000640142228677855 1905 1569.36363636364 1651 3.52509190519924e-05 126 2.66115300032469 -1.99158273128776 -1 3.1066076828549 1645 2286 1139 1651 2715 1186 1902 1831 126 1902 880 1509 M15187 GENTILE_UV_RESPONSE_CLUSTER_D6 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D6.html Cluster d6: genes progressively down-regulated in WS1 cells (fibroblast) through 18 h after irradiation with high dose UV-C. 12907719 34/54 John Newman 2.34973885117722e-06 8.21581875658796e-06 1150 1940.27272727273 1654 2.13612850986397e-07 1104 1.54672545571542 1.54558637481076 1 2.87510201849711 1146 3311 2007 3111 1104 1447 1654 1311 3126 1929 1197 1510 M16734 KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3.html Genes with high histone H3 trimethylation mark at K27 (H3K27me3) in PC3 cells (prostate cancer) by ChIP-chip assay on a 12K CpG array (high-CpG-density promoters, HCP). 18488029 54/143 Jessica Robertson 7.27510647597006e-06 1.94251560948124e-05 1530 1880.90909090909 1655 6.61375503080719e-07 1273 1.85672201283247 1.92135312591135 1 3.19770076219084 1529 3208 1273 2498 1580 2368 1597 1655 1672 1332 1978 1511 M19170 MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP.html The 'NPM1-mutated signature 1': genes up-regulated in pediatric AML (acute myeloid leukemia) samples with mutated NPM1 [GeneID=4869] compared to all AML cases with the intact gene. 17597811 192/448 Arthur Liberzon 7.84587608180645e-07 4.09418433400279e-06 1785 1550.36363636364 1656 7.13261716353489e-08 586 1.71757571450951 2.13731219908432 1 3.38258902594713 1782 1996 853 1656 612 3053 2706 667 2019 586 1124 1512 M2631 FARMER_BREAST_CANCER_APOCRINE_VS_BASAL http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_APOCRINE_VS_BASAL.html Genes which best discriminate between two groups of breast cancer according the status of ESR1 and AR [GeneID=2099;367]: apocrine (ESR1- AR+) vs basal (ESR1- AR-). 15897907 219/571 Leona Saunders 7.65108270965936e-08 9.84971801578675e-07 3965 2105.54545454545 1656 6.95552997795095e-09 304 1.70333295666874 -1.5890158225324 -1 3.7397777285072 3965 1086 304 640 975 2468 4436 4011 1656 569 3051 1513 M1227 TRAYNOR_RETT_SYNDROM_DN http://www.broadinstitute.org/gsea/msigdb/cards/TRAYNOR_RETT_SYNDROM_DN.html Genes down-regulated in primary fibroblasts from Rett syndrom patients who carry mutations inactivating MECP2 [GeneID=4204]. 12418965 14/31 John Newman 1.05947344766895e-05 2.635187142132e-05 1660 1688.63636363636 1656 9.63162318093896e-07 766 1.44056513727741 1.45359201247558 1 2.41124131051218 1656 1460 1455 1955 1713 2073 1137 2282 1543 766 2535 1514 M1424 LEE_LIVER_CANCER_DENA_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_DENA_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) induced by diethylnitrosamine (DENA) [PubChem=5921]. 15565109 43/159 Yujin Hoshida 9.76761253856293e-06 2.47068767398751e-05 1660 1706.18181818182 1657 8.87968718664719e-07 1047 1.73008306863434 -1.39775317007669 -1 2.91354405504641 1657 1351 1067 2161 1685 1136 2449 2898 1551 1047 1766 1515 M9946 LU_TUMOR_ANGIOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LU_TUMOR_ANGIOGENESIS_UP.html Up-regulated genes of putative pathways stimulated in tumor endothelial cells by papillary serous ovarian epithelial tumor cells. 17308118 18/40 Jessica Robertson 0.000150958905813326 0.000268358661851763 1530 1695 1657 1.37244786599167e-05 514 1.84110189724183 1.87710855028831 1 2.40337484002099 1530 2314 1092 1625 3041 2234 1884 1716 1657 1038 514 1516 M8416 BROWNE_HCMV_INFECTION_10HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_10HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 10 h time point that were not down-regulated at the previous time point, 8 h. 11711622 34/92 John Newman 5.81474038250171e-05 0.000114727888136434 1660 1638.27272727273 1658 5.28626734135231e-06 561 1.86746119864323 2.02833993268404 1 2.68969814115932 1658 2424 2372 2090 2253 1550 1223 566 1015 2309 561 1517 M19367 GRAHAM_CML_DIVIDING_VS_NORMAL_DIVIDING_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_DIVIDING_VS_NORMAL_DIVIDING_DN.html Genes down-regulated in dividing CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients compared to the dividing cells from normal donors. 17717066 3/23 Arthur Liberzon 0.00138603025886271 0.00209717074363276 1070 1918.27272727273 1659 0.000138689550443374 818 2.54802914711823 2.54802914711823 1 2.49455796084041 1068 1709 4148 2914 2976 864 818 1339 1659 2454 1152 1518 M10290 KOBAYASHI_EGFR_SIGNALING_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOBAYASHI_EGFR_SIGNALING_24HR_UP.html Genes up-regulated in H1975 cells (non-small cell lung cancer, NSCLC) resistant to gefitinib [PubChem=123631] after treatment with EGFR inhibitor CL-387785 [PubChem=2776] for 24h. 17145885 93/193 Arthur Liberzon 0.000320090177721901 0.000535120432680995 1655 1887 1659 2.91033417183848e-05 1170 1.77615544548212 -1.90561114813952 -1 2.12399544186098 1652 1952 1170 1836 2675 1502 2681 1633 2468 1529 1659 1519 M17507 MILI_PSEUDOPODIA http://www.broadinstitute.org/gsea/msigdb/cards/MILI_PSEUDOPODIA.html Transcripts significantly enriched in pseudopodia of NIH/3T3 cells (fibroblast) in response to both chemotactic (lysophosphatidic acid, LPA [PubChem=3988]) and haptotactic (fibronectin, FN1 [GeneID=2335) migratory stimuli. 18451862 21/56 Jessica Robertson 0.000445591722637191 0.000727034405389234 1630 2071 1660 4.05165453762162e-05 865 1.61953873724939 1.61953873724939 1 1.8579119055553 1630 2995 2736 2652 2744 1660 865 1620 1542 3168 1169 1520 M12518 BACOLOD_RESISTANCE_TO_ALKYLATING_AGENTS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BACOLOD_RESISTANCE_TO_ALKYLATING_AGENTS_DN.html Genes down-regulated in D-341 MED (OBR) cells (medulloblastoma) resistant to both carmustine and O6-BG [PubChem=2578;4578]. 12479369 52/140 John Newman 0.000169621899421081 0.000298895125607565 540 1888.18181818182 1661 1.54213617116183e-05 539 2.04748927578474 2.13068696785624 1 2.63776487229331 539 3768 1661 3271 3394 1242 1330 675 2025 1737 1128 1521 M9630 KOMMAGANI_TP63_GAMMA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KOMMAGANI_TP63_GAMMA_TARGETS.html Genes changed in H1299 cells (non-small cell lung cancer, NSCLC) transiently transfected to express the TP63 [GeneID=8626] gamma splice variant. 16462763 8/16 Arthur Liberzon 0.000724463163106431 0.00114300121966977 1640 1814.09090909091 1662 7.2469945262318e-05 491 2.14994289160101 2.57883970455875 1 2.31196869760761 1636 1946 4243 1703 2883 2241 778 1591 491 1662 781 1522 M6023 BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_DN http://www.broadinstitute.org/gsea/msigdb/cards/BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_DN.html Genes down-regulated in pre B lymphocyte after induction of physiological DNA double-strand breaks (DSB) by RAG2 [GeneID=5897]; the changes are independent of ATM [GeneID=472] signaling. 18849970 41/95 Jessica Robertson 2.84886339465384e-07 2.29907642774426e-06 1800 1637.90909090909 1666 2.58987614869458e-08 247 1.62653137988915 1.93747007300695 1 3.35228680618515 1796 1435 1390 2468 247 2166 1666 979 2577 2024 1269 1523 M2157 DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN.html Genes down-regulated in MCF7 cells (breast cancer) at 24 h of estradiol [PubChem=5757] treatment. 20406972 343/817 Jessica Robertson 3.52213773897944e-10 8.46396792043982e-09 1960 1720.36363636364 1666 3.20194339958483e-11 188 1.73232480200462 1.87455769885313 1 5.11155038271076 1959 672 188 730 764 3971 3351 2332 1666 229 3062 1524 M13661 CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5 http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5.html The 'group 5 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 but not ERBB2 [GeneID=2099;2064]. 18794137 301/708 Jessica Robertson 4.55005605203368e-07 2.92102274825625e-06 4160 2258.36363636364 1667 4.13641544825442e-08 30 1.52911047413013 -1.42798190526993 -1 3.09338349235559 4156 30 756 857 416 3484 4190 4392 1667 412 4482 1525 M1766 TESAR_JAK_TARGETS_MOUSE_ES_D3_DN http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_JAK_TARGETS_MOUSE_ES_D3_DN.html Genes down-regulated in mES cells (mouse embryonic stem cells) after tratment with JAK inhibitor I [PubChem=5494425]. 17597760 8/15 Jessica Robertson 2.92649929426703e-06 9.64273840055e-06 2025 1845.63636363636 1667 2.92650314825333e-07 200 3.00838213779529 -2.95185143897241 -1 5.51559576762018 2024 200 4445 439 1254 1527 2543 3101 1155 1667 1947 1526 M8537 HOFMANN_CELL_LYMPHOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_CELL_LYMPHOMA_DN.html Genes down-regulated in lymph nodes from patients with mantle cell lymphoma (MCL) compared to the non-malignant hyperplastic lymph nodes. 11468180 28/91 Kevin Vogelsang 8.9748160212459e-08 1.11259227184017e-06 2840 2189.09090909091 1668 8.1589239885183e-09 47 1.51649916938167 1.5618650633658 1 3.30024168525401 2837 1036 1579 1079 47 4276 3938 3716 1668 1459 2445 1527 M2070 YAGUE_PRETUMOR_DRUG_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAGUE_PRETUMOR_DRUG_RESISTANCE_DN.html Down-regulated genes common to all pretumorigenic cells with acquired drug resistance. 17283147 8/27 Jessica Robertson 0.000685499909590683 0.00108632146646667 565 1934.27272727273 1668 6.8571146099821e-05 562 1.92597940917373 1.92597940917373 1 2.08667681306316 637 2626 4501 3047 3544 565 562 937 2361 1668 829 1528 M1640 YIH_RESPONSE_TO_ARSENITE_C1 http://www.broadinstitute.org/gsea/msigdb/cards/YIH_RESPONSE_TO_ARSENITE_C1.html Genes in cluster 1: strongly up-regulated in HFW cells (fibroblast) upon treatment with sodium arsenite [PubChem=26435] at all time points. 12016162 27/53 John Newman 0.000360773271861317 0.000598013283318759 1370 1948.45454545455 1669 3.28029498073696e-05 651 1.83091717505223 2.32546915763087 1 2.15718413581352 1366 3770 1781 972 3222 1585 1487 1669 1806 3124 651 1529 M9884 BRUNEAU_HEART_GREAT_VESSELS_AND_VALVULOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/BRUNEAU_HEART_GREAT_VESSELS_AND_VALVULOGENESIS.html Genes for which mutations result in developmental defects in the great vessels formation and valvulogenesis, a major class of congenital heart disease. 18288184 6/14 Jessica Robertson 0.00020305969055067 0.000352555601114244 1485 1785.54545454545 1669 2.03078247894339e-05 207 2.14994289160101 2.57883970455875 1 2.71340189169244 1482 2461 4546 1998 2595 1758 1669 786 207 1327 812 1530 M18308 REACTOME_THROMBOXANE_SIGNALLING_THROUGH_TP_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THROMBOXANE_SIGNALLING_THROUGH_TP_RECEPTOR.html Genes involved in Thromboxane signalling through TP receptor 8/26 Reactome 9.60364999603745e-07 4.61694568892485e-06 3330 2187.18181818182 1671 9.60365414639416e-08 742 1.80763187243173 -1.86063887095452 -1 3.52546320557307 3326 780 4032 1423 742 3534 4206 1671 1494 786 2065 1531 M6889 KEGG_RIBOFLAVIN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIBOFLAVIN_METABOLISM.html Riboflavin metabolism 4/19 KEGG 2.70241111422619e-06 9.05182164493491e-06 1675 1688.18181818182 1673 2.70241440059344e-07 162 1.69132345722454 1.69132345722454 1 3.11786729440182 1673 1760 3801 2740 3173 1806 661 162 782 1620 392 1532 M16515 CREIGHTON_AKT1_SIGNALING_VIA_MTOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_AKT1_SIGNALING_VIA_MTOR_UP.html Genes in the AKT1 [GeneID=207] pathway which are independent of MTOR [GeneID=2475], insensitive to RAD001 (everolimus) [PubChem=6442177]. 17213801 29/58 Arthur Liberzon 2.97460477167938e-05 6.39403576150898e-05 980 1538.36363636364 1674 2.70422271987813e-06 515 1.60184388868619 -1.6861803461776 -1 2.4557896078197 976 2051 2088 2735 2042 515 1100 1023 1674 1932 786 1533 M17034 REACTOME_INTEGRATION_OF_ENERGY_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTEGRATION_OF_ENERGY_METABOLISM.html Genes involved in Integration of energy metabolism 66/186 Reactome 2.78752244796688e-05 6.03899837904882e-05 1395 1955.63636363636 1675 2.53414342550392e-06 1211 1.38459352414054 1.44111354977723 1 2.13527926825968 1393 1426 1353 1713 2021 1211 1243 4465 3021 1675 1991 1534 M15425 VANTVEER_BREAST_CANCER_ESR1_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_ESR1_DN.html Down-regulated genes from the optimal set of 550 markers discriminating breast cancer samples by ESR1 [GeneID=2099] expression: ER(+) vs ER(-) tumors. 11823860 181/450 Arthur Liberzon 2.64954879983031e-06 8.90658943759313e-06 1480 1624.27272727273 1675 2.40868362799478e-07 540 1.8444366231819 2.0712933753373 1 3.40485938686914 1479 1675 540 1559 1173 2281 1736 2377 1970 1230 1847 1535 M12 PID_RHOA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RHOA_PATHWAY.html RhoA signaling pathway 18832364 31/67 Pathway Interaction Database 7.73513929831408e-06 2.0443803018556e-05 1605 2006.81818181818 1676 7.03196954089482e-07 707 2.29071212000587 -1.38771013895409 -1 3.92654511129341 2919 2311 1308 1264 1601 3034 3276 1603 707 1676 2376 1536 M1511 GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_DN.html Genes down-regulated in glioblastoma cell lines displaying spherical growth (cluster-1) compared to those displaying semiadherent or adherent growth phenotype (cluster-2). 18037961 15/34 Jessica Robertson 4.05433962001838e-06 1.23367762723417e-05 1790 1776.09090909091 1676 3.68577008336885e-07 1054 1.42558444832225 -1.00812729020616 -1 2.55792253396529 1790 1054 1676 2093 1344 1859 1618 1156 2921 2612 1414 1537 M751 REACTOME_DARPP_32_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DARPP_32_EVENTS.html Genes involved in DARPP-32 events 14/30 Reactome 1.43450693988509e-05 3.39808281680866e-05 2205 1835.81818181818 1679 1.30410572150275e-06 186 1.45588988437163 1.00050710453056 1 2.37812893414769 2202 1388 2682 1432 1819 1679 729 3415 186 3146 1516 1538 M13897 REACTOME_CD28_DEPENDENT_PI3K_AKT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CD28_DEPENDENT_PI3K_AKT_SIGNALING.html Genes involved in CD28 dependent PI3K/Akt signaling 13/29 Reactome 6.97576430778294e-05 0.000134908920950354 1365 1946.63636363636 1679 6.34180500479408e-06 794 1.02014751682828 1.11595091223302 1 1.44307408623221 1362 1744 3100 1679 2300 1365 794 1406 2526 3677 1460 1539 M924 REACTOME_PLATELET_CALCIUM_HOMEOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_CALCIUM_HOMEOSTASIS.html Genes involved in Platelet calcium homeostasis 8/19 Reactome 1.94926648001869e-05 4.4298073352898e-05 1420 1818.18181818182 1680 1.94928357860892e-06 896 1.51536512326843 1.54803536340711 1 2.41149616054879 1416 983 4054 1733 1946 1090 896 2127 2944 1131 1680 1540 M11355 KEGG_TIGHT_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TIGHT_JUNCTION.html Tight junction 69/153 KEGG 2.53053927938782e-07 2.17979909250208e-06 4175 2069.18181818182 1681 2.30049051860174e-08 136 2.35741874061504 -2.32915937656835 -1 4.87858528549536 4173 1681 550 136 214 4012 2618 4673 310 757 3637 1541 M11520 BIOCARTA_TPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TPO_PATHWAY.html TPO Signaling Pathway 18/42 BioCarta 6.40707457112333e-05 0.000125254699375402 1060 1995.45454545455 1682 5.82478288398966e-06 444 1.01861634242147 -1.01861634242147 -1 1.45291456960773 1056 3421 3238 1682 2848 444 1140 507 3020 3870 724 1542 M1273 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1.html Cluster PAM1: genes up-regulated in hepatocellular carcinoma (HCC) vs normal liver tissue from mice deficient for TXNIP [GeneID=10628]. 16607285 177/408 Leona Saunders 1.48606905950255e-07 1.58989032256369e-06 4430 2122.09090909091 1682 1.3509719635313e-08 94 1.55543388936262 -1.41764360567763 -1 3.29682896985233 4430 681 805 538 94 2725 4068 4167 1682 714 3439 1543 M847 BOYLAN_MULTIPLE_MYELOMA_C_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_UP.html Genes up-regulated in group C of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 31/69 Jessica Robertson 5.30313187910382e-08 7.3867843043764e-07 2955 1943.27272727273 1682 4.82102909721509e-09 15 1.58041044773133 2.12660784407795 1 3.54208544029322 2951 1490 1646 1857 15 3848 3719 588 1114 1682 2466 1544 M366 LANDIS_ERBB2_BREAST_TUMORS_324_UP http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_TUMORS_324_UP.html Up-regulated genes from the 324 genes identified by two analytical methods as changed in the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 101/218 Leona Saunders 1.91498141708615e-06 7.1687063813697e-06 2335 1698.81818181818 1683 1.74089371270572e-07 1005 1.4333406752311 -1.60677944437174 -1 2.69536041274756 2332 1092 1955 1171 1005 1678 2559 1808 1683 1251 2153 1545 M3274 POMEROY_MEDULLOBLASTOMA_DESMOPLASIC_VS_CLASSIC_UP http://www.broadinstitute.org/gsea/msigdb/cards/POMEROY_MEDULLOBLASTOMA_DESMOPLASIC_VS_CLASSIC_UP.html Top up-regulated marker genes for medulloblastoma classification: desmoplastic vs classic morphology. 11807556 55/133 Jean Junior 3.9683483879926e-06 1.21302547593825e-05 1635 1746.63636363636 1683 3.60759595099687e-07 960 2.08068967057985 2.00494182112085 1 3.73895232138381 1633 1824 1815 1678 1336 2942 2299 1683 960 1941 1102 1546 M15383 CONRAD_STEM_CELL http://www.broadinstitute.org/gsea/msigdb/cards/CONRAD_STEM_CELL.html Supplementary Table 2. Genelist comparing microarray expression profiles of spermatogonial cells, haGSCs and hES (H1) cells. Examples of expression rates of different hES cell enriched and germ cell specific genes, surface markers for germ cell selection and signal transduction in all three cell types (spermatogonial cells = SC). 18849962 21/84 Jessica Robertson 2.55372535122086e-06 8.66528384925486e-06 1570 1746.81818181818 1683 2.32157119595441e-07 341 1.84421121513408 2.28430638510802 1 3.4124844794931 1569 2696 1902 2040 1151 2643 1683 341 414 3166 1610 1547 M1983 SCHOEN_NFKB_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/SCHOEN_NFKB_SIGNALING.html Genes down-regulated in A375 cells (melanoma) treated with KINK-1, a small molecule inhibitor of NFKB. 18544741 31/67 Jessica Robertson 0.000122861124315957 0.000222546280844443 1060 1827.72727272727 1683 1.11698169227793e-05 1001 1.89200050417946 1.8874084424339 1 2.52603983136337 1060 2863 1115 1405 2463 2333 2451 1530 2201 1683 1001 1548 M11159 SMID_BREAST_CANCER_RELAPSE_IN_LIVER_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_LIVER_UP.html Genes up-regulated in liver relapse of breast cancer. 18451135 2/6 Jessica Robertson 0.00608582352030618 0.00855373995685505 1530 1802.8 1683.5 0.000678038652604171 158 1.36206281919861 -1.36206281919861 -1 1.02951848999827 1527 796 4469 NA 3395 1188 561 1923 158 2171 1840 1549 M18256 KEGG_SULFUR_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SULFUR_METABOLISM.html Sulfur metabolism 4/18 KEGG 9.26206218223703e-06 2.36652254012883e-05 2525 1765 1685 9.26210078607163e-07 113 1.47721724977715 -1.58172582579463 -1 2.49780690282034 2525 216 3805 1685 1699 2161 3175 863 113 1621 1552 1550 M16517 BIOCARTA_WNT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_WNT_PATHWAY.html WNT Signaling Pathway 19/48 BioCarta 1.03366675344524e-05 2.58071403437939e-05 1630 1633.81818181818 1685 9.39701463768341e-07 263 1.71317122659521 1.97420973221761 1 2.87321452209591 1627 2698 2236 1364 2061 2245 1685 263 1035 2419 339 1551 M1133 DARWICHE_PAPILLOMA_RISK_LOW_UP http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_LOW_UP.html Genes up-regulated during skin tumor progression from low risk papilloma vs normal skin. 17525749 110/307 Arthur Liberzon 0.00307690164038232 0.00447219636688323 1170 1952.09090909091 1685 0.000280110310389065 1060 1.48971054391279 1.67559626560056 1 1.27935990041131 1169 2801 1685 2528 3067 1178 1060 1595 2237 2947 1206 1552 M19708 KEGG_TYPE_II_DIABETES_MELLITUS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TYPE_II_DIABETES_MELLITUS.html Type II diabetes mellitus 21/67 KEGG 4.42657515094429e-05 9.00300831481118e-05 1690 1733.72727272727 1686 4.02424019969954e-06 1013 1.50496963786961 1.5177736642637 1 2.2255187360609 1686 1783 1913 1013 2175 1328 1293 2891 1250 2077 1662 1553 M842 REACTOME_PURINE_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_CATABOLISM.html Genes involved in Purine catabolism 5/15 Reactome 3.68310975365029e-06 1.14830687329376e-05 1690 2160.72727272727 1688 3.68311585804838e-07 179 2.09319468152991 2.09319468152991 1 3.77964251997214 1688 3493 4036 3691 2992 1192 1171 179 1403 2892 1031 1554 M17951 NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_UP.html Top 100 probe sets contrubuting to the positive side of the 1st principal component; predominantly associated with spindle cell and pleomorphic sarcoma samples. 17464315 51/136 Nikolaos Papanikolaou 0.000839020338747508 0.00131273766523233 695 2000.27272727273 1688 7.63036808454546e-05 692 1.51530365057161 1.534250962161 1 1.59619549302056 692 2806 729 2888 3132 1688 1523 1644 3655 1429 1817 1555 M9131 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCEROPHOSPHOLIPID_METABOLISM.html Glycerophospholipid metabolism 36/81 KEGG 1.3161918949978e-05 3.16453320675201e-05 2830 1941.63636363636 1690 1.19654524493855e-06 840 1.62932400364899 -1.33525040175446 -1 2.67984289137248 2826 1437 2008 1684 1783 1690 3447 1412 840 1138 3093 1556 M1514 KANG_IMMORTALIZED_BY_TERT_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_IMMORTALIZED_BY_TERT_DN.html Down-regulated genes in the signature of adipose stromal cells (ADSC) immortalized by forced expression of telomerase (TERT) [GeneID=7015]. 15579653 60/211 Kevin Vogelsang 1.80145289502753e-07 1.78847632756335e-06 1255 1605.36363636364 1690 1.63768458412557e-08 325 2.07927462647018 2.40484290142414 1 4.36828890973296 1253 1823 325 1245 2233 2681 2411 1690 1491 520 1987 1557 M5574 CAFFAREL_RESPONSE_TO_THC_24HR_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_24HR_3_DN.html Genes down-regulated in EVSA-T cells (breast cancer) after treatment with 3 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 24 h. 18454173 13/26 Jessica Robertson 1.70554359655694e-05 3.94480616656753e-05 1695 1727.63636363636 1691 1.55050619897958e-06 418 1.47398651412899 -1.47398651412899 -1 2.37278036248154 1691 1221 2455 1257 1877 1709 3288 418 867 3083 1138 1558 M226 PID_VEGFR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_VEGFR1_PATHWAY.html VEGFR1 specific signals 18832364 23/43 Pathway Interaction Database 1.00023966597323e-05 2.52267119200783e-05 1020 1640.45454545455 1693 9.09312921487056e-07 406 1.53268742835571 1.50473680721213 1 2.57605407042278 1017 3238 1836 1721 1693 406 604 1674 3013 2293 550 1559 M155 PID_S1P_META_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_META_PATHWAY.html Sphingosine 1-phosphate (S1P) pathway 18832364 10/30 Pathway Interaction Database 3.94933619242807e-07 2.75940760315158e-06 2455 1909.54545454545 1694 3.59030627399495e-08 193 1.23062749038405 0.923408048702839 1 2.50067310121739 2454 193 1831 1694 351 2068 1516 4522 1690 1360 3326 1560 M18095 GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP.html Up-regulated genes from the set G (Fig. 5a): specific to cells expressing both MLL-AF4 [GeneID=4297;4299] and AF4-MLL fusion proteins. 17130830 148/379 Arthur Liberzon 4.55046224120159e-07 2.92102274825625e-06 1720 1436.09090909091 1694 4.1367847112871e-08 357 1.96472701940918 2.14100549094995 1 3.97463377069958 1717 2220 357 875 722 1847 1694 2585 1325 634 1821 1561 M702 REACTOME_ACYL_CHAIN_REMODELLING_OF_PE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACYL_CHAIN_REMODELLING_OF_PE.html Genes involved in Acyl chain remodelling of PE 4/22 Reactome 1.9951238322739e-05 4.52305286794169e-05 1695 2027.63636363636 1695 1.99514174483621e-06 41 3.17112867683882 -3.17112867683882 -1 5.03593073528353 1695 3352 3960 2441 3502 1412 1526 353 41 2662 1360 1562 M2160 MARSON_FOXP3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_FOXP3_TARGETS_DN.html Genes down-regulated by FOXP3 [GeneID=50943] in both ex vivo and hybridoma cells. 17237765 34/84 Arthur Liberzon 2.7367643709043e-06 9.13424347724897e-06 3810 2278.36363636364 1696 2.4879707049098e-07 464 1.37145615774096 1.48023238379288 1 2.52623504432306 3807 464 1696 1163 1186 3437 4590 3277 1273 1028 3141 1563 M12971 KYNG_DNA_DAMAGE_BY_GAMMA_RADIATION http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_GAMMA_RADIATION.html Genes specifically responding to gamma radiation. 15897889 67/154 Jessica Robertson 0.00031216956122398 0.000522811495316501 935 1844.90909090909 1697 2.83830786731754e-05 935 1.66060804619927 1.94030236210773 1 1.99195394444619 935 2466 1697 1804 2672 1443 1409 1239 2744 2302 1583 1564 M2492 TURJANSKI_MAPK11_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TURJANSKI_MAPK11_TARGETS.html Examples of transcription factors whose activities are regulated by MAPK11 [GeneID=5600] phosphorylation. 17496919 3/5 Arthur Liberzon 0.000113658173741861 0.000206996580705153 1560 2038.18181818182 1698 1.13663987341555e-05 218 2.90883983979762 2.90883983979762 1 3.91708524787227 1559 2935 4203 2339 3379 1594 1421 618 218 2456 1698 1565 M5519 PAL_PRMT5_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PAL_PRMT5_TARGETS_DN.html Genes down-regulated in NIH-3T3 cells (fibroblast) after knockdown of PRMT5 [GeneID=10419] by RNAi. 15485929 18/42 John Newman 0.00369145349345349 0.00530991775814453 1455 2029.18181818182 1699 0.000336151099651081 981 2.3274888272684 2.73010454622203 1 1.93540338331867 1451 3972 1224 3387 3091 1217 981 1699 1864 1778 1657 1566 M1838 LABBE_TGFB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_TGFB1_TARGETS_UP.html Up-regulated genes in NMuMG cells (mammary epithelium) after stimulation with TGFB1 [GeneID=7040]. 17210685 78/206 Jessica Robertson 4.25251488203934e-07 2.82656521095551e-06 2895 1689.90909090909 1699 3.86592336730384e-08 358 1.92541582716917 2.16680301780179 1 3.90515468134846 2892 572 544 358 389 3972 2837 1758 1699 872 2696 1567 M4844 KEGG_CHEMOKINE_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CHEMOKINE_SIGNALING_PATHWAY.html Chemokine signaling pathway 87/239 KEGG 2.86880148372444e-07 2.30751325380193e-06 1635 1737.90909090909 1700 2.60800168892401e-08 250 1.31209865737047 1.37374774833419 1 2.70347691886691 1632 824 1417 1229 250 2184 1918 1976 3320 1700 2667 1568 M254 PID_MYC_REPRESS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MYC_REPRESS_PATHWAY.html Validated targets of C-MYC transcriptional repression 18832364 48/110 Pathway Interaction Database 2.03563957962052e-05 4.59932838481281e-05 1890 1889 1703 1.85059855949873e-06 1256 2.02786914028644 2.44922280522583 1 3.21498682657457 1890 2419 1274 1579 1929 2908 3084 1468 1269 1256 1703 1569 M15122 OZEN_MIR125B1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/OZEN_MIR125B1_TARGETS.html Potential targets of MIR125B1 [GeneID=406911] microRNA which are up-regulated in prostate cancer. 17891175 17/45 Jessica Robertson 5.30595078184749e-06 1.5197851689326e-05 1965 1815.09090909091 1703 4.82360325341869e-07 969 1.45435391826063 -1.40718045434377 -1 2.56139043356167 1962 969 2175 1426 1457 1619 1982 3454 1361 1703 1858 1570 M10332 MODY_HIPPOCAMPUS_POSTNATAL http://www.broadinstitute.org/gsea/msigdb/cards/MODY_HIPPOCAMPUS_POSTNATAL.html Genes up-regulated in hyppocampus at late postnatal stages (clusters 11 and 15). 11438693 51/117 John Newman 5.85955134227515e-07 3.4235028683673e-06 2870 1984.81818181818 1703 5.32686627538876e-08 505 1.68813549214343 -1.41333057336639 -1 3.37255296078237 2867 1181 1603 788 505 3307 2264 2736 1703 1695 3184 1571 M19844 VALK_AML_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_1.html Top 40 genes from cluster 1 of acute myeloid leukemia (AML) expression profile; 57% of the samples are FAB M1 subtype, 43% have 11q23 abnormalities, and 36% have up-regulated EVI1 [GeneID=2122] expression. 15084694 18/45 Jessica Robertson 8.25857809450895e-05 0.000156552172131347 2050 1729.18181818182 1704 7.50808011772217e-06 549 2.16944981013054 2.2451573471174 1 3.01760525131363 2050 2342 1165 2083 3114 1987 1399 549 1589 1039 1704 1572 M6778 BIOCARTA_IL10_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL10_PATHWAY.html IL-10 Anti-inflammatory Signaling Pathway 11/19 BioCarta 7.31175827978321e-06 1.950079641381e-05 2770 1827.90909090909 1705 6.64707507338055e-07 888 1.24414014851235 -1.25834992311026 -1 2.14192685283105 2770 888 2165 1740 1582 1366 1705 1994 1636 2814 1447 1573 M11023 GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_DN.html Down-regulated genes from the set G (Fig. 5a): specific to cells expressing both MLL-AF4 [GeneID=4297;4299] and AF4-MLL fusion proteins. 17130830 23/64 Arthur Liberzon 2.15044447843824e-05 4.8192170377626e-05 1705 1721.54545454545 1705 1.95496863525269e-06 590 1.78094675351734 1.81224749272266 1 2.8103124007653 1705 2009 1890 1861 1947 1078 590 4550 813 1422 1072 1574 M16473 KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION.html Aldosterone-regulated sodium reabsorption 20/55 KEGG 8.89849870674915e-05 0.000166527016532854 2805 2016.09090909091 1706 8.08987150102576e-06 1134 1.79713659103254 -2.0871980834564 -1 2.48211284517628 2801 1647 1527 1134 2376 2178 4060 1161 1581 2006 1706 1575 M6176 HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_UP.html Genes whose expression correlated with higher risk of late recurrence of hepatocellular carcinoma (HCC). 18923165 44/110 Yujin Hoshida 1.03222226245277e-05 2.57988938147647e-05 1915 1825.09090909091 1706 9.38388277807471e-07 744 1.65921610036392 1.49801876646319 1 2.78280882549501 1913 1352 744 1697 1706 1815 1675 3546 2176 1077 2375 1576 M12705 SIG_CD40PATHWAYMAP http://www.broadinstitute.org/gsea/msigdb/cards/SIG_CD40PATHWAYMAP.html Genes related to CD40 signaling 21/36 Signaling Gateway 0.000283667044795489 0.000478841416394691 1205 1779.36363636364 1707 2.57912388459052e-05 908 1.25315967020592 -1.14251172441295 -1 1.52068291062553 1202 1646 2445 1707 2646 916 1917 908 3046 2080 1060 1577 M6241 VALK_AML_CLUSTER_8 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_8.html Top 40 genes from cluster 8 of aculte myeloid leukemia (AML) expression profile; 69% of the samples are FAB M2 subtype. 15084694 13/38 Jessica Robertson 0.000116330592690651 0.000211616908908537 2405 1770.09090909091 1707 1.0576067674716e-05 157 1.65550164980801 2.05748231727364 1 2.22352064917954 2405 1611 1707 1866 2450 2707 2316 1343 157 1280 1629 1578 M1875 JU_AGING_TERC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JU_AGING_TERC_TARGETS_UP.html Cytokines, growth factors, and secreted proteins that show increased expression on a protein array of samples from aged TERC [GeneID=7012] knockout mice. 17486088 4/12 Jessica Robertson 0.00171837215087564 0.00257015381391742 1110 2099.90909090909 1708 0.000171970236005568 425 1.83857908752951 1.83857908752951 1 1.740636899751 1108 2294 4522 3444 3232 788 425 1708 3009 1641 928 1579 M6376 MCCABE_BOUND_BY_HOXC6 http://www.broadinstitute.org/gsea/msigdb/cards/MCCABE_BOUND_BY_HOXC6.html Genes whose promoters where bound by HOXC6 [GeneID=3223] in LNCaP cells (prostate cancer), according to a ChIP-chip analysis. 18339881 247/926 Jessica Robertson 1.01511927355998e-06 4.79038158701114e-06 1845 1659.54545454545 1709 9.22836129049486e-08 725 1.64706787978182 1.95085481653103 1 3.20266980988898 1843 2382 1842 1395 725 2208 1709 1358 1578 1953 1262 1580 M10620 REACTOME_EICOSANOID_LIGAND_BINDING_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EICOSANOID_LIGAND_BINDING_RECEPTORS.html Genes involved in Eicosanoid ligand-binding receptors 3/14 Reactome 0.0011237636358668 0.00173075713619206 1210 2074.54545454545 1710 0.000112433232077039 1035 2.94879343248783 2.94879343248783 1 2.97680334219142 1208 1710 4008 2681 3391 1262 1625 1035 2224 2449 1227 1581 M2177 FIGUEROA_AML_METHYLATION_CLUSTER_6_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_6_UP.html Cluster 6 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 83/199 Arthur Liberzon 1.39256053530887e-06 5.86253407200259e-06 1710 2251 1710 1.26596492434136e-07 687 1.45293824922638 1.77992191854968 1 2.77860655142267 1710 3634 2883 4226 851 1526 1465 687 2864 3703 1212 1582 M16718 DING_LUNG_CANCER_MUTATED_FREQUENTLY http://www.broadinstitute.org/gsea/msigdb/cards/DING_LUNG_CANCER_MUTATED_FREQUENTLY.html The lung adenocarcinoma TSP (tumor sequencing project) genes with significantly higher frequencies of nonsense, splice site, and frame-shift mutations. 18948947 11/25 Jessica Robertson 1.06556662571979e-05 2.64752486639299e-05 3670 2267.63636363636 1714 9.68701624373083e-07 52 1.94299581632714 -1.87756479370573 -1 3.25077720159132 4650 1223 1108 691 1714 4570 3666 2536 52 1067 3667 1583 M12210 YOKOE_CANCER_TESTIS_ANTIGENS http://www.broadinstitute.org/gsea/msigdb/cards/YOKOE_CANCER_TESTIS_ANTIGENS.html Genes up-regulated in both colorectal cancer cells and normal testis relative to normal colon epithelium. 18281482 25/74 Jessica Robertson 1.98816190455346e-06 7.34741852108635e-06 1795 1790.27272727273 1715 1.80742154661585e-07 993 1.34885137160973 1.39661075784418 1 2.53120786476668 1794 1199 2166 2557 1023 1608 993 2087 2983 1568 1715 1584 M10184 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP.html Genes up-regulated in monocytes by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 146/354 Arthur Liberzon 0.000125826280556948 0.000227127099649406 1580 1831 1717 1.14394070556194e-05 1006 1.46389143346155 1.57588752512512 1 1.94972981286038 1071 1580 1006 1979 2469 1951 1571 1577 2908 2312 1717 1585 M1909 BIOCARTA_EGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EGF_PATHWAY.html EGF Signaling Pathway 25/53 BioCarta 0.00016200750183684 0.000286586316952598 1465 1979.45454545455 1719 1.4729039387517e-05 843 0.923265594988947 -0.968437853832412 -1 1.19559954348868 1464 1872 3251 1020 2518 843 1719 1556 2553 3779 1199 1586 M1134 DARWICHE_PAPILLOMA_RISK_LOW_DN http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_LOW_DN.html Genes down-regulated during skin tumor progression from low risk papilloma vs normal skin. 17525749 120/288 Arthur Liberzon 9.98508354410309e-07 4.72749354697327e-06 4660 2332.81818181818 1719 9.07735279637294e-08 718 1.59801809154148 -1.18212555590852 -1 3.11064644736354 4656 1005 1317 1476 718 2578 3956 2462 1719 1556 4218 1587 M18608 MURATA_VIRULENCE_OF_H_PILORI http://www.broadinstitute.org/gsea/msigdb/cards/MURATA_VIRULENCE_OF_H_PILORI.html Selected genes up-regulated in WT-A10 cells (gastric epithelium) expressing the H. pilori virulence gene CagA. 17237808 14/38 Arthur Liberzon 2.99820765492178e-06 9.80432733493613e-06 1940 1744.63636363636 1719 2.72564703722902e-07 1223 2.27045786438687 -2.39777594602722 -1 4.15668871643951 1937 1970 1461 2172 1223 1265 2595 1623 1335 1891 1719 1588 M19586 VALK_AML_WITH_CEBPA http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_WITH_CEBPA.html Genes that best predicted acute myeloid leukemia (AML) with mutations in CEBPA [GeneID=1050]. 15084694 23/66 Jessica Robertson 6.04498753477698e-06 1.68411483876129e-05 2485 1687.63636363636 1721 5.49545831343976e-07 1290 1.48787257518072 -1.60653604672824 -1 2.59617275772466 2481 1290 1731 1831 1501 1470 1757 1527 1457 1798 1721 1589 M11 PID_PRL_SIGNALING_EVENTS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PRL_SIGNALING_EVENTS_PATHWAY.html Signaling events mediated by PRL 18832364 20/41 Pathway Interaction Database 0.0268086004917585 0.0348184872240523 1010 2079.63636363636 1722 0.00246736063530044 1006 1.50650996905631 1.46905367201323 1 0.802981251939969 1006 2509 2066 1186 3732 1536 1506 1722 2827 3105 1681 1590 M11090 DITTMER_PTHLH_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DITTMER_PTHLH_TARGETS_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer) after knockdown of PTHLH [GeneID=5744] by RNAi. 16551631 93/198 Leona Saunders 1.78635289902256e-06 6.85265479395647e-06 1245 1806.27272727273 1723 1.62395849954956e-07 966 1.59031812009193 1.85016006835371 1 3.00193553331154 1244 2976 2307 2013 966 2196 1617 1136 1723 2443 1248 1591 M11410 LUCAS_HNF4A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LUCAS_HNF4A_TARGETS_UP.html Genes up-regulated in Tet-On HEK293 cells (embryonic kidney) by expression of HNF4A [GeneID=3172]. 16007190 44/96 Leona Saunders 8.54493615577777e-07 4.26956588478944e-06 2000 1572.81818181818 1724 7.76812679516879e-08 653 1.62267230814244 -1.66036679918352 -1 3.18488185584367 1998 850 1641 1123 653 2089 1789 1838 1724 1908 1688 1592 M17086 BUCKANOVICH_T_LYMPHOCYTE_HOMING_ON_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BUCKANOVICH_T_LYMPHOCYTE_HOMING_ON_TUMOR_UP.html Genes up-regulated in microdissected endothelial samples from ovarian cancer tumors with tumor-infiltrating lymphocytes (TIL) vs those without TILs. 18157142 19/41 Jessica Robertson 2.14252059314286e-06 7.71109946195657e-06 3490 2062.54545454545 1725 1.94774789062605e-07 357 1.50805904588963 -0.950409017936809 -1 2.81840571073074 3488 357 1725 1247 1061 4018 2568 1627 731 2429 3437 1593 M7918 SCIAN_INVERSED_TARGETS_OF_TP53_AND_TP73_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCIAN_INVERSED_TARGETS_OF_TP53_AND_TP73_UP.html Genes that were inversely correlated in H1299 cells (lung cancer): up-regulated by P53 [GeneID=7157] and down-regulated by P73 [GeneID=7161]. 17982488 5/20 Jessica Robertson 0.000177179411003758 0.000311426376580499 1730 1994.54545454545 1726 1.77193539233821e-05 47 5.55876916266923 5.55876916266923 1 7.1250783304264 1726 1988 4315 2417 3044 1521 1631 702 47 2904 1645 1594 M12095 BIOCARTA_IL1R_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL1R_PATHWAY.html Signal transduction through IL1R 27/52 BioCarta 7.53277602904039e-05 0.000144193580359817 1600 1740.27272727273 1727 6.84821269348657e-06 658 1.4704009552956 -1.43513781547912 -1 2.06445512780208 1598 2197 2529 2216 2318 658 1561 1199 2124 1727 1016 1595 M14174 NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_DN http://www.broadinstitute.org/gsea/msigdb/cards/NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_DN.html Genes down-regulated in K562 cells (bone marrow) after treatment with dasatinib [PubChem=3062316] or imatinib [PubChem=5291]. 17213809 12/18 Arthur Liberzon 0.00107175108830928 0.00165640686009804 1730 1836.90909090909 1727 9.74794144088146e-05 789 1.29474080730196 -1.35052066199213 -1 1.31606394579391 1727 2247 2735 2781 2897 925 789 1090 857 2964 1194 1596 M14036 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_DN.html Genes down-regulated in monocytes by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 27/74 Arthur Liberzon 1.45079346351943e-06 6.01097981436963e-06 1480 1836.45454545455 1729 1.31890401840759e-07 873 1.4877557156865 1.82579415725866 1 2.83928588587693 1476 2114 1278 2644 873 1708 2156 1336 3124 1729 1763 1597 M154 SCHAVOLT_TARGETS_OF_TP53_AND_TP63 http://www.broadinstitute.org/gsea/msigdb/cards/SCHAVOLT_TARGETS_OF_TP53_AND_TP63.html Genes up-regulated by TP53 [GeneID=7157] and down-regulated by an isoform of TP63 [GeneID=8626] in primary HEK cells (epidermal keratinocytes). 17404570 19/30 Leona Saunders 8.86626647732339e-05 0.000166122849711065 1325 1587.54545454545 1729 8.06056710796705e-06 383 1.60474457386583 1.86375038774918 1 2.2170098947068 1325 2014 1729 2109 2374 1103 383 2187 1333 1919 987 1598 M19703 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_WS http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_WS.html Human environmental stress response genes not changed in primary fibroblasts from patients with Warner syndrom (WS) . 15897889 10/19 Jessica Robertson 1.41950116558248e-06 5.92850486802096e-06 2110 1707.81818181818 1729 1.29045643771357e-07 659 1.72822481193315 2.127339348111 1 3.30199598743753 2110 659 1818 1217 861 2067 1729 1569 2637 2715 1404 1599 M13809 LIAO_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/LIAO_METASTASIS.html Genes up-regulated in the samples with intrahepatic metastatic hepatocellular carcinoma (HCC) vs primary HCC. 18504433 340/853 Jessica Robertson 4.24637718179609e-07 2.82649481163302e-06 950 1772.36363636364 1730 3.86034363765446e-08 388 1.62103356599662 1.91378570483726 1 3.28780883046878 2350 1328 947 1253 388 3934 2075 1730 1872 949 2670 1600 M16476 KEGG_CELL_ADHESION_MOLECULES_CAMS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CELL_ADHESION_MOLECULES_CAMS.html Cell adhesion molecules (CAMs) 63/183 KEGG 1.93835624495376e-14 9.76681436973474e-13 2935 1853.90909090909 1731 1.76214204086706e-15 88 2.2070290627207 2.18708661372 1 9.68900643058742 2931 296 88 517 1326 3134 2326 3654 1731 183 4207 1601 M1088 REACTOME_METABOLISM_OF_PORPHYRINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_PORPHYRINS.html Genes involved in Metabolism of porphyrins 10/22 Reactome 1.13453705674491e-05 2.79960013054588e-05 3740 1906.27272727273 1731 1.03140264325416e-06 155 2.1745565279194 -0.795218371566784 -1 3.61891551737161 3738 1703 1502 444 1731 2837 2612 1418 155 2700 2129 1602 M12456 VERNELL_RETINOBLASTOMA_PATHWAY_DN http://www.broadinstitute.org/gsea/msigdb/cards/VERNELL_RETINOBLASTOMA_PATHWAY_DN.html Cluster 2: genes down-regulated by RB1, CDNK2A [GeneID=1029;5925], and one of the E2Fs (E2F1, E2F2, or E2F3 [GeneID=1869;1870;1871]). 12923195 20/44 Kevin Vogelsang 0.011121455999994 0.0151409479418861 885 1933.09090909091 1732 0.00101618894599976 883 1.35679549652235 -1.21488396703154 -1 0.902544251490284 883 1732 1539 1699 3263 1034 1810 2470 3099 1549 2186 1603 M766 KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM.html Glycine, serine and threonine metabolism 15/34 KEGG 8.14637913666656e-07 4.17201449556497e-06 2010 1879.63636363636 1733 7.40580195744595e-08 630 1.92756751257109 2.19600261359756 1 3.79038398324263 2009 3319 1547 3445 630 1733 1479 759 2002 2603 1150 1604 M4605 FONTAINE_FOLLICULAR_THYROID_ADENOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_FOLLICULAR_THYROID_ADENOMA_UP.html Genes up-regulated in follicular thyroid adenoma (FTA) compared to other thyroid tumors. 17968324 44/122 Arthur Liberzon 4.74709483976948e-06 1.39117488550093e-05 1695 1875.90909090909 1733 4.31555007540097e-07 1285 1.39604978484932 1.63311060908945 1 2.47830142009181 1693 1433 2400 2138 1412 1861 1285 1733 1933 3355 1392 1605 M549 REACTOME_DOWNREGULATION_OF_ERBB2_ERBB3_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNREGULATION_OF_ERBB2_ERBB3_SIGNALING.html Genes involved in Downregulation of ERBB2:ERBB3 signaling 7/19 Reactome 0.00265235216237466 0.0038913344498709 980 2222.90909090909 1734 0.000265552322789747 638 2.4982551180985 2.4982551180985 1 2.20067199841007 977 3981 3927 2302 3539 1734 1463 1212 638 3196 1483 1606 M703 REACTOME_ACYL_CHAIN_REMODELLING_OF_PS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACYL_CHAIN_REMODELLING_OF_PS.html Genes involved in Acyl chain remodelling of PS 3/16 Reactome 1.59267097825567e-05 3.71861295670457e-05 1560 1928.45454545455 1735 1.59268239307461e-06 24 3.17112867683882 -3.17112867683882 -1 5.13451575688454 1560 2647 3961 1735 3590 1508 1938 325 24 2447 1478 1607 M15381 REACTOME_TCR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TCR_SIGNALING.html Genes involved in TCR signaling 25/65 Reactome 1.45271038741326e-06 6.01223711442581e-06 2515 1835.54545454545 1735 1.3206466787928e-07 874 1.43473137728175 -1.50135814640984 -1 2.73804471921405 2515 1288 2172 1046 874 1735 2310 3409 1488 1996 1358 1608 M3652 DER_IFN_ALPHA_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_ALPHA_RESPONSE_UP.html Genes up-regulated in HT1080 cells (fibrosarcoma) by treatment with interferon alpha for 6 h. 9861020 81/205 Yujin Hoshida 1.19057233769412e-05 2.91180687600974e-05 1845 1792.63636363636 1735 1.08234434614024e-06 278 1.67656767763882 1.93275158755178 1 2.77969931664851 1555 1531 1735 1493 1843 3323 2729 278 1844 1444 1944 1609 M11280 PENG_LEUCINE_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/PENG_LEUCINE_DEPRIVATION_UP.html Genes up-regulated in BJAB cells (B-lymphoma) after leucine [PubChem=857] deprivation. 12101249 96/216 Broad Institute 1.14903505679775e-05 2.82941580460025e-05 1500 2119 1736 1.04458278011042e-06 672 1.44844525424837 1.42384294940104 1 2.40807908579964 1498 4055 3036 3423 1736 1146 679 968 2757 3339 672 1610 M5542 SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER.html 50 genes up-regulated in the pancreatic cancer cell lines (AsPC1, Hs766T, MiaPaCa2, Panc1) but not in the non-neoplastic cells (HPDE) by the combination of decitabine and TSA [PubChem=451668;5562]. 12839967 21/66 John Newman 6.59898978121554e-07 3.66257540976655e-06 3995 2038.90909090909 1737 5.99908341873662e-08 553 2.22880922229628 -1.83137887909785 -1 4.42882627769206 3992 1648 873 1287 553 2336 2578 3603 1737 1253 2568 1611 M2026 NAKAMURA_ADIPOGENESIS_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_ADIPOGENESIS_LATE_UP.html Genes up-regulated in mesenchymal stem cells during late phase of adipogenesis, defined as days 7 to 14 of culturing with adipogenic hormones. 12646203 77/185 Arthur Liberzon 5.06872593925679e-06 1.46798824174025e-05 1185 1778.45454545455 1737 4.60794328860763e-07 1182 1.7244646298313 2.09043620673916 1 3.04659878922432 1182 2465 1500 2104 1434 2297 1650 1737 1931 1474 1789 1612 M527 GAUSSMANN_MLL_AF4_FUSION_TARGETS_D_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_D_DN.html Down-regulated genes from the set D (Fig. 5a): specific signature shared by cells expressing MLL-AF4 [GeneID=4297;4299] alone and those expressing both MLL-AF4 and AF4-MLL fusion proteins. 17130830 5/17 Arthur Liberzon 0.000688654644654508 0.0010905831919064 1385 1917 1738 6.88868148128311e-05 904 1.88197419745846 -1.88197419745846 -1 2.03783019869139 1383 904 4168 2558 2847 1332 1294 1176 1819 1868 1738 1613 M4308 SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1 http://www.broadinstitute.org/gsea/msigdb/cards/SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1.html Genes up-regulated in the pancreatic cancer cell lines (AsPC1, Hs766T, MiaPaCa2, Panc1) but not in the non-neoplastic cells (HPDE) by decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 12839967 283/867 John Newman 3.33190605161621e-13 1.40614572694171e-11 2265 1582.63636363636 1738 3.02900550146974e-14 88 1.83091131177985 1.9167795680256 1 7.26265024014248 2261 1473 106 88 642 3461 2400 2471 1738 162 2607 1614 M5319 APPEL_IMATINIB_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/APPEL_IMATINIB_RESPONSE.html Genes up-regulated by imatinib [PubChem=5291] during dendritic cell differentiation. 15756019 25/65 Kevin Vogelsang 3.06817566092851e-05 6.56505531831553e-05 1705 1865.63636363636 1739 2.78928950119819e-06 1040 1.72724894765715 -1.57595133179231 -1 2.64081087910302 1703 1040 1134 2596 2057 1355 1739 3122 2102 1567 2107 1615 M17487 RIGGINS_TAMOXIFEN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/RIGGINS_TAMOXIFEN_RESISTANCE_UP.html Genes up-regulated SUM44/LCCTam cells (breast cancer) resistant to 4-hydroxytamoxifen [PubChem=63062] relative to the parental SUM44 cells sensitive to the drug. 18974135 63/145 Leona Saunders 1.15803885216581e-05 2.8470986680215e-05 2630 1690.36363636364 1739 1.05276813446423e-06 599 1.5762707779459 -1.54113182739612 -1 2.61903348172756 2627 1340 785 982 1739 2016 2989 1949 964 599 2604 1616 M99 PID_TXA2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TXA2PATHWAY.html Thromboxane A2 receptor signaling 18832364 32/89 Pathway Interaction Database 4.62118719855072e-07 2.95428147508986e-06 1985 1704.36363636364 1740 4.20108015386335e-08 420 1.39389052709923 1.37500486557571 1 2.81732895969395 1983 1190 1424 1362 420 1917 1462 2527 2424 1740 2299 1617 M1326 MANTOVANI_NFKB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MANTOVANI_NFKB_TARGETS_DN.html NF-kB-controlled genes down-regulated in endothelial cells in response to viral GPCR protein. 17906691 7/22 Jessica Robertson 2.4134799151534e-05 5.34478586125181e-05 2540 1899.63636363636 1740 2.41350612753792e-06 680 1.50527132564895 -0.822105440841086 -1 2.35056555480886 2536 897 4310 1358 2007 2853 1740 992 680 2269 1254 1618 M11954 XU_HGF_SIGNALING_NOT_VIA_AKT1_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_SIGNALING_NOT_VIA_AKT1_48HR_UP.html Genes up-regulated in DU-145 cells (prostate cancer) in the absence and presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 23/61 Arthur Liberzon 1.62017300118176e-06 6.47240467479771e-06 2045 1736 1743 1.47288563122443e-07 870 1.26567782963372 1.27874102384334 1 2.40060440182725 2041 870 1943 2037 919 1743 933 1584 2613 2789 1624 1619 M17954 STARK_HYPPOCAMPUS_22Q11_DELETION_DN http://www.broadinstitute.org/gsea/msigdb/cards/STARK_HYPPOCAMPUS_22Q11_DELETION_DN.html Genes down-regulated in hyppocampus of mice carrying a hemizygotic microdeletion in the 22q11.2 region. 18469815 8/21 Jessica Robertson 0.000104334656762482 0.000191730275132938 1745 1777.90909090909 1743 1.04339555660469e-05 632 0.900401518794912 -0.86554260575491 -1 1.2234442034036 1743 662 4339 1856 2446 1176 2047 966 632 2404 1286 1620 M16763 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NEUROTROPHIN_SIGNALING_PATHWAY.html Neurotrophin signaling pathway 81/152 KEGG 4.25386451017052e-06 1.28438202929504e-05 2765 1914 1745 3.86715703214355e-07 241 1.69963473849842 1.98033831218769 1 3.03878282329833 2765 1337 1745 241 1361 3306 3053 2565 575 1443 2663 1621 M2587 BIOCARTA_HSP27_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HSP27_PATHWAY.html Stress Induction of HSP Regulation 13/25 BioCarta 9.90963644214829e-07 4.71342355680631e-06 3405 1976.72727272727 1745 9.00876445984374e-08 86 2.28734736650994 2.44360132310929 1 4.45355313889186 3402 370 1060 354 712 3475 4040 2492 86 1745 4008 1622 M15267 FUJII_YBX1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FUJII_YBX1_TARGETS_UP.html Genes up-regulated in MCF-7 cells (breast cancer) after knockdown of YBX1 [GeneID=4904] by RNAi. 18316615 31/70 Jessica Robertson 1.17572558464426e-05 2.88452884274503e-05 3545 2227.54545454545 1746 1.06884715273856e-06 313 2.42398411676501 -1.91282462442279 -1 4.02251534447897 3543 1361 656 996 1746 4205 3380 3358 313 1089 3856 1623 M8451 SENESE_HDAC3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC3_TARGETS_UP.html Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC3 [GeneID=8841] by RNAi. 17470557 325/930 Leona Saunders 1.02659537823165e-05 2.57115229417077e-05 1310 2001.90909090909 1747 9.33272880644291e-07 1307 1.68682602143661 1.72443291663084 1 2.83002410965239 1307 3726 2001 2315 1704 1684 1747 1430 2671 1831 1605 1624 M7735 BOYLAN_MULTIPLE_MYELOMA_C_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_DN.html Genes down-regulated in group C of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 36/102 Jessica Robertson 3.47489444616845e-06 1.09606456061272e-05 1750 1660.27272727273 1747 3.15899994069782e-07 327 1.85489379327874 2.02536244980144 1 3.36305773048756 1747 327 865 1769 1283 2175 1974 3384 1524 1359 1856 1625 M14105 DACOSTA_LOW_DOSE_UV_RESPONSE_VIA_ERCC3_XPCS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_LOW_DOSE_UV_RESPONSE_VIA_ERCC3_XPCS_DN.html Genes down-regulated in fibroblasts expressing the XP/CS mutant form of ERCC3 [GeneID=2071], after low dose UVC irradiation. 15608684 12/28 Arthur Liberzon 9.2433185724272e-05 0.000172005307788235 1800 1863.09090909091 1749 8.40336995825689e-06 181 5.02790383837703 5.02790383837703 1 6.91844809465294 1798 3486 1749 2385 2389 1641 1498 1058 181 2965 1344 1626 M8155 MCBRYAN_PUBERTAL_BREAST_3_4WK_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_3_4WK_DN.html Genes down-regulated during pubertal mammary gland development between weeks 3 and 4. 17486082 20/47 Arthur Liberzon 1.79765030275769e-06 6.88218081594978e-06 3925 1787 1750 1.6342288833129e-07 630 1.89291529773184 1.36829281114462 1 3.57183572615894 3924 630 1548 1386 972 1750 2291 1782 1014 2011 2349 1627 M4008 FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL.html Genes which best discriminate between two groups of breast cancer according to the status of ESR1 and AR [GeneID=2099;367]: apocrine (ESR1- AR+) and luminal (ESR1+ AR+). 15897907 206/551 Leona Saunders 7.08105583198292e-07 3.8227912014599e-06 1000 1994.81818181818 1750 6.43732555557845e-08 581 1.53014249791221 -1.48905948575509 -1 3.03011855676298 3831 996 863 1000 581 1770 4109 3597 1750 850 2596 1628 M1368 SCHAEFFER_SOX9_TARGETS_IN_PROSTATE_DEVELOPMENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_SOX9_TARGETS_IN_PROSTATE_DEVELOPMENT_UP.html Predicted targets of SOX9 [GeneID=6662] that are up-regulated during early prostate development. 18794802 14/29 Jessica Robertson 1.23092877367379e-06 5.46742391794822e-06 1750 1871.54545454545 1750 1.11902678399552e-07 766 1.30372584328418 1.11816119963088 1 2.50769260264883 1750 766 1635 1425 797 2716 1972 4091 1197 1894 2344 1629 M12763 RAMALHO_STEMNESS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAMALHO_STEMNESS_DN.html Genes depleted in embryonic, neural and hematopoietic stem cells. 12228720 57/149 John Newman 0.000206125187408141 0.000357080454046044 935 1668.45454545455 1750 1.87404093167253e-05 933 1.73528375963775 1.91081924880407 1 2.18655550990956 933 1957 942 1750 2572 1598 1800 1542 2087 1249 1923 1630 M4391 PEREZ_TP53_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/PEREZ_TP53_TARGETS.html Genes up-regulated in the HMEC cells (primary mammary epithelium) upon expression of TP53 [GeneID=7157] off adenoviral vector. 17563751 661/1775 Leona Saunders 4.14621454440293e-10 9.7633976658654e-09 1755 1629.09090909091 1751 4.14621454517652e-11 2 1.6583246436237 1.81178892757125 1 4.85560058653518 1751 2 4199 196 263 3015 2010 2189 1643 66 2586 1631 M12889 LINDGREN_BLADDER_CANCER_CLUSTER_2A_UP http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_2A_UP.html Genes whose expression profile is specific to Cluster IIa of urothelial cell carcinoma (UCC) tumors. 16532037 7/10 Leona Saunders 1.08393308713583e-05 2.68888853696057e-05 3610 2106.54545454545 1752 1.08393837427135e-06 386 1.51879691291971 -1.64486827135042 -1 2.53732297391935 3606 386 4162 1544 1752 3107 3862 893 391 1499 1970 1632 M1391 SHIN_B_CELL_LYMPHOMA_CLUSTER_7 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_7.html Cluster 7 of genes distinguishing among different B lymphocyte neoplasms. 19010892 13/37 Jessica Robertson 4.46722058356132e-05 9.07386027506214e-05 2220 1811 1753 4.06119208682049e-06 927 1.55772093132519 -1.69373909253363 -1 2.30158783678814 2218 2171 1582 2396 2177 1486 1408 927 2536 1753 1267 1633 M1633 SARTIPY_BLUNTED_BY_INSULIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SARTIPY_BLUNTED_BY_INSULIN_RESISTANCE_UP.html Genes up-regulated in 3T3-L1 cells (adipocyte) by insulin [GeneID=3630] but displayed blunted response to insulin the insulin resistant cells. 14530283 13/26 John Newman 0.000399271337262068 0.000657639889775062 1210 1787.36363636364 1754 3.63039834749661e-05 969 1.13216201496779 0.991351697143826 1 1.31682972934232 1209 1743 2319 1872 2724 1021 1142 1938 2970 1754 969 1634 M1470 SESTO_RESPONSE_TO_UV_C5 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C5.html Cluster 5: genes changed in primary keratinocytes by UVB irradiation. 11867738 38/82 John Newman 1.55825389223849e-05 3.65098886951479e-05 1625 1854.09090909091 1754 1.41660448128818e-06 1379 1.34897781201246 1.45263573445338 1 2.18812022872678 1621 2392 2468 1754 1851 1884 1485 1379 2373 1506 1682 1635 M6469 DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN.html Genes down-regulated in Kasumi-1 cells (acute myeloid leukaemia (AML) with the t(8;21) translocation) after knockdown of the AML1 MTG8 fusion [GeneID=861;862] by RNAi. 16652140 16/39 Leona Saunders 2.21598224761452e-05 4.9518802156994e-05 485 1647.27272727273 1755 2.01454960794118e-06 68 1.63178045860188 1.63178045860188 1 2.56789536242756 481 2700 1755 2974 2865 196 68 475 3833 2124 649 1636 M1144 OZANNE_AP1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OZANNE_AP1_TARGETS_DN.html Cancer motility and invasion genes down-regulated by the AP-1 transcription factor. 16799638 4/8 Arthur Liberzon 0.000552619890885281 0.000887753448299084 2245 1921.63636363636 1755 5.52757363936981e-05 419 1.70254290480086 1.64684345704472 1 1.89915424757424 2242 1401 4182 1419 2804 1881 1453 1952 419 1630 1755 1637 M18762 COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP.html 'Late-TGFB1 signature': genes overexpressed in primary hepatocytes at a late phase of TGFB1 [GeneID=7040] treatment; is associated with a more invasive phenotype. 18506891 67/156 Yujin Hoshida 1.62968614703845e-06 6.48828316484466e-06 2545 1812.36363636364 1756 1.48153395841499e-07 500 1.60916019767226 1.26753181894317 1 3.05145966795942 2541 577 1008 500 923 2857 1895 3970 1756 712 3197 1638 M8731 BIOCARTA_SPPA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SPPA_PATHWAY.html Aspirin Blocks Signaling Pathway Involved in Platelet Activation 17/42 BioCarta 2.98134971008325e-06 9.77467038716671e-06 1220 1899 1757 2.71032159117608e-07 1195 1.39177821231307 1.57047978166857 1 2.54869670314511 1216 2815 2121 1757 1219 1398 1815 1288 2686 3379 1195 1639 M5223 BRUNEAU_SEPTATION_ATRIAL http://www.broadinstitute.org/gsea/msigdb/cards/BRUNEAU_SEPTATION_ATRIAL.html Genes for which mutations result in atrial septation defects, a major class of congenital heart disease. 18288184 3/18 Jessica Robertson 3.47751683140643e-05 7.29764615851793e-05 1760 2148.27272727273 1758 3.47757125165991e-06 90 6.00900434550934 6.00900434550934 1 9.08632149094512 1758 3225 4544 2656 4159 1461 1322 424 90 2472 1520 1640 M5988 REACTOME_SLC_MEDIATED_TRANSMEMBRANE_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SLC_MEDIATED_TRANSMEMBRANE_TRANSPORT.html Genes involved in SLC-mediated transmembrane transport 93/268 Reactome 6.18692736247107e-07 3.51417474188357e-06 2790 2025.27272727273 1760 5.62448100216729e-08 513 1.70242664411359 1.74631152847895 1 3.39403922844154 2789 929 776 1496 530 3813 2507 4158 1760 513 3007 1641 M2421 PARK_OSTEOBLAST_DIFFERENTIATION_BY_PHENYLAMIL_UP http://www.broadinstitute.org/gsea/msigdb/cards/PARK_OSTEOBLAST_DIFFERENTIATION_BY_PHENYLAMIL_UP.html Genes up-regulated in M2-10B4 cells (osteoblast) in response to phenylamil [PubChem=4755]. 19433444 6/19 Arthur Liberzon 1.41762999360861e-05 3.36525539516208e-05 3135 1794 1760 1.4176390372264e-06 206 1.89468552745636 -2.189722813574 -1 3.09780114405762 3131 206 4664 988 1852 1760 3177 714 434 551 2257 1642 M10277 MULLIGHAN_NPM1_SIGNATURE_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_SIGNATURE_3_UP.html The 'NPM1 signature 3': genes up-regulated in pediatric AML (acute myeloid leukemia) with mutated NPM1 [GeneID=4869] compared to the AML cases with intact NPM1 and MLL [GeneID=4297]. 17597811 235/533 Arthur Liberzon 4.74004227338519e-07 3.00566144696657e-06 2850 2019 1761 4.30913026787114e-08 429 1.63097358804724 2.10783788482297 1 3.29205661158053 2850 1903 1347 1746 429 4564 3157 1417 2109 926 1761 1643 M1845 RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN.html Down-regulated genes in breast tumors from transgenic mice overexpressing ERBB2 and CDC25A [GeneID=2064;993] compared to those from mice overexpressing ERBB2 only. 17283130 128/267 Jessica Robertson 1.83483027966882e-06 6.97587836865205e-06 3210 2063.09090909091 1761 1.6680289181312e-07 681 1.75328808433627 -1.77044170672257 -1 3.30460247713371 3206 1628 932 1347 979 2591 4016 2656 1761 681 2897 1644 M13767 LEE_EARLY_T_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_EARLY_T_LYMPHOCYTE_DN.html Genes down-regulated at early stages of progenitor T lymphocyte maturation compared to the late stages. 15210650 42/109 Arthur Liberzon 0.0030793797579165 0.00447441040173541 1015 1989.18181818182 1761 0.000280336226071867 1014 1.52426879681482 1.62266388165213 1 1.30891868390754 1014 2915 1869 1578 3655 1311 1124 2473 3134 1761 1047 1645 M2307 WANG_NFKB_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WANG_NFKB_TARGETS.html Representative genes up-regulated in C2C12 cells (myoblast) lacking NFkB activity due to expression of a super repressor form of NFKBIA [GeneID=4792]. 17438126 26/61 Arthur Liberzon 5.56398230344504e-06 1.57444571702557e-05 1405 1650.63636363636 1761 5.05817852297015e-07 765 2.30217473545529 3.05208552062693 1 4.04164881583673 1405 2008 765 2563 1478 1761 1814 1997 1280 1305 1781 1646 M17726 KEGG_DRUG_METABOLISM_OTHER_ENZYMES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DRUG_METABOLISM_OTHER_ENZYMES.html Drug metabolism - other enzymes 15/80 KEGG 3.27930467938518e-05 6.9438869080881e-05 1980 1811.63636363636 1763 2.98123051044768e-06 508 2.03305011008791 2.99159100062541 1 3.09024790063941 1977 508 905 806 2076 3691 4278 1763 837 1981 1106 1647 M183 PID_IL6_7_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL6_7_PATHWAY.html IL6-mediated signaling events 18832364 38/74 Pathway Interaction Database 9.40679608704732e-06 2.39827238650183e-05 1735 2195.63636363636 1763 8.55166937183736e-07 1006 1.10461603024128 1.03192779872381 1 1.86544353418249 1732 2362 3154 1763 1668 1236 1006 2998 3176 3361 1696 1648 M14142 BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN.html Genes down-regulated in the invasive ductal carcinoma (IDC) compared to the invasive lobular carcinoma (ILC), the two major pathological types of breast cancer. 18490921 34/81 Jessica Robertson 0.000204064148808802 0.000354164667154833 840 1760.72727272727 1767 1.85530072299425e-05 639 1.72561476486857 1.92358499856394 1 2.1766180645408 837 1544 639 1562 2566 2104 2045 2340 3117 847 1767 1649 M10664 XU_GH1_AUTOCRINE_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_GH1_AUTOCRINE_TARGETS_UP.html Genes up-regulated in MFCF-7 cells (breast cancer) upon stable autocrine expression of HG1 [GeneID=2688]. 15845533 144/405 John Newman 7.38695765420739e-05 0.000141807798310593 1600 1845.81818181818 1767 6.71564154394312e-06 1220 1.6248262100441 1.77082354105418 1 2.28557288010851 1599 1817 1220 2658 2312 2482 1767 1268 2352 1333 1496 1650 M13950 KEGG_ASTHMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ASTHMA.html Asthma 12/39 KEGG 1.08553723753402e-05 2.6900198281779e-05 3180 2099.09090909091 1768 9.8685690354016e-07 1135 2.07022503121304 -2.14402510222135 -1 3.45840812015945 3180 1309 1135 1768 1718 2508 2950 3782 1276 1174 2290 1651 M18090 NUYTTEN_NIPP1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NUYTTEN_NIPP1_TARGETS_DN.html Genes down-regulated in PC3 cells (prostate cancer) after knockdown of NIPP1 [GeneID=5511] by RNAi. 17724462 547/1300 Jessica Robertson 4.88376207005347e-07 3.06773579896388e-06 2045 1663.81818181818 1771 4.88376314335474e-08 396 1.49069875396366 1.61250273687174 1 3.00407984797802 1771 396 4307 580 472 2506 1865 2045 2043 585 1732 1652 M9025 OUILLETTE_CLL_13Q14_DELETION_UP http://www.broadinstitute.org/gsea/msigdb/cards/OUILLETTE_CLL_13Q14_DELETION_UP.html Genes up-regulated in chronic lymphocytic leukemia (CLL) samples bearing deletions in the 13q14 region. 18281475 52/129 Jessica Robertson 1.27713634242857e-05 3.08646771563706e-05 995 1928.45454545455 1772 1.16103977861478e-06 525 1.39217842660752 -1.28408685333919 -1 2.2953161954637 995 2356 2361 2912 1772 525 1732 1685 2372 3095 1408 1653 M17702 KERLEY_RESPONSE_TO_CISPLATIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/KERLEY_RESPONSE_TO_CISPLATIN_DN.html Genes genes down-regulated in NT2/D1 cells (embryonal carcinoma) in response to treatment with cisplatin [PubChem=2767]. 15940259 3/10 Leona Saunders 0.000509484631559328 0.000821557117511015 1900 1833.72727272727 1773 5.09601477829703e-05 525 2.03842594896113 -2.03842594896113 -1 2.29890142399802 1899 795 4172 1822 2788 1662 2340 1002 525 1393 1773 1654 M11403 KANNAN_TP53_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANNAN_TP53_TARGETS_DN.html Primary down-regulated targets of TP53 [GeneID=7157] in the H1299 (lung cancer) cell line. 11402317 15/37 Broad Institute 1.19473519194369e-05 2.92046380252902e-05 2830 2295.27272727273 1774 1.08612880012662e-06 1179 2.72827880945336 2.72827880945336 1 4.52211934974703 2830 2435 1678 1179 1753 4553 3339 1702 1391 2614 1774 1655 M17534 LEE_DOUBLE_POLAR_THYMOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/LEE_DOUBLE_POLAR_THYMOCYTE.html Genes enriched in the double polar (DP) thymocyte compared to all other T lymphocyte differentiation stages. 15210650 13/34 Arthur Liberzon 1.28102312138185e-05 3.09267096692188e-05 4290 2086 1774 1.16457325511414e-06 165 2.24225011861416 -1.59481264175356 -1 3.69613402867418 4286 650 1501 1191 1774 2350 2965 2844 165 1279 3941 1656 M10 PID_BCR_5PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BCR_5PATHWAY.html BCR signaling pathway 18832364 44/107 Pathway Interaction Database 0.000151153309142285 0.000268602353674913 995 1840.45454545455 1775 1.37421541170984e-05 449 1.13271999184564 -1.11443097833537 -1 1.47848972428094 991 2154 3179 1271 2504 449 1437 1775 2966 2621 898 1657 M8976 WATANABE_COLON_CANCER_MSI_VS_MSS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_COLON_CANCER_MSI_VS_MSS_DN.html Down-regulated genes discriminating between MSI (microsatellite instability) and MSS (microsatellite stability) colon cancers. 17047040 29/123 Leona Saunders 1.37084065772039e-06 5.83638198535578e-06 4415 1823.54545454545 1776 1.24621955627711e-07 328 2.39302921240265 2.80074565913903 1 4.57813973859568 4415 1776 953 332 840 2408 2477 2317 328 1534 2679 1658 M18630 ROVERSI_GLIOMA_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROVERSI_GLIOMA_COPY_NUMBER_DN.html Genes in the most frequently homozygous deleted loci in a panel of glioma cell lines. 16247447 27/83 Arthur Liberzon 0.000213327741485472 0.000368739873331213 1730 2168 1777 1.93953118253006e-05 1583 1.83162989376114 -1.98356834663015 -1 2.29861472217094 3262 1777 1726 2252 2579 1661 3107 1734 1583 1730 2437 1659 M1563 MA_PITUITARY_FETAL_VS_ADULT_DN http://www.broadinstitute.org/gsea/msigdb/cards/MA_PITUITARY_FETAL_VS_ADULT_DN.html Down-regulated in human fetal pituitary tissue, compared to adult pituitary tissue 15894316 18/32 John Newman 4.52002770067738e-05 9.1520361246926e-05 1330 1716.54545454545 1777 4.1092005181286e-06 455 1.18292667320562 1.14518694313565 1 1.74620511403388 1328 2783 2999 2521 3098 887 639 455 1803 1777 592 1660 M10454 MCLACHLAN_DENTAL_CARIES_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCLACHLAN_DENTAL_CARIES_UP.html Genes up-regulated in pulpal tissue extracted from carious teeth. 15869869 138/455 John Newman 6.0106790056836e-11 1.71744157442886e-09 1720 2097.54545454545 1777 5.46425364167984e-12 157 1.66582226594273 1.94499793324915 1 5.33710419772148 1719 1765 157 1777 1430 3786 3124 2466 3201 615 3033 1661 M19245 COULOUARN_TEMPORAL_TGFB1_SIGNATURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/COULOUARN_TEMPORAL_TGFB1_SIGNATURE_DN.html 'Early-TGFB1 signature': genes overexpressed in primary hepatocytes at an early phase of TGFB1 [GeneID=7040] treatment; is associated with a less invasive phenotype. 18506891 100/254 Yujin Hoshida 1.17515009749464e-05 2.88452884274503e-05 2485 1852.72727272727 1779 1.06832397701198e-06 689 1.55174862825976 -1.49355073436443 -1 2.57507160348567 2485 689 880 1779 1745 1512 2834 2765 2189 754 2748 1662 M14877 BASAKI_YBX1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BASAKI_YBX1_TARGETS_DN.html Genes down-regulated in SKOC-3 cells (ovarian cancer) after YB-1 (YBX1) [GeneID=4904] knockdown by RNAi. 17072343 264/667 Arthur Liberzon 5.74942182925993e-07 3.39317263122318e-06 4120 2272.90909090909 1781 5.2267484834538e-08 497 1.6124551323011 -1.70908546780853 -1 3.22363678390724 4118 802 758 576 497 3346 4151 3737 1781 646 4590 1663 M7669 LEE_TARGETS_OF_PTCH1_AND_SUFU_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_TARGETS_OF_PTCH1_AND_SUFU_UP.html Genes up-regulated in medulloblastoma tumors from animals with inactivating mutations of one copy of PTCH1 or SUFU [GeneID=5727;51684] in conjunction with TP53 [GeneID=7157] loss. 17452975 35/93 Jessica Robertson 0.00127913543767402 0.00195308851773882 755 1909.81818181818 1781 0.000116352705927267 751 1.5908352265827 1.6390338386534 1 1.57542608321646 751 2740 1227 2606 2933 2017 1781 1331 2984 1072 1566 1664 M3126 KEGG_LEISHMANIA_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LEISHMANIA_INFECTION.html Leishmania infection 38/98 KEGG 0.000863212100718096 0.00134923679251668 1765 1951.72727272727 1782 7.85046349703725e-05 1256 1.71020433286457 -1.58072645933708 -1 1.79405521985621 1761 2421 2028 1323 2863 1256 1782 1646 2405 2593 1391 1665 M14512 BIOCARTA_RACCYCD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RACCYCD_PATHWAY.html Influence of Ras and Rho proteins on G1 to S Transition 22/48 BioCarta 0.000167391461310367 0.000295441200640444 1305 2008.18181818182 1782 1.52185635441827e-05 921 1.07829540209692 -1.13159808348439 -1 1.39114932921776 1303 1782 2977 1099 2526 921 1172 2387 3217 3238 1468 1666 M4047 BIOCARTA_NKT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NKT_PATHWAY.html Selective expression of chemokine receptors during T-cell polarization 5/30 BioCarta 0.000249886456142004 0.000426271544769359 1525 2211.90909090909 1785 2.49914560048303e-05 762 1.72099530465279 -1.72099530465279 -1 2.12016302338513 1522 3350 3869 3085 3561 1074 1785 762 1052 2884 1387 1667 M1471 AFFAR_YY1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/AFFAR_YY1_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) expressing ~25% of YY1 [GeneID=7528]. 16611997 142/397 Kevin Vogelsang 3.7522167943794e-08 5.51187708415733e-07 825 1539.63636363636 1787 3.41110623488678e-09 291 1.85257125117023 2.05041035124887 1 4.23816966431275 821 2221 291 1912 772 2197 1967 1632 2394 942 1787 1668 M18168 CASTELLANO_NRAS_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_NRAS_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) isolated from NRAS [GeneID=4893] knockout mice. 16909116 53/117 Leona Saunders 0.000178686766437441 0.000313722812860939 1180 1764.63636363636 1788 1.62455710228915e-05 867 1.4723742148834 1.46275397285795 1 1.88553179705741 1176 1588 1788 2092 2541 1399 977 867 2665 2440 1878 1669 M4661 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_GRANULOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_GRANULOCYTE_UP.html Genes up-regulated in granulocytes by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 39/109 Arthur Liberzon 0.000193126236465945 0.000336928348503135 1215 2160 1789 1.75584720063129e-05 701 1.65543606607601 1.75919782801774 1 2.10120884688882 1212 4226 1789 3655 3535 1067 920 701 3052 2289 1314 1670 M1844 RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP.html Up-regulated genes in breast tumors from transgenic mice overexpressing ERBB2 and CDC25A [GeneID=2064;993] compared to those from mice overexpressing ERBB2 only. 17283130 68/174 Jessica Robertson 4.53177105114699e-06 1.34574646043567e-05 2800 1910.72727272727 1791 4.11980035104606e-07 597 1.82558846213434 -1.54568946101767 -1 3.25045036893367 2797 834 597 1643 1386 3046 2465 2690 1791 1141 2628 1671 M17557 DANG_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DANG_MYC_TARGETS_DN.html Genes down-regulated by MYC [GeneID=4609] and whose promoters are bound by MYC, according to MYC Target Gene Database. 14519204 16/42 Chi Dang 0.000131783457036203 0.000236761277670313 1360 1710.72727272727 1791 1.19810319758578e-05 658 1.68512465168395 2.42788960152934 1 2.23327328140866 1359 1791 2171 1429 2481 1962 2441 658 676 2737 1113 1672 M9728 BARRIER_COLON_CANCER_RECURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_COLON_CANCER_RECURRENCE_UP.html Up-regulated genes from the 70-gene prognosis predictor for stage 2 colon cancer, based on non-neoplastic mucosa gene expression profiles. 17043639 26/59 Arthur Liberzon 6.4044655594928e-06 1.75710337305523e-05 2485 1838.63636363636 1792 5.82225836703736e-07 741 1.51222274465196 -1.92730394388876 -1 2.6284762021413 2484 741 2801 2089 1527 1094 2141 1372 1158 3026 1792 1673 M9948 KIM_WT1_TARGETS_8HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_8HR_DN.html Genes down-regulated in UB27 cells (osteosarcoma) at 8 hr after inducing the expression of a mutant form of WT1 [GeneID=7490]. 17430890 97/204 Arthur Liberzon 5.58342170684315e-06 1.57899300653392e-05 1795 2063.27272727273 1792 5.075850797423e-07 1479 1.61416088136755 1.81351216839354 1 2.83304737408349 1792 3205 1643 2620 1479 2587 1491 1648 2721 1673 1837 1674 M4752 WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_DN.html Genes down-regulated in rectal cancer patients resistant to radiotherapy (non-responders) relative to the sensitive ones (responders). 16585155 97/204 Arthur Liberzon 1.49926776916215e-05 3.53754721364241e-05 1115 1707.81818181818 1793 1.36297998777257e-06 730 1.77400701543924 2.10207178843146 1 2.88643132641593 1115 2106 1675 1639 1832 1837 1793 730 2008 2926 1125 1675 M6891 HOUSTIS_ROS http://www.broadinstitute.org/gsea/msigdb/cards/HOUSTIS_ROS.html Genes known to modulate ROS or whose expression changes in response to ROS 16612386 23/53 Nick Houstis 0.00399840061343997 0.00572631579296446 1365 1977.27272727273 1794 0.000364153279096393 462 1.58043403793189 -1.61538415758981 -1 1.29525533163039 1363 2744 2641 2977 3545 703 462 1612 2427 1794 1482 1676 M752 REACTOME_NEUROTRANSMITTER_RECEPTOR_BINDING_AND_DOWNSTREAM_TRANSMISSION_IN_THE_POSTSYNAPTIC_CELL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEUROTRANSMITTER_RECEPTOR_BINDING_AND_DOWNSTREAM_TRANSMISSION_IN_THE_POSTSYNAPTIC_CELL.html Genes involved in Neurotransmitter Receptor Binding And Downstream Transmission In The Postsynaptic Cell 51/156 Reactome 6.40732865678566e-07 3.60874303914634e-06 1360 1946.27272727273 1795 5.82484592988272e-08 541 1.21351955890882 1.18509561078896 1 2.41421510220968 1360 1269 2703 1795 541 1244 1229 3074 3236 3017 1941 1677 M9709 TAVOR_CEBPA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAVOR_CEBPA_TARGETS_UP.html Genes up-regulated in KCL22 cells (chronic myelogenous leukemia, CML, with BCR-ABL1 [GeneID=613;25] fusion) by expression of CEBPA [GeneID=1050]. 14517214 23/67 Kevin Vogelsang 1.17823216230268e-05 2.88614527577122e-05 4450 2581.63636363636 1795 1.07112588408275e-06 869 1.95518139675558 -2.07589925156965 -1 3.24438003945687 4449 1046 1324 1279 1750 3862 4574 3140 869 1795 4310 1678 M10100 CHOI_ATL_ACUTE_STAGE http://www.broadinstitute.org/gsea/msigdb/cards/CHOI_ATL_ACUTE_STAGE.html Acute stage-specific genes for adult T cell leukemia (ATL). 16909099 2/15 Leona Saunders 0.00530936297245202 0.00749989392639672 1265 2143 1795.5 0.000591325956596267 536 1.22833632130144 -1.22833632130144 -1 0.954078727268833 1264 1815 4191 NA 3204 904 536 1776 3979 2162 1599 1679 M10480 GU_PDEF_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GU_PDEF_TARGETS_DN.html Integrin, VEGF, Wnt and TGFbeta signaling pathway genes down-regulated in PC-3 cells (prostate cancer) after knockdown of PDEF [GeneID=25803] by RNAi. 17483333 23/92 Jessica Robertson 1.61379950965565e-06 6.4579543144717e-06 3390 2190.81818181818 1796 1.46709153950163e-07 114 2.01628045496648 -1.40929658243035 -1 3.8249838129656 3387 1374 1322 547 916 4116 3517 4198 114 1796 2812 1680 M2234 BHAT_ESR1_TARGETS_VIA_AKT1_UP http://www.broadinstitute.org/gsea/msigdb/cards/BHAT_ESR1_TARGETS_VIA_AKT1_UP.html Genes bound by ESR1 [GeneID=2099] and up-regulated by estradiol [PubChem=5757] in MCF-7 cells (breast cancer) expressing constitutevly active form of AKT1 [GeneID=207]. 18838536 181/425 Arthur Liberzon 2.96119360035041e-07 2.33605272916533e-06 3790 2067.27272727273 1796 2.69199454447844e-08 261 1.58606510459317 -1.48209426842765 -1 3.26486845454853 3789 809 1138 1114 261 1796 4163 4175 2121 842 2532 1681 M7388 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN.html Genes down-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 10 days after transduction. 16818636 86/278 Arthur Liberzon 1.11771831421146e-07 1.31268872691602e-06 1385 1684.45454545455 1797 1.01610760999779e-08 310 1.88990937914752 1.85681806845309 1 4.06324778814365 1384 2066 310 1506 401 2373 1797 2811 2433 743 2705 1682 M7880 SPIRA_SMOKERS_LUNG_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/SPIRA_SMOKERS_LUNG_CANCER_UP.html Up-regulated genes that distinguished smokers with and without lung cancer. 17334370 23/72 Jessica Robertson 4.26195624570311e-06 1.28514663397145e-05 4160 2451.72727272727 1797 3.8745131838294e-07 488 1.65347242541519 1.65085864566333 1 2.95609285227777 4159 488 1439 752 1362 3653 4518 3524 1028 1797 4249 1683 M19895 KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM.html Nicotinate and nicotinamide metabolism 13/31 KEGG 1.59470066139412e-07 1.65326710161346e-06 2660 2003.90909090909 1799 1.44972797908021e-08 110 1.38689379547007 1.89225906937722 1 2.9309929726562 2657 1799 1702 2209 110 4134 3008 296 1675 1742 2711 1684 M644 FOURNIER_ACINAR_DEVELOPMENT_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FOURNIER_ACINAR_DEVELOPMENT_LATE_UP.html Genes up-regulated late in HMEC cells (mammary epithelium) during acinar development in vitro. 16849555 11/24 Arthur Liberzon 3.08201951169248e-05 6.59166747229164e-05 2395 1719.72727272727 1799 2.8018751719129e-06 389 1.9311002469933 2.39315990385566 1 2.95124134533257 1799 1887 1102 2395 3102 1416 2395 389 1235 2103 1094 1685 M2425 YANG_BCL3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BCL3_TARGETS_DN.html Genes down-regulated in neonatal cardiac myocytes upon knockdown of BCL3 [GeneID=602] by RNAi. 19451226 3/24 Arthur Liberzon 0.000943273859803739 0.00146606345175467 1415 1994.72727272727 1799 9.436744936744e-05 604 3.32806253801357 3.32806253801357 1 3.44736417046302 1413 2140 4666 1116 3243 1799 2425 1237 604 2477 822 1686 M571 REACTOME_NUCLEAR_SIGNALING_BY_ERBB4 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEAR_SIGNALING_BY_ERBB4.html Genes involved in Nuclear signaling by ERBB4 21/70 Reactome 2.97414622078454e-05 6.39403576150898e-05 1895 1652.63636363636 1801 2.70380584415602e-06 387 2.60302594340781 -2.31273038214407 -1 3.99070353088398 1895 2429 1294 1907 2041 931 1608 2274 387 1612 1801 1687 M16097 NOUZOVA_METHYLATED_IN_APL http://www.broadinstitute.org/gsea/msigdb/cards/NOUZOVA_METHYLATED_IN_APL.html Genes whose CpG islands are hyper-methylated in the NB4 cell line (APL, acute promyelocytic leukemia) compared to PBMC (normal peripheral peripheral blood mononuclear cells). 15302897 46/112 Kevin Vogelsang 5.65543212792412e-07 3.34613067568844e-06 1805 1836.81818181818 1802 5.14130325612623e-08 494 1.67542129154468 1.70709521245198 1 3.35323245919353 1802 941 1929 1293 494 2640 2835 4190 999 1191 1891 1688 M2408 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_3 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_3.html Genes regulated in MCF7 cells (breast cancer) by expression of the truncated (611-CTF) form of ERBB2 [GeneID=2064] at both 15 h and 60 h time points. 19364815 10/27 Arthur Liberzon 7.04101203097834e-06 1.89730778477082e-05 3740 2204.18181818182 1802 6.40094051414252e-07 192 2.99934391007092 -2.75577170368099 -1 5.17676947327326 3739 1802 969 1194 1558 3601 4141 2652 192 1370 3028 1689 M3284 KUMAR_TARGETS_OF_MLL_AF9_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/KUMAR_TARGETS_OF_MLL_AF9_FUSION.html Myeloid leukemia model in mice with germ-line MLL-AF9 fusion knock-in [GeneID=4297;4300]: genes changed in comparison among the leukemic, preleukemic and wild-type animals. 14615372 232/605 Kevin Vogelsang 1.07257846210238e-06 4.95063560953846e-06 1805 1694.90909090909 1803 9.75071804566358e-08 677 1.5858206042882 1.63242665476859 1 3.07529264405173 1803 916 677 1278 750 2335 1845 2900 2529 1100 2511 1690 M1526 MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_7 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_7.html Cluster 7: genes up-regulated in SW260 cells (colon cancer) by curcumin and sulindac [PubChem=969516;5352]. 10969808 14/28 John Newman 5.0526724996606e-05 0.000101226264785847 1510 2097.18181818182 1804 4.59344413324632e-06 209 4.11214406923112 4.11214406923112 1 6.00443959081201 1509 3852 2107 3651 4028 1611 674 473 209 3151 1804 1691 M4491 CROONQUIST_NRAS_VS_STROMAL_STIMULATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_NRAS_VS_STROMAL_STIMULATION_DN.html Genes down-regulated in ANBL-6 cell line (multiple myeloma, MM) expressing an activated form of NRAS [GeneID=4893] off a plasmid vector compared to those co-cultured with bone marrow stromal cells. 12791645 92/194 Arthur Liberzon 2.51415277799852e-06 8.5863063599357e-06 940 1698.54545454545 1806 2.28559604651696e-07 420 2.00374812575509 2.33605427297703 1 3.71060019619627 940 2267 420 1333 2413 2759 2194 1806 1566 895 2091 1692 M2364 PURBEY_TARGETS_OF_CTBP1_AND_SATB1_UP http://www.broadinstitute.org/gsea/msigdb/cards/PURBEY_TARGETS_OF_CTBP1_AND_SATB1_UP.html Genes up-regulated in HEK-293 cells (fibroblast) upon knockdown of both CTBP1 and SATB1 [GeneID=1487, 6304] by RNAi. 19103759 82/216 Arthur Liberzon 7.8442149419844e-05 0.000149727051805046 1480 2106.90909090909 1806 7.13135876866249e-06 541 2.25299502253191 2.53612673361627 1 3.14975538753469 1478 3953 983 2592 3581 2769 2238 541 1527 1708 1806 1693 M821 SCHLESINGER_METHYLATED_IN_COLON_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SCHLESINGER_METHYLATED_IN_COLON_CANCER.html Genes expressed in normal colon; they undergo down-regulation in tumors through DNA methylation. 17200670 3/11 Leona Saunders 1.39803319462977e-07 1.52231708717588e-06 1640 1783.09090909091 1807 1.39803328258213e-08 2 4.36785386451565 4.36785386451565 1 9.28802466109645 1639 3070 4293 637 3745 1827 1807 36 2 2462 96 1694 M5914 LANDEMAINE_LUNG_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/LANDEMAINE_LUNG_METASTASIS.html Genes associated with metastasis of breast cancer in the lung compared to the non-lung metastasis. 18676831 10/31 Jessica Robertson 7.22296026534056e-05 0.000139172663665238 1625 1923.09090909091 1807 6.56654310714072e-06 235 3.11288385549047 3.11288385549047 1 4.38802839116375 1623 3002 1807 3096 3513 1890 1196 529 235 2712 1551 1695 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 0.000443864296970048 0.000724468162870653 850 2239.72727272727 1807 4.4395297888215e-05 849 1.72412317098254 1.72412317098254 1 1.97885747941336 849 1807 4432 2432 2764 1300 885 1663 4061 3207 1237 1696 M1135 DARWICHE_PAPILLOMA_RISK_HIGH_UP http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_HIGH_UP.html Genes up-regulated during skin tumor progression from normal skin to high risk papilloma. 17525749 91/262 Arthur Liberzon 0.000100088021899178 0.000184796087714557 1175 1800.81818181818 1810 9.09932505902523e-06 1173 1.64364090875205 1.84189415029735 1 2.24295170897249 1173 2043 1369 2409 2415 1627 1245 1810 1871 2345 1502 1697 M13013 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA.html Genes whose expression is coregulated with that of IL3RA [GeneID=3563] in hematopoietic stem cells (HSC). 15711547 13/24 Arthur Liberzon 4.66745770277244e-06 1.37126688371108e-05 2220 1966.54545454545 1814 4.24315236831632e-07 493 1.68628690371295 1.71708199965443 1 2.99739578811103 2217 2317 1814 1060 1403 2518 1728 3497 493 1282 3303 1698 M2072 BAE_BRCA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BAE_BRCA1_TARGETS_UP.html Genes concordantly up-regulated in DU-145 and MCF-7 cells (lprostate, breast cancer) upon expression of BRCA1. 15520196 68/139 Arthur Liberzon 2.31738504406197e-05 5.15389953321043e-05 4410 2045.90909090909 1814 2.1067358679598e-06 293 1.82047759950308 2.12759367121144 1 2.85328791658625 4406 293 711 827 1966 2269 4611 1814 933 633 4042 1699 M2584 KAAB_HEART_ATRIUM_VS_VENTRICLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAAB_HEART_ATRIUM_VS_VENTRICLE_DN.html Genes down-regulated in the ventricles of healthy hearts, compared to atria. 15103417 195/447 John Newman 9.36562517206281e-07 4.54790876230947e-06 1815 1842.27272727273 1815 8.51420832646154e-08 694 1.74011466067248 1.9082346404084 1 3.39794468496843 1812 2385 1503 1574 694 2811 2331 1969 1815 1441 1930 1700 M17243 REACTOME_ACTIVATED_TAK1_MEDIATES_P38_MAPK_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_TAK1_MEDIATES_P38_MAPK_ACTIVATION.html Genes involved in activated TAK1 mediates p38 MAPK activation 14/17 Reactome 2.17810235971212e-05 4.87653495346919e-05 2485 1887.90909090909 1816 1.980112658398e-06 1181 1.3379196794248 -1.45514696134564 -1 2.10870986640077 2482 1699 2387 1691 1948 1816 2669 1181 1563 1888 1443 1701 M13167 FREDERICK_PRKCI_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/FREDERICK_PRKCI_TARGETS.html Genes down-regulated in H1703 cells (non-small cell lung cancer, NSCLC) after knockdown of PRKCI [GeneID=5584] by RNAi. 18427549 5/23 Jessica Robertson 0.000184276100747071 0.000322689763864266 1645 2104.36363636364 1817 1.8429138348731e-05 1077 2.07758576609802 -2.07758576609802 -1 2.65127503762265 1644 1077 4314 1698 2563 1704 1950 3086 1817 1165 2130 1702 M13387 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_6 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_6.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 6. 12554760 56/111 Arthur Liberzon 1.41574973663724e-06 5.9181117447655e-06 4425 2320.81818181818 1818 1.28704604336821e-07 421 1.72913779060653 -1.7187770494974 -1 3.3042219823736 4421 583 551 1062 860 2844 4460 4335 1818 421 4174 1703 M10967 VICENT_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VICENT_METASTASIS_UP.html The metastasis gene signature: genes up-regulated during metastasis of NSCLC (non-small cell lung carcinoma) tumors to bone. 18381434 9/23 Jessica Robertson 0.000238286949708641 0.000408417207876625 890 1882.18181818182 1820 2.38312504867065e-05 606 1.56831298402334 1.83452394486975 1 1.94272006322559 888 2601 4461 2503 3463 932 753 832 1845 1820 606 1704 M166 PID_ATF2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATF2_PATHWAY.html ATF-2 transcription factor network 18832364 49/92 Pathway Interaction Database 3.8298202746208e-05 7.94797954245929e-05 1825 1711 1822 3.48171540618757e-06 440 1.79285086884165 2.02325875128172 1 2.68670557713047 1822 1345 717 462 2127 2957 3465 1908 1313 440 2265 1705 M6541 WU_HBX_TARGETS_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_3_UP.html Genes up-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] both in SK-Hep-1 cells (hepatocellular carcinoma) and normal primary hepatocytes. 11439330 14/36 John Newman 5.12306871857353e-05 0.00010233034959606 825 1821.18181818182 1824 4.65744365609485e-06 616 1.06299315907052 1.07114170616638 1 1.55032278617702 824 1462 2487 2784 2213 1005 616 1824 3108 2509 1201 1706 M5370 FONTAINE_FOLLICULAR_THYROID_ADENOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_FOLLICULAR_THYROID_ADENOMA_DN.html Genes down-regulated in follicular thyroid adenoma (FTA) compared to other thyroid tumors. 17968324 46/119 Arthur Liberzon 6.43781581278888e-08 8.68424121760708e-07 2100 1947.72727272727 1824 5.85256000107037e-09 22 2.02767715506404 -2.11504623985489 -1 4.49243243560169 2097 2985 998 1824 22 2349 1467 4023 1478 995 3187 1707 M13709 NIKOLSKY_BREAST_CANCER_12Q13_Q21_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_12Q13_Q21_AMPLICON.html Genes within amplicon 12q13-q21 identified in a copy number alterations study of 191 breast tumor samples. 19010930 30/63 Jessica Robertson 6.1589180445643e-06 1.70773313354014e-05 2510 1956.72727272727 1827 5.59903207870315e-07 1082 1.15497958030845 -1.20752378726439 -1 2.01275792430645 2508 1121 2411 1827 1510 1383 2346 1500 2972 2864 1082 1708 M10320 REACTOME_BIOLOGICAL_OXIDATIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BIOLOGICAL_OXIDATIONS.html Genes involved in Biological oxidations 43/219 Reactome 1.39517496844823e-06 5.8634887014784e-06 4635 2567.54545454545 1828 1.26834168475249e-07 129 1.76830847858178 -1.49621459230025 -1 3.38167648785602 4635 129 780 1683 852 3683 4539 3960 1828 1527 4627 1709 M4388 BIOCARTA_CDMAC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CDMAC_PATHWAY.html Cadmium induces DNA synthesis and proliferation in macrophages 10/29 BioCarta 0.00139442473207289 0.00210783041757856 1260 2027.72727272727 1829 0.000126846304051595 890 1.75532103073892 -1.75532103073892 -1 1.7170723094579 1256 3378 2784 2016 2991 890 1133 1061 1829 3474 1493 1710 M14811 LEE_LIVER_CANCER_ACOX1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_ACOX1_DN.html Genes down-regulated in hepatocellular carcinoma of ACOX1 [GeneID=51] knockout mice. 15565109 38/128 Yujin Hoshida 7.6101578709487e-07 4.0113835526733e-06 2160 1779.81818181818 1829 6.91832773038853e-08 602 2.0666966770074 2.46157117478267 1 4.07685002837223 2157 1829 764 1918 602 2780 1750 2619 1647 1233 2279 1711 M1245 LI_WILMS_TUMOR_VS_FETAL_KIDNEY_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_VS_FETAL_KIDNEY_2_UP.html Genes up-regulated in Wilm's tumor vs fetal kidney. 15531917 19/44 Arthur Liberzon 0.00115342352632717 0.00177211234241611 1180 2014.09090909091 1831 0.000104911699217755 1018 2.65816469081423 2.99213214237004 1 2.67344979813828 1177 3651 1329 2551 3521 1831 1945 1018 1689 1920 1523 1712 M991 REACTOME_TRANSFERRIN_ENDOCYTOSIS_AND_RECYCLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSFERRIN_ENDOCYTOSIS_AND_RECYCLING.html Genes involved in Transferrin endocytosis and recycling 13/29 Reactome 0.00144483187636544 0.00217700391403487 965 1935.45454545455 1832 0.000131434693741233 826 1.43900885206881 -1.43900885206881 -1 1.40027629068181 962 2085 2716 3234 2967 826 907 1140 1832 3079 1542 1713 M621 REACTOME_ARMS_MEDIATED_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ARMS_MEDIATED_ACTIVATION.html Genes involved in ARMS-mediated activation 11/23 Reactome 1.55679058726456e-05 3.6493850384801e-05 1630 1564.36363636364 1833 1.41527418520308e-06 268 1.75322547298197 2.0222888575047 1 2.84395566309101 1629 2319 2080 968 1850 1744 1833 1958 268 2099 460 1714 M2329 BILANGES_RAPAMYCIN_SENSITIVE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_RAPAMYCIN_SENSITIVE_GENES.html Genes translationally regulated in MEF cells (embryonic fibroblasts) by rapamycin (sirolimus) [PubChem=6610346] but not in response to serum deprivation. 17562867 22/63 Arthur Liberzon 4.00201112748901e-05 8.25414795044609e-05 1070 1940.09090909091 1833 3.6382581179692e-06 816 1.21897559332106 -1.21897559332106 -1 1.819401299565 1066 2399 3327 3306 2137 985 991 816 1833 3251 1230 1715 M16912 BALDWIN_PRKCI_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BALDWIN_PRKCI_TARGETS_UP.html Genes up-regulated in U87MG cells (glioblastoma multiforme) after knockdown of PRKCI [GeneID=5584] by RNAi. 16331246 28/80 Jessica Robertson 7.43834610937015e-07 3.95193762681502e-06 1835 1865 1834 6.76213511302323e-08 595 1.5798600160111 1.96142223645682 1 3.12024065525098 1834 1448 1834 1784 595 2431 1989 3325 1104 1839 2332 1716 M6034 REACTOME_SEROTONIN_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEROTONIN_RECEPTORS.html Genes involved in Serotonin receptors 2/12 Reactome 0.00300052817687399 0.00437203825772125 1545 2107.4 1835 0.000333837462381866 370 3.36354643817181 3.36354643817181 1 2.90069989945894 1808 3009 4001 NA 3507 1542 1543 1275 370 2157 1862 1717 M17372 LEE_LIVER_CANCER_MYC_TGFA_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_TGFA_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) tissue of MYC and TGFA [GeneID=4609;7039] double transgenic mice. 15565109 33/113 Yujin Hoshida 1.7721742522295e-06 6.81275918531608e-06 4685 2558.81818181818 1835 1.61106879979753e-07 859 1.84582626897982 1.77550213743926 1 3.48595183031147 4681 859 895 955 963 3627 4535 4356 1835 987 4454 1718 M3812 KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS.html Amyotrophic lateral sclerosis (ALS) 28/69 KEGG 2.75909313369071e-06 9.19375517427172e-06 3590 2381.27272727273 1836 2.50826963087928e-07 1190 1.84263258748876 -1.65992520990871 -1 3.39224683124489 3586 1642 1654 1749 1190 3343 3403 3627 1254 1836 2910 1719 M1240 JOHANSSON_BRAIN_CANCER_EARLY_VS_LATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOHANSSON_BRAIN_CANCER_EARLY_VS_LATE_DN.html Genes down-regulated in early vs late brain tumors induced by retroviral delivery of PDGFB [GeneID=5155]. 15750623 44/85 Leona Saunders 6.1147892089481e-07 3.48587618407917e-06 2175 1942.90909090909 1837 5.55890082593057e-08 527 1.65565570204777 1.56996302034094 1 3.30291948956123 2171 599 1372 1825 527 2932 2591 3198 1837 1295 3025 1720 M2458 SANDERSON_PPARA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SANDERSON_PPARA_TARGETS.html Hepatic genes regulated by fasting or in response to WY14643 [PubChem=5694] and which require intact PPARA [GeneID=5465]. 19805517 15/18 Arthur Liberzon 2.53425482640883e-06 8.63046374749401e-06 2185 1945.54545454545 1837 2.30387067791624e-07 630 1.33746341498693 -1.2480242641144 -1 2.47566531004259 2183 1213 2210 2694 1147 1415 1837 630 3265 3268 1539 1721 M1186 HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_UP.html Genes up-regulated in MCF7 cells (breast cancer, normal TP53 [GeneID=7157]) undergoing mitotic arrest and apoptosis after treatment with 100 nM docetaxel [PubChem=148124]. 17099726 27/141 Arthur Liberzon 0.0273564452118918 0.0355004802331377 1790 2191.90909090909 1838 0.00251842345591652 1249 1.636505469369 -1.53488994728801 -1 0.867230519188125 1788 1283 1566 1838 3406 1249 1367 3500 3772 2150 2192 1722 M14827 FERRARI_RESPONSE_TO_FENRETINIDE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FERRARI_RESPONSE_TO_FENRETINIDE_UP.html Genes up-regulated in HUVEC cells (umbilical vein endothelium) by fenretinide [PubChem=1744]. 15958647 15/31 Arthur Liberzon 3.12404213455166e-05 6.67544981418562e-05 1740 1984.09090909091 1838 2.84007863402748e-06 1487 1.53773137674647 1.51480295297037 1 2.34698459434733 1737 1696 1553 1704 2060 2264 2004 2798 2684 1487 1838 1723 M12135 MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_DN.html Genes down-regulated in apoptotic tissues (neuroepithelium) after MDM4 [GeneID=4194] knockout. 15608685 65/231 Arthur Liberzon 0.000636903634596344 0.00101342289701816 860 1976.27272727273 1839 5.79170994560856e-05 858 1.77279096723895 1.7797805387031 1 1.94025554647589 858 2608 926 2513 2818 1839 1722 2385 2761 1593 1716 1724 M1356 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX2_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX2_UP.html Early prostate development genes (up-regulated at 6 hr dihydrotestosterone [PubChem=10635]) which are also up-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 5/9 Jessica Robertson 0.00663631870092335 0.00928015202403068 915 2074.81818181818 1840 0.000665622072689459 913 2.28884681330478 2.28884681330478 1 1.70041434534351 913 1755 4326 1584 3195 1840 2144 1421 2234 1874 1537 1725 M11472 RIZKI_TUMOR_INVASIVENESS_3D_DN http://www.broadinstitute.org/gsea/msigdb/cards/RIZKI_TUMOR_INVASIVENESS_3D_DN.html Genes down-regulated in three-dimentional (3D) cultures of preinvasive (S3-C) vs invasive (T4-2) breast cancer cells. 18316601 223/565 Jessica Robertson 1.52263727963204e-05 3.5800693890395e-05 4410 2471.54545454545 1841 1.38422528911487e-06 565 1.77708927256986 2.08952367805066 1 2.88807560265473 4410 1712 565 1096 1841 2851 4193 3416 1684 890 4529 1726 M18437 REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS.html Genes involved in G alpha (q) signalling events 61/199 Reactome 1.5289750254582e-05 3.5931679886144e-05 1385 1904.09090909091 1842 1.3899869561495e-06 796 1.66004686289321 1.86732728048449 1 2.69689914502798 1381 1861 796 2505 1842 1725 1089 3480 2787 1048 2431 1727 M15380 KORKOLA_EMBRYONIC_CARCINOMA_VS_SEMINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_EMBRYONIC_CARCINOMA_VS_SEMINOMA_DN.html Top 25 most highly expressed genes in seminoma relative to embryonic carcinoma tumors. 16424014 13/90 Arthur Liberzon 0.000216709705315103 0.000373896052690196 1440 1828.72727272727 1842 1.97028231928565e-05 723 2.40951409032508 2.40951409032508 1 3.01852233883622 1439 1842 1717 2502 2590 1797 1991 723 2080 2365 1070 1728 M2058 NIELSEN_GIST_VS_SYNOVIAL_SARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_GIST_VS_SYNOVIAL_SARCOMA_DN.html Top 20 genes whose down-regulation correlated with gastrointestinal stromal tumors (GIST) compared to synovial sarcoma. 11965276 12/45 Arthur Liberzon 5.505256448224e-06 1.56159998283158e-05 420 1440.27272727273 1842 5.00479111324278e-07 416 2.22364611322398 2.01840425121236 1 3.90667750939054 1957 512 457 1152 1871 2617 1979 2622 418 416 1842 1729 M2701 ST_MYOCYTE_AD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_MYOCYTE_AD_PATHWAY.html Myocyte Adrenergic Pathway is a specific case of the generalized Adrenergic Pathway. 20/54 Signaling Transduction KE 3.11303691300704e-06 1.00743722198557e-05 2380 2066.90909090909 1843 2.83003756183203e-07 766 1.4135635432598 1.40652847428121 1 2.5818142248423 2379 1650 1843 766 1239 2484 1760 4514 982 2008 3111 1730 M1318 GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN.html Genes down-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of ELK3 [GeneID=2004] and HIF1A [GeneID=3091] by RNAi. 17704799 97/214 Jessica Robertson 3.04350161481311e-06 9.91094410494389e-06 890 1694.45454545455 1843 2.766823477483e-07 886 1.65807437835843 1.88129227929517 1 3.03270785767121 886 1858 1122 1843 1231 2388 1779 1495 2111 1916 2010 1731 M4862 REACTOME_RECYCLING_OF_BILE_ACIDS_AND_SALTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RECYCLING_OF_BILE_ACIDS_AND_SALTS.html Genes involved in Recycling of bile acids and salts 5/27 Reactome 0.000705816796835627 0.00111550000336315 1670 1987.54545454545 1844 7.06041076907001e-05 728 1.81036982585818 1.9552986316379 1 1.9538037289019 1666 1708 3912 2321 2890 1844 2572 947 1301 728 1974 1732 M11680 HATADA_METHYLATED_IN_LUNG_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/HATADA_METHYLATED_IN_LUNG_CANCER_DN.html Genes with unmethylated DNA in lung cancer samples. 16407832 22/217 Arthur Liberzon 0.00109061740138346 0.00168445390338922 1630 1895.54545454545 1844 9.9196221302714e-05 800 1.74629575702176 -1.80713388960901 -1 1.77040088808625 1628 2715 1281 2080 3701 800 2049 1844 2206 1716 831 1733 M16966 BIOCARTA_STATHMIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STATHMIN_PATHWAY.html Stathmin and breast cancer resistance to antimicrotubule agents 10/22 BioCarta 2.26014306651599e-05 5.04094736301472e-05 1960 1772.09090909091 1845 2.0546966237755e-06 379 1.32941179201224 1.27335204860543 1 2.08830261917356 1486 1845 1991 1043 1960 1006 379 4115 1776 1959 1933 1734 M12824 SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4 http://www.broadinstitute.org/gsea/msigdb/cards/SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4.html Cluster 4 of method A: up-regulation of these genes in patients with non-small cell lung cancer (NSCLC) predicts good survival outcome. 18641660 126/338 Arthur Liberzon 2.12129511006823e-06 7.66413946474922e-06 2820 1804.18181818182 1845 1.92845195952443e-07 363 1.68890019960109 -1.7945057228185 -1 3.15801678327147 2819 555 617 1341 1059 1845 3707 2824 2308 363 2408 1735 M19520 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREEN_DN.html Genes from the green module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 13/42 Arthur Liberzon 5.26304207478912e-07 3.21966255384619e-06 3635 2018.72727272727 1846 4.78458484896619e-08 102 1.94355099457138 2.78320359223848 1 3.90176146650753 3632 770 1846 1274 464 4345 4311 858 102 2353 2251 1736 M9172 MURAKAMI_UV_RESPONSE_1HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/MURAKAMI_UV_RESPONSE_1HR_DN.html Genes down-regulated in primary keratinocytes at 1 h after UVB irradiation. 11532376 8/18 Arthur Liberzon 1.1187163750898e-06 5.09951841796771e-06 130 1803.27272727273 1846 1.11871693827704e-07 19 1.6423321702157 1.6423321702157 1 3.17715734906597 633 1846 4611 3242 3939 128 19 130 2778 2410 100 1737 M1401 BYSTROEM_CORRELATED_WITH_IL5_DN http://www.broadinstitute.org/gsea/msigdb/cards/BYSTROEM_CORRELATED_WITH_IL5_DN.html Genes whose expression in bone marrow samples correlated inversely with increased levels of serum IL5 [GeneID=3567]. 14525773 43/136 Kate Stafford 3.81898139540567e-06 1.18045823343476e-05 1850 1881.45454545455 1847 3.47180729526728e-07 738 1.47271075019067 -1.42236086084577 -1 2.65279044705829 1847 3180 2592 1892 1319 738 960 1322 1978 3281 1587 1738 M2862 FINETTI_BREAST_CANCERS_KINOME_BLUE http://www.broadinstitute.org/gsea/msigdb/cards/FINETTI_BREAST_CANCERS_KINOME_BLUE.html Genes in the blue cluster of protein kinases distinguishing between luminal A and basal breast cancer subtypes. 18245477 20/50 Jessica Robertson 4.90383495000911e-05 9.86239080503978e-05 2205 1992 1847 4.45813114607307e-06 1350 1.3783856857606 1.70223613886291 1 2.01837974131387 1487 2511 2203 2896 2203 1801 1350 1847 1789 2016 1809 1739 M4035 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_RED_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_RED_UP.html Genes from the red module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 11/21 Arthur Liberzon 1.54619919127001e-05 3.62818698562407e-05 2320 1548.27272727273 1848 1.40564550758209e-06 624 1.05749100897204 1.06648490720125 1 1.7163634526721 2317 771 2026 1309 1848 1964 624 1043 2092 1064 1973 1740 M7615 RIZKI_TUMOR_INVASIVENESS_2D_DN http://www.broadinstitute.org/gsea/msigdb/cards/RIZKI_TUMOR_INVASIVENESS_2D_DN.html Genes down-regulated in monolayer (2D) cultures of preinvasive (S3-C) vs invasive (T4-2) breast cancer cells. 18316601 36/112 Jessica Robertson 2.73198772613488e-06 9.12480006034785e-06 4000 2265.18181818182 1849 2.4836282897796e-07 856 1.64632561985451 -1.48419673812037 -1 3.03281749352297 4000 856 1849 921 1184 3143 4262 4308 950 2032 1412 1741 M14019 DING_LUNG_CANCER_MUTATED_RECURRENTLY http://www.broadinstitute.org/gsea/msigdb/cards/DING_LUNG_CANCER_MUTATED_RECURRENTLY.html The lung adenocarcinoma TSP (tumor sequencing project) genes bearing recurrent somatic mutations. 18948947 5/13 Arthur Liberzon 8.43378184960479e-06 2.19356774649125e-05 1855 1881.63636363636 1850 8.4338138576801e-07 17 5.55876916266923 5.55876916266923 1 9.46621839573152 1853 1850 4561 1635 2645 2065 1468 243 17 2916 1445 1742 M2208 CARD_MIR302A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CARD_MIR302A_TARGETS.html Potential targets of MIR302A [GeneID=407028]. 18710938 59/130 Arthur Liberzon 0.00198203653835697 0.00294664442218933 770 2120.36363636364 1850 0.000180347678319844 766 1.37060263027242 1.3682186913795 1 1.26784661927766 766 3766 2371 3169 3779 997 1257 1596 2834 1850 939 1743 M13720 KEGG_LYSINE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LYSINE_DEGRADATION.html Lysine degradation 20/50 KEGG 0.00201698882965954 0.00299101571385588 1805 2059.90909090909 1851 0.00018353094622351 644 1.96451213352185 -1.72055274647435 -1 1.81256884793125 1804 2660 2757 3635 3013 644 772 1420 1851 3103 1000 1744 M1376 GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN.html Genes down-regulated in MMH-RT cells (hepatocytes displaying an invasive, metastatic phenotype) during epithelial to mesenchymal transition (EMT). 16607286 157/350 Jessica Robertson 9.29559198506601e-06 2.37121088960367e-05 1965 2004.54545454545 1851 8.45057387425072e-07 917 1.93520824481447 2.2153052491591 1 3.27160974521848 1965 2908 917 1482 1664 3074 2151 1851 1586 1557 2895 1745 M15676 BECKER_TAMOXIFEN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BECKER_TAMOXIFEN_RESISTANCE_DN.html Genes down-regulated in a breast cancer cell line resistant to tamoxifen [PubChem=5376] compared to the parental line sensitive to the drug. 15657362 39/132 Jean Junior 2.98448524072215e-06 9.77467038716671e-06 3255 1846.09090909091 1851 2.71317208130487e-07 722 1.49818324894896 -1.5227782464313 -1 2.74355114465301 3253 722 1851 886 1220 2059 3481 2152 1170 1286 2227 1746 M1555 RUAN_RESPONSE_TO_TNF_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TNF_DN.html Adipocyte abundant genes down-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to TNF [GeneID=7124]. 12732648 58/126 John Newman 7.89245412607156e-07 4.10477691839859e-06 1855 1844.63636363636 1851 7.17496087043131e-08 616 1.44334449536037 -0.971484516767643 -1 2.8419267605696 1851 709 1172 2073 616 1025 1831 3549 2591 2766 2108 1747 M2616 ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY.html Genes transiently induced only by the second pulse of EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 606/2731 Yaara Zwang 3.47279568624687e-15 1.93800754388692e-13 1855 1609.72727272727 1852 3.47279568624689e-16 3 1.80636477259137 1.92872525610736 1 8.3938385066923 1852 3 4685 422 269 2696 1961 2266 1344 30 2179 1748 M5872 KEGG_STEROID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STEROID_BIOSYNTHESIS.html Steroid biosynthesis 5/21 KEGG 0.00353738381502153 0.00509879438855456 1420 2315.09090909091 1854 0.000354302735049927 1283 2.30269326825228 -2.30269326825228 -1 1.92961578363256 1422 2962 3787 3970 3587 1417 1416 1283 1605 1854 2163 1749 M8582 RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_DN.html Genes down-regulated in peripheral blood monocytes by CSF2RB (GM-CSF) and IL4 [GeneID=1437;3565]. 16527888 210/541 Arthur Liberzon 6.42081950290027e-06 1.75952983570706e-05 1855 2096.72727272727 1854 5.83712567498849e-07 882 1.42394409005915 1.59817696709455 1 2.47472235291001 1854 1816 882 1533 1528 3280 2279 3060 2949 1849 2034 1750 M19872 TAVOR_CEBPA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAVOR_CEBPA_TARGETS_DN.html Genes down-regulated in KCL22 cells (chronic myelogenous leukemia, CML, with BCR-ABL1 [GeneID=613;25] fusion) by expression of CEBPA [GeneID=1050]. 14517214 22/60 Kevin Vogelsang 0.00748252342913096 0.0103859907550082 1255 2308.54545454545 1856 0.00068255403941266 578 1.49746181931906 1.77280900361697 1 1.08572193777661 1254 3240 1698 3527 3364 1378 578 1856 4012 3243 1244 1751 M11682 BONCI_TARGETS_OF_MIR15A_AND_MIR16_1 http://www.broadinstitute.org/gsea/msigdb/cards/BONCI_TARGETS_OF_MIR15A_AND_MIR16_1.html Potential targets of MIR15A and MIR16-1 [GeneID=406948;406950] microRNAs in prostate cancer. 18931683 55/140 Jessica Robertson 1.43167568478243e-05 3.39515802575428e-05 1235 2368.18181818182 1856 1.30153181969452e-06 1231 1.53918793957024 1.87072810066565 1 2.5144028617689 1231 4265 2569 4229 1818 1856 1770 1592 2168 2932 1620 1752 M18085 LIANG_SILENCED_BY_METHYLATION_2 http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_SILENCED_BY_METHYLATION_2.html Genes up-regulated in T24 cells (bladder carcinoma) after treatment with decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 11861364 44/108 John Newman 0.000210183429056118 0.000363841724623927 1860 2093.90909090909 1858 1.910941020277e-05 696 1.79743406637279 2.0455472276488 1 2.25951612092475 1858 1825 696 1705 2574 3613 2728 1779 2435 1074 2746 1753 M137 PID_VEGF_VEGFR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_VEGF_VEGFR_PATHWAY.html VEGF and VEGFR signaling network 18832364 5/10 Pathway Interaction Database 0.000542315904335326 0.00087179839715792 1005 1873.72727272727 1859 5.42448297753365e-05 708 1.99941215311302 1.99941215311302 1 2.23606255799525 1004 2798 3898 2443 2862 708 765 972 2579 1859 723 1754 M690 REACTOME_KERATAN_SULFATE_KERATIN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KERATAN_SULFATE_KERATIN_METABOLISM.html Genes involved in Keratan sulfate/keratin metabolism 15/32 Reactome 1.82048447111421e-05 4.16745981027905e-05 2025 1723.63636363636 1859 1.65499957788112e-06 363 2.01753568635484 2.27799317038786 1 3.23018454721347 2025 363 1014 1609 1900 2729 2417 2224 1341 1479 1859 1755 M5408 RODWELL_AGING_KIDNEY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODWELL_AGING_KIDNEY_DN.html Genes whose expression decreases with age in normal kidney. 15562319 83/233 John Newman 1.37675458625769e-05 3.28653692878427e-05 3965 2453.54545454545 1859 1.2516029109359e-06 1316 1.5979096779662 -1.6931119071708 -1 2.61857819407069 3961 1859 1798 1589 1803 2510 4337 3899 1425 1316 2492 1756 M12272 MISSIAGLIA_REGULATED_BY_METHYLATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/MISSIAGLIA_REGULATED_BY_METHYLATION_UP.html Genes up-regulated in PaCa44 and CFPAC1 cells (pancreatic cancer) after treatment with decitabine [PubChem=451668], a DNA hypomethylating agent similar to azacitidine [PubChem=9444]. 15637593 125/288 Leona Saunders 1.37927425840086e-06 5.84912142521847e-06 2685 1743.72727272727 1860 1.25388647557068e-07 270 1.81002541556832 -1.71619452572704 -1 3.46216001262537 2681 1169 398 893 1922 1533 2808 3002 1860 270 2645 1757 M1597 BURTON_ADIPOGENESIS_PEAK_AT_2HR http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_PEAK_AT_2HR.html Cluster 2: genes maximally expressed at 2 h time point during differentiation of 3T3-L1 fibroblasts into adipocytes (cluster 2) in response to adipogenic hormones. 12137940 41/83 John Newman 1.04051003294935e-06 4.8607019400924e-06 1160 1794.27272727273 1860 9.45918659153061e-08 736 1.35175006833339 1.27830011644246 1 2.62530684433771 1157 1867 2420 1188 736 1620 1930 2479 2782 1698 1860 1758 M19875 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP.html Genes up-regulated in nsopharyngeal carcinoma relative to the normal tissue. 16912175 196/518 Leona Saunders 4.62089620720528e-06 1.36529127534451e-05 560 1762.63636363636 1861 4.20082355727114e-07 445 1.77731859801987 2.10946888981159 1 3.16043793660751 558 2936 445 2311 2194 2170 1861 1178 2457 1585 1694 1759 M6413 RUTELLA_RESPONSE_TO_HGF_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_HGF_DN.html Genes down-regulated in peripheral blood monocytes by HGF [GeneID=3082]. 16527888 169/404 Arthur Liberzon 1.6025081669665e-05 3.73599665194279e-05 1865 1773.72727272727 1861 1.45683621814563e-06 778 1.46058647718539 1.61955651453731 1 2.36381927171302 1193 2731 1263 2380 1861 1400 1132 1861 2964 1948 778 1760 M15188 KAAB_FAILED_HEART_VENTRICLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAAB_FAILED_HEART_VENTRICLE_DN.html Genes down-regulated in the ventricles of failing hearts (DCM and ICM) compared to the healthy controls. 15103417 37/95 Arthur Liberzon 8.40706350678186e-05 0.000158852820938628 1030 1961.18181818182 1862 7.64307708260464e-06 621 1.64566184737253 1.77422413390021 1 2.28522898543586 1029 2861 1862 3067 2353 1449 621 1624 2385 2952 1370 1761 M56 PID_LPA4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LPA4_PATHWAY.html LPA4-mediated signaling events 18832364 11/19 Pathway Interaction Database 0.00038743702881555 0.000639947098001292 515 1774.27272727273 1863 3.5227752391118e-05 233 1.15774217288601 1.15774217288601 1 1.35159452830078 513 1746 1863 2295 2778 436 233 2063 4116 2816 658 1762 M961 REACTOME_TRANSPORT_TO_THE_GOLGI_AND_SUBSEQUENT_MODIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_TO_THE_GOLGI_AND_SUBSEQUENT_MODIFICATION.html Genes involved in Transport to the Golgi and subsequent modification 19/38 Reactome 1.61930414714503e-05 3.76391827059604e-05 630 1764.54545454545 1864 1.47210551464813e-06 275 1.12485966957146 1.12485966957146 1 1.81914800851145 626 2780 2858 3089 1864 650 275 1102 3475 1918 773 1763 M1651 RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP.html Genes up-regulated in the brain cortex of mice that were exposed to an enriched learning environment for 2 or 14 days. 11070096 15/38 John Newman 1.2350153186018e-06 5.47519563194705e-06 2355 1740.09090909091 1864 1.1227418290033e-07 162 1.64674330540726 -0.715572658394619 -1 3.16710903627689 2353 368 1864 1702 799 3127 2532 1306 162 2615 2313 1764 M1816 KYNG_DNA_DAMAGE_BY_4NQO_OR_UV http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_4NQO_OR_UV.html 4NQO treatment and UV irradiation responding genes. 15897889 47/98 Jessica Robertson 1.83789657009967e-06 6.97587836865205e-06 3395 2048.63636363636 1864 1.67081645954009e-07 982 1.44285950825008 -1.25542022036336 -1 2.71950579437513 3394 1864 2215 1525 982 1202 3582 1548 1617 2435 2171 1765 M19848 ENK_UV_RESPONSE_EPIDERMIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ENK_UV_RESPONSE_EPIDERMIS_UP.html Genes up-regulated in epidermis after to UVB irradiation. 16434974 225/554 Lauren Kazmierski 2.34566954618774e-07 2.09367761779729e-06 3720 2304.09090909091 1865 2.13242708753292e-08 196 1.69952838997819 -1.37419409081934 -1 3.52798264353314 3718 679 826 1663 196 3945 4231 3366 1865 927 3929 1766 M18757 ONDER_CDH1_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_1_UP.html Genes up-regulated in HMLE cells (mmortalized nontransformed mammary epithelial) by expression of a dominant-negative form of E-cadhedrin (CDH1) [GeneID=999]. 18483246 111/263 Jessica Robertson 3.90037377039294e-06 1.19850173692205e-05 1865 2114.18181818182 1865 3.5458006230652e-07 1123 1.77437247876642 1.96711570694106 1 3.1919001398873 1865 2386 1211 1626 1328 3502 2637 3413 1755 1123 2410 1767 M16141 CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_UP.html All marker genes up-regulated in the 'interferon' subclass of hepatocellular carcinoma (HCC). 18701503 13/132 Yujin Hoshida 1.13440972378969e-05 2.79960013054588e-05 3500 1985.36363636364 1865 1.03128688482828e-06 590 2.43958980602805 -1.47163608778621 -1 4.05998615909972 3497 1224 1261 1348 1730 2127 2406 1865 590 2363 3428 1768 M1078 REACTOME_CREATION_OF_C4_AND_C2_ACTIVATORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CREATION_OF_C4_AND_C2_ACTIVATORS.html Genes involved in Creation of C4 and C2 activators 5/11 Reactome 0.00660207163381181 0.009235017216729 1325 2231.09090909091 1866 0.000662176834937809 1218 1.65707010302454 1.65707010302454 1 1.23234163829351 1324 2326 4095 2555 3193 1218 1724 1478 3189 1866 1574 1769 M18968 HAHTOLA_SEZARY_SYNDROM_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_SEZARY_SYNDROM_DN.html Genes down-regulated in monocytes isolated from peripheral blood samples of Sezary syndrom patients compared to those from healthy normal donors. 16914566 17/79 Arthur Liberzon 0.00332912637016628 0.00481193281017865 2120 1910 1867 0.000303106803043363 515 2.22318376340511 2.83182952638934 1 1.88342429734192 2118 1740 1431 1695 3120 2782 2284 1243 515 2215 1867 1770 M1489 FIRESTEIN_CTNNB1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/FIRESTEIN_CTNNB1_PATHWAY.html Genes required for CTNNB1 [GeneID=1499] activity in DLD-1 cell (colon cancer with APC [GeneID=324] deletions), based on shRNA screen. 18794900 33/72 Jessica Robertson 9.20571649946401e-06 2.35469364172971e-05 2190 1923 1869 8.36886820022048e-07 1092 1.63506279961618 1.68175034422696 1 2.76600648006088 2189 1869 2640 1266 1659 1642 1092 2394 1390 2228 2784 1771 M8646 BOYLAN_MULTIPLE_MYELOMA_C_D_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_D_DN.html Genes down-regulated both in group C and D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 166/419 Jessica Robertson 4.8419635074269e-07 3.053666136433e-06 1870 1589.90909090909 1869 4.40178597553758e-08 365 1.65748031257007 1.55174985625466 1 3.34139022556892 1869 811 365 1275 436 2291 2017 2850 2475 552 2548 1772 M8321 WEST_ADRENOCORTICAL_TUMOR_MARKERS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_TUMOR_MARKERS_DN.html Top down-regulated genes in pediatric adrenocortical tumors (ACT) compared to the normal tissue. 17234769 13/40 Arthur Liberzon 0.00167764735299113 0.00251084493647923 1235 1755.90909090909 1871 0.000152629821720486 1075 2.03053431617453 1.87835848835003 1 1.92989204128293 1233 2019 1075 1204 2990 2049 1871 2180 1186 1274 2234 1773 M2345 FARDIN_HYPOXIA_11 http://www.broadinstitute.org/gsea/msigdb/cards/FARDIN_HYPOXIA_11.html Genes in the hypoxia signature, based on analysis of 11 neuroblastoma cell lines in hypoxia and normal oxygen conditions. 20624283 25/53 Paolo Fardin 1.83120688587241e-05 4.18791384441099e-05 1575 1815.36363636364 1871 1.66474738946143e-06 1198 1.56369565439196 1.86965568298046 1 2.50234658538674 1945 2117 1699 2334 1901 1871 1575 2214 1544 1571 1198 1774 M1191 HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer, mutated TP53 [GeneID=7157]) undergoing aberrant mitosis and necrosis after treatment with 2 nM docetaxel [PubChem=148124]. 17099726 20/54 Arthur Liberzon 2.9725720396375e-06 9.75453261746592e-06 2455 1848.72727272727 1872 2.70234186917511e-07 553 2.7053229291127 2.81967274242024 1 4.95501384480735 2071 2453 967 825 1216 2615 2453 3764 553 1547 1872 1775 M4623 KORKOLA_TERATOMA http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_TERATOMA.html Genes predicting the teratoma (T) subtype of nonseminomatous male germ cell tumors (NSGCT). 15870693 21/87 Leona Saunders 3.00397067641368e-05 6.45124041689941e-05 2340 1694.45454545455 1874 2.7309197224105e-06 639 2.16668695178435 -2.76163235122754 -1 3.31868795678272 2339 1874 990 1392 2044 2056 2585 1185 639 1615 1920 1776 M13424 JAZAG_TGFB1_SIGNALING_VIA_SMAD4_UP http://www.broadinstitute.org/gsea/msigdb/cards/JAZAG_TGFB1_SIGNALING_VIA_SMAD4_UP.html Genes up-regulated in PANC-1-S4KD cells (pancreatic cancer; SMAD4 [GeneID=4089] knocked down by RNAi) after stimulation by TGF1B [GeneID=7040] for 2 h. 15592526 83/199 Leona Saunders 4.15887348128806e-07 2.81825276987931e-06 2065 1720.09090909091 1874 3.78079478861862e-08 375 2.17971082851814 2.38181639722312 1 4.42193836422854 2061 2574 899 1874 375 2299 1440 1703 1066 1980 2650 1777 M16637 LIU_CDX2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_CDX2_TARGETS_UP.html Genes up-regulated in HET1A cells (esophagus epithelium) engineered to stably express CDX2 [GeneID=1045]. 16990345 24/58 Arthur Liberzon 1.17740195124524e-06 5.28984232361955e-06 745 2356.72727272727 1875 1.07036598306443e-07 519 2.28540904110716 -2.19924940698 -1 4.40792146322418 3972 745 519 774 784 4592 3291 4159 1875 745 4468 1778 M1190 ZHAN_MULTIPLE_MYELOMA_CD1_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_UP.html Top 50 up-regulated genes in cluster CD-1 of multiple myeloma samples with the characteristic expression spike of CCND1 [GeneID=595]. 16728703 24/75 Kevin Vogelsang 0.000275589707738307 0.000466382582326366 1875 1809.45454545455 1875 2.50567487617213e-05 1045 1.85656699739718 1.68404084279297 1 2.26067485429819 1875 1045 1367 2127 2636 1942 1471 1286 1377 2378 2400 1779 M4987 KIM_WT1_TARGETS_12HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_12HR_DN.html Genes down-regulated in UB27 cells (osteosarcoma) at 12 hr after inducing the expression of a mutated form of WT1 [GeneID=7490]. 17430890 143/315 Arthur Liberzon 1.64596004734227e-06 6.51433174142389e-06 1415 1761.27272727273 1876 1.49632843526459e-07 929 1.57707060180636 1.48752709847637 1 2.98960489718755 1412 2186 1933 1672 929 2227 1876 2972 2000 962 1205 1780 M16617 GAJATE_RESPONSE_TO_TRABECTEDIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAJATE_RESPONSE_TO_TRABECTEDIN_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) by trabectedin [PubChem=3199]. 12198119 19/37 John Newman 0.000284573640204245 0.000480198803744002 1630 2040.36363636364 1876 2.58736779038975e-05 1193 1.20600307622811 -0.957818738564733 -1 1.46291743774433 1626 1734 1804 2126 2647 1193 2231 3267 2486 1454 1876 1781 M1604 JACKSON_DNMT1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JACKSON_DNMT1_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) upon Cre-lox knockout of DNMT1 [GeneID=1786]. 11137995 72/165 John Newman 0.00463792704126156 0.00659985609333486 1165 2254.72727272727 1876 0.000422521221438333 1164 1.39966196689909 1.56239878030503 1 1.11555667161758 1164 2835 1876 2354 3126 1842 1830 1873 3307 2846 1749 1782 M12801 DORN_ADENOVIRUS_INFECTION_32HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_32HR_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) 32 h after infection with adenovirus Ad12. 15681441 17/29 Arthur Liberzon 0.0351289201291838 0.0450627209760075 1250 1980.72727272727 1878 0.00324570151807119 1106 1.87724706458388 -1.52366720408126 -1 0.923729158285454 1250 1785 1523 1878 3444 1106 1297 2419 2923 2221 1942 1783 M2086 LI_INDUCED_T_TO_NATURAL_KILLER_UP http://www.broadinstitute.org/gsea/msigdb/cards/LI_INDUCED_T_TO_NATURAL_KILLER_UP.html Genes up-regulated in ITNK cells (T-lymphocyte progenitors (DN3 cells) reprogrammed to natural killer (NK) cells by ablation of BCL11B [GeneID=64919] gene), compared to the parental DN3 cells. 20538915 210/480 Arthur Liberzon 3.30589490765692e-07 2.47466829669015e-06 3760 2171.36363636364 1878 3.00535945857007e-08 43 1.51726007252605 -1.42256243751259 -1 3.10935128237566 3758 43 541 636 300 3602 3919 4144 1878 403 4661 1784 M11367 MAHADEVAN_IMATINIB_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAHADEVAN_IMATINIB_RESISTANCE_DN.html Top genes down-regulated in the GIST (gastrointestinal stromal tumor) cell line resistant to imatinib [PubChem=5291] compared to the parental cell line sensitive to the drug. 17325667 12/33 Arthur Liberzon 4.13657352228309e-05 8.48315653249889e-05 1485 1620.54545454545 1879 3.76059209336045e-06 560 2.14728643743315 1.88730740040905 1 3.19563772343659 1483 649 560 1581 2459 2223 2216 1879 1895 627 2254 1785 M6181 DORN_ADENOVIRUS_INFECTION_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_48HR_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) 48 h after infection with adenovirus Ad12. 15681441 17/33 Arthur Liberzon 0.0351289201291838 0.0450627209760075 1255 1981.72727272727 1879 0.00324570151807119 1107 1.87724706458388 -1.52366720408126 -1 0.923729158285454 1251 1786 1524 1879 3445 1107 1298 2420 2924 2222 1943 1786 M18175 REACTOME_P75NTR_SIGNALS_VIA_NFKB http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P75NTR_SIGNALS_VIA_NFKB.html Genes involved in p75NTR signals via NF-kB 9/23 Reactome 1.99072172407227e-06 7.35108116548674e-06 4640 2473.54545454545 1880 1.99072350741236e-07 240 1.86239727997114 -1.56741886946991 -1 3.49476302546642 4639 893 3977 958 1070 3402 4554 1880 240 1241 4355 1787 M1876 JU_AGING_TERC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JU_AGING_TERC_TARGETS_DN.html Cytokines, growth factors, and secreted proteins that show decreased expression on a protein array of samples from aged TERC [GeneID=7012] knockout mice. 17486088 5/7 Jessica Robertson 0.00686619188913737 0.00958729892505891 1795 2581.18181818182 1880 0.00068874996724199 740 1.39955048466052 1.39955048466052 1 1.0325101793279 1791 3200 4523 3455 3977 1566 740 1813 4201 1880 1247 1788 M2413 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7.html Genes regulated in MCF7 cells (breast cancer) by expression of the truncated (611-CTF) form of ERBB2 [GeneID=2064] at 60 h time point. 19364815 273/662 Arthur Liberzon 8.61657578119441e-07 4.28842420876208e-06 2120 1653.18181818182 1880 7.83325377816924e-08 472 1.679765821351 1.88119154312872 1 3.29576630114668 2119 2100 472 1082 659 3509 1880 1836 1928 572 2028 1789 M7968 BIOCARTA_CARM1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CARM1_PATHWAY.html Transcription Regulation by Methyltransferase of CARM1 6/15 BioCarta 0.00158207969671184 0.00237236014681333 1010 1891.36363636364 1881 0.000158320716585667 296 1.22021190488854 1.22021190488854 1 1.17072241019504 1009 2726 3882 1881 2995 967 793 2174 296 3036 1046 1790 M184 PID_ECADHERIN_KERATINOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ECADHERIN_KERATINOCYTE_PATHWAY.html E-cadherin signaling in keratinocytes 18832364 16/40 Pathway Interaction Database 3.79583597790884e-07 2.69640744894893e-06 2575 1689.36363636364 1881 3.45076057530449e-08 121 1.91578441795628 -1.64229001261487 -1 3.89995710936042 2572 1302 1881 420 337 2592 1698 2106 121 2721 2833 1791 M1657 LEE_CALORIE_RESTRICTION_MUSCLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_CALORIE_RESTRICTION_MUSCLE_DN.html Down-regulated in the gastrocnemius muscle of aged (30-month) mice subjected to caloric restriction diet since young adulthood. 10464095 35/90 John Newman 6.57381972499582e-06 1.79306863977476e-05 1210 1897.18181818182 1881 5.97621760755262e-07 490 1.12250832965734 -1.01597507744987 -1 1.94748194588601 1210 1916 2953 3004 1534 553 490 1881 2887 3550 891 1792 M11358 BIOCARTA_ARF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARF_PATHWAY.html Tumor Suppressor Arf Inhibits Ribosomal Biogenesis 14/28 BioCarta 1.08284127472907e-06 4.97470020919648e-06 3470 2041.09090909091 1885 9.84401643367759e-08 217 2.44284834410169 -1.40420807124584 -1 4.73539784416948 3470 1885 1878 1756 753 2173 1936 4064 217 2502 1818 1793 M55 PID_S1P_S1P3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P3_PATHWAY.html S1P3 pathway 18832364 19/42 Pathway Interaction Database 1.45330978885695e-07 1.56650146009823e-06 2510 1859.27272727273 1885 1.32119080441994e-08 91 1.39562112973029 1.14490775402113 1 2.96138032917275 2509 1737 1888 1486 91 2043 1428 2802 1885 1450 3133 1794 M1600 MCCLUNG_COCAIN_REWARD_4WK http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_COCAIN_REWARD_4WK.html Genes up-regulated in the nucleus accumbens (a major reward center in the brain) after 4 weeks of cocaine [PubChem=5760] treatment. 14566342 51/125 John Newman 4.2800641997241e-07 2.82882663468366e-06 1730 1926.18181818182 1885 3.89096821127622e-08 394 1.47567698590975 1.5110711683114 1 2.9928008738977 1730 1107 2729 2100 394 1852 1885 3337 1429 2331 2294 1795 M15382 BROWNE_HCMV_INFECTION_10HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_10HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 10 h time point that were not up-regulated at the previous time point, 8 h. 11711622 86/261 John Newman 6.87310339011115e-06 1.86062174962801e-05 1390 2413.63636363636 1886 6.24829532975262e-07 985 1.5130677748691 1.63321259024078 1 2.61619532100951 1387 4432 2732 4488 1550 1462 1563 1886 2848 3217 985 1796 M9375 DAZARD_UV_RESPONSE_CLUSTER_G1 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G1.html Cluster G1: genes most highly up-regulated in NHEK cells (normal keratinocyte) between 6 h and 12 h after UV-B irradiation. 12771951 62/137 John Newman 4.38688387597063e-07 2.86707640764273e-06 3470 2365.81818181818 1886 3.98807704612022e-08 405 1.44430496223207 -1.07335736141603 -1 2.92609629574804 3468 1014 1886 1331 405 3726 4596 2485 1624 1724 3765 1797 M2240 JOHNSTONE_PARVB_TARGETS_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_3_UP.html Genes up-regulated upon overexpression of PARVB [GeneID=29780] in MDA-MB-231 cells (breast cancer) cultured in 3D Matrigel only. 17998334 325/767 Arthur Liberzon 3.73200661510554e-07 2.6805936035782e-06 3575 2181 1886 3.39273386199167e-08 329 1.61022849827327 -1.41312584671398 -1 3.27944131383752 3572 535 725 585 329 3903 4162 3228 1886 894 4172 1798 M10547 BIOCARTA_MAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MAL_PATHWAY.html Role of MAL in Rho-Mediated Activation of SRF 17/42 BioCarta 2.33117145434636e-06 8.17654897834358e-06 4100 2080.36363636364 1888 2.11924902228529e-07 248 2.14338729354431 -1.05392242070482 -1 3.98582608670124 4096 874 1496 557 1101 3169 3439 1888 248 2211 3805 1799 M1612 BURTON_ADIPOGENESIS_1 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_1.html Strongly up-regulated at 2 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 26/47 John Newman 1.74524271437941e-05 4.01680125716203e-05 710 1649.36363636364 1888 1.58659687218773e-06 707 1.4450351424273 1.44062355271748 1 2.32202645862779 707 2234 2318 2008 1888 764 1003 1069 2532 2549 1071 1800 M9399 BOYLAN_MULTIPLE_MYELOMA_PCA1_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_PCA1_UP.html Top up-regulated genes from principal component 1 (PCA1) which captures variation between normal plasma cells and tumors arising from aberrant expression of BCL2L1 and MYC [GeneID=598;4609]. 17483317 65/199 Arthur Liberzon 4.16397113496832e-07 2.81825276987931e-06 2100 1780.54545454545 1888 3.78542902099022e-08 376 1.81074321194587 1.637636821601 1 3.67342069931835 2099 702 451 981 376 3227 2423 4535 1888 553 2351 1801 M1441 REACTOME_P38MAPK_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P38MAPK_EVENTS.html Genes involved in p38MAPK events 10/15 Reactome 0.000351459556853751 0.000584021093410169 1895 1881.72727272727 1891 3.19559742368708e-05 1149 1.29812181544715 -1.58407590061431 -1 1.53432429747862 1891 1311 1746 1384 2696 2086 2709 1149 2351 1960 1416 1802 M7160 JAZAG_TGFB1_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/JAZAG_TGFB1_SIGNALING_UP.html Genes up-regulated in PANC-1-puro cells (pancreatic cancer) stimulated by TGF1B [GeneID=7040] for 2 h. 15592526 100/228 Leona Saunders 8.27698312983208e-07 4.21381153484506e-06 3455 2208.90909090909 1891 7.52453294895831e-08 634 1.69819634491027 -1.58176955825948 -1 3.33665935400071 3453 2607 1655 1633 634 1891 2686 2996 1814 1781 3148 1803 M1866 WANG_TUMOR_INVASIVENESS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_TUMOR_INVASIVENESS_DN.html Down-regulated genes in the subpopulation of invasive PyMT cells (breast cancer) compared to the general population of PyMT cells. 17440055 146/318 Jessica Robertson 9.50660062857659e-06 2.41452198078645e-05 1885 2124.27272727273 1891 8.64240155325238e-07 1506 1.55306955804964 1.78845652743401 1 2.62111401857864 1881 3046 2342 1891 1675 2353 1786 1926 1640 3321 1506 1804 M1289 HUI_MAPK14_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUI_MAPK14_TARGETS_UP.html Genes up-regulated in fetal liver (days E13.5 and E15.5) samples from embryo-specific Cre-lox knockout of MAPK14 [GeneID=1432]. 17468757 13/34 Leona Saunders 1.42437703004563e-06 5.93300512248339e-06 1575 1774.81818181818 1892 1.29488904750089e-07 864 1.28620151471581 1.43534748196198 1 2.45729864197717 1574 1561 1892 2078 864 2011 2067 1987 2480 1275 1734 1805 M19826 ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_UP.html Genes up-regulated in BxPC3 cells (pancreatic cancer) after treatment with TNF [GeneID=7124] or IKI-1, an inhibitor of IkappaB kinase (IKK). 19010928 139/341 Jessica Robertson 2.91474734423346e-06 9.61189729421391e-06 2985 1908.72727272727 1895 2.64977382358737e-07 412 1.48145386493801 -1.48765352509776 -1 2.71686466640554 3312 412 854 918 1208 1895 3282 2981 2271 878 2985 1806 M619 REACTOME_TRIGLYCERIDE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRIGLYCERIDE_BIOSYNTHESIS.html Genes involved in Triglyceride Biosynthesis 22/42 Reactome 5.46111396068523e-07 3.29104283013232e-06 2015 1717.54545454545 1897 4.96465028755584e-08 340 1.77117830059756 -1.12389446275668 -1 3.54955050498294 2015 1645 1897 1904 478 918 1026 3996 340 2186 2488 1807 M19460 WOOD_EBV_EBNA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WOOD_EBV_EBNA1_TARGETS_DN.html Genes down-regulated in the Ad/AH cells (adenocarcinoma) engineered to stably express the Epstein-Barr virus (EBV) gene EBNA1. 17486072 26/74 Arthur Liberzon 1.79552031541849e-05 4.11835937251642e-05 2925 1892.45454545455 1897 1.63230451785995e-06 608 2.05698413670156 -1.84252203738286 -1 3.29721374138786 2922 865 884 608 1897 2654 2182 4043 965 1045 2752 1808 M9911 WOO_LIVER_CANCER_RECURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WOO_LIVER_CANCER_RECURRENCE_DN.html Genes negatively correlated with recurrence free survival in patients with hepatitis B-related (HBV) hepatocellular carcinoma (HCC). 18381945 48/146 Yujin Hoshida 1.3890542786123e-05 3.30915523618568e-05 2080 2036 1897 1.26278459001467e-06 451 1.1919750857948 -1.34195435164927 -1 1.9520541551351 2078 451 2913 2550 1806 1104 1858 1849 2669 3221 1897 1809 M9823 REN_MIF_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/REN_MIF_TARGETS_DN.html Genes down-regulated in SK-N-DZ cells (neuroblastoma) after knockdown of MIF [GeneID=4282] by antisense RNA. 16449971 3/9 Leona Saunders 1.7504354942235e-05 4.0267750250031e-05 1900 1824 1898 1.75044928248624e-06 337 1.14272693544559 -1.14272693544559 -1 1.83579763825509 1600 1899 4279 2880 3046 528 560 337 1898 2460 577 1810 M10845 GOLDRATH_IMMUNE_MEMORY http://www.broadinstitute.org/gsea/msigdb/cards/GOLDRATH_IMMUNE_MEMORY.html 'Memory genes' expressed uniquely in CD8+ [GeneID=925] memory T lymphocytes (compared with effector or naive cells) 15548615 45/90 Kate Stafford 7.26834026985396e-07 3.88363084430281e-06 2635 2061.90909090909 1900 6.60758424651165e-08 589 1.79828075267725 -1.31323631162072 -1 3.55660129564832 2632 1271 924 1900 589 4342 3636 2890 1037 805 2655 1811 M3456 FERNANDEZ_BOUND_BY_MYC http://www.broadinstitute.org/gsea/msigdb/cards/FERNANDEZ_BOUND_BY_MYC.html Genes identified by ChIP within the high-affinity group of MYC [GeneID=4609] targets. 12695333 137/334 Yujin Hoshida 4.97762338918169e-07 3.09762857924374e-06 3770 2278.36363636364 1904 4.52511319581569e-08 446 1.80374121152086 2.17332266580509 1 3.63215135502454 3766 1904 1276 1336 446 2754 3881 2447 1435 1769 4048 1812 M7405 HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_DN.html Genes down-regulated during differentiation from pre-BI to large pre-BII lymphocyte. 11779835 48/132 Arthur Liberzon 9.20399998257893e-06 2.35469364172971e-05 1575 1826.81818181818 1904 8.36730771726673e-07 962 1.63110322210006 1.87261119071706 1 2.75930813362576 1575 1023 962 2199 1658 2294 1904 2071 2572 1786 2051 1813 M6698 RAMASWAMY_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMASWAMY_METASTASIS_UP.html Up-regulated genes in metastatic vs primary solid tumors. 12469122 47/101 John Newman 0.000126998313825295 0.000228890037917436 1100 2202.27272727273 1905 1.15459677806177e-05 624 2.48875764833567 2.6217141352968 1 3.31167535178434 1098 4646 1483 4011 3611 1626 1905 624 2313 2071 837 1814 M563 REACTOME_SIGNALING_BY_EGFR_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_EGFR_IN_CANCER.html Genes involved in Signaling by EGFR in Cancer 68/143 Reactome 1.90025725661955e-06 7.14082237732094e-06 1410 2032.72727272727 1906 1.72750808906819e-07 999 1.33832979176143 1.5447947817584 1 2.51752287451252 1408 2467 3060 1300 999 1906 1497 2048 2662 3691 1322 1815 M12275 BROWNE_HCMV_INFECTION_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_24HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 24 h time point that were not up-regulated at the previous time point, 20 h. 11711622 97/260 John Newman 0.000206000007712351 0.000357080454046044 1725 2035.81818181818 1906 1.87290272121553e-05 1345 1.62565523192354 1.8017773474949 1 2.04841737533508 1721 3049 2126 1718 2570 2558 2016 1711 1906 1674 1345 1816 M9664 BIOCARTA_GPCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GPCR_PATHWAY.html Signaling Pathway from G-Protein Families 22/55 BioCarta 1.91789419817149e-06 7.1687063813697e-06 2020 1890.63636363636 1908 1.74354170012393e-07 364 1.57380492289638 1.39873443501389 1 2.95949983149022 2018 1293 2029 364 1007 1887 1908 4423 1145 2183 2540 1817 M18415 REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE.html Genes involved in Sema4D induced cell migration and growth-cone collapse 15/48 Reactome 0.0200876031388127 0.0264263077789097 1905 2190.36363636364 1908 0.00184303608940063 853 2.77470316733772 3.31515902387072 1 1.60041545419796 1904 2668 1751 2714 3573 1908 1492 1649 853 3254 2328 1818 M9230 LIU_CMYB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_CMYB_TARGETS_DN.html Genes down-regulated in MCF-7 cells (breast cancer) by overexpression of CMYB [GeneID=4602] off adenovirus vector. 16205643 5/9 Arthur Liberzon 5.64551152196202e-05 0.000111671029936319 2160 1780.27272727273 1908 5.64565495019186e-06 309 2.29954591222166 -2.29954591222166 -1 3.32188663625482 2158 790 4123 1340 2269 2211 2286 1029 309 1160 1908 1819 M11156 ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN.html Genes down-regulated in normal tissue adjacent to liver tumor, compared to the normal liver samples. 18413731 267/547 Jessica Robertson 5.85166403751372e-07 3.4235028683673e-06 3215 1902.09090909091 1909 5.31969599451596e-08 503 1.41732069691643 -1.32833828265383 -1 2.83151982439982 3214 803 2313 1523 503 1060 2914 3003 1917 1764 1909 1820 M779 REACTOME_DOWNSTREAM_SIGNAL_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNSTREAM_SIGNAL_TRANSDUCTION.html Genes involved in Downstream signal transduction 55/111 Reactome 3.05194399077773e-07 2.36072070403987e-06 1610 2071.45454545455 1910 2.77449492196174e-08 274 1.11540034298432 1.2286267906771 1 2.29415890585509 1607 1910 2949 1021 274 1701 1595 2942 3118 3715 1954 1821 M2047 KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_UP.html Genes up-regulated in response to hydorgen peroxyde [PubChem=784] in CS-B cells (Cockaine syndrome fibroblast, CS) with defficient ERCC6 [GeneID=2074]. 12606941 35/85 Arthur Liberzon 1.93213268553975e-06 7.19711745980863e-06 1290 1737 1910 1.75648580220196e-07 957 1.63631943610766 1.87154807787704 1 3.07602932490809 1289 2393 1910 1938 1012 2436 1941 1036 957 2372 1823 1822 M2429 SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12 http://www.broadinstitute.org/gsea/msigdb/cards/SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12.html Cluster 12 of method A: up-regulation of these genes in patients with non-small cell lung cancer (NSCLC) predicts good survival outcome. 18641660 151/534 Arthur Liberzon 1.5522611581304e-06 6.26916441855309e-06 2280 1977.63636363636 1911 1.41114750305949e-07 903 1.76723672165492 2.02982784914125 1 3.36085907879853 2277 1525 1147 1654 903 3259 2187 2720 1663 1911 2508 1823 M3261 KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY.html Toll-like receptor signaling pathway 63/144 KEGG 8.81669429236048e-06 2.27380459295549e-05 2390 2116.18181818182 1913 8.01520875112704e-07 1485 1.2635495534107 -1.39163405193664 -1 2.1445358101247 2390 1682 2626 1485 1646 1794 3298 1870 2505 2069 1913 1824 M8240 REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL.html Genes involved in Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell 36/119 Reactome 0.000829563931350721 0.00129924351013017 1790 1958.45454545455 1914 7.5443354909023e-05 985 1.77983737495914 1.91831294560028 1 1.87777028783061 1789 2504 1352 2232 2857 2445 1914 985 2338 1356 1771 1825 M1182 LA_MEN1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LA_MEN1_TARGETS.html Genes up-regulated in cells expressing MEN1 [GeneID=4221]. 16449969 20/35 Arthur Liberzon 0.00286683455147214 0.00418765171701947 1760 2007.36363636364 1914 0.00026096156110616 1362 1.68899573962192 1.89343384676867 1 1.46813175396725 1760 2895 1525 2368 3056 2047 1362 1606 1914 1546 2002 1826 M3335 HELLER_HDAC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_HDAC_TARGETS_UP.html Genes up-regulated in at least one of three multiple myeloma (MM) cell lines by TSA [PubChem=5562]. 18172295 253/635 Jessica Robertson 2.04532228638529e-06 7.48647225274829e-06 1915 1804.81818181818 1914 1.85938562537039e-07 1041 1.53861700532557 1.67510038990036 1 2.88273613884499 1914 2101 1123 1088 1041 2795 2050 2509 2208 1112 1912 1827 M1367 BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_UP.html Genes from cluster 1: up-regulated in group C of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 19/52 Jessica Robertson 2.31488029210712e-06 8.14379057718767e-06 2210 1919.81818181818 1914 2.10443884351832e-07 1079 1.803150185344 2.25603780794291 1 3.3542729511094 2206 1606 1796 2367 1098 2713 2166 1914 1079 2430 1743 1828 M11404 CERVERA_SDHB_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/CERVERA_SDHB_TARGETS_1_DN.html Genes turned off in Hep3B cells (hepatocellular carcinoma, HCC) upon knockdown of SDHB [GeneID=6390] by RNAi. 18519664 22/73 Jessica Robertson 4.30673186365847e-07 2.8384452198458e-06 3845 2326.72727272727 1915 3.91521155158805e-08 396 2.13184759125323 -2.1981233713257 -1 4.32242300003744 3842 1548 736 1038 396 4225 3903 1915 2508 831 4652 1829 M13449 CAIRO_HEPATOBLASTOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_HEPATOBLASTOMA_DN.html Genes down-regulated in hepatoblastoma samples compared to normal liver tissue. 19061838 155/467 Arthur Liberzon 4.37564051461894e-07 2.86372226976318e-06 4580 2195.54545454545 1918 3.97785580445668e-08 403 1.80747592052471 -1.65114813878567 -1 3.66220004370699 4578 550 495 1073 403 2600 4483 3193 1918 739 4119 1830 M1592 SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_UP.html Genes up-regulated in 3T3-L1 cells (adipocyte) by insulin [GeneID=3630] which continued to respond normally to insulin in the insulin resistant cells. 14530283 30/52 John Newman 7.1076648002995e-08 9.30349643972164e-07 2060 1783 1919 6.46151366357352e-09 29 1.25530462369843 1.31461716519829 1 2.76747167203598 2059 735 1592 1919 29 2195 1900 3112 2687 1288 2097 1831 M2151 DUTERTRE_ESTRADIOL_RESPONSE_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DUTERTRE_ESTRADIOL_RESPONSE_6HR_UP.html Genes up-regulated in MCF7 cells (breast cancer) at 6 h of estradiol [PubChem=5757] treatment. 20406972 150/303 Jessica Robertson 6.97496225367569e-07 3.80263376832652e-06 3485 2356 1919 6.34087678640435e-08 411 1.63586494170826 1.77347152830661 1 3.24085209378777 3484 411 799 1238 572 4257 3904 4355 1919 659 4318 1832 M2312 AZARE_STAT3_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/AZARE_STAT3_TARGETS.html Genes up-regulated in RPWE-1 cells by activated STAT3 [GeneID=6774]. 17438134 22/48 Arthur Liberzon 0.00470665325203357 0.00669358942003925 1720 2086.63636363636 1919 0.000428795715596058 556 2.70018619981958 3.03790961473447 1 2.14605379808461 1720 3124 2009 2576 3128 1803 1585 1788 556 2745 1919 1833 M152 REACTOME_NUCLEAR_EVENTS_KINASE_AND_TRANSCRIPTION_FACTOR_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEAR_EVENTS_KINASE_AND_TRANSCRIPTION_FACTOR_ACTIVATION.html Genes involved in Nuclear Events (kinase and transcription factor activation) 18/31 Reactome 1.22656779881212e-06 5.45840142947162e-06 2480 1770.81818181818 1921 1.11506225696546e-07 174 1.3466109370057 1.11529343754363 1 2.59053434862605 2480 174 2567 1015 795 1921 1201 3192 1164 2324 2646 1834 M2118 SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN.html Genes down-regulated in pleura relapse of breast cancer. 18451135 15/84 Jessica Robertson 2.00834828823272e-05 4.55083175950606e-05 3975 2483.81818181818 1921 1.82578783853552e-06 623 2.34722833202335 -2.17348833245079 -1 3.72524918250695 4403 1455 629 1115 1921 3873 3974 3972 906 623 4451 1835 M2218 BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G123, defined by unsupervised clustering. 17187432 28/80 Yujin Hoshida 2.44748648773683e-06 8.47040006021771e-06 2585 1938.36363636364 1921 2.22499019141341e-07 474 1.53865832526807 1.6628947682791 1 2.85265277729224 2585 474 1921 1507 1124 3480 2487 2658 1230 2286 1570 1836 M2370 GOBERT_CORE_OLIGODENDROCYTE_DIFFERENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/GOBERT_CORE_OLIGODENDROCYTE_DIFFERENTIATION.html Oligodendrocyte core differentiation genes: up-regulated in Oli-neo cells (oligodendroglial precursor) at 10 h after treatment with PD174265, dexamethasone or isotretinoin [PubChem=4709, 5743, 5282379]. 19139271 29/66 Arthur Liberzon 1.06136640967008e-06 4.91916777462895e-06 2655 2030.36363636364 1921 9.64879019741157e-08 743 1.81846934621191 2.04118238361422 1 3.52829602484535 2654 1921 1350 1345 743 3540 2992 2819 861 992 3117 1837 M260 ABE_INNER_EAR http://www.broadinstitute.org/gsea/msigdb/cards/ABE_INNER_EAR.html Genes prefentially expressed in human inner ear tissue (cochlea and vestibule), at least 10-fold higher from a mixture of 29 other tissues. 12471561 33/83 John Newman 1.51507879283081e-06 6.16259679429782e-06 2095 1810.27272727273 1922 1.37734530565857e-07 564 1.82134838889423 1.56425392102185 1 3.46872357635739 2093 1833 1922 1165 891 3190 2479 1928 564 1216 2632 1838 M2477 ALFANO_MYC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ALFANO_MYC_TARGETS.html Genes up-regulated hT-RPE cells (immortalized retinal pigment epithelium) by MYC [GeneID=4609]. 20123981 183/489 Arthur Liberzon 3.14638309806631e-05 6.71400327756773e-05 1655 1912.81818181818 1923 2.86038917974962e-06 1207 1.43978028968165 1.59780854648759 1 2.19616911183881 1651 2330 1769 1923 2063 2123 1690 1207 2259 2207 1819 1839 M287 BIOCARTA_ERK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERK_PATHWAY.html Erk1/Erk2 Mapk Signaling pathway 21/54 BioCarta 1.30645277009605e-05 3.14434395514642e-05 1500 2069.63636363636 1925 1.18769138948e-06 1113 1.33915814362161 1.47159538536772 1 2.20395102797775 1500 1925 2412 1445 1781 2585 1985 1113 2976 3160 1884 1840 M2106 KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_DN.html Genes whose expression was significantly and negatively correlated with the number of perineuronal oligodendrocytes in the layer III of BA9 brain region. 18762803 19/111 Jessica Robertson 8.90612158698335e-05 0.00016660313675291 1150 1722.45454545455 1925 8.09680195303215e-06 117 1.48337930971025 1.5567327396514 1 2.04865977259112 1147 2594 2043 3532 2718 470 117 978 2696 1925 727 1841 M70 PID_PS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PS1_PATHWAY.html Presenilin action in Notch and Wnt signaling 18832364 34/83 Pathway Interaction Database 1.91553275518353e-05 4.36160665247329e-05 3090 2198.45454545455 1926 1.74140857624315e-06 1006 1.79447361608127 2.13672904550081 1 2.86007898938728 3089 2472 2021 1086 1910 3768 3853 1480 1006 1926 1572 1842 M5876 REACTOME_CTLA4_INHIBITORY_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CTLA4_INHIBITORY_SIGNALING.html Genes involved in CTLA4 inhibitory signaling 9/24 Reactome 4.45400881864076e-07 2.90229850530109e-06 2395 2145.81818181818 1927 4.45400971135976e-08 440 1.17076695996716 1.17076695996716 1 2.369651398192 2394 1894 4023 2181 440 3260 1813 464 1807 3401 1927 1843 M903 REACTOME_REGULATION_OF_SIGNALING_BY_CBL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_SIGNALING_BY_CBL.html Genes involved in Regulation of signaling by CBL 11/26 Reactome 0.00155462467547082 0.002332683710937 1650 2099.72727272727 1927 0.000141429485026344 1093 1.04227428650057 1.14360937432339 1 1.00279218833541 1648 2209 2623 1927 3003 1497 1135 1093 2803 3561 1598 1844 M17788 LINDGREN_BLADDER_CANCER_CLUSTER_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_1_DN.html Down-regulated genes whose expression profile is specific to Custer I of urothelial cell carcinoma (UCC) tumors. 16532037 290/653 Leona Saunders 4.072999290235e-07 2.7892494272413e-06 1930 2051.72727272727 1927 3.70272731299576e-08 366 1.56214375289571 1.67415949813768 1 3.17165694522603 1927 1764 404 1571 366 3560 2876 3225 2681 910 3285 1845 M12153 HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_DN.html Genes down-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with high risk of myelodysplastic syndrom (MDS) compared to the low risk patients. 12411319 17/55 Arthur Liberzon 3.7114859667128e-05 7.74010825100854e-05 2690 1855.36363636364 1927 3.37413507491841e-06 601 2.23432631725883 2.20411380064242 1 3.35768577726181 2688 1927 1080 1175 2114 2641 1679 1419 601 2218 2867 1846 M1671 KYNG_RESPONSE_TO_H2O2 http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_RESPONSE_TO_H2O2.html Genes up-regulated in response to hydrogen peroxide [PubChem=784] in CS-B cells (Cockayne syndrome fibroblast, CS) expressing ERCC6 [GeneID=2074] off a plasmid vector. 12606941 58/120 John Newman 0.000301159959284708 0.000506182054952704 780 1840.27272727273 1928 2.73819266583939e-05 699 1.62461767484123 1.71416898709498 1 1.95711888316133 699 2688 2379 1928 2772 779 754 780 3151 3598 715 1847 M8773 HO_LIVER_CANCER_VASCULAR_INVASION http://www.broadinstitute.org/gsea/msigdb/cards/HO_LIVER_CANCER_VASCULAR_INVASION.html Gene expression signature of vascular invasion of hepatocellular carcinoma (HCC). 17009164 9/40 Yujin Hoshida 0.000471209738468941 0.000764573696144549 1825 2320 1929 4.7130968567569e-05 280 2.00840940492846 1.59634191361933 1 2.2879675796139 1823 1704 4608 1989 2775 1805 1929 4238 280 1826 2543 1848 M13930 JIANG_TIP30_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_TIP30_TARGETS_DN.html Down-regulated genes in HepG2 cells (liver cancer) overexpressing an oncogenic variant of tumor suppressor TIP30 [GeneID=10553] compared to its wild type form. 17440068 13/42 Jessica Robertson 1.02091306621047e-05 2.55965683695145e-05 3720 2463.63636363636 1932 9.28107094365962e-07 103 2.85931341277736 -2.14616620563892 -1 4.79916522742807 3717 1932 1188 1863 1702 3530 4021 3924 103 1756 3364 1849 M12851 BIOCARTA_CELL2CELL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CELL2CELL_PATHWAY.html Cell to Cell Adhesion Signaling 12/19 BioCarta 0.00119045329713772 0.00182421980064989 780 2136.36363636364 1936 0.000108281632532474 311 0.926702596469793 0.926702596469793 1 0.927768079861235 779 1936 2762 3247 3040 627 311 1828 4182 3610 1178 1850 M1473 BIOCARTA_BLYMPHOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BLYMPHOCYTE_PATHWAY.html B Lymphocyte Cell Surface Molecules 4/18 BioCarta 0.000450611422804377 0.000734712987912774 1940 2171.09090909091 1938 4.50702821683991e-05 696 1.17908539990417 1.17908539990417 1 1.35066358450234 1938 1520 3817 2924 3497 1101 827 1041 3864 2657 696 1851 M18149 RUTELLA_RESPONSE_TO_HGF_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_HGF_UP.html Genes up-regulated in peripheral blood monocytes by HGF [GeneID=3082]. 16527888 268/649 Arthur Liberzon 2.06704441174057e-05 4.6545747781914e-05 1620 2147.90909090909 1938 1.87914893930466e-06 1522 1.47183851555726 1.71642214885974 1 2.33066519516455 1620 2410 1522 1890 1938 3133 2775 1855 2514 2042 1928 1852 M2591 GHANDHI_DIRECT_IRRADIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GHANDHI_DIRECT_IRRADIATION_UP.html Genes significantly (FDR < 10%) up-regulated in IMR-90 cells (fibroblast) in response to direct irradiation. 19108712 58/143 Itai Pashtan 2.98874305598286e-07 2.3381051686704e-06 4330 2281.09090909091 1938 2.71703951091775e-08 267 1.60982512301744 -1.66155480147812 -1 3.31355332580786 4326 1263 919 508 267 1938 3955 4121 2329 1293 4173 1853 M588 GAUSSMANN_MLL_AF4_FUSION_TARGETS_F_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_F_DN.html Down-regualted genes from the set F (Fig. 5a): specific signature shared by cells expressing AF4-MLL [GeneID=4299;4297] alone and those expressing both AF4-MLL and MLL-AF4 fusion proteins. 17130830 20/49 Arthur Liberzon 7.33766188815977e-05 0.000140976972562184 2460 1883.36363636364 1939 6.67082421153449e-06 356 1.36138279706352 1.57849166066715 1 1.91626830303001 2456 356 1517 814 2310 3374 2584 3115 1055 1197 1939 1854 M4925 STEARMAN_LUNG_CANCER_EARLY_VS_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/STEARMAN_LUNG_CANCER_EARLY_VS_LATE_UP.html Up-regulated genes classifying non-tumor lung tissues by age after incution of lung cancer by urethane injection [PubChem=5641]: early (24-26 weeks) vs late (46 weeks). 18172294 72/192 Jessica Robertson 1.23746362288097e-06 5.48086440153141e-06 1655 2236.63636363636 1940 1.12496756266759e-07 800 1.37017142128152 1.48829353169704 1 2.63496540155557 1654 2941 3094 2968 800 1940 1773 1798 3086 2847 1702 1855 M7416 ST_GAQ_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GAQ_PATHWAY.html G alpha q Pathway 19/35 Signaling Transduction KE 1.45397971169583e-05 3.43761298133536e-05 1945 2192.18181818182 1941 1.32180847375887e-06 1001 1.00801593552708 -1.06326831504777 -1 1.64469674159613 1941 1552 2887 2522 1825 1001 1933 2248 2852 3899 1454 1856 M19929 BROWNE_HCMV_INFECTION_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_48HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 48 h time point that were not up-regulated at the previous time point, 24 h. 11711622 118/381 John Newman 5.59799125913211e-06 1.58215844633854e-05 2950 2064 1942 5.0890959122762e-07 589 1.76454720735806 1.91055498545592 1 3.09643255564581 2946 1246 1200 589 1480 4426 2756 2724 1942 1185 2210 1857 M2551 KEGG_ARGININE_AND_PROLINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ARGININE_AND_PROLINE_METABOLISM.html Arginine and proline metabolism 26/66 KEGG 4.15256336256363e-07 2.81825276987931e-06 3735 2151.36363636364 1944 3.77505831488375e-08 374 1.86117641405027 -1.90480781242313 -1 3.77573358797733 3735 739 1132 1944 374 4002 3586 1718 2167 1042 3226 1858 M2135 LUI_THYROID_CANCER_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_CLUSTER_1.html Cluster 1: genes with similar expression profiles across follicular thyrorid carcinoma (FTC) samples. 15608688 38/82 Leona Saunders 2.66713851985634e-07 2.23182341143693e-06 1695 1825.90909090909 1944 2.4246716756392e-08 227 1.25540093371371 1.2500261074954 1 2.59330231194116 1692 1828 2388 1959 227 2358 1609 1944 1866 2197 2017 1859 M11361 KYNG_DNA_DAMAGE_BY_4NQO http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_4NQO.html Genes specifically responding to 4NQO treatment of primary fibroblasts. 15897889 27/66 Jessica Robertson 0.00018771428715913 0.000328219831950628 2235 1815.54545454545 1945 1.70663914303076e-05 557 1.62447783497855 1.91385535194988 1 2.06866725868471 2235 1285 1945 884 2813 2549 2765 1238 1968 1732 557 1860 M5497 NIKOLSKY_BREAST_CANCER_1Q21_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_1Q21_AMPLICON.html Genes within amplicon 1q21 identified in a copy number alterations study of 191 breast tumor samples. 19010930 15/50 Jessica Robertson 0.000422410172894642 0.000692587148419976 1680 1851.18181818182 1946 3.84082999462955e-05 441 1.86642329311013 -1.45135768928074 -1 2.15551609864786 1678 1839 1946 2250 2735 1333 1964 1825 441 1988 2364 1861 M9362 IWANAGA_CARCINOGENESIS_BY_KRAS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_CARCINOGENESIS_BY_KRAS_DN.html Cluster 4: genes down-regulated in lung tissue samples from mice with tumor-bearing genotypes (activated KRAS [GeneID=3845] alone or together with inactivated PTEN [GeneID=5728]). 18281487 86/239 Jessica Robertson 3.19853290383583e-07 2.43791532721343e-06 1760 2065.54545454545 1948 2.90775760805798e-08 286 1.65485502146134 -1.28271233085764 -1 3.39525817999761 1759 3014 1835 3590 286 1573 1015 1948 2083 3431 2187 1862 M18424 FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP.html Genes up-regulated early in HMEC cells (mammary epithelium) during acinar development in vitro. 16849555 14/33 Arthur Liberzon 0.00125950054360793 0.00192436242169767 1505 1935 1950 0.000114565653313056 205 2.1166283012611 -1.39319620970732 -1 2.10110492825042 2240 2598 1916 1745 2930 1501 2191 1950 205 2504 1505 1863 M6051 DORSAM_HOXA9_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DORSAM_HOXA9_TARGETS_DN.html HOXA9 [GeneID=3205] targets down-regulated in hematopoietic stem cells. 14604967 21/53 Broad Institute 0.000116062653321393 0.000211211492607397 1370 1905.63636363636 1951 1.05517069769236e-05 380 1.68879549859419 1.50521517471157 1 2.26875204724886 1370 1876 2168 2878 2449 1165 380 1951 2855 2627 1243 1864 M2699 BIOCARTA_SODD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SODD_PATHWAY.html SODD/TNFR1 Signaling Pathway 8/15 BioCarta 0.000657757295855297 0.00104498571714011 2785 2219.90909090909 1952 6.57952067095033e-05 1066 1.60341894008788 -1.89351768026001 -1 1.74707744901126 2785 1895 3870 2404 2840 1952 1734 1066 1693 2390 1790 1865 M13903 NELSON_RESPONSE_TO_ANDROGEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/NELSON_RESPONSE_TO_ANDROGEN_UP.html Genes up-regulated in LNCaP cells (prostate cancer) in response to synthetic androgen R1881 [PubChem=13766]. 12185249 69/158 Broad Institute 2.52455791265871e-07 2.17979909250208e-06 2805 1907.18181818182 1952 2.29505291123493e-08 103 1.37595840324975 -1.38877089848529 -1 2.84749175109769 2805 103 1806 1003 212 3192 1952 3412 2108 875 3511 1866 M4780 WANG_SMARCE1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_SMARCE1_TARGETS_DN.html Genes down-regulated in BT549 cells (breast cancer) by expression of SMARCE1 [GeneID=6605] off a retroviral vector. 16135788 255/682 John Newman 2.19688774788543e-05 4.91624450171496e-05 2360 2321 1954 1.99719062362829e-06 1056 1.77825371729725 2.00642820974411 1 2.80043578488696 2357 3044 1371 1894 1954 4026 3200 1932 1840 1056 2857 1867 M4229 SESTO_RESPONSE_TO_UV_C6 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C6.html Cluster 6: genes changed in primary keratinocytes by UVB irradiation. 11867738 24/61 John Newman 2.63494946172689e-06 8.87682708082428e-06 2235 2278.45454545455 1954 2.3954114705659e-07 1169 1.12155982498782 1.36153695545287 1 2.07101325003745 2233 1923 2672 3010 1169 1543 1651 1954 3472 3749 1687 1868 M1836 LABBE_WNT3A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_WNT3A_TARGETS_UP.html Up-regulated genes in NMuMG cells (mammary epithelium) after stimulation with WNT3A [GeneID=89780]. 17210685 79/192 Jessica Robertson 5.7361752606152e-07 3.38962386774815e-06 2000 1722.81818181818 1954 5.21470614203525e-08 496 1.93093534574112 -1.64195530102859 -1 3.86066643481813 2000 1954 574 1263 496 2933 1788 2200 2086 1195 2462 1869 M1286 HOSHIDA_LIVER_CANCER_SUBCLASS_S3 http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_SUBCLASS_S3.html Genes from 'subtype S3' signature of hepatocellular carcinoma (HCC): hepatocyte differentiation. 19723656 170/490 Jessica Robertson 3.82911379475753e-07 2.69822966048628e-06 3855 2153.36363636364 1954 3.48101314656122e-08 54 1.78414329516374 1.79579368984863 1 3.63178429756331 3852 54 644 533 344 3331 3821 4152 1954 601 4401 1870 M18694 LIU_COMMON_CANCER_GENES http://www.broadinstitute.org/gsea/msigdb/cards/LIU_COMMON_CANCER_GENES.html Low abundance transcripts common to nasopharyngeal carcinoma (NPC), breast and liver tumors. 18332864 64/184 Jessica Robertson 1.46131371063885e-05 3.45321031167607e-05 2285 2288.09090909091 1955 1.32847583387672e-06 387 1.76219912162693 2.23560086643551 1 2.87396905991195 2281 1955 2325 1848 1827 4637 4657 387 925 3068 1259 1871 M18810 REACTOME_PD1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PD1_SIGNALING.html Genes involved in PD-1 signaling 9/21 Reactome 0.000125419595111461 0.000226567549226024 2585 2080.18181818182 1956 1.25426674207454e-05 779 1.93886965713515 1.71597743607958 1 2.58310369135062 2584 779 4021 1956 2491 1829 1746 1312 2171 1810 2183 1872 M547 REACTOME_SULFUR_AMINO_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SULFUR_AMINO_ACID_METABOLISM.html Genes involved in Sulfur amino acid metabolism 15/27 Reactome 2.24079607354546e-05 5.00255855199334e-05 2160 1985.27272727273 1957 2.0371080885068e-06 765 1.30681428501069 -1.46632309504564 -1 2.05439126615351 2156 765 2140 2121 1957 3006 4080 1118 1147 1478 1870 1873 M8981 BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_DN.html Genes down-regulated in ALL (acute lymphoblastic leukemia) patients who developed t-ML (treatment related myeloid leukemia). 16341039 21/51 Arthur Liberzon 4.28941888094525e-06 1.29013248242148e-05 1285 1907.72727272727 1957 3.89947931291078e-07 186 2.46294034628756 2.46294034628756 1 4.40175295264084 1284 3340 2062 3058 1741 1957 2129 186 968 3164 1096 1874 M13522 DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN.html Common down-regulated transcripts in fibroblasts expressing either XP/CS or TDD mutant forms of ERCC3 [GeneID=2071], after UVC irradiation. 15608684 338/799 Arthur Liberzon 2.00295918286779e-06 7.37882604631955e-06 1060 2106.18181818182 1957 1.82087364221477e-07 954 1.50963732178141 1.66390697995329 1 2.83191099213897 1058 4126 2746 2992 1028 1392 1957 1742 2523 2650 954 1875 M1092 REACTOME_FGFR1_LIGAND_BINDING_AND_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FGFR1_LIGAND_BINDING_AND_ACTIVATION.html Genes involved in FGFR1 ligand binding and activation 2/18 Reactome 0.0128362304462474 0.0173795365128909 1760 2430.1 1957.5 0.00143445093626411 1539 1.83561607901882 -1.83561607901882 -1 1.18087613869188 1756 3259 4102 NA 3605 1737 1539 1586 2847 2159 1711 1876 M7399 KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM.html Porphyrin and chlorophyll metabolism 18/48 KEGG 2.42295186877783e-05 5.36069521109202e-05 2090 1822.27272727273 1958 2.20270777651818e-06 354 1.88482056974189 -0.943466909974319 -1 2.94236367223461 2089 1553 1958 870 1975 2981 2988 1583 354 2321 1373 1877 M144 PID_CERAMIDE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CERAMIDE_PATHWAY.html Ceramide signaling pathway 18832364 34/69 Pathway Interaction Database 8.57250032591534e-05 0.000161652863288689 910 1657.09090909091 1958 7.79348579947267e-06 368 1.17556957873555 -1.22733670454968 -1 1.62918009801188 906 1958 2706 2010 2361 368 824 951 2605 2754 785 1878 M12533 WALLACE_PROSTATE_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WALLACE_PROSTATE_CANCER_DN.html Genes down-regulated in prostate tumor vs normal tissue samples. 18245496 2/10 Jessica Robertson 0.024998035408733 0.0325805996105082 1885 2273.9 1958.5 0.00280891349067819 853 2.01170736737527 2.01170736737527 1 1.09347026567899 1885 2830 4454 NA 3725 2003 853 1882 1025 2168 1914 1879 M12494 REACTOME_PHOSPHORYLATION_OF_CD3_AND_TCR_ZETA_CHAINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHOSPHORYLATION_OF_CD3_AND_TCR_ZETA_CHAINS.html Genes involved in Phosphorylation of CD3 and TCR zeta chains 7/18 Reactome 4.30544375089913e-06 1.29246056481187e-05 4480 2585.36363636364 1959 4.30545209250253e-07 982 1.79375629915151 -1.87153516222344 -1 3.2052776555983 4479 982 3969 1108 1411 4482 4240 1959 1060 1000 3749 1880 M879 REACTOME_FATTY_ACID_TRIACYLGLYCEROL_AND_KETONE_BODY_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FATTY_ACID_TRIACYLGLYCEROL_AND_KETONE_BODY_METABOLISM.html Genes involved in Fatty acid, triacylglycerol, and ketone body metabolism 93/250 Reactome 1.09377285506134e-06 5.01508767007578e-06 2145 1689.18181818182 1959 9.94339453502002e-08 660 1.59011814058124 -1.33964073719068 -1 3.08036151055096 2435 2141 1959 1615 755 660 1292 2062 1318 2202 2142 1881 M2565 HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP.html Genes distinguishing asparaginase resistant and sensitive ALL (B- and T-lineage ALL); here - genes up-regulated in the drug resistant samples. 15295046 14/41 Arthur Liberzon 2.25532381397157e-05 5.03259399631941e-05 2710 2129.81818181818 1959 2.0503153951746e-06 427 1.80517163420608 2.25171612450699 1 2.83612383455268 2706 2083 1866 2201 1959 3661 4655 427 484 1906 1480 1882 M10084 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_DN.html Genes down-rgulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 6h. 16818636 22/66 Arthur Liberzon 3.8201687167135e-07 2.69732965324932e-06 3055 2123.72727272727 1960 3.47288125460287e-08 342 2.12620582629757 2.57970486916178 1 4.32819597733289 3055 1295 938 871 342 4579 4067 2108 1960 1714 2432 1883 M10445 DORSAM_HOXA9_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DORSAM_HOXA9_TARGETS_UP.html HOXA9 [GeneID=3205] targets up-regulated in hematopoietic stem cells. 14604967 33/66 Broad Institute 2.09675058934735e-06 7.59916453954163e-06 2480 2222.18181818182 1960 1.90613871608805e-07 1053 1.55264763331298 1.60616608813369 1 2.90534125156839 2478 2308 2545 1629 1053 3443 3454 1960 1904 1845 1825 1884 M1790 NADELLA_PRKAR1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NADELLA_PRKAR1A_TARGETS_UP.html Epithelial and mesenchymal markers up-regulated in MEF cells (embryonic fibroblasts) after knockout of PRKAR1A [GeneID=5573]. 18413734 5/14 Jessica Robertson 1.07515071603389e-06 4.95128411507793e-06 110 2079.45454545455 1960 1.07515123621132e-07 110 5.05471798239466 5.05471798239466 1 9.80222499001535 1960 2963 4467 2973 3437 1478 1010 110 110 2911 1455 1885 M12617 KEGG_TYPE_I_DIABETES_MELLITUS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TYPE_I_DIABETES_MELLITUS.html Type I diabetes mellitus 23/78 KEGG 0.0839184282471183 0.0965721401684667 1590 2120.72727272727 1964 0.00793650793650794 1331 1.87486478936403 -1.94071454505894 -1 0.695694591979698 1588 2841 1649 1796 3683 1331 2164 2299 2223 1790 1964 1886 M1694 HARRIS_BRAIN_CANCER_PROGENITORS http://www.broadinstitute.org/gsea/msigdb/cards/HARRIS_BRAIN_CANCER_PROGENITORS.html Genes from the brain cancer stem (cancer stem cell, CSC) signature. 19074870 24/60 Leona Saunders 0.000449251549832707 0.000732750700492887 1840 2067.63636363636 1964 4.08493923266783e-05 746 1.5401449282365 1.73192661636708 1 1.76491765353258 1836 1369 1065 2028 2745 2801 2789 1964 3726 746 1675 1887 M513 ZHAN_MULTIPLE_MYELOMA_MF_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_MF_DN.html Top 50 down-regulated genes in cluster MF of multiple myeloma samples with characteristic expression spike of MAF family transcription factors. 16728703 23/66 Arthur Liberzon 3.91927943683288e-06 1.20352185065523e-05 4545 2482.90909090909 1964 3.56298765364543e-07 312 1.84085145137867 -1.85344713581172 -1 3.3102669821559 4541 1964 1362 652 1329 4032 4440 3441 312 1425 3814 1888 M15545 VALK_AML_CLUSTER_15 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_15.html Top 40 genes from cluster 15 of acute myeloid leukemia (AML) expression profile; 88% of the samples are FAB M1 or M2 subtype, 63% have mutations in CEBPA [GeneID=1050]. 15084694 24/59 Jessica Robertson 0.0014614113683697 0.0022005699460734 2315 2117.45454545455 1965 0.00013294391412866 1239 1.5458071595487 -1.61312763539603 -1 1.50155791975384 2313 1965 1903 3009 2969 1239 1667 1456 2631 2879 1261 1889 M12338 GERY_CEBP_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/GERY_CEBP_TARGETS.html Genes changed in NIH 3T3 cells (embryonic fibroblast) by expression of one or more of C/EBP proteins: CEBPA, CEBPB, CEBPG, and CEBPD [GeneID=1050;1051;1054;1052]. 15985538 108/229 Kevin Vogelsang 7.39297681922603e-06 1.96838007811893e-05 3675 2379.18181818182 1967 6.72091060275233e-07 1044 1.74322358909166 -1.54858829919109 -1 2.99857013836168 3674 1528 1044 1327 1585 2760 4397 2893 1967 1707 3289 1890 M1895 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_4NQO_IN_OLD http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_4NQO_IN_OLD.html Human environmental etress response genes not changed in primary fibroblasts from old donors in response to 4NQO treatment. 15897889 6/20 Jessica Robertson 7.15978680191765e-07 3.84756432956263e-06 2720 2042.90909090909 1968 7.1597891087333e-08 204 1.69359477452492 2.127339348111 1 3.35206404225377 2718 204 4446 1349 615 2752 1968 4478 329 2063 1550 1891 M4253 VALK_AML_CLUSTER_4 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_4.html Top 40 genes from cluster 4 of acute myeloid leukemia (AML) expression profile; 87% of the samples are FAB M1 subtype, 53% bear mutations in CEBPA [GeneID=1050]. 15084694 25/59 Jessica Robertson 8.6207759382285e-07 4.28842420876208e-06 1970 1683.18181818182 1969 7.83707210573741e-08 660 1.69392037145854 2.15878490680672 1 3.32353808259668 1969 1371 1528 2046 660 2383 2245 711 2273 2002 1327 1892 M4077 FOURNIER_ACINAR_DEVELOPMENT_LATE_2 http://www.broadinstitute.org/gsea/msigdb/cards/FOURNIER_ACINAR_DEVELOPMENT_LATE_2.html Genes identified by method 2 as coordinately down-regulated late in HMEC cells (mammary epithelium) during acinar development in vitro. 16849555 222/454 Arthur Liberzon 1.35311931565988e-05 3.24001896432407e-05 715 2177.36363636364 1970 1.23011603468108e-06 713 1.78454919319395 2.138699065634 1 2.92847250283803 713 3876 1743 2594 1793 2579 1970 1401 1922 3356 2004 1893 M9775 HAHTOLA_MYCOSIS_FUNGOIDES_CD4_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_CD4_UP.html Genes up-regulated in T helper cells (defines as CD4+) isolated from patients with mucosis fungoides compared to those from normal control donors. 16914566 50/116 Arthur Liberzon 4.7600174318762e-05 9.58961379439892e-05 2310 2077.09090909091 1971 4.32738220440111e-06 713 1.53361899405986 -1.48145747022584 -1 2.25251741612029 2309 713 1665 1290 2197 1971 3515 2856 1841 1609 2882 1894 M18322 ZHANG_TARGETS_OF_EWSR1_FLI1_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TARGETS_OF_EWSR1_FLI1_FUSION.html Genes up-regulated in RD-EF cells (rhabdomyosarcoma) engineered to express EWSR1-FLI1 fusion [GeneID=2130;2313] and which are also highly expressed in Ewing's famliy tumors. 15930281 85/188 Kevin Vogelsang 7.39907343549566e-07 3.94000660440144e-06 1780 1799.54545454545 1971 6.7264326581495e-08 420 1.4439777364244 1.47998987246452 1 2.85256476758285 1780 420 1971 837 594 3177 2240 2759 2088 1584 2345 1895 M16626 BIOCARTA_CK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CK1_PATHWAY.html Regulation of ck1/cdk5 by type 1 glutamate receptors 13/32 BioCarta 4.3493319666736e-05 8.87672891804551e-05 1995 1737.27272727273 1972 3.95401632181956e-06 287 1.48537488487686 1.12696566110504 1 2.19987320809616 1994 1972 2315 1316 2166 1892 816 2730 287 2348 1274 1896 M15137 TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_UP.html Genes up-regulated in ductal vs lobular carcinoma breast tumor cells. 17389037 15/38 Arthur Liberzon 2.47831197973924e-05 5.45741068470774e-05 1975 2042.27272727273 1973 2.25303627136268e-06 364 2.18429019292403 2.18429019292403 1 3.40366085785556 1973 2787 1805 2881 3435 2375 1969 364 847 2608 1421 1897 M5589 HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_UP.html Genes up-regulated during differentiation from pre-BI to large pre-BII lymphocyte. 11779835 28/61 Arthur Liberzon 1.1402532047819e-06 5.17224547462841e-06 1465 1927.09090909091 1975 1.03659435979276e-07 771 1.26902520954878 1.37782267437132 1 2.45212734543453 1461 1286 1975 2294 771 2403 1958 1610 2933 2285 2222 1898 M683 REACTOME_LATENT_INFECTION_OF_HOMO_SAPIENS_WITH_MYCOBACTERIUM_TUBERCULOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LATENT_INFECTION_OF_HOMO_SAPIENS_WITH_MYCOBACTERIUM_TUBERCULOSIS.html Genes involved in Latent infection of Homo sapiens with Mycobacterium tuberculosis 16/38 Reactome 0.00024743597309056 0.000422706879293608 1135 2029.36363636364 1976 2.24967097108314e-05 862 1.50169202201513 -1.3013364616353 -1 1.85199641343642 1131 2166 1976 3136 2613 862 1351 1822 3047 2724 1495 1899 M7714 AMIT_EGF_RESPONSE_240_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_240_HELA.html Genes whose expression peaked at 240 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 35/85 Leona Saunders 6.53669858384581e-05 0.000127559879464173 655 1576.81818181818 1976 5.94262982914017e-06 323 1.41869864800094 1.45800487183475 1 2.01946921568841 653 2423 2495 3190 2344 323 332 713 2500 1976 396 1900 M18053 BIOCARTA_LEPTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LEPTIN_PATHWAY.html Reversal of Insulin Resistance by Leptin 6/35 BioCarta 0.00141397633979008 0.00213394303647546 1190 2216.54545454545 1977 0.000141487684440335 899 1.3279466114641 1.3279466114641 1 1.29641493606525 1190 1810 3861 2411 3078 1121 1082 1977 3918 3035 899 1901 M19043 ST_ADRENERGIC http://www.broadinstitute.org/gsea/msigdb/cards/ST_ADRENERGIC.html Adrenergic Pathway 22/55 Signaling Transduction KE 9.86961258364513e-06 2.49320779336717e-05 1825 2132.63636363636 1977 8.97241532805109e-07 1630 1.19918243827526 1.16333582694125 1 2.01775425669176 1821 1733 2475 1977 1689 2119 1630 1936 2477 3239 2363 1902 M4697 ZHAN_MULTIPLE_MYELOMA_HP_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_HP_DN.html Top 50 down-regulated genes in cluster HP of multiple myeloma samples characterized by a hyperploid signature. 16728703 23/60 Arthur Liberzon 6.13952053781633e-06 1.70530046204042e-05 1485 1757.90909090909 1977 5.58139788308084e-07 319 1.53283829216141 1.36096863523612 1 2.67159100121092 1481 2280 2258 2863 1507 947 1234 2170 1977 2301 319 1903 M8256 REACTOME_GENERIC_TRANSCRIPTION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GENERIC_TRANSCRIPTION_PATHWAY.html Genes involved in Generic Transcription Pathway 127/490 Reactome 3.9456651173007e-06 1.2084566496517e-05 1190 2320.45454545455 1978 3.58697472164208e-07 763 1.17685240157701 -1.28809730546435 -1 2.11548215621961 1186 3228 3642 3920 1333 763 1978 1282 2962 3933 1298 1904 M11718 BOYLAN_MULTIPLE_MYELOMA_D_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_D_DN.html Genes down-regulated in group D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 51/120 Jessica Robertson 0.000371275357135492 0.000614551862782379 1425 2057.72727272727 1980 3.3758002630822e-05 1423 1.61843081037834 1.65733141555722 1 1.89982412262712 1423 2108 1800 2646 2707 1980 1738 2723 2470 1428 1612 1905 M2529 BIOCARTA_PDGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PDGF_PATHWAY.html PDGF Signaling Pathway 26/52 BioCarta 2.45343218436656e-05 5.41279812426633e-05 1665 2075.54545454545 1981 2.23041776852936e-06 1130 1.01054292994218 -0.968437853832412 -1 1.57599097104883 1662 1961 3001 1149 1981 1130 2148 2004 2652 3500 1643 1906 M691 REACTOME_KERATAN_SULFATE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KERATAN_SULFATE_DEGRADATION.html Genes involved in Keratan sulfate degradation 6/12 Reactome 0.001393650388618 0.00210733969701967 1620 1962.27272727273 1981 0.000139452517847839 388 2.77505564762306 2.77505564762306 1 2.7146893206883 1618 900 3958 1457 2978 1981 2359 2247 388 2049 1650 1907 M4204 AMIT_EGF_RESPONSE_40_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_40_HELA.html Genes whose expression peaked at 40 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 26/55 Leona Saunders 2.05348482036854e-05 4.63294649410061e-05 1285 2204.09090909091 1981 1.86682180717392e-06 869 1.31278807629513 1.29590405337998 1 2.07977848643097 1283 3315 2892 2945 1932 1490 1394 869 3116 3028 1981 1908 M2462 DE_YY1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DE_YY1_TARGETS_UP.html Genes up-regulated in SaOS-2 cells (osteosarcoma) upon knockdown of YY1 [GeneID=7528] by RNAi. 18339860 10/26 Jessica Robertson 0.000205069877188498 0.000355778394855721 1495 1954.72727272727 1981 1.86444540891738e-05 850 1.80824867304149 1.8064193469484 1 2.27954404341303 1492 1981 1452 3086 2568 1240 880 2339 2898 2716 850 1909 M2287 CHANGOLKAR_H2AFY_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANGOLKAR_H2AFY_TARGETS_UP.html Genes up-regulated in liver tissue upon knockout of H2AFY [GeneID=9555]. 17242180 34/73 Arthur Liberzon 1.58899527741305e-05 3.71394136581927e-05 2085 2191.18181818182 1982 1.44455159488593e-06 1100 1.44942877815044 -1.1189109048681 -1 2.34712396441001 2082 1959 2299 2607 1856 1100 1893 3592 1973 2760 1982 1910 M5622 DAZARD_UV_RESPONSE_CLUSTER_G2 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G2.html Cluster G2: genes increasingly up-regulated in NHEK cells (normal keratinocyte) and reaching maximum levels at 12 h and 24 h after UV-B irradiation. 12771951 40/79 John Newman 0.0054540935092112 0.007695839260513 1060 2062.45454545455 1983 0.000497060186509471 1057 1.40776626732958 -1.34776974992375 -1 1.08768263411014 1057 2361 1784 1539 3150 1354 1565 1983 2960 2761 2173 1911 M13015 REACTOME_NOREPINEPHRINE_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NOREPINEPHRINE_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Norepinephrine Neurotransmitter Release Cycle 6/21 Reactome 0.00260661270231313 0.00382782423160117 1860 2568.09090909091 1985 0.000260967525274958 1705 3.06908479856712 3.06908479856712 1 2.71152376944012 1859 3166 3995 4049 3057 1867 1795 1728 1985 3043 1705 1912 M913 REACTOME_NEPHRIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEPHRIN_INTERACTIONS.html Genes involved in Nephrin interactions 15/33 Reactome 5.83849374947156e-06 1.63533662343238e-05 2870 2088.45454545455 1985 5.30773567643527e-07 450 1.44113023155154 -1.32936712719342 -1 2.52133654690301 2868 1212 1638 450 1492 2682 2135 4534 811 1985 3166 1913 M1243 WIEMANN_TELOMERE_SHORTENING_AND_CHRONIC_LIVER_DAMAGE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WIEMANN_TELOMERE_SHORTENING_AND_CHRONIC_LIVER_DAMAGE_UP.html Genes up-regulated by telomere shortening due to the knockout of TERC [GeneID=7012] in the presence of chronic liver damage. 15608677 8/28 Leona Saunders 9.73076619069652e-05 0.000180159503633362 1465 2093.54545454545 1985 9.73119231210581e-06 625 0.96283044819025 -0.98326192055772 -1 1.31778533658786 1462 1985 4272 2448 2433 625 715 1187 3768 3309 825 1914 M18532 KIM_MYCN_AMPLIFICATION_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYCN_AMPLIFICATION_TARGETS_UP.html Genes positively correlated with amplifications of MYCN [GeneID=4613] in the SCLC (small cell lung cancer) cell lines. 16116477 62/163 Arthur Liberzon 4.01109867066284e-06 1.22131308451761e-05 2105 1976.54545454545 1985 3.64645998529416e-07 992 1.85519752422762 2.12114563014537 1 3.33174275592703 2104 2147 1908 1593 1342 3342 2622 1684 992 2023 1985 1915 M3475 CHEN_HOXA5_TARGETS_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_HOXA5_TARGETS_6HR_UP.html Genes up-regulated 6 h after induction of HoxA5 [GeneID=3205] expression in a breast cancer cell line. 15757903 5/11 Arthur Liberzon 0.0172742382387557 0.0229441837831091 1950 2639.36363636364 1986 0.00174100056434673 1465 1.25813482674599 1.25813482674599 1 0.753897196599568 1947 2491 4502 3904 3489 1848 1986 1760 3762 1879 1465 1916 M15891 GESERICK_TERT_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GESERICK_TERT_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) with TERT [GeneID=7015] knockout, after expression of the gene off a retroviral vector. 16501597 14/26 Lauren Kazmierski 0.00199357475290768 0.00296004160080018 1100 2179.09090909091 1987 0.000181398506033679 1100 1.34294514645151 1.34294514645151 1 1.2412955767754 1100 3975 2643 3415 3011 1348 1308 1293 1987 2505 1385 1917 M8876 PODAR_RESPONSE_TO_ADAPHOSTIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/PODAR_RESPONSE_TO_ADAPHOSTIN_DN.html Down-regulated genes in MM1.S cells (multiple myeloma) treated with adaphostin [PubChem=387042], a tyrosine kinase inhibitor with anticancer properties. 17308109 13/33 Jessica Robertson 8.4353586836902e-06 2.19356774649125e-05 2040 1865.63636363636 1987 7.66853729742831e-07 321 3.17998429627131 3.90222548621131 1 5.41530417225887 2040 2172 1370 3105 1629 2813 1987 1260 321 1755 2070 1918 M4723 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN.html Genes down-regulated in normal hematopoietic progenitors by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 107/303 Arthur Liberzon 1.25370797130832e-05 3.03768125829927e-05 1625 1889.27272727273 1990 1.13974101439689e-06 533 1.55884085952183 1.79405868320612 1 2.57403907388139 1622 1584 533 2168 1766 2203 1990 2845 2840 813 2418 1919 M1444 STONER_ESOPHAGEAL_CARCINOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/STONER_ESOPHAGEAL_CARCINOGENESIS_DN.html Genes down-regulated in esophagus by the carcinogen NMBA [PubChem=13643] and brought back to normal by a diet with PEITC [PubChem=16741] or black raspberries. 18676871 5/8 Jessica Robertson 1.1905579280969e-05 2.91180687600974e-05 3760 2418.45454545455 1990 1.1905643065718e-06 37 2.29946421496688 -1.22073854704435 -1 3.81244323946542 3756 1990 4385 1337 2980 4529 3585 286 37 1875 1843 1920 M9726 KEGG_PANCREATIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PANCREATIC_CANCER.html Pancreatic cancer 43/90 KEGG 2.54146212657931e-05 5.5755110136473e-05 2100 2018.36363636364 1991 2.31044680570931e-06 1033 1.37020493530244 -1.02337382709778 -1 2.13045909090965 2098 1354 2096 1187 1991 1033 2118 4549 1181 2942 1653 1921 M3911 GEISS_RESPONSE_TO_DSRNA_UP http://www.broadinstitute.org/gsea/msigdb/cards/GEISS_RESPONSE_TO_DSRNA_UP.html Genes up-pregulated by dsRNA in GRE cells (glioma; no interferon system). 11487589 30/55 John Newman 6.6861358715357e-08 8.90091837898191e-07 2400 2053.54545454545 1991 6.07830552248873e-09 24 1.25320886271313 -1.31370504450833 -1 2.77165168769268 2396 1445 2429 1596 24 1991 1954 2372 3063 3330 1989 1922 M10814 BECKER_TAMOXIFEN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BECKER_TAMOXIFEN_RESISTANCE_UP.html Genes up-regulated in a breast cancer cell line resistant to tamoxifen [PubChem=5376] compared to the parental line sensitive to the drug. 15657362 29/83 Jean Junior 8.75813047113701e-07 4.34402381396637e-06 2670 2018.36363636364 1993 7.96193996156637e-08 666 2.44316591146502 3.37473235681517 1 4.78859107437042 2669 3362 1210 2661 666 2944 2361 1642 760 1934 1993 1923 M5133 GRANDVAUX_IRF3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRANDVAUX_IRF3_TARGETS_UP.html Genes up-regulated in Jurkat cells (T lymphocyte) by expression of a constitutively active form of IRF3 [GeneID=3661]. 11991981 14/30 Yujin Hoshida 3.6397987572493e-07 2.63211373093676e-06 4630 2482 1993 3.30890850857945e-08 326 1.97403311969171 -2.16851240202435 -1 4.02609642875359 4629 1140 1596 1993 326 4282 4017 2405 1502 1897 3515 1924 M1163 BAKER_HEMATOPOIESIS_STAT3_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BAKER_HEMATOPOIESIS_STAT3_TARGETS.html STAT3 [GeneID=6774] targets in hematopoietic signaling. 17934481 11/20 Arthur Liberzon 0.00640153573962511 0.00895985557822081 1355 2204.09090909091 1994 0.000583658099469014 992 1.27564492536048 1.39170989859795 1 0.954806070968816 1353 3251 1994 3522 3678 992 1160 1536 3451 2105 1203 1925 M1843 LABBE_TARGETS_OF_TGFB1_AND_WNT3A_DN http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_TARGETS_OF_TGFB1_AND_WNT3A_DN.html Down-regulated genes in NMuMG cells (mammary epithelium) after stimulation with both TGFB1 and WNT3A [GeneID=7040;89780]. 17210685 70/200 Jessica Robertson 2.41023086578306e-07 2.1310078937848e-06 4490 2553.36363636364 1994 2.19111920894385e-08 200 1.77917785469699 -1.61631114679307 -1 3.6883322649714 4489 1909 1233 1667 200 3635 4285 3878 1994 1217 3580 1926 M7014 BIOCARTA_MYOSIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MYOSIN_PATHWAY.html PKC-catalyzed phosphorylation of inhibitory phosphoprotein of myosin phosphatase 16/49 BioCarta 0.0138528805031896 0.0186536201258467 1680 2170.18181818182 1995 0.00126735323737462 1224 1.6895334815077 -2.01226165089527 -1 1.0679244745704 1679 2785 1995 2517 3320 1346 1224 1554 3135 2720 1597 1927 M17033 LINDSTEDT_DENDRITIC_CELL_MATURATION_A http://www.broadinstitute.org/gsea/msigdb/cards/LINDSTEDT_DENDRITIC_CELL_MATURATION_A.html Maturation of monocyte-derived dendritic cells (DC) in response to inflammatory stimuli: genes up-regulated only at 8 hr after the stimulation (cluster A). 12356685 45/96 Arthur Liberzon 1.278277484708e-05 3.08763314089777e-05 1615 1994.81818181818 1996 1.1620771927371e-06 435 1.74298075555393 1.60177480655768 1 2.87358750733647 1611 1276 638 1996 1773 3142 3138 2803 2737 435 2394 1928 M14698 HOEBEKE_LYMPHOID_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOEBEKE_LYMPHOID_STEM_CELL_UP.html Genes up-regulated in the common lymphoid progenitor (CLP, defined as CD34+CD38-CD7+ [GeneID=947;952;924]) compared to a multipotent cord blood cell (defined as CD34+CD38+CD7-). 17170726 62/163 Arthur Liberzon 1.71489398458813e-07 1.73563568288985e-06 2000 1901 1997 1.55899465296696e-08 131 1.5956766749546 1.82530279866699 1 3.35990850830853 1997 1684 1633 1743 131 2120 2617 3307 2211 2022 1446 1929 M12428 MCBRYAN_PUBERTAL_BREAST_4_5WK_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_4_5WK_DN.html Genes down-regulated during pubertal mammary gland development between week 4 and 5. 17486082 140/319 Arthur Liberzon 2.19984377630025e-06 7.86305715922423e-06 1880 2050.36363636364 1997 1.99985997817354e-07 1071 1.20850043124078 1.32775804516583 1 2.2548179783301 1880 2039 2383 2835 1071 1997 1842 2408 2880 1910 1309 1930 M1478 LIAN_NEUTROPHIL_GRANULE_CONSTITUENTS http://www.broadinstitute.org/gsea/msigdb/cards/LIAN_NEUTROPHIL_GRANULE_CONSTITUENTS.html Granule constituents expressed during mouse promyelocytic cell line differentiation to neutrophils. 11468144 22/68 Kevin Vogelsang 0.000164267057982621 0.000290254688426306 1955 2138.72727272727 1998 1.49344840516174e-05 1141 1.88669416722445 -1.87084081258789 -1 2.43939945200031 1952 1924 1141 2167 2523 2006 3262 2884 1951 1718 1998 1931 M2371 WACKER_HYPOXIA_TARGETS_OF_VHL http://www.broadinstitute.org/gsea/msigdb/cards/WACKER_HYPOXIA_TARGETS_OF_VHL.html Genes down-regulated by VHL [GeneID=7428] and re-expressed under hypoxia conditions in renal carcinoma cells. 19158274 14/23 Arthur Liberzon 0.036599909809789 0.0468855050215066 2000 2289.54545454545 1999 0.00338394253241756 894 1.07310829554026 -0.864554195237921 -1 0.521284928583264 1999 1841 2358 2379 4119 1798 894 1863 3875 1905 2154 1932 M1572 LEE_CALORIE_RESTRICTION_MUSCLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_CALORIE_RESTRICTION_MUSCLE_UP.html Up-regulated in the gastrocnemius muscle of aged (30-month) mice subjected to caloric restriction diet since young adulthood. 10464095 25/68 John Newman 1.8673516642048e-06 7.03409155825055e-06 3860 2150.45454545455 2000 1.69759386291609e-07 624 2.23764499982922 -1.56336634925214 -1 4.21456783310868 3856 624 1146 1215 993 3576 3538 2873 1021 2000 2813 1933 M12362 DAVICIONI_RHABDOMYOSARCOMA_PAX_FOXO1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_RHABDOMYOSARCOMA_PAX_FOXO1_FUSION_UP.html Genes up-regulated in RMS cells (rhabdomyosarcoma) expressing PAX3 or PAX7 fusions with FOXO1 [GeneID=5077;5081;2308] compared to the fusion negative cell lines. 16849537 35/95 Arthur Liberzon 4.66896238160608e-05 9.42643589840848e-05 2505 2089.36363636364 2001 4.24460133806103e-06 1170 1.5642721648892 1.63145347784012 1 2.30180139511635 2503 1279 1254 1344 2189 4031 3017 1170 2001 1309 2886 1934 M1435 GALINDO_IMMUNE_RESPONSE_TO_ENTEROTOXIN http://www.broadinstitute.org/gsea/msigdb/cards/GALINDO_IMMUNE_RESPONSE_TO_ENTEROTOXIN.html Genes up-regulated in macrophages by aerolysin-related cytotoxic enterotoxin (Act) from Aeromonas hydrophila. 12824169 74/135 Kevin Vogelsang 4.06197635340978e-06 1.23519929864233e-05 3015 2439.90909090909 2001 3.69271259388267e-07 779 1.80325571787014 1.99873979412235 1 3.23522426055227 3015 2001 1103 1410 1345 4223 3302 4289 1482 779 3890 1935 M8009 KAAB_FAILED_HEART_ATRIUM_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAAB_FAILED_HEART_ATRIUM_UP.html Genes up-regulated in atria of failing hearts (DCM and ICM) compared to healthy controls. 15103417 28/91 John Newman 2.62305609720858e-05 5.73036870467104e-05 1935 1961.72727272727 2001 2.38462488398358e-06 1213 1.57361499514099 1.64028555638 1 2.43988697371347 1933 2233 2164 1755 2001 2645 1213 1894 1370 2284 2087 1936 M4113 SENESE_HDAC2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC2_TARGETS_UP.html Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC2 [GeneID=3066] by RNAi. 17470557 74/166 Leona Saunders 3.09671394491923e-07 2.38671078057426e-06 1420 1843 2002 2.8151948916472e-08 277 1.5415145407337 1.4925421809627 1 3.16791253769315 1418 2002 2739 1885 277 2050 1521 2103 2082 2342 1854 1937 M4740 BENPORATH_ES_CORE_NINE http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_ES_CORE_NINE.html Set 'Core 9': 'embryonic stem cell' transcription regulators that are preferentially and coordinately overexpressed in the high-grade, ER-negative breast cancer tumors. 18443585 7/16 Jessica Robertson 0.000353292293154642 0.000586650491042755 2305 2119.09090909091 2002 3.53348472675298e-05 1050 1.56545823422763 -1.57548926836192 -1 1.84918813510286 2303 1151 4341 1737 2717 1368 2002 2842 1050 2270 1529 1938 M13526 AMIT_EGF_RESPONSE_20_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_20_HELA.html Genes whose expression peaked at 20 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 9/15 Leona Saunders 0.00130038380594325 0.00198101382140769 1620 2244 2002 0.000130114538235367 952 1.12605629173235 1.16743131177972 1 1.11261131263111 1617 2089 4346 2002 2965 1362 952 4434 2398 1244 1275 1939 M882 BIOCARTA_CXCR4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CXCR4_PATHWAY.html CXCR4 Signaling Pathway 19/45 BioCarta 6.49740396905825e-05 0.000126914693618203 2620 2248.90909090909 2004 5.90690533552378e-06 1095 1.41184674729712 -1.4740994123721 -1 2.01085225014313 2617 1300 1981 1095 2276 2004 3535 3168 1802 3000 1960 1940 M3642 DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_DN.html 'PAX-FKHR signature': genes down-regulated by PAX3- or PAX7-FOXO1 [GeneID=5081;5077;2308] fusion in primary alveolar rhabdomyosarcoma(ARMS) tumors. 16849537 16/28 Arthur Liberzon 2.632035181549e-05 5.74462825372083e-05 2120 1761.18181818182 2004 2.39278788291741e-06 582 1.97603173708745 2.73888567414697 1 3.06305372958133 2120 762 1186 1126 2004 2513 2608 1770 582 2121 2581 1941 M9011 KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION.html Vasopressin-regulated water reabsorption 29/62 KEGG 4.98367041191129e-05 9.9972087115652e-05 580 1855 2007 4.53071210073956e-06 178 1.20425907047952 1.26961786117845 1 1.7608093310074 580 2007 2693 2704 3170 178 334 770 3986 3625 358 1942 M18356 XU_HGF_TARGETS_INDUCED_BY_AKT1_6HR http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_TARGETS_INDUCED_BY_AKT1_6HR.html Genes changed in DU-145 cells (prostate cancer) in the absence but not presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 6 h. 17099727 10/36 Arthur Liberzon 0.00152157874198953 0.00228676009780722 1930 2334 2007 0.00013842110241679 1019 1.13151894578923 -1.17304841624699 -1 1.09222774044501 1930 3030 2351 3646 2975 1019 1300 2007 3868 1964 1584 1943 M13671 COATES_MACROPHAGE_M1_VS_M2_UP http://www.broadinstitute.org/gsea/msigdb/cards/COATES_MACROPHAGE_M1_VS_M2_UP.html Up-regulated genes distinguishing between M1 (pro-inflammatory) and M2 (anti-inflammatory) macrophage subtypes. 18199539 54/119 Jessica Robertson 4.61724634628454e-07 2.95428147508986e-06 3450 2371.27272727273 2007 4.19749755938967e-08 419 1.21653804318506 1.11567976021658 1 2.45886444644158 3446 590 1794 1159 419 3422 2007 4286 2623 1851 4487 1944 M2344 FARDIN_HYPOXIA_9 http://www.broadinstitute.org/gsea/msigdb/cards/FARDIN_HYPOXIA_9.html Genes in the hypoxia signature, based on analysis of nine neuroblastoma cell lines in hypoxia and normal oxygen conditions. 19832978 4/11 Paolo Fardin 0.000591674764373022 0.000945952898618894 2840 2277.09090909091 2008 5.91832358993298e-05 538 1.50945827793583 0.829197998241968 1 1.66855639620538 2838 1231 4651 1995 2822 2008 1159 3155 538 1646 3005 1945 M6121 REACTOME_INITIAL_TRIGGERING_OF_COMPLEMENT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INITIAL_TRIGGERING_OF_COMPLEMENT.html Genes involved in Initial triggering of complement 10/18 Reactome 0.00398458543091243 0.00571002058998644 1555 2377 2009 0.000362892778691389 1535 1.41779207712256 1.41779207712256 1 1.16260240565755 1554 1891 1535 3569 3103 1565 2344 2009 4017 2699 1861 1946 M1516 HU_GENOTOXIN_ACTION_DIRECT_VS_INDIRECT_4HR http://www.broadinstitute.org/gsea/msigdb/cards/HU_GENOTOXIN_ACTION_DIRECT_VS_INDIRECT_4HR.html Genes discriminating between direct (cisplatin, MMS, mitomycin C [PubChem=2767;4156;5746]) and indirect (paclitaxel, hydroxyurea, etoposide [PubChem=4666;3657;36462]) acting genotoxins at 4 h time point. 15120960 32/65 John Newman 7.18743875793755e-06 1.92870586612568e-05 2015 1857.63636363636 2011 6.53405658139454e-07 861 2.16983615589199 2.88397746028069 1 3.73941260120422 2011 861 1538 1484 1567 2765 2394 2026 1496 2142 2150 1947 M1906 VANASSE_BCL2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANASSE_BCL2_TARGETS_UP.html Genes up-regulated in primary B lymphocytes engineered to overexpress BCL2 [GeneID=12043]. 15561778 22/78 Arthur Liberzon 0.00705003257793259 0.00982058640314866 2465 2193.81818181818 2011 0.000642975155662732 1411 1.39605788077208 1.65165540842509 1 1.02460544665971 2464 2011 1587 2403 3798 1772 1703 1411 3096 2194 1693 1948 M1960 MIKKELSEN_MCV6_LCP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MCV6_LCP_WITH_H3K4ME3.html Genes with low-CpG-density promoters (LCP) bearing the tri-methylation mark at H3K4 (H3K4me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state). 18509334 107/271 Jessica Robertson 2.82012573580597e-07 2.29742234705141e-06 3035 1826.18181818182 2011 2.56375099755545e-08 71 1.71022037813662 -1.79841491860716 -1 3.52496551724545 3031 71 493 1103 240 2501 4481 2700 2011 631 2826 1949 M8104 KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM.html Amino sugar and nucleotide sugar metabolism 19/54 KEGG 5.92017339128139e-05 0.000116562741645145 2015 1808.81818181818 2012 5.38212064403038e-06 537 1.3713624287023 -1.14663023243862 -1 1.9717146087903 1661 2012 3128 3044 2256 731 1016 1079 2015 2418 537 1950 M15964 CHESLER_BRAIN_D6MIT150_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_D6MIT150_QTL_TRANS.html Neurologically relevant genes modulated in brain tissue by a trans-regulatory QTL (quantitative trait locus) near D6Mit150 marker. 15711545 2/17 Jean Junior 0.0294483214578319 0.0380570420163818 1400 2278.6 2017.5 0.00331567191148197 1399 1.25416119826726 1.25416119826726 1 0.650770538861658 1399 1901 4376 NA 3641 1680 2343 2134 1529 2165 1618 1951 M13447 LANDIS_ERBB2_BREAST_PRENEOPLASTIC_DN http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_PRENEOPLASTIC_DN.html Down-regulated genes from top 82 genes out of the 324-gene signature identified in the pre-neoplastic tissue adjacent to the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 34/74 Leona Saunders 2.57679552911526e-07 2.19144534472488e-06 4175 2411.90909090909 2020 2.34254166447983e-08 218 1.49027099520527 -1.2361416866493 -1 3.08279654986131 4172 1360 1937 2082 218 2020 1894 4566 2316 1927 4039 1952 M2661 REACTOME_REGULATED_PROTEOLYSIS_OF_P75NTR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATED_PROTEOLYSIS_OF_P75NTR.html Genes involved in Regulated proteolysis of p75NTR 7/13 Reactome 3.38402523791253e-05 7.1333973301206e-05 2280 1698.36363636364 2021 3.38407677133766e-06 161 2.01299884268454 -1.15425804175272 -1 3.05116551891408 2280 786 3976 755 2115 745 939 2646 161 2258 2021 1953 M5082 FRASOR_TAMOXIFEN_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_TAMOXIFEN_RESPONSE_DN.html Genes preferentially down-regulated in MCF-7 cells (breast cancer) by tamoxifen [PubChem=5376] but not by estradiol or fulvestrant (ICI 182780) [PubChem=5757;3478439]. 16849584 7/18 Arthur Liberzon 0.00036643029276376 0.000606746414095752 2025 2007.27272727273 2021 3.66490728811531e-05 119 2.7168191555031 -2.14836012201647 -1 3.19469989493525 2021 1511 4111 1346 2725 1656 2195 2506 119 1498 2392 1954 M8702 DAZARD_RESPONSE_TO_UV_NHEK_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_RESPONSE_TO_UV_NHEK_DN.html Genes down-regulated in NHEK cells (normal keratinocytes) by UV-B irradiation. 12771951 189/494 John Newman 2.78810867134728e-05 6.03899837904882e-05 1425 2656.09090909091 2022 2.53467636935657e-06 1325 1.28266429183477 1.35119709167602 1 1.97808701438837 1421 4487 3454 4331 2022 1552 1325 1563 3105 3969 1988 1955 M8123 BERNARD_PPAPDC1B_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERNARD_PPAPDC1B_TARGETS_DN.html Genes down-regulated in ZR-75-1 cells (breast cancer, amplified 8p11-12 region) upon knockdown of PPAPDC1B [GeneID=84513] by RNAi. 18757432 37/91 Jessica Robertson 2.50706317604773e-06 8.57525404595596e-06 2725 2343.36363636364 2023 2.2791509391243e-07 1031 1.43332433527474 1.12612993142929 1 2.65456557789748 2723 1031 2023 1953 1140 2477 1844 4422 1702 2525 3937 1956 M90 PID_WNT_CANONICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_WNT_CANONICAL_PATHWAY.html Canonical Wnt signaling pathway 18832364 10/33 Pathway Interaction Database 3.42556360550411e-06 1.08387515566457e-05 1400 2012.09090909091 2025 3.1141535812482e-07 365 1.01789136465396 1.165600961977 1 1.84731836199315 1397 2025 2809 3054 1277 799 365 3240 3338 2693 1136 1957 M1437 WANG_IMMORTALIZED_BY_HOXA9_AND_MEIS1_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_IMMORTALIZED_BY_HOXA9_AND_MEIS1_DN.html Down-regulated genes in myeloid progenitors immortalized by HOXA9 [GeneID=3205] vs those immortalized by HOXA9 and MEIS1 [GeneID=4211]. 15755900 12/33 Kevin Vogelsang 0.000102080403500121 0.000187882470856861 900 1969.36363636364 2025 9.28046730520692e-06 418 1.31019313305635 1.31019313305635 1 1.78447585625245 897 2558 2025 3713 2923 418 659 886 4149 2967 468 1958 M11778 BOHN_PRIMARY_IMMUNODEFICIENCY_SYNDROM_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOHN_PRIMARY_IMMUNODEFICIENCY_SYNDROM_DN.html Genes down-regulated in B lymphocytes from patients with primary immunodefiency syndrom. 17195838 41/103 Jessica Robertson 1.07961980640805e-05 2.67960721018439e-05 2805 1949.81818181818 2025 9.81477367754982e-07 1062 1.52406343142151 -1.49583405664569 -1 2.5469578470063 2802 2360 2086 1184 1716 1285 2634 2341 1062 2025 1953 1959 M800 REACTOME_G_ALPHA1213_SIGNALLING_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_ALPHA1213_SIGNALLING_EVENTS.html Genes involved in G alpha (12/13) signalling events 37/97 Reactome 3.16236639315494e-07 2.41919601397908e-06 3125 2043 2026 2.87487895247818e-08 281 1.43516228775944 -1.54072971529897 -1 2.94627173978447 3125 601 1563 876 281 2909 4179 3660 2026 970 2283 1960 M13254 GRAHAM_CML_QUIESCENT_VS_NORMAL_DIVIDING_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_NORMAL_DIVIDING_DN.html Genes down-regulated in quescent CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloblastic leukemia) patients compared to the dividing cells from normal donors. 17717066 6/24 Arthur Liberzon 0.000439546106957046 0.000717920201185332 1230 2283.63636363636 2028 4.3963307151821e-05 548 0.979724003291219 0.979724003291219 1 1.12588754119243 1228 2028 4147 3692 3297 1170 548 859 3782 3050 1319 1961 M581 ZIRN_TRETINOIN_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZIRN_TRETINOIN_RESPONSE_UP.html Genes up-regulated in MS427 cells (Wilms tumor with normal WT1 [GeneID=7490]) after treatment with 10 microM tretinoin (ATRA) [PubChem=444795] for 24 h. 15897880 14/25 Leona Saunders 3.26741886827864e-06 1.04584185906788e-05 2030 1967.90909090909 2028 2.97038520093441e-07 1260 1.55633338783219 1.62559137153792 1 2.8333341240891 1745 2404 1739 2320 1260 2030 2028 2552 2792 1374 1403 1962 M7890 WAESCH_ANAPHASE_PROMOTING_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/WAESCH_ANAPHASE_PROMOTING_COMPLEX.html Subunits of the anaphase promoting complex (APC). 15637585 8/18 Leona Saunders 0.000434557649863464 0.000711011573764033 1615 2621.45454545455 2029 4.34642651416484e-05 152 5.05471798239466 5.05471798239466 1 5.81658284816633 1612 4411 4248 3996 4307 1996 1921 856 152 3308 2029 1963 M1428 SANSOM_APC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_APC_TARGETS_UP.html Top genes up-regulated at day 5 of Cre-Lox induced APC [GeneID=324] knockout in the intestine. 15198980 84/216 Kevin Vogelsang 2.14852010211004e-06 7.72083220742916e-06 2685 2219.36363636364 2029 1.95320200032521e-07 1063 1.66160025608621 1.67657629009902 1 3.10502556685367 2685 1953 1169 1297 1063 3999 2851 2841 2029 1561 2965 1964 M15569 KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY.html NOD-like receptor signaling pathway 36/72 KEGG 0.000150036471790489 0.00026692137692112 1700 2012.36363636364 2030 1.3640609546755e-05 1141 1.57227017579442 -1.46217753871223 -1 2.0537822153766 1697 2653 2181 2565 2502 1141 1310 1835 2789 2030 1433 1965 M1930 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_UP.html Genes from the yellow module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 21/51 Arthur Liberzon 1.79850711952436e-05 4.12319195797024e-05 2245 1935.36363636364 2030 1.63501983867868e-06 171 1.39914811443377 1.13820469188232 1 2.24248428097558 2245 171 2045 1999 1898 1729 1546 2030 2582 2082 2962 1966 M17002 REACTOME_BILE_SALT_AND_ORGANIC_ANION_SLC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BILE_SALT_AND_ORGANIC_ANION_SLC_TRANSPORTERS.html Genes involved in Bile salt and organic anion SLC transporters 2/12 Reactome 8.94193782725574e-06 2.297254422068e-05 3440 2154.2 2030.5 9.93552596050751e-07 150 2.39094242784929 -3.33567567151949 -1 4.05408794959633 3438 393 4030 NA 1721 2607 1312 4471 150 1080 2340 1967 M553 REACTOME_SIGNALING_BY_ERBB2 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ERBB2.html Genes involved in Signaling by ERBB2 58/128 Reactome 1.10411445775045e-06 5.04768814538399e-06 1885 2217 2031 1.00374091988454e-07 759 1.51879144859841 1.59326644657485 1 2.94062592157682 1882 3358 2534 901 759 2031 1862 3354 2451 3597 1658 1968 M1138 CROONQUIST_NRAS_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_NRAS_SIGNALING_UP.html Genes up-regulated in ANBL-6 cell line (multiple myeloma, MM) expressing a constantly active form of NRAS [GeneID=4893] off a plasmid vector compared to those grown in the presence of IL6 [GeneID=3569]. 12791645 20/65 Arthur Liberzon 2.42143475430761e-05 5.35986927665822e-05 2875 2373.90909090909 2031 2.20132855117477e-06 750 1.55193215216737 1.23240117004507 1 2.4227347728091 2874 750 1460 1435 1974 3236 2781 4553 2031 1550 3469 1969 M8943 TING_SILENCED_BY_DICER http://www.broadinstitute.org/gsea/msigdb/cards/TING_SILENCED_BY_DICER.html Epigenetically silenced genes up-regulated in HCT116 cells (colon cancer) hypomorphic for DICER1 [GeneID=23405]. 18413723 20/68 Jessica Robertson 0.00114035457820356 0.00175375830438526 1020 1934.09090909091 2032 0.000103722372937022 839 3.01817173617485 3.01817173617485 1 3.04051520610166 1020 3126 1192 2032 3474 1667 2061 1100 2227 2537 839 1970 M196 PID_IL23_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL23_PATHWAY.html IL23-mediated signaling events 18832364 23/54 Pathway Interaction Database 4.40730377560726e-05 8.9691854690861e-05 3250 2037.45454545455 2034 4.00672006407012e-06 1108 1.60744718384963 -1.71836699243338 -1 2.37802092480144 3248 1289 1164 1397 2172 1800 3104 2034 2815 1108 2281 1971 M5218 SILIGAN_BOUND_BY_EWS_FLT1_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/SILIGAN_BOUND_BY_EWS_FLT1_FUSION.html Genes bound by EWSR1-FLT1 [GeneID=2130;2321] fusion but whose expression did not change in STA-ET-7.2 cells (Ewing's sarcoma) after knockdown of EWSR1-FLT1 by RNAi. 15735734 25/89 Leona Saunders 0.00531305317355439 0.00750134593892012 1810 2330 2034 0.000484175261479427 1196 1.74230371637333 1.7295129008878 1 1.35323617468034 1809 3671 2460 3703 3148 1655 1721 2234 2034 1999 1196 1972 M3444 REACTOME_TRANSMEMBRANE_TRANSPORT_OF_SMALL_MOLECULES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSMEMBRANE_TRANSPORT_OF_SMALL_MOLECULES.html Genes involved in Transmembrane transport of small molecules 162/475 Reactome 9.16560159819214e-08 1.12434578767352e-06 2305 1718.72727272727 2035 8.33236543640716e-09 257 1.75809756837672 1.79315076380022 1 3.8230810069501 2305 549 306 677 574 3293 2277 4155 2035 257 2478 1973 M15593 MOROSETTI_FACIOSCAPULOHUMERAL_MUSCULAR_DISTROPHY_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOROSETTI_FACIOSCAPULOHUMERAL_MUSCULAR_DISTROPHY_DN.html Genes down-regulated in FSHD (facioscapulohumeral muscular dystrophy) mesoangioblasts. 17761758 8/20 Arthur Liberzon 1.32689012876898e-06 5.73149528453711e-06 4660 2033.72727272727 2035 1.32689092105648e-07 137 2.5309492876022 -2.04840606790462 -1 4.84928279244716 4658 1750 4145 441 877 2280 2035 2182 137 1134 2732 1974 M1130 MCBRYAN_TERMINAL_END_BUD_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_TERMINAL_END_BUD_DN.html The 'TEB profile genes': down-regulated during pubertal mammary gland development specifically in the TEB (terminal end bud) structures. 17486082 9/15 Arthur Liberzon 1.31899709810547e-05 3.16965148806268e-05 2740 2460.18181818182 2035 1.31900492706092e-06 1318 1.57865998027734 -1.52033918527745 -1 2.59610785777129 2739 1318 4180 2035 1824 1965 2899 3476 1999 1811 2816 1975 M63 PID_AVB3_OPN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AVB3_OPN_PATHWAY.html Osteopontin-mediated events 18832364 31/54 Pathway Interaction Database 2.09381460421476e-06 7.59916453954163e-06 4415 2607.36363636364 2036 1.9034696336107e-07 666 1.5835238099629 -1.48890077891274 -1 2.96311729027963 4413 1441 1977 666 1051 3203 3553 4426 1854 2036 4061 1976 M1755 SANSOM_APC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_APC_TARGETS.html Genes up-regulated after Cre-lox knockout of APC [GeneID=324] in the small intestine. 17377531 144/346 Arthur Liberzon 7.86500633170095e-07 4.09504663003896e-06 3920 2491.90909090909 2038 7.15000831222216e-08 614 1.79999887768487 2.0463849089999 1 3.54485280809685 3916 2038 1094 1465 614 3457 3734 4214 1620 1073 4186 1977 M12861 GENTILE_UV_RESPONSE_CLUSTER_D2 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D2.html Cluster d2: genes down-regulated consistently in WS1 cells (fibroblast) between 6 h and 24 h after irradiation with high dose UV-C. 12907719 20/56 John Newman 0.0104513878639471 0.0142784849943021 1225 2427.09090909091 2039 0.000954670118285343 1223 1.90993966716658 2.1414582836267 1 1.28827947077478 1223 4277 2039 3781 4547 1321 1405 1490 2183 2536 1896 1978 M10334 WANG_CLIM2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_CLIM2_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) engineered to conditionally express a dominant negative form of CLIM2 [GeneID=8861] by a Tet Off system. 17452977 155/426 Arthur Liberzon 2.18153780438195e-06 7.82148902167853e-06 1845 2102.45454545455 2040 1.98321815237773e-07 1067 1.6473039170993 1.9507406145079 1 3.07492285835487 1844 3109 1909 2228 1067 3132 2150 1168 1670 2810 2040 1979 M13714 LEE_METASTASIS_AND_ALTERNATIVE_SPLICING_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_METASTASIS_AND_ALTERNATIVE_SPLICING_DN.html Down-regulated genes displaying alternative splicing in MDA-MB-435 cells (breast cancer) whose metastatic potential has been reduced by expression of NME1 [GeneID=4830]. 18245461 28/87 Jessica Robertson 2.32197408873139e-06 8.16077481033895e-06 3890 2370 2043 2.11088776313252e-07 948 1.60912853893067 -1.47784529269903 -1 2.99281600071628 3887 1728 1562 2043 1099 2250 4541 3031 1718 948 3263 1980 M2011 MIKKELSEN_NPC_ICP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_ICP_WITH_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K27 (H3K27me3) in neural progenitor cells (NPC). 17603471 4/16 Arthur Liberzon 4.80530533458058e-07 3.03472517491167e-06 2045 2137.36363636364 2043 4.80530637367406e-08 466 1.67824021823807 -1.45877996391278 -1 3.38489870073471 2043 906 4597 1546 466 2122 3308 3227 2070 1644 1582 1981 M13036 KEGG_PRION_DISEASES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRION_DISEASES.html Prion diseases 24/49 KEGG 2.83924675576986e-05 6.13120290209104e-05 1660 1918.36363636364 2044 2.58116672618662e-06 380 1.66279162545766 1.84340220571512 1 2.56030840768248 1659 2813 2044 1182 3600 2455 1636 380 2095 2375 863 1982 M2475 LIU_IL13_MEMORY_MODEL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_IL13_MEMORY_MODEL_DN.html Genes down-regulated in BEAS-2B cells (bronchial epithelium) stimulated with IL13 [GeneID=3596] on days 1 to 3 and then rested for the next 3 days (repeated-stimulation or memory model) 20123980 3/9 Arthur Liberzon 0.00016792949706654 0.000296279225622668 2045 2142.72727272727 2044 1.67942188558562e-05 991 1.07148900351736 -1.07148900351736 -1 1.38188634454431 2044 991 4673 1974 2549 1776 2084 1034 2571 2478 1396 1983 M5823 BROWNE_HCMV_INFECTION_1HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_1HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 1 h time point that were not up-regulated at the previous time point, 30 min. 11711622 40/179 Arthur Liberzon 0.000276380006144591 0.000467213819911094 1605 2101 2045 2.51286121017856e-05 933 1.685273640084 1.49163973444806 1 2.05162069595381 1605 3020 1377 2452 2639 2045 1320 3127 2831 933 1762 1984 M16811 BIOCARTA_ERK5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERK5_PATHWAY.html Role of Erk5 in Neuronal Survival 16/34 BioCarta 3.01622332840851e-05 6.47162203155782e-05 2830 2095.36363636364 2048 2.7420588017672e-06 336 1.92016947293133 2.36108742103164 1 2.94013863431227 2829 1790 1672 623 2048 3781 3151 2021 336 2118 2680 1985 M1835 KEGG_GLIOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLIOMA.html Glioma 32/75 KEGG 0.00017987315379757 0.000315451197116547 2650 2072 2049 1.63534420004144e-05 935 1.79429380961935 -1.36283995326233 -1 2.29621914059795 2649 2049 1632 935 2544 2637 1853 1670 1345 2588 2890 1986 M2842 BIOCARTA_FIBRINOLYSIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FIBRINOLYSIS_PATHWAY.html Fibrinolysis Pathway 5/15 BioCarta 3.01593761851902e-05 6.47162203155782e-05 2250 2129.36363636364 2049 3.0159785507596e-06 1155 2.06045824519532 2.27202897534296 1 3.15494698605425 2247 1897 3836 1541 2079 2688 2708 1876 2049 1155 1347 1987 M11850 TANG_SENESCENCE_TP53_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TANG_SENESCENCE_TP53_TARGETS_UP.html Genes up-regulated in WI-38 cells (senescent primary fibroblasts) after inactivation of TP53 [GeneID=7157] by GSE56 polypeptide. 17533371 19/61 Leona Saunders 0.00302561193755771 0.0044053678583165 1220 2300.90909090909 2050 0.000275434638625841 1041 2.09934761676718 2.09934761676718 1 1.80793235819215 1218 3242 2003 3446 3235 1675 2659 1736 2050 3005 1041 1988 M1546 APPIERTO_RESPONSE_TO_FENRETINIDE_UP http://www.broadinstitute.org/gsea/msigdb/cards/APPIERTO_RESPONSE_TO_FENRETINIDE_UP.html Genes up-regulated in A2780 cells (ovarian carcinoma) exposed to fenretinide [PubChem=1744]. 17213814 28/71 Arthur Liberzon 4.179800030532e-05 8.56055198560881e-05 990 1697.63636363636 2051 3.79989040458698e-06 338 1.57745300903665 1.71014488128737 1 2.34532511304575 986 2991 2051 2142 2226 721 1109 734 2196 3180 338 1989 M13630 GENTILE_UV_HIGH_DOSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_HIGH_DOSE_DN.html Selected genes down-regulated in WS1 (fibroblast) in response to irradiation with high dose UV-C. 12907719 232/485 John Newman 6.06143246594651e-06 1.68568976471367e-05 1715 2621.45454545455 2053 5.51040833313536e-07 1382 1.42597872694246 1.59755976773493 1 2.48796325817704 1712 4621 2798 4041 1505 2053 1901 1382 3220 3740 1863 1990 M15927 RODRIGUES_DCC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_DCC_TARGETS_DN.html Genes down-regulated in HCT8/S1 cells (colon cancer) which normally lack DCC [GeneID=9423] compared to those stably expressing wild type DCC off a plasmid vector. 17334389 98/207 Arthur Liberzon 1.03665599854016e-07 1.2391876408532e-06 3410 2470.63636363636 2055 9.42414588534678e-09 60 1.45509535649171 1.50438583959118 1 3.14172087731686 3406 1252 1557 873 60 4488 3724 4138 2055 1317 4307 1991 M11064 HALMOS_CEBPA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HALMOS_CEBPA_TARGETS_UP.html Genes up-regulated in H358 cells (lung cancer) by inducible expression of CEBPA [GeneID=1050] off plasmid vector. 15205324 44/99 Kevin Vogelsang 1.6559153107601e-06 6.53716861518268e-06 2055 1920.09090909091 2055 1.50537868831844e-07 928 2.09727600940994 2.26025273653332 1 3.97457740083819 2055 2192 936 1325 932 3366 2431 2974 1243 928 2739 1992 M6041 DAIRKEE_CANCER_PRONE_RESPONSE_E2 http://www.broadinstitute.org/gsea/msigdb/cards/DAIRKEE_CANCER_PRONE_RESPONSE_E2.html 'Cancer prone response profile' (CPRP): genes changed in response to estradiol [PubChem=5757] in epithelial cell cultures from patients at high risk of breast cancer. 18381411 25/58 Jessica Robertson 0.000233447686128021 0.000400562379053792 1595 2219.81818181818 2056 2.12247692314564e-05 1426 2.50536070763389 2.50536070763389 1 3.1111949580211 1592 3091 1426 3367 2604 2286 1843 2184 2056 2001 1968 1993 M758 REACTOME_ABC_FAMILY_PROTEINS_MEDIATED_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ABC_FAMILY_PROTEINS_MEDIATED_TRANSPORT.html Genes involved in ABC-family proteins mediated transport 15/45 Reactome 4.72827027425992e-05 9.53385305730723e-05 2340 2099.90909090909 2057 4.29851990723008e-06 942 2.28944150372555 2.39800838925277 1 3.36475834821282 2337 2057 1499 2031 2195 3292 2675 2717 942 1480 1874 1994 M1179 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_6 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_6.html Amplification hot spot 6: colocolized fragile sites and cancer genes in the 17p13-p11.1 region. 16751803 6/9 Arthur Liberzon 0.000195733775147862 0.000341007073305859 2590 1957 2057 1.95751017555181e-05 30 3.51734271653262 -1.47591627039601 -1 4.45776753289138 2587 1663 4231 2096 2586 2012 1423 727 30 2057 2115 1995 M12710 AMIT_EGF_RESPONSE_120_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_120_HELA.html Genes whose expression peaked at 120 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 67/122 Leona Saunders 3.68019383956567e-06 1.14830687329376e-05 1725 2267 2057 3.34563635987722e-07 1303 1.72217188114948 1.81663146478706 1 3.10969358247595 1916 2738 1884 1724 1303 3805 2691 2881 2216 1722 2057 1996 M1884 YOSHIMURA_MAPK8_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/YOSHIMURA_MAPK8_TARGETS_UP.html Genes up-regulated in vascular smooth muscle cells (VSMC) by MAPK8 (JNK1) [GeneID=5599]. 16311603 622/2045 Jessica Robertson 4.45983779145486e-11 1.31438993023632e-09 2070 1787.54545454545 2058 4.45983779154436e-12 4 1.67829567319824 1.78526430751955 1 5.44832594378399 2066 4 4537 674 335 3151 2058 2478 1830 60 2470 1997 M2443 PLASARI_TGFB1_TARGETS_1HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_TARGETS_1HR_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) upon stimulation with TGFB1 [GeneID=7040] for 1 h. 19752192 26/46 Arthur Liberzon 7.97989058721704e-05 0.000151698853110341 1470 2238 2058 7.25470913667518e-06 1468 1.29940515402815 1.24777024106771 1 1.81390904638804 1468 3152 2058 2847 2335 1897 1566 1980 3161 2552 1602 1998 M17517 WU_HBX_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_2_DN.html Genes down-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] in primary hepatocytes. 11439330 9/22 John Newman 0.00135150226127025 0.00205198715840807 1810 2217.72727272727 2062 0.00013523249167737 748 1.38837591059763 -1.29166728925028 -1 1.36404082041111 1807 2902 4399 2922 2972 748 1226 2230 2062 1814 1313 1999 M16128 XU_GH1_EXOGENOUS_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_GH1_EXOGENOUS_TARGETS_UP.html Genes up-regulated in MFCF-7 cells (breast cancer) by exogenous HG1 [GeneID=2688]. 15845533 25/121 John Newman 1.41679153133333e-07 1.53682525829351e-06 2065 1753 2062 1.28799238415833e-08 87 1.46115077262326 1.69485304122784 1 3.10486455283708 2062 164 1446 2317 87 2124 1439 3463 2764 1237 2180 2000 M2375 EHRLICH_ICF_SYNDROM_DN http://www.broadinstitute.org/gsea/msigdb/cards/EHRLICH_ICF_SYNDROM_DN.html Down-regulated in B lymphocytes from patients with ICF syndrom caused by mutations in DNMT3B [GeneID=1789] compared to normals. 11741835 9/26 John Newman 2.85060601288668e-05 6.15006435376933e-05 1925 2394.09090909091 2062 2.85064258034275e-06 1540 2.16539936536563 2.45401111610034 1 3.33315037923358 1922 1982 4411 2739 2062 2815 2719 2044 1540 1815 2286 2001 M7912 DELLA_RESPONSE_TO_TSA_AND_BUTYRATE http://www.broadinstitute.org/gsea/msigdb/cards/DELLA_RESPONSE_TO_TSA_AND_BUTYRATE.html Genes up-regulated in HT-29 cells (colon cancer) by the combination of trichostatin A (TSA) and sodium butyrate [PubChem=5562;5222465]. 11423116 27/46 John Newman 0.0138236217324145 0.0186334909509681 1165 2328.54545454545 2063 0.00126465943910055 1165 1.78503138569228 1.78503138569228 1 1.12859297195751 1165 3798 2572 2063 3524 1748 1699 1553 3112 2638 1742 2002 M3009 HORTON_SREBF_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/HORTON_SREBF_TARGETS.html Genes up-regulated in liver from mice transgenic for SREBF1 or SREBF2 [GeneID = 6720, 6721] and down-regulated in mice lacking SCAP [GeneID=22937]. 14512514 13/35 Arthur Liberzon 1.00100820573882e-05 2.52267583202372e-05 3855 1992 2064 9.10011600356826e-07 648 1.27720655768435 -1.38481918792713 -1 2.14665594483575 3855 648 2235 2133 1694 2225 2064 1353 1085 1758 2862 2003 M319 RAY_TARGETS_OF_P210_BCR_ABL_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAY_TARGETS_OF_P210_BCR_ABL_FUSION_DN.html Genes down-regulated in HL-60 cells (acute myeloid leukemia, AML) by expression of p210 BCR-ABL [GeneID=613;25] fusion protein. 15155749 6/21 Arthur Liberzon 0.000128336121999676 0.000231034601494614 1525 2098.27272727273 2065 1.28343534174235e-05 322 1.31192216007651 1.31192216007651 1 1.74377227227062 1521 2408 4539 3337 3178 876 322 640 2832 2065 1363 2004 M2620 ZWANG_EGF_INTERVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_EGF_INTERVAL_DN.html Genes repressed in the time interval between two pulses of EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 139/310 Yaara Zwang 9.57269549339857e-08 1.16513379433937e-06 3070 2324 2065 8.70245082720742e-09 53 1.47367658089757 1.4977865632294 1 3.19625536231362 3066 1090 1822 1205 53 4303 3112 3467 2065 1671 3710 2005 M657 REACTOME_GASTRIN_CREB_SIGNALLING_PATHWAY_VIA_PKC_AND_MAPK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GASTRIN_CREB_SIGNALLING_PATHWAY_VIA_PKC_AND_MAPK.html Genes involved in Gastrin-CREB signalling pathway via PKC and MAPK 75/232 Reactome 2.46863549119791e-06 8.52470590401873e-06 1665 2117 2066 2.24421660115957e-07 1100 1.61908540755978 1.86732728048449 1 3.00012097159411 1663 2499 1100 2618 1126 2066 1433 3475 3049 1589 2669 2006 M3958 ZHAN_MULTIPLE_MYELOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_UP.html Genes most significantly up-regulated in multiple myeloma samples, compared to normal bone marrow plasma cells. 11861292 64/151 Kevin Vogelsang 0.000117534318209439 0.000213475122143191 2070 2093.36363636364 2066 1.06855089012416e-05 1226 1.20094689669121 -0.967966366751005 -1 1.61133690273622 1690 1630 2737 1226 2452 1382 2066 2919 2423 2436 2066 2007 M15537 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_UP.html Genes from the turquoise module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphocholine (oxPAPC). 16912112 46/122 Arthur Liberzon 0.000110497711772187 0.000201868334255153 975 2078.54545454545 2067 1.00457510951131e-05 971 1.8101125266316 2.02149783802725 1 2.44473196487229 971 3832 2067 2374 2437 2415 2416 1451 1489 2018 1394 2008 M622 REACTOME_PROLONGED_ERK_ACTIVATION_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROLONGED_ERK_ACTIVATION_EVENTS.html Genes involved in Prolonged ERK activation events 13/26 Reactome 3.18283173891449e-05 6.7715346844185e-05 2705 2150.09090909091 2068 2.89352526109197e-06 193 1.89371200221224 2.0222888575047 1 2.88600893109207 2705 2245 1853 1084 2068 3109 3137 4135 193 1747 1375 2009 M7578 REACTOME_SEMA3A_PLEXIN_REPULSION_SIGNALING_BY_INHIBITING_INTEGRIN_ADHESION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMA3A_PLEXIN_REPULSION_SIGNALING_BY_INHIBITING_INTEGRIN_ADHESION.html Genes involved in SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion 9/34 Reactome 0.0274212957542615 0.0355649576264792 1685 2216.54545454545 2068 0.00277656588575703 379 1.30281385583616 1.39420956736212 1 0.690022609581248 1685 379 4020 1524 3422 1869 1284 3004 2559 2568 2068 2010 M10351 BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN.html Genes down-regulated in T24 (bladder cancer) cells in response to the photodynamic therapy (PDT) stress. 17952126 436/943 Jessica Robertson 8.22078727753586e-07 4.20093884215191e-06 2390 2253.36363636364 2069 7.47344577219701e-08 633 1.38429423232784 1.7240985549951 1 2.72056884446631 2389 799 2002 1526 633 4573 3044 2069 2543 2027 3182 2011 M487 BUCKANOVICH_T_LYMPHOCYTE_HOMING_ON_TUMOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BUCKANOVICH_T_LYMPHOCYTE_HOMING_ON_TUMOR_DN.html Genes down-regulated in microdissected endothelial samples from ovarian cancer tumors with tumor-infiltrating lymphocytes (TIL) vs those without TILs. 18157142 11/39 Jessica Robertson 0.00285565235633407 0.00417261831673884 3290 2410.27272727273 2072 0.000259942346456404 1522 2.10859360741769 -2.52586375761085 -1 1.83406412274424 3289 1844 1577 2208 3055 1946 2072 4462 1778 1522 2760 2012 M273 PID_EPHA2_FWD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHA2_FWD_PATHWAY.html EPHA2 forward signaling 18832364 26/46 Pathway Interaction Database 0.00052225872032515 0.000840709159547802 2060 2163.36363636364 2073 4.748934006486e-05 1272 1.38197421548964 1.515910824792 1 1.55351101008297 2060 1960 2389 1272 2779 2722 1791 2322 1800 2073 2629 2013 M2243 REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING.html Genes involved in Sema4D in semaphorin signaling 17/55 Reactome 0.027781132278167 0.0360017659998591 1880 2181 2074 0.00255802514673934 1026 2.1429660966518 2.50723135212584 1 1.13084828988356 1878 2343 1623 2571 3644 2074 1847 1726 1026 2802 2457 2014 M967 REACTOME_TRAF6_MEDIATED_IRF7_ACTIVATION_IN_TLR7_8_OR_9_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF6_MEDIATED_IRF7_ACTIVATION_IN_TLR7_8_OR_9_SIGNALING.html Genes involved in TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling 16/50 Reactome 4.36280134622939e-06 1.30466414221001e-05 3410 2251.27272727273 2074 3.96619090735252e-07 446 1.22382792718993 -1.71466420355662 -1 2.18504223955562 3408 1883 2681 1926 1374 2553 4137 446 2074 2726 1556 2015 M17173 MCCLUNG_DELTA_FOSB_TARGETS_8WK http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_DELTA_FOSB_TARGETS_8WK.html Genes up-regulated in the nucleus accumbens (a major reward center in brain) 8 weeks after induction of deltaFosB, a FOSB [GeneID=2354] splice variant. 14566342 34/99 John Newman 7.55737669734848e-06 2.00645139964731e-05 2075 2137.54545454545 2074 6.87036605305119e-07 454 2.13060875514579 2.41766030495222 1 3.65844342503435 2074 3669 2024 3201 1592 1860 2181 1579 454 2758 2121 2016 M3003 MEINHOLD_OVARIAN_CANCER_LOW_GRADE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MEINHOLD_OVARIAN_CANCER_LOW_GRADE_UP.html Genes up-regulated in low grade (LMP and G1) serous ovarian carcinomas vs the higher grade invasive tumors (G2 and G3). 15558012 11/31 Arthur Liberzon 0.000634298626158231 0.00100962070726137 2150 2017.18181818182 2077 5.76801435855558e-05 805 1.94415516841205 1.64705490187565 1 2.12896755716202 2150 2023 2077 2689 2816 1304 805 2220 1426 2830 1849 2017 M18030 ST_TUMOR_NECROSIS_FACTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_TUMOR_NECROSIS_FACTOR_PATHWAY.html Tumor Necrosis Factor Pathway. 21/37 Signaling Transduction KE 0.00089262231111024 0.00139288316678741 1535 2233 2078 8.11804261124218e-05 1327 1.33437279005526 -1.41216062263316 -1 1.39305288172887 1534 2078 2769 2657 2868 1409 1327 1496 2925 3629 1871 2018 M14385 WANG_CISPLATIN_RESPONSE_AND_XPC_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_CISPLATIN_RESPONSE_AND_XPC_DN.html Genes down-regulated in fibroblasts with defective XPC [GeneID=7508] in response to cisplatin [PubChem=2767]. 15107491 172/382 John Newman 3.31250022064541e-05 7.00784471058437e-05 1135 1955.27272727273 2078 3.01140917946697e-06 1132 1.48047037548308 1.68744665040725 1 2.2481687403842 1135 2832 2293 2233 2078 1489 1756 1132 2517 2787 1256 2019 M14136 FOURNIER_ACINAR_DEVELOPMENT_EARLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/FOURNIER_ACINAR_DEVELOPMENT_EARLY_DN.html Genes down-regulated early in HMEC cells (mammary epithelium) during acinar development in vitro. 16849555 5/12 Arthur Liberzon 0.0603947908572993 0.0757521386395354 1670 2342.72727272727 2080 0.00621018481501129 792 0.948147073574608 0.948147073574608 1 0.388371679237885 1667 792 4110 1884 3526 2186 1478 2080 3733 1867 2447 2020 M193 PID_NEPHRIN_NEPH1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NEPHRIN_NEPH1_PATHWAY.html Nephrin/Neph1 signaling in the kidney podocyte 18832364 21/46 Pathway Interaction Database 2.52752342422397e-06 8.61379982975528e-06 2865 1928.81818181818 2081 2.29775120730482e-07 662 1.40720254139115 -1.37091739040529 -1 2.60518524401973 2865 1693 1852 662 1145 2107 3379 2213 718 2081 2502 2021 M3185 HELLER_SILENCED_BY_METHYLATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_SILENCED_BY_METHYLATION_DN.html Genes down-regulated in at least one of three multiple myeloma (MM) cell lines treated with the DNA hypomethylating agent decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 18172295 76/163 Jessica Robertson 5.84876909101582e-06 1.63723607888292e-05 2085 2199 2081 5.31707694564545e-07 959 1.72659219894737 1.55424473556551 1 3.02044977575825 2081 3016 1310 2711 1493 1738 2051 3774 2607 959 2449 2022 M2658 BOYLAN_MULTIPLE_MYELOMA_D_CLUSTER_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_D_CLUSTER_UP.html Genes from cluster 3: up-regulated in group D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 15/39 Jessica Robertson 4.02303239576924e-05 8.28656255234052e-05 1170 1859 2081 3.65736905898038e-06 635 1.14153310397038 1.15737855243593 1 1.70310304065261 1166 2081 3079 2875 2138 680 635 1222 2557 3266 750 2023 M526 REACTOME_TETRAHYDROBIOPTERIN_BH4_SYNTHESIS_RECYCLING_SALVAGE_AND_REGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TETRAHYDROBIOPTERIN_BH4_SYNTHESIS_RECYCLING_SALVAGE_AND_REGULATION.html Genes involved in Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation 9/21 Reactome 2.57395570165831e-07 2.19144534472488e-06 1970 2225.09090909091 2084 2.57395599979451e-08 243 1.47921224350217 1.78617954078323 1 3.05992025304975 1968 2931 3920 2177 243 1586 1424 2084 3275 3399 1469 2024 M11205 IVANOVA_HEMATOPOIESIS_MATURE_CELL http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_MATURE_CELL.html Genes in the expression cluster 'MBC Shared': up-regulated in mature blood cell populations from adult bone marrow and fetal liver. 12228721 200/466 John Newman 1.82394026369202e-06 6.95442154244167e-06 3415 2518.18181818182 2085 1.65812888714231e-07 806 1.49674497826676 1.69645998721286 1 2.82180124388504 3413 806 1189 1960 977 4674 2964 4113 2085 1208 4311 2025 M12636 RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP.html Genes up-regulated in peripheral blood monocytes by CSF2RB (GM-CSF) and IL4 [GeneID=1437;3565]. 16527888 227/507 Arthur Liberzon 9.24340771859265e-05 0.000172005307788235 1130 1981.90909090909 2085 8.40345100703609e-06 1009 1.51236571204894 1.74904202594611 1 2.08103098407789 1129 3174 2085 2751 2390 1697 1828 1159 2400 2179 1009 2026 M12664 SESTO_RESPONSE_TO_UV_C3 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C3.html Cluster 3: genes changed in primary keratinocytes by UVB irradiation. 11867738 22/52 John Newman 0.017815627877618 0.0235963912477439 725 2251.81818181818 2086 0.0016328687439885 722 0.909389169905052 -0.909389169905052 -1 0.540876104377774 722 2202 3122 2023 3341 940 1475 2086 3607 3664 1588 2027 M19437 ALONSO_METASTASIS_NEURAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ALONSO_METASTASIS_NEURAL_UP.html Neural-related genes up-regulated in melanoma tumors that developed metastases compared to primary melanoma that did not. 17409456 12/34 Jessica Robertson 3.36052834820329e-05 7.0934395674237e-05 1520 2011.18181818182 2086 3.05507243800419e-06 872 1.65050837775951 1.73256175105164 1 2.50319913297653 1516 3028 1882 3138 2086 2140 2402 872 1069 2249 1741 2028 M3618 BIOCARTA_TNFR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TNFR1_PATHWAY.html TNFR1 Signaling Pathway 18/35 BioCarta 8.87503926855824e-05 0.000166220759442302 2270 1806.72727272727 2087 8.06854301592416e-06 904 1.54805446035392 -1.50277209568661 -1 2.13854575388265 2269 2163 2302 2087 2375 1317 1019 2358 904 1773 1307 2029 M870 LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_DN.html Genes down-regulated in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of congenic B.D. chr3 (BD, large HSC size) vs parental B6 strain (tiny HSC size). 17220891 38/65 Leona Saunders 4.99325657085403e-05 0.000100121524565777 2090 2063.27272727273 2087 4.53942718591462e-06 472 1.6021873074102 -1.61317450987812 -1 2.34226083795862 2087 3797 2364 3907 2817 782 1507 472 1859 2594 510 2030 M2286 REACTOME_PEROXISOMAL_LIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PEROXISOMAL_LIPID_METABOLISM.html Genes involved in Peroxisomal lipid metabolism 11/24 Reactome 3.2514216045632e-05 6.89107265444738e-05 970 1834.27272727273 2088 2.95588150812024e-06 193 0.914834727804431 -0.914834727804431 -1 1.39166286081863 967 2088 3288 3243 2263 324 193 400 3411 3557 443 2031 M2083 WANG_METASTASIS_OF_BREAST_CANCER_ESR1_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_METASTASIS_OF_BREAST_CANCER_ESR1_DN.html Genes whose expression in primary ER(+) [GeneID=2099] breast cancer tumors negatively correlates with developing distant metastases. 15721472 21/46 Arthur Liberzon 5.32560028323989e-06 1.52448154717545e-05 3000 2172 2088 4.84146652282738e-07 494 1.16306466446556 -1.08392383285669 -1 2.04780567880701 3000 494 2267 1961 1458 1673 3338 3310 2567 2088 1736 2032 M19965 NGO_MALIGNANT_GLIOMA_1P_LOH http://www.broadinstitute.org/gsea/msigdb/cards/NGO_MALIGNANT_GLIOMA_1P_LOH.html Proteins with reduced expression in mulignant glioma cell line (A172) which bears loss of heterozygosity (LOH) in the 1p region. 17440165 22/43 Jessica Robertson 0.000456367728096862 0.000743064341161186 795 2178.72727272727 2089 4.14965840422217e-05 792 2.456818823694 3.10183115808784 1 2.80992208249517 792 4330 2120 2190 3999 1430 1212 846 2089 3248 1710 2033 M12228 BOYAULT_LIVER_CANCER_SUBCLASS_G12_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G12_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G12, defined by unsupervised clustering 17187432 9/33 Yujin Hoshida 4.09937951894955e-06 1.24495738339583e-05 2560 2208.09090909091 2090 4.09938708117977e-07 777 1.03199260643624 1.20944185748109 1 1.8502106193112 2557 2090 4563 1401 1385 2779 2229 777 1561 3422 1525 2034 M1981 ONO_FOXP3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONO_FOXP3_TARGETS_UP.html Genes up-regulated in CD4+ [GeneID=920] T lymphocytes transduced with FOXP3 [GeneID=50943]. 17377532 11/32 Jessica Robertson 0.0254230581555309 0.0330831575997828 2840 2506.27272727273 2091 0.00233833527465123 1524 1.83936719975814 -2.1160209617168 -1 0.995324567841335 2836 3683 2091 3302 3922 1985 2724 1707 1751 1524 2044 2035 M18724 XU_AKT1_TARGETS_6HR http://www.broadinstitute.org/gsea/msigdb/cards/XU_AKT1_TARGETS_6HR.html Genes up-regulated in DU-145 cells (prostate cancer) expressing a dominant negative form of AKT1 [GeneID=207] upon sham-treatment for 6 h (as a control for the HGF [GeneID=3082] experiments). 17099727 22/54 Arthur Liberzon 3.08131678703629e-07 2.37875625437431e-06 1830 2190.36363636364 2092 2.80119747145923e-08 276 1.28250576450662 1.23840420254103 1 2.63631235003555 1828 2076 2092 2098 276 2753 2190 4313 2798 1715 1955 2036 M6897 NATSUME_RESPONSE_TO_INTERFERON_BETA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NATSUME_RESPONSE_TO_INTERFERON_BETA_UP.html Genes up-regulated in T98 cells (glioma) 48 h after treatment with interferon beta. 16140920 75/170 John Newman 0.001044428496821 0.00161684570072785 820 1961.27272727273 2093 9.49931508036424e-05 818 1.66417439193061 1.74222868075219 1 1.69796795515078 818 3828 2093 2158 3106 1153 1040 996 2343 2690 1349 2037 M2092 KAMIKUBO_MYELOID_CEBPA_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/KAMIKUBO_MYELOID_CEBPA_NETWORK.html Network of differentially expressed myeloid genes centered around CEBPA [GeneID=1050]. 20478528 14/48 Arthur Liberzon 3.45062466593868e-05 7.26072168144978e-05 1840 1949.90909090909 2093 3.13698071726677e-06 1133 2.18435626335565 -2.3374208147267 -1 3.3047626192856 1837 2347 1133 1782 2093 2160 2639 2173 1754 1385 2146 2038 M1965 MIKKELSEN_MEF_LCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_LCP_WITH_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MEF cells (embryonic fibroblasts). 18509334 27/127 Jessica Robertson 7.22741406502416e-07 3.87109955014435e-06 3285 2076.63636363636 2094 6.57037858124253e-08 474 2.62729313333519 -2.63981177707856 -1 5.19755223453691 3284 2397 474 1233 585 3148 4473 2094 1302 716 3137 2039 M2500 PHONG_TNF_RESPONSE_VIA_P38_COMPLETE http://www.broadinstitute.org/gsea/msigdb/cards/PHONG_TNF_RESPONSE_VIA_P38_COMPLETE.html Genes whose expression changes in Calu-6 cells (lung cancer) by TNF [GeneID=7124] were blocked completely by p38 inhibitor LY479754. 20516219 177/382 Arthur Liberzon 3.47578304965963e-06 1.09606456061272e-05 1585 1862.45454545455 2094 3.15980776460567e-07 1284 1.51142757231469 1.7406579001602 1 2.74032842146881 1583 2183 2094 2102 1284 2327 2363 1477 2127 1389 1558 2040 M185 PID_ALK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALK1_PATHWAY.html ALK1 signaling events 18832364 11/33 Pathway Interaction Database 0.00279825798623065 0.00409513957635128 1950 2222.27272727273 2098 0.000254711230962846 1300 1.11934208973405 1.17444007830574 1 0.97693919795723 1948 2350 2616 2477 3050 2081 1560 2068 2897 2098 1300 2041 M7705 AKL_HTLV1_INFECTION_UP http://www.broadinstitute.org/gsea/msigdb/cards/AKL_HTLV1_INFECTION_UP.html Genes up-regulated in WE17/10 cells (CD4+ [GeneID=920] T lymphocytes) infected by HTLV1 (and thus displaying low CD7 [GeneID=924]) compared to the uninfected (i.e., CD7+) cells. 17287851 25/47 Arthur Liberzon 8.54339837394537e-07 4.26956588478944e-06 2580 1881.09090909091 2098 7.76672881059892e-08 483 1.50851206758829 -1.89561235443897 -1 2.96081512519182 2580 483 2768 2256 652 1589 1834 1830 2117 2485 2098 2042 M19891 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_12 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_12.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 12. 12554760 61/134 Arthur Liberzon 1.49726131836484e-05 3.53459271428597e-05 3795 2462 2098 1.36115591674827e-06 300 1.34197621437262 1.61735781104782 1 2.18366551936637 3792 300 1838 1002 1831 4311 3279 3613 2098 1437 3581 2043 M2380 IKEDA_MIR30_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR30_TARGETS_DN.html Genes down-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-30 microRNA. 19188439 25/48 Arthur Liberzon 5.83295154940092e-05 0.00011503876666874 2105 1773.72727272727 2102 5.30282382419396e-06 617 2.06714793372612 1.92575308302544 1 2.97641828832268 2102 2634 1185 1031 2254 2622 2145 2245 617 993 1683 2044 M1824 MATZUK_LUTEAL_GENES http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_LUTEAL_GENES.html Luteal genes, based on mouse models with female fertility defects. 18989307 5/34 Jessica Robertson 0.0454781302095836 0.0578162013462042 1720 2355.09090909091 2103 0.00464365710761522 839 2.0939212418656 -2.0939212418656 -1 0.947507929158196 1716 3040 4491 3186 3490 1635 1275 2254 839 1877 2103 2045 M1141 SAENZ_DETOX_PATHWAY_AND_CARCINOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SAENZ_DETOX_PATHWAY_AND_CARCINOGENESIS_DN.html Detoxification pathway genes down-regulated in enterocytes of transgenic mice expressing SV40 T antigen. 17334401 11/56 Arthur Liberzon 8.50434780924048e-06 2.20660984684944e-05 2495 2354.45454545455 2104 7.73125516721162e-07 1244 1.16899137967056 1.30046052141032 1 1.98961537916306 2495 1939 1758 3762 1635 1905 1244 2289 4051 2104 2717 2046 M14829 HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN http://www.broadinstitute.org/gsea/msigdb/cards/HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN.html Genes down-regulated in hematopoietic precursor cells conditionally expressing HOXA9 and MEIS1 [GeneID=3205;4211]. 16507773 66/178 Kevin Vogelsang 7.55652624711931e-07 3.99660067652382e-06 2105 2082.18181818182 2105 6.86957167511326e-08 600 1.8181542563677 1.91275284182965 1 3.58763074310923 2105 2225 779 1624 600 3379 3092 2978 1901 931 3290 2047 M19867 ALCALAY_AML_BY_NPM1_LOCALIZATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/ALCALAY_AML_BY_NPM1_LOCALIZATION_DN.html Genes down-regulated in acute myeloid leukemia (AML) with respect to cellular localization of NPM1 [GeneID=4869]: cytoplasmic vs. nucleolar. 15831697 113/279 Kevin Vogelsang 3.45280868675248e-07 2.54800968600349e-06 1495 1925.63636363636 2105 3.13891748059691e-08 310 1.65607469573922 1.79542761535148 1 3.38614867687219 1491 2105 637 1732 310 2812 2304 3471 2362 1041 2917 2048 M13336 PETRETTO_HEART_MASS_QTL_CIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_HEART_MASS_QTL_CIS_DN.html Down-regulated cis-regulated expression quantitative loci (cis-eQTL) in the heart that colocalize with previously mapped cardiac mass QTLs. 18443592 24/74 Jessica Robertson 4.93827540349715e-05 9.91888492961323e-05 3380 2382.81818181818 2106 4.48944204999884e-06 1292 1.70275987616718 2.09275939836879 1 2.49181915972234 3376 2428 1415 1619 2207 4623 3518 1292 1691 1936 2106 2049 M1352 NIKOLSKY_BREAST_CANCER_15Q26_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_15Q26_AMPLICON.html Genes within amplicon 15q26 identified in a copy number alterations study of 191 breast tumor samples. 19010930 11/44 Jessica Robertson 1.02820210867465e-05 2.5738007912657e-05 2500 1902.27272727273 2106 9.34733558326098e-07 262 2.1615980700032 2.59545484195161 1 3.62620604871061 2498 2702 1504 3087 2435 2452 1874 262 442 2106 1563 2050 M8478 DER_IFN_GAMMA_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_GAMMA_RESPONSE_DN.html Genes down-regulated in HT1080 (fibrosarcoma) cells by treatment with interferon gamma for 6 h. 9861020 4/12 Yujin Hoshida 2.3338504682428e-06 8.17982295750619e-06 4670 2491.72727272727 2107 2.33385291933253e-07 212 0.831821999615109 -0.833563607707029 -1 1.54679675811239 4667 212 4377 1729 1154 3658 3756 2107 275 1637 3837 2051 M10382 IIZUKA_LIVER_CANCER_EARLY_RECURRENCE http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_EARLY_RECURRENCE.html Genes down-regulated in hepatocellular carcinoma (HCC) tumors with higher risk of early intrahepatic recurrence. The single up-regulated gene (GenBank Accession=AC000063) has been excluded from the signature. 12648972 11/27 Yujin Hoshida 0.0179832150392531 0.0238116263560159 2135 2117.27272727273 2108 0.00164835616129392 1250 2.07525113660091 2.43904644835919 1 1.23130281308709 2134 1888 1488 2825 3342 2172 1250 2064 2269 2108 1750 2052 M17454 MASSARWEH_TAMOXIFEN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MASSARWEH_TAMOXIFEN_RESISTANCE_UP.html Genes up-regulated in breast cancer tumors (formed by MCF-7 xenografts) resistant to tamoxifen [PubChem=5376]. 18245484 380/965 Jessica Robertson 5.88239326636265e-07 3.42421053989756e-06 4630 2305.36363636364 2110 5.34763167200586e-08 386 1.52618479669615 -1.50275808488901 -1 3.04895818133922 4628 534 788 1124 510 2960 4667 4151 2110 386 3501 2053 M1307 GROSS_HIF1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HIF1A_TARGETS_DN.html Genes down-regulated in SEND cells (skin endothelium) at normal oxygen (normoxia) conditions after knockdown of HIF1A [GeneID=3091] by RNAi. 17704799 20/46 Jessica Robertson 6.75877349579115e-05 0.000131526630403976 1680 2115.18181818182 2111 6.14452831428956e-06 1274 1.56514625160442 -1.01677163822354 -1 2.22032365608034 1677 1877 2337 2972 2287 2111 1274 1279 3025 2534 1894 2054 M18843 JI_METASTASIS_REPRESSED_BY_STK11 http://www.broadinstitute.org/gsea/msigdb/cards/JI_METASTASIS_REPRESSED_BY_STK11.html Adenocarcinoma metastatic program genes up-regulated in A549 and H2126 cells (lung cancer) lacking functional STK11 [GeneID=6794] but down-regulated by the normal gene. 17676035 20/42 Jessica Robertson 3.65923264709809e-05 7.64815530075898e-05 4335 2495.27272727273 2111 3.3266304655246e-06 949 1.98065372797951 -2.09931285531928 -1 2.98023111127645 4331 1651 1333 1522 2111 3419 4358 2948 949 1199 3627 2055 M233 PID_EPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPO_PATHWAY.html EPO signaling pathway 18832364 24/58 Pathway Interaction Database 0.00011147038310797 0.000203407404690011 1925 2190.54545454545 2113 1.01341846845181e-05 866 1.04395871870279 -1.18603147341422 -1 1.40870846304291 1921 866 2844 1055 2440 1710 3063 1833 2883 3368 2113 2056 M1116 CAIRO_PML_TARGETS_BOUND_BY_MYC_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_PML_TARGETS_BOUND_BY_MYC_UP.html Genes up-regulated in MEF cells (embryonic fibroblasts) after knockout of PML [GeneID=5371] and whose promoters were bound by MYC [GeneID=4609]. 15735755 15/35 Lauren Kazmierski 0.000275739975233835 0.000466468420197023 1700 2156.27272727273 2116 2.50704128674608e-05 228 2.77372693208363 3.35755243491443 1 3.37738648516551 1699 3452 1757 2621 2637 2898 2749 1576 228 1986 2116 2057 M7946 KEGG_NOTCH_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NOTCH_SIGNALING_PATHWAY.html Notch signaling pathway 16/52 KEGG 0.000261847375354884 0.000445216546049704 3175 2390.09090909091 2117 2.38071405477577e-05 232 2.18805367329062 2.41202977519189 1 2.6804468885973 3173 1880 1848 1734 2625 4292 4677 1473 232 2117 2240 2058 M1364 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX6_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX6_UP.html Early prostate development genes (up-regulated at 48 hr dihydrotestosterone [PubChem=10635]) which are also up-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 7/15 Jessica Robertson 0.000341348961543827 0.000568834009172964 1435 2250.72727272727 2117 3.41401406483228e-05 1007 2.39826719588337 2.41440420080086 1 2.84468021343754 1435 1229 4330 1420 2708 2891 3683 2384 1554 1007 2117 2059 M2029 KOYAMA_SEMA3B_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOYAMA_SEMA3B_TARGETS_DN.html Genes down-regulated in NCI-H1299 cells (large cell neuroendocrine carcinoma) stably expressing SEMA3B [GeneID=7869]. 18985860 238/616 Jessica Robertson 1.75350604746363e-07 1.76328955759969e-06 2070 2163 2117 1.5940965338423e-08 133 1.52852861068208 1.69568126434869 1 3.21468373142608 2070 3073 1756 2933 133 3399 2548 2117 2589 2021 1154 2060 M62 PID_EPHB_FWD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHB_FWD_PATHWAY.html EPHB forward signaling 18832364 33/76 Pathway Interaction Database 2.49895641586852e-05 5.49254679397744e-05 1550 2268.18181818182 2119 2.27180436517997e-06 1550 1.43288202452095 1.41608862406636 1 2.23132251252849 1550 3337 2440 1854 1986 2875 2119 2515 2078 1842 2354 2061 M12730 KORKOLA_EMBRYONAL_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_EMBRYONAL_CARCINOMA_UP.html Genes from the 12p region that were up-regulated in embryonic carcinoma tumors compared to normal testis. 16424014 29/69 Arthur Liberzon 0.000617811756948018 0.000985386621190747 2300 2303.72727272727 2119 5.61804837513721e-05 1596 1.58213914099246 2.1663501576875 1 1.73864023399997 2297 1596 2119 1966 2808 2925 3081 1748 1979 2781 2041 2062 M2398 SERVITJA_LIVER_HNF1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SERVITJA_LIVER_HNF1A_TARGETS_DN.html Genes down-regulated in liver tissue upon knockout of HNF1A [GeneID=6927]. 19289501 80/290 Arthur Liberzon 7.54849033138853e-07 3.99660067652382e-06 4185 2546.54545454545 2120 6.86226629216039e-08 598 1.53149696978806 1.55837701459729 1 3.0219908965546 4184 1479 1027 2120 598 3360 3523 4147 2114 824 4636 2063 M1547 BIOCARTA_HDAC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HDAC_PATHWAY.html Control of skeletal myogenesis by HDAC and calcium/calmodulin-dependent kinase (CaMK) 21/43 BioCarta 0.000269133732870666 0.000456446135444061 2385 1681.90909090909 2121 2.44696965987369e-05 460 1.284614483218 1.47937064795247 1 1.56862055476225 773 2121 2382 2383 2629 592 460 782 2850 2624 905 2064 M9494 BIOCARTA_BCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BCR_PATHWAY.html BCR Signaling Pathway 21/57 BioCarta 0.00113211742201979 0.00174223390462553 1650 2152.54545454545 2122 0.00010297276621654 1340 1.56814989450447 -1.36236686623658 -1 1.58140011272355 1650 2400 2122 1370 2907 1340 2810 2641 2413 2079 1946 2065 M4038 PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_DN.html Genes down-regulated in CD38+ [GeneID=952] CLL (chronic lymphocytic leukemia) cells. 17287849 8/31 Arthur Liberzon 8.56776395095403e-08 1.08243085183469e-06 2125 1855.27272727273 2122 8.56776428128365e-09 51 2.15611397668918 1.84849303866345 1 4.7015935680051 2122 519 4133 854 51 2418 2159 4447 177 1133 2395 2066 M3447 AMIT_SERUM_RESPONSE_60_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_60_MCF10A.html Genes whose expression peaked at 60 min after stimulation of MCF10A cells with serum. 17322878 33/82 Leona Saunders 1.88424313315085e-05 4.29662448756442e-05 1655 2249.27272727273 2123 1.71296297399977e-06 1653 1.47092253849811 1.90326573215502 1 2.34789988666268 1653 2543 2123 1789 1905 2886 2779 2971 1989 2227 1877 2067 M1007 FERRANDO_TAL1_NEIGHBORS http://www.broadinstitute.org/gsea/msigdb/cards/FERRANDO_TAL1_NEIGHBORS.html Nearest neighbors of TAL1 [GeneID=6886], based on the close agreement of their expression profiles with that of TAL1 in pediatric T cell acute lymphoblastic leukemia (T-ALL) 12086890 11/40 Jean Junior 3.79911002803574e-05 7.89473596069866e-05 3505 2319.81818181818 2123 3.45379603204057e-06 544 2.09051972951747 -2.15969276616247 -1 3.13501267592022 3501 772 894 1373 2123 4557 4246 3485 690 544 3333 2068 M1264 WANG_RESPONSE_TO_BEXAROTENE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_BEXAROTENE_DN.html Genes down-regulated in the mouse lung cancer model and which reverted to normal levels upon treatment with bexarotene [PubChem=82146]. 16247446 22/51 Leona Saunders 3.16710543277963e-05 6.75514613473162e-05 2640 1972.36363636364 2124 2.87922820648969e-06 715 1.67595281012502 1.78403821287244 1 2.55478954144849 2640 1204 1442 1111 2064 2761 2996 2451 715 2188 2124 2069 M4932 GAJATE_RESPONSE_TO_TRABECTEDIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAJATE_RESPONSE_TO_TRABECTEDIN_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) by trabectedin [PubChem=3199]. 12198119 61/142 John Newman 0.000252752483287126 0.000430846903122398 2265 1926.72727272727 2124 2.29801387325044e-05 752 1.97262263110955 -1.99415454484327 -1 2.42680957433722 2264 2299 752 1367 2616 1484 2124 3406 1686 1049 2147 2070 M3283 BOWIE_RESPONSE_TO_TAMOXIFEN http://www.broadinstitute.org/gsea/msigdb/cards/BOWIE_RESPONSE_TO_TAMOXIFEN.html Genes up-regulated by tamoxifen [PubChem=5376] in HMEC-E6 cells (mammary epithelial cells damaged by expression of HPV-16 E6 [GeneID=1489078]). 17016442 15/52 Arthur Liberzon 2.9135213515771e-07 2.31211682689763e-06 1245 1867 2125 2.64865612492994e-08 255 1.1648517233976 1.1499186399393 1 2.39971755241137 1245 2125 2511 2616 255 1539 917 2239 2946 2609 1535 2071 M1509 BRACHAT_RESPONSE_TO_CISPLATIN http://www.broadinstitute.org/gsea/msigdb/cards/BRACHAT_RESPONSE_TO_CISPLATIN.html Genes up-regulated in FL5.12 cells (pro-B lymphocyte) in response to cisplatin [PubChem=2767]. 12447701 16/27 John Newman 0.0145509990687976 0.0195375305548382 1400 2313.63636363636 2128 0.0013316492185341 802 1.36363343345672 -1.36363343345672 -1 0.851906773870239 1398 3898 2136 3983 3378 829 802 1568 3803 2128 1527 2072 M9639 HAN_SATB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAN_SATB1_TARGETS_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer) after knockdown of SATB1 [GeneID=6304] by RNAi. 18337816 272/684 Jessica Robertson 1.82842345299081e-07 1.79622480098846e-06 4170 2245.54545454545 2129 1.66220327722854e-08 146 1.71314055175886 -1.5338526857985 -1 3.59791256445307 4167 915 497 548 146 3063 4365 3634 2129 568 4669 2073 M3649 BROWNE_HCMV_INFECTION_2HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_2HR_UP.html Genes up-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 2 h time point that were not up-regulated at the previous time point, 1 h. 11711622 18/49 Arthur Liberzon 5.80365664819714e-06 1.62849910499712e-05 3600 2489.18181818182 2130 5.27606541677215e-07 962 1.42105342248028 1.46490731039288 1 2.48715624659113 3597 1498 1475 962 1489 4432 4006 2130 2371 1352 4069 2074 M2365 PURBEY_TARGETS_OF_CTBP1_AND_SATB1_DN http://www.broadinstitute.org/gsea/msigdb/cards/PURBEY_TARGETS_OF_CTBP1_AND_SATB1_DN.html Genes down-regulated in HEK-293 cells (fibroblast) upon knockdown of both CTBP1 and SATB1 [GeneID=1487, 6304] by RNAi. 19103759 92/356 Arthur Liberzon 7.75220330383368e-06 2.04658167221209e-05 2130 2317 2130 7.04748238239116e-07 634 1.34673736138285 -1.38974373593097 -1 2.30823327871285 2130 3761 2912 4578 1603 634 2101 678 2910 3177 1003 2075 M18342 ST_G_ALPHA_I_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_G_ALPHA_I_PATHWAY.html G alpha i Pathway 26/60 Signaling Transduction KE 1.24304292250523e-05 3.01495814433722e-05 1395 2198.36363636364 2131 1.13004540545074e-06 1299 1.24264499055558 1.43787567572405 1 2.0534011879116 1392 3280 2713 2393 1764 2131 1315 1299 2357 3501 2037 2076 M14024 GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP.html Genes up-regulated in erythroid progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 16/39 Arthur Liberzon 3.93321759345282e-05 8.13733229267988e-05 3510 2281.81818181818 2131 3.57571628573339e-06 763 1.08350702667091 1.41278982032623 1 1.6196571811981 3507 763 2498 1739 2131 3054 4614 1231 1384 2727 1452 2077 M2602 BIOCARTA_RANKL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RANKL_PATHWAY.html Bone Remodelling 8/19 BioCarta 0.000497545579545479 0.00080341095304966 1880 2026.72727272727 2132 4.97657012882761e-05 651 0.7377010799032 -0.7377010799032 -1 0.834582083918784 1879 2132 3819 2224 2785 651 1036 1337 2323 3292 816 2078 M11106 BIOCARTA_GSK3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GSK3_PATHWAY.html Inactivation of Gsk3 by AKT causes accumulation of b-catenin in Alveolar Macrophages 23/55 BioCarta 1.59899520664509e-05 3.72966228886953e-05 2135 2294.54545454545 2132 1.45364257137854e-06 1443 1.14326687316941 1.37701493730396 1 1.85057587066979 2132 1781 2754 1443 1860 2924 1682 2835 3078 2788 1963 2079 M2000 MIKKELSEN_ES_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 K27 trimethylation mark (H327me3) in embryonic stem cells (ES). 17603471 14/81 Arthur Liberzon 8.8031381352064e-05 0.0001652042663259 960 2160.27272727273 2132 8.00317309639667e-06 486 1.76824832107809 1.76824832107809 1 2.44445241819379 958 3937 2132 4462 2369 684 486 1759 3564 2512 900 2080 M8779 LI_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LI_LUNG_CANCER.html Proteins showing significant overexpression in lung cancer cell lines relative to normal bronchial epithelial cell lines. 16369491 37/87 Arthur Liberzon 1.59487348785375e-06 6.40409354248728e-06 3215 2466.27272727273 2133 1.44988604004226e-07 912 2.01593992573588 1.88698575437248 1 3.8270180672857 3211 1438 1737 1147 912 4437 3730 3351 1116 2133 3917 2081 M9371 MILICIC_FAMILIAL_ADENOMATOUS_POLYPOSIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MILICIC_FAMILIAL_ADENOMATOUS_POLYPOSIS_UP.html Top genes up-regulated in colon epithelium biopsies from FAP (familial adenomatous polyposis) patients with mutated APC [GeneID=324]. 18829530 6/58 Jessica Robertson 4.47165966136622e-07 2.90229850530109e-06 2145 1985.45454545455 2135 4.47166056117477e-08 12 3.4897718026624 3.4897718026624 1 7.06335497881551 2142 2135 4431 2041 2987 2440 2219 65 12 2062 1306 2082 M7700 KUROKAWA_LIVER_CANCER_EARLY_RECURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KUROKAWA_LIVER_CANCER_EARLY_RECURRENCE_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) with early recurrence. 15288478 13/24 Yujin Hoshida 1.6489260646466e-05 3.82139838720769e-05 1840 2352.63636363636 2135 1.49903493061136e-06 316 5.05471798239466 5.05471798239466 1 8.16244067149114 1840 3782 1880 2804 3624 2135 2287 316 1729 3687 1795 2083 M2388 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_TRANS.html Transcripts in hematopoietic stem cells (HSC) which are trans-regulated (i.e., modulated by a QTL (quantitative trait locus) not in a close proximity to the gene). 15711547 575/1453 Jean Junior 3.14194128624381e-07 2.41362899464566e-06 3575 2248.90909090909 2136 3.14194173047468e-08 311 1.67003949555195 1.98025541027477 1 3.42906636798143 3575 395 4378 413 311 3491 3350 2136 1986 823 3880 2084 M8526 CHEN_LUNG_CANCER_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_LUNG_CANCER_SURVIVAL.html Protein profiles associated with survival in lung adenocarcinoma. 14573703 22/62 Kate Stafford 5.82516705144059e-06 1.63257971310111e-05 3430 2203.63636363636 2137 5.29562043217614e-07 288 2.42944547723878 -1.82330673680491 -1 4.25109910740225 3429 2203 1314 796 1491 3731 3103 2137 288 1717 4031 2085 M19667 CHENG_RESPONSE_TO_NICKEL_ACETATE http://www.broadinstitute.org/gsea/msigdb/cards/CHENG_RESPONSE_TO_NICKEL_ACETATE.html Genes down-regulated in HPL1D cells (lung epithelium) upon exposure to nickel acetate [PubChem=9756]. 12915101 33/71 John Newman 3.98893605225733e-07 2.76826476128525e-06 2140 1980.36363636364 2137 3.62630615955686e-08 357 1.33685281344657 -1.39973673051761 -1 2.71584614636529 2137 955 2177 3182 357 1468 3029 2157 2903 1846 1573 2086 M15638 RIZ_ERYTHROID_DIFFERENTIATION_APOBEC2 http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_APOBEC2.html Selected genes whose expression profile follows that of APOBEC2 [GeneID=10930] in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). 17213805 11/48 Leona Saunders 5.52348466472489e-05 0.000109534698006351 3795 2140.18181818182 2138 5.02147576939971e-06 595 1.95642808596408 -2.06198036650298 -1 2.83222326443581 3791 1313 1113 1582 2237 4224 2445 2138 595 1516 2588 2087 M1379 HE_PTEN_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HE_PTEN_TARGETS_DN.html Genes down-regulated in the intestine after the tissue specific knockout of PTEN [GeneID=5728] by Cre-lox. 17237784 4/8 Jessica Robertson 9.54338200945425e-07 4.60984738132019e-06 920 2088.72727272727 2138 9.54338610788303e-08 16 0.818335095595333 0.818335095595333 1 1.59621636497584 920 2138 4334 3351 3432 330 16 1425 4144 2678 208 2088 M1445 GUO_HEX_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GUO_HEX_TARGETS_DN.html Genes down-regulated in day 6 embryoid bodies derived from embryonic stem cells (ES) with HEX [GeneID=3087] knockout. 12791650 48/106 Kevin Vogelsang 4.42656209546529e-08 6.37275056111917e-07 3905 2522.36363636364 2138 4.02414744048273e-09 9 1.62747449549184 -1.30794413064844 -1 3.68571657385537 3905 448 941 1780 9 4463 2797 4677 2028 2138 4560 2089 M11521 KEGG_GLYCOLYSIS_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOLYSIS_GLUCONEOGENESIS.html Glycolysis / Gluconeogenesis 32/81 KEGG 1.8518513537285e-06 6.99820600288043e-06 2095 2060.27272727273 2139 1.68350264775213e-07 989 1.59790110063121 -1.52319108806167 -1 3.01091804486782 2091 2425 2225 2614 989 1671 1762 2229 2511 2139 2007 2090 M1420 MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_DN.html Down-regulated genes discriminating multiple myeloma samples by the ype of immunoglobulin light chain they produce: Ig lambda (IGLL) vs Ig kappa (IGLK). 12623842 17/32 Kate Stafford 0.000169667314151968 0.000298895125607565 2370 2106.72727272727 2139 1.54254909603446e-05 1266 1.62242504232715 2.05702978626751 1 2.09015785060733 2369 2665 1982 2746 2530 2443 1783 1315 1936 1266 2139 2091 M1458 ABBUD_LIF_SIGNALING_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/ABBUD_LIF_SIGNALING_1_UP.html Genes up-regulated in AtT20 cells (pituitary cancer) after treatment with LIF [GeneID=3976]. 14576184 32/73 Kevin Vogelsang 3.38592348023675e-06 1.07423408452196e-05 3085 1993.18181818182 2139 3.07811699215842e-07 334 1.65138487928152 -1.48196535874676 -1 2.99935522777436 3084 334 1053 1728 1273 2139 2918 3186 2232 1420 2558 2092 M10949 AMUNDSON_GENOTOXIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_GENOTOXIC_SIGNATURE.html Genes discriminating genotoxic (DNA damaging) agents from other kinds of stresses. 15824734 55/151 Arthur Liberzon 4.71034294478858e-07 2.99087629258527e-06 3810 2095.27272727273 2140 4.28213086663991e-08 427 1.75474062352362 -1.48859447407319 -1 3.54324918749674 3809 2766 1326 2074 427 1350 2140 2854 2366 1387 2549 2093 M10196 WILLIAMS_ESR1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WILLIAMS_ESR1_TARGETS_DN.html The 'ER-alpha profile': genes down-regulated in T47D cells (breast cancer, ESR2 [GeneID=2100] Tet-Off) upon activation of ESR1 [GeneID=2099] by estradiol (E2) [PubChem=5757]. 17700529 3/10 Jessica Robertson 3.68283907202953e-05 7.68720886036987e-05 2140 2715 2140 3.68290010831951e-06 527 1.63981553367187 -1.76355639142255 -1 2.4660561010669 2593 527 4306 1823 2140 4685 4235 4314 1708 1397 2137 2094 M7995 HOSHIDA_LIVER_CANCER_SUBCLASS_S2 http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_SUBCLASS_S2.html Genes from 'subtype S2' signature of hepatocellular carcinoma (HCC): proliferation, MYC and AKT1 [GeneID=4609;207] activation. 19723656 93/210 Jessica Robertson 8.92540812889293e-05 0.000166897296456474 1235 2109.90909090909 2142 8.1143365941806e-06 560 1.89526394222692 2.06809452133148 1 2.61697306169843 1232 3919 2194 2762 2872 2142 2012 560 1926 2445 1145 2095 M19971 RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP.html Genes up-regulated in peripheral blood mononucleocytes by HGF [GeneID=3082] compared to those regulated by CSF2RB (GM-CSF) and IL4 [GeneID=1437;3565]. 16527888 273/678 Arthur Liberzon 5.42844670197283e-05 0.000107786869684088 1705 2188.18181818182 2143 4.93507332018852e-06 1301 1.44363104214842 1.5734214062117 1 2.09355892262619 1704 1993 1301 1937 2231 3022 2433 2143 3011 2201 2094 2096 M8492 KEGG_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_APOPTOSIS.html Apoptosis 59/107 KEGG 1.75004559566517e-06 6.76068727228936e-06 2625 1974.09090909091 2144 1.59095180707702e-07 957 1.55142726329357 1.80836931951353 1 2.93185158167272 2625 1177 1682 970 957 3378 3114 2399 1008 2144 2261 2097 M2539 KUMAR_AUTOPHAGY_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/KUMAR_AUTOPHAGY_NETWORK.html Genes defining the Mycobacterium tuberculosis strain-independent regulatory axis of the host macrophage cells. 20211141 41/126 Arthur Liberzon 0.00919531905943036 0.012639854829126 1685 2255.54545454545 2144 0.000839452641688191 950 1.40125761252109 1.23763304868822 1 0.972282466304981 1683 3147 2131 2796 3334 2237 950 1467 2896 2026 2144 2098 M15822 OZANNE_AP1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OZANNE_AP1_TARGETS_UP.html Cancer motility and invasion genes up-regulated by the AP-1 transcription factor. 16799638 17/40 Arthur Liberzon 4.08782021637399e-05 8.39418296841741e-05 2145 2461.90909090909 2145 3.71626924921944e-06 872 1.66660173283132 -1.34783231706388 -1 2.48306193794654 3999 1301 872 1826 2145 3477 3024 2752 2143 1262 4280 2099 M1609 LEE_CALORIE_RESTRICTION_NEOCORTEX_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_CALORIE_RESTRICTION_NEOCORTEX_DN.html Down-regulated in the neocortex of aged (30-month) mice subjected to caloric restriction since young adulthood. 10888876 74/204 John Newman 1.76727297630018e-06 6.80479964415993e-06 2980 2551 2145 1.60661308723871e-07 962 1.69875464945131 1.90850350607481 1 3.208513646568 2977 2145 1473 2112 962 4213 4465 2944 1736 1563 3471 2100 M1837 LABBE_WNT3A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_WNT3A_TARGETS_DN.html Down-regulated genes in NMuMG cells (mammary epithelium) after stimulation with WNT3A [GeneID=89780]. 17210685 61/248 Jessica Robertson 4.37092932210014e-06 1.30626114817355e-05 3135 2273.63636363636 2145 3.97358000565975e-07 1150 1.50851219658763 -1.76012711624456 -1 2.69302920327033 3134 2855 2145 3419 1375 1564 2928 1150 2374 1955 2111 2101 M984 BIOCARTA_TOLL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TOLL_PATHWAY.html Toll-Like Receptor Pathway 37/78 BioCarta 3.05191549090038e-05 6.53324622675157e-05 2150 2220.18181818182 2146 2.77450711721961e-06 1021 1.08042968330343 -1.15712989156307 -1 1.65271447199514 2146 2540 3277 2108 2055 1098 2985 1021 2710 3335 1147 2102 M5388 BROWNE_HCMV_INFECTION_18HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_18HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 18 h time point that were not up-regulated at the previous time point, 16 h. 11711622 120/313 John Newman 0.000812679527702814 0.00127535708868566 1900 2319 2146 7.39072624264478e-05 1675 1.58978699704551 1.67029848770643 1 1.68194569128763 1900 3333 2240 1675 2853 2871 2753 2056 2146 1734 1948 2103 M1093 REACTOME_SYNTHESIS_OF_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI.html Genes involved in Synthesis of glycosylphosphatidylinositol (GPI) 10/18 Reactome 6.21328118444736e-07 3.52487114168527e-06 3580 2240.45454545455 2147 5.6484390356496e-08 48 1.30843712955313 -0.616207050567385 -1 2.6079316138129 3576 1509 2772 1460 531 2147 2697 1917 48 3486 4502 2104 M1753 ZHENG_FOXP3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_UP.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are up-regulated both in developing (located in the thymus) and mature (from peripheral blood) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 18/39 Jessica Robertson 0.0003129586360506 0.000523758631618968 1240 2234.45454545455 2147 2.84548331375846e-05 739 1.36358562169455 1.5820043463078 1 1.63527398500579 1240 3677 2147 4356 2673 987 930 1117 3773 2940 739 2105 M1137 DARWICHE_PAPILLOMA_RISK_HIGH_DN http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_HIGH_DN.html Genes down-regulated during skin tumor progression from normal skin to high risk papilloma. 17525749 139/333 Arthur Liberzon 4.20311924350306e-07 2.82579867647853e-06 4115 2607.27272727273 2148 3.82101822410262e-08 381 1.49260507627523 -1.13050637935944 -1 3.02738626971839 4114 1627 1581 2148 381 3724 4289 2237 2039 2028 4512 2106 M454 ROSS_AML_WITH_MLL_FUSIONS http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_AML_WITH_MLL_FUSIONS.html Top 100 probe sets for pediatric acute myeloid leukemia (AML) subtypes with chimeric MLL fusions [GeneID=4297]. 15226186 58/138 Kate Stafford 3.32386667164857e-06 1.05956729410512e-05 1575 2114.81818181818 2148 3.02170153956193e-07 1268 1.43987134000024 1.59449243371845 1 2.61833252929731 1573 2148 2335 3141 1268 1853 1484 2539 2556 2765 1601 2107 M1899 BASSO_CD40_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/BASSO_CD40_SIGNALING_DN.html Gene down-regulated by CD40 [GeneID=958] signaling in Ramos cells (EBV negative Burkitt lymphoma). 15331443 33/105 Kevin Vogelsang 0.00315879362542675 0.00458411487418698 1770 2257.63636363636 2148 0.000287576200679476 1230 1.73396461065331 2.03549021615275 1 1.48232099640944 1769 2917 1551 3181 3225 2148 2000 1230 2317 2643 1853 2108 M37 PID_NFKAPPAB_CANONICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFKAPPAB_CANONICAL_PATHWAY.html Canonical NF-kappaB pathway 18832364 17/38 Pathway Interaction Database 0.0247994962071141 0.0323567867354017 1085 2320 2149 0.00228032194400661 1083 1.46238382458804 -1.46238382458804 -1 0.796483863444396 1083 3155 2902 2149 3388 1682 1794 1843 2356 3382 1786 2109 M10839 BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN http://www.broadinstitute.org/gsea/msigdb/cards/BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN.html Down-regulated genes in MDA-MB-435 cells (breast cancer) undergoing G2/M arrest after treatment with 2-methoxyestradiol (2ME2) [PubChem=1573]. 17234781 87/294 Jessica Robertson 1.5197572172707e-05 3.57688715225038e-05 4475 2600.18181818182 2150 1.38160701439624e-06 1010 1.52933016062314 -1.40691825618652 -1 2.48564034149294 4472 1170 1612 1010 1839 2377 4000 4358 2150 1468 4146 2110 M5688 CADWELL_ATG16L1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CADWELL_ATG16L1_TARGETS_UP.html Genes up-regulated in Paneth cell (part of intestiinal epithelium) of mice with hypomorphic (reduced function) form of ATG16L1 [GeneID=55054]. 18849966 49/138 Jessica Robertson 0.000152564150784524 0.000270903982787525 1740 2048.09090909091 2150 1.38704301572756e-05 850 1.97889015881597 -2.13842251943804 -1 2.58027814968295 1739 2150 850 2910 2505 1922 2374 2376 2472 1106 2125 2111 M16894 KEGG_COMPLEMENT_AND_COAGULATION_CASCADES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_COMPLEMENT_AND_COAGULATION_CASCADES.html Complement and coagulation cascades 27/95 KEGG 0.000269652281968948 0.000457160127824345 2630 2149.09090909091 2151 2.45168489737404e-05 1093 1.48170829543582 1.58608416932438 1 1.8089207576329 1506 2074 1093 2686 2630 2151 2629 1504 3484 1725 2158 2112 M1430 BROWN_MYELOID_CELL_DEVELOPMENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWN_MYELOID_CELL_DEVELOPMENT_UP.html Genes defining differentiation potential of the bipotential myeloid cell line FDB. 16769770 102/326 Kevin Vogelsang 3.23259038160338e-07 2.45845509149669e-06 3725 2124.27272727273 2151 2.93871896053377e-08 289 1.50640450291159 -1.74287560734373 -1 3.08867664271012 3725 928 923 1467 289 3314 4478 2151 2586 1016 2490 2113 M17728 BLALOCK_ALZHEIMERS_DISEASE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BLALOCK_ALZHEIMERS_DISEASE_DN.html Genes down-regulated in brain from patients with Alzheimer's disease. 14769913 838/1930 John Newman 0.000103663873487319 0.000190721991033207 990 2457.54545454545 2151 1.03668709594231e-05 988 1.49335763203641 1.74217293766506 1 2.03038887421186 988 3912 4400 1942 2444 2258 1752 1778 2151 3695 1713 2114 M3996 JIANG_HYPOXIA_NORMAL http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_HYPOXIA_NORMAL.html Genes up-regulated in RPTEC cells (normal kidney) by hypoxia. 12692265 235/525 John Newman 1.26390355464573e-06 5.54746019276978e-06 2155 2178.63636363636 2151 1.14900389160086e-07 807 1.63177591643442 1.91481454137489 1 3.13492635375583 2151 3821 1561 2985 807 2739 2189 1714 2136 1526 2336 2115 M5505 HUPER_BREAST_BASAL_VS_LUMINAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUPER_BREAST_BASAL_VS_LUMINAL_DN.html Genes down-regulated in basal mammary epithelial cells compared to the luminal ones. 17409405 46/112 Jessica Robertson 9.45900468479058e-06 2.40765322938233e-05 2710 1938.63636363636 2152 8.59913214043284e-07 623 2.28510802430978 -2.3421829986192 -1 3.85760806042675 2707 2152 623 747 1671 2296 3423 2935 1134 709 2928 2116 M672 CHIN_BREAST_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIN_BREAST_CANCER_COPY_NUMBER_UP.html Genes from common regions of gains observed in more than 15% of 148 primary breast cancer tumors. 17001317 10/37 Arthur Liberzon 0.00297380569313862 0.00433579759740124 1335 2147 2153 0.000270712099882475 1329 1.90755134028769 1.90755134028769 1 1.64758005363763 1331 2672 2153 1527 3062 1959 1396 2175 3310 2703 1329 2117 M118 PID_INTEGRIN_A9B1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN_A9B1_PATHWAY.html Alpha9 beta1 integrin signaling events 18832364 15/34 Pathway Interaction Database 4.23163521154928e-05 8.65914524075106e-05 2960 2260.27272727273 2155 3.84701509818026e-06 1005 1.53699213855773 1.69413822333013 1 2.28237467836261 2956 1136 1005 1389 2155 4073 3495 1747 2467 1476 2964 2118 M18181 HUMMEL_BURKITTS_LYMPHOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUMMEL_BURKITTS_LYMPHOMA_DN.html Down-regulated genes constituting the molecular signature of Burkitt 's lymphoma. 16760442 10/23 Arthur Liberzon 7.92085416047867e-05 0.000150882612178874 1990 1820.90909090909 2156 7.20103577850642e-06 761 1.60819018615364 -1.42250368518733 -1 2.24633592504783 1990 978 2156 2407 2332 761 786 2191 2346 2702 1381 2119 M14591 WEIGEL_OXIDATIVE_STRESS_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/WEIGEL_OXIDATIVE_STRESS_RESPONSE.html Oxidative stress genes down-regulated in ARPE-19 cells (retinal pigmented epithelium) in response to HNE, tBH and H2O2 [PubChem=5283344;6410;784]. 12419474 43/100 John Newman 9.45112921460252e-06 2.40695605976236e-05 1790 2056.72727272727 2156 8.59197256053976e-07 246 2.12017493842736 2.80458038267391 1 3.57927353112495 1786 3018 2370 1761 2156 2661 2721 246 752 3592 1561 2120 M1303 GROSS_HYPOXIA_VIA_ELK3_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_UP.html Genes up-regulated in SEND cells (skin endothelium) at hypoxia with ELK3 [GeneID=2004] knockdown by RNAi. 17704799 177/372 Jessica Robertson 1.52229060003373e-05 3.5800693890395e-05 955 2261.81818181818 2159 1.38391012148158e-06 952 1.41729009296286 1.54025837967383 1 2.30334007520317 952 3139 2056 2859 1840 2185 1525 1787 3248 3130 2159 2121 M17758 KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM.html Alanine, aspartate and glutamate metabolism 16/35 KEGG 2.07358515247376e-06 7.54997670900702e-06 4400 2491.45454545455 2160 1.88507918810055e-07 877 1.49560508798558 -1.12852085098343 -1 2.80014402611596 4400 877 1652 2160 1046 4618 3897 2679 1175 1203 3699 2122 M1125 MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN.html Pubertal genes down-regulated by TGFB1 [GeneID=7040]. 17486082 51/106 Arthur Liberzon 7.98203015462595e-07 4.11774058972012e-06 4320 2560.54545454545 2162 7.25639368242184e-08 622 1.92445197802232 -2.0878293459283 -1 3.78825790517009 3908 1184 715 1706 622 4176 3846 4320 2162 1211 4316 2123 M1203 TERAMOTO_OPN_TARGETS_CLUSTER_7 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_7.html Cluster 7: genes down-regulated early (within 24 h) after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 12/27 Arthur Liberzon 0.0426111639073599 0.0543188014335932 2165 2418.90909090909 2162 0.00395087130296098 1269 1.32009407595198 1.22562396986282 1 0.61042422593884 2162 2720 1828 3757 3841 2071 1269 1845 2954 2245 1916 2124 M18311 REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS.html Genes involved in Metabolism of vitamins and cofactors 29/56 Reactome 3.17595623963809e-06 1.02285436006489e-05 2480 2151.45454545455 2165 2.887237113191e-07 750 1.22226925918706 -0.899480859372726 -1 2.229476454879 2477 1727 2952 3007 1245 750 1070 4088 2165 2780 1405 2125 M16646 WEBER_METHYLATED_HCP_IN_FIBROBLAST_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_HCP_IN_FIBROBLAST_DN.html Unmethylated germline-specific genes with high-CpG-density promoters (HCP) in primary fibroblasts. 17334365 15/79 Jessica Robertson 3.24871867994926e-07 2.45845509149669e-06 2445 1906.90909090909 2165 2.95338105425863e-08 52 2.11496000805056 -2.79341228026694 -1 4.33643657171717 2445 3245 1583 2285 2165 2278 3384 52 672 1994 873 2126 M19693 DAZARD_RESPONSE_TO_UV_NHEK_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_RESPONSE_TO_UV_NHEK_UP.html Genes up-regulated in NHEK cells (normal keratinocytes) by UV-B irradiation. 12771951 192/538 John Newman 2.89997549680958e-06 9.57666326853395e-06 4525 2519 2166 2.63634483589028e-07 938 1.51835427646636 -1.29236876620881 -1 2.78542216001923 4525 1625 1361 938 1206 2478 3998 3557 2166 1783 4072 2127 M615 KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION.html Intestinal immune network for IgA production 18/53 KEGG 4.67625943170795e-05 9.43303990399633e-05 3690 2393.36363636364 2167 4.25123530177179e-06 1050 2.03656909899587 -1.53480613999856 -1 2.99655233938109 3687 1050 1216 1198 2191 4464 4153 2167 1086 1347 3768 2128 M552 REACTOME_PROLACTIN_RECEPTOR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROLACTIN_RECEPTOR_SIGNALING.html Genes involved in Prolactin receptor signaling 8/41 Reactome 0.0015098358576593 0.00226983985530687 2170 2374.27272727273 2167 0.000151086266159808 1004 1.97032227765007 -1.97032227765007 -1 1.90422715633977 2167 3658 3928 3523 2989 1215 1890 1164 1004 3298 1281 2129 M19259 IYENGAR_RESPONSE_TO_ADIPOCYTE_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/IYENGAR_RESPONSE_TO_ADIPOCYTE_FACTORS.html Genes up-regulated in MCF-7 cells (breast cancer) in response to growth medium from L3T3-L1 cells (differentiated to pre-adipocytes). 14508521 9/17 John Newman 3.96896092613046e-05 8.19680515638931e-05 3695 2036.90909090909 2168 3.96903181484113e-06 89 2.20152634417821 -0.983161388768916 -1 3.28835935398148 3695 518 4395 530 2168 3616 2643 1027 89 2579 1146 2130 M12369 RICKMAN_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_METASTASIS_DN.html Genes down-regulated in metastatic vs non-metastatic HNSCC (head and neck squamous cell carcinoma) samples. 18679425 203/416 Jessica Robertson 1.63552248229894e-06 6.49115128016012e-06 3075 2273.09090909091 2169 1.48683972561746e-07 250 1.54827319746577 1.59622387782432 1 2.9358906788042 3073 250 1449 1351 924 3920 2169 4094 1780 2315 3679 2131 M1320 INGRAM_SHH_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/INGRAM_SHH_TARGETS_UP.html Genes up-regulated in 10T1/2 cells (multipotent mesoderma) by expression of SHH [GeneID=6469]. 17873912 70/288 Jessica Robertson 1.19021133202373e-06 5.33715818360116e-06 2170 1962 2170 1.08201088721335e-07 679 1.74637183116259 1.8648422089805 1 3.3657991797057 2170 704 1028 1075 786 3574 3451 3048 2222 679 2845 2132 M1942 MEISSNER_BRAIN_HCP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_HCP_WITH_H3_UNMETHYLATED.html Genes with high-CpG-density promoters (HCP) that have no histone H3 methylation marks in brain. 18600261 13/152 Jessica Robertson 0.000311940791582389 0.000522615140992161 1780 2153.27272727273 2170 2.8362275531376e-05 1187 1.37571352349315 1.43120279608423 1 1.65029563490767 1778 2170 2354 3901 2671 1187 1198 1564 2998 2361 1504 2133 M2270 STEGER_ADIPOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/STEGER_ADIPOGENESIS_UP.html Genes up-regulated during adipogenesis of 3T3-L1 cells (fibroblast). 18285465 13/32 Arthur Liberzon 4.40302720137829e-05 8.96679072823063e-05 3125 2525.36363636364 2171 4.00283211361561e-06 703 1.70313836358771 -1.86224186268867 -1 2.51965648364524 3122 1218 874 1767 2171 4591 4260 3399 2016 703 3658 2134 M19107 GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP.html Genes up-regulated in myeloid progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 19/46 Arthur Liberzon 4.00573037812206e-06 1.2204715573394e-05 2735 2153.63636363636 2172 3.64157970156418e-07 1341 1.91610391825216 -1.41951508936738 -1 3.44133399530429 2735 2512 1854 2405 1341 3093 1849 2172 1443 2422 1864 2135 M1408 KIM_GERMINAL_CENTER_T_HELPER_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_GERMINAL_CENTER_T_HELPER_DN.html Genes down-regulated in germinal center T helper cells compared to other CD4+ [GeneID=920] T lymphocyte types. 15213097 15/40 Kate Stafford 0.000434953958493147 0.000711411605409734 2175 2133.45454545455 2172 3.95490886781733e-05 1097 1.56166493759417 -1.48251418370324 -1 1.79690512640935 2172 1697 1904 2500 2741 1721 2567 2827 1792 1097 2450 2136 M12898 REACTOME_GAP_JUNCTION_TRAFFICKING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAP_JUNCTION_TRAFFICKING.html Genes involved in Gap junction trafficking 13/27 Reactome 0.0083190010111367 0.0114993624596421 2160 2271.45454545455 2173 0.000759147793495065 1043 2.09646589834017 2.28939630864819 1 1.48613384740199 2160 1931 1043 2729 3218 2691 1855 3508 2173 1273 2405 2137 M2509 ABDELMOHSEN_ELAVL4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ABDELMOHSEN_ELAVL4_TARGETS.html Major ELAVL4 [GeneID=1996] associated mRNAs encoding proteins with functions in neuronal physiology. 20584986 23/33 Arthur Liberzon 1.66729169328298e-06 6.56548644934792e-06 3700 2350.45454545455 2174 1.5157208698707e-07 289 1.62189018340236 -0.794307790164124 -1 3.07255410348636 3696 1495 2174 892 935 4514 3684 2148 289 3327 2701 2138 M4861 VERHAAK_AML_WITH_NPM1_MUTATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_AML_WITH_NPM1_MUTATED_UP.html Genes up-regulated in acute myeloid leukemia (AML) patients with mutated NPM1 [GeneID=4869]. 16109776 125/356 Kevin Vogelsang 9.46105003410404e-08 1.15454376197426e-06 2180 2087.18181818182 2176 8.60095494634032e-09 307 1.7847255993694 1.94156049260799 1 3.87347609282681 2176 1333 307 1568 1537 4161 3807 2494 2406 405 2765 2139 M13077 WANG_RECURRENT_LIVER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RECURRENT_LIVER_CANCER_DN.html Genes down-regulated in samples from patients with recurrent hepatocellular carcinoma (HCC). 17975138 9/21 Yujin Hoshida 2.17256132119107e-05 4.86645427872913e-05 2565 2370.63636363636 2179 2.17258256158545e-06 1224 1.6874226883972 -2.82502317599512 -1 2.66011970172328 2564 2644 4568 3288 1973 1341 2179 1224 1309 3423 1564 2140 M2093 KAMIKUBO_MYELOID_MN1_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/KAMIKUBO_MYELOID_MN1_NETWORK.html Network of differentially expressed myeloid genes centered around MN1 [GeneID=4330]. 20478528 16/31 Arthur Liberzon 2.4817547701509e-05 5.46242501311749e-05 1540 1879.27272727273 2179 2.25616615139343e-06 366 1.206191148552 1.60402770598053 1 1.87936634975088 1536 2621 2179 3043 2762 1647 683 366 2334 2739 762 2141 M195 PID_CMYB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CMYB_PATHWAY.html C-MYB transcription factor network 18832364 65/152 Pathway Interaction Database 7.24860078772221e-06 1.93840524397298e-05 1735 2229.36363636364 2180 6.58965879150604e-07 1522 1.62621557208209 2.04715560641877 1 2.80126268840052 1733 3050 1634 2061 1576 2836 3004 1522 2660 2180 2267 2142 M1127 HUMMERICH_MALIGNANT_SKIN_TUMOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_MALIGNANT_SKIN_TUMOR_DN.html Genes down-regulated in malignant skin tumors (squamous cell carcinoma, SCC) formed by treatment with DMBA and TPA [PubChem=6001;4792] in the two stage skin carcinogenesis model. 16247483 17/49 Leona Saunders 0.00802551411565605 0.0111100617861047 1820 2593.45454545455 2180 0.000732267388795637 1513 2.68841769679555 3.55306749089301 1 1.92045248621224 1816 3451 1513 4148 3216 2180 1723 2085 2106 3387 2903 2143 M19134 KENNY_CTNNB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KENNY_CTNNB1_TARGETS_DN.html Genes down-regulated in HC11 cells (mammary epithelium) by expression of constantly active CTNNB1 [GeneID=1499]. 15642117 41/91 Yujin Hoshida 0.000399685992048287 0.000658091552613588 2065 2226.72727272727 2180 3.63416930595751e-05 827 1.72958130058957 2.44175437308823 1 2.01150597643399 2063 3115 1934 2750 3476 2259 1508 827 2180 2773 1609 2144 M17537 JI_RESPONSE_TO_FSH_DN http://www.broadinstitute.org/gsea/msigdb/cards/JI_RESPONSE_TO_FSH_DN.html Down-regulated in ovarian epithelial cells (MCV152) 72 hours following FSH treatment, compared to untreated 15386376 54/115 John Newman 5.63658920060495e-05 0.000111541625819404 1900 1895.36363636364 2180 5.12430329095272e-06 491 1.88410298305641 2.17203157437667 1 2.72209132594877 1898 2416 2246 1642 2317 2975 2180 491 1541 2520 623 2145 M2434 GUO_TARGETS_OF_IRS1_AND_IRS2 http://www.broadinstitute.org/gsea/msigdb/cards/GUO_TARGETS_OF_IRS1_AND_IRS2.html Transcripts dependent upon IRS1 and IRS2 [GeneID=3667, 8660] for normal expression in liver. 19596788 65/168 Arthur Liberzon 3.92419487492641e-06 1.20424212075345e-05 3465 2386 2181 3.56745624966198e-07 1209 1.89804516414108 2.29330054428267 1 3.41293393556205 3461 1259 1287 1709 1330 4567 3491 2977 1209 2181 2775 2146 M5298 BIOCARTA_STEM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STEM_PATHWAY.html Regulation of hematopoiesis by cytokines 4/15 BioCarta 0.00851715643193516 0.0117524720377056 1930 2493.90909090909 2182 0.000854997749328074 1014 1.46121539824585 1.46121539824585 1 1.03076987881014 1928 2182 3858 3229 3239 2109 1014 2564 3861 1623 1826 2147 M7914 HENDRICKS_SMARCA4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HENDRICKS_SMARCA4_TARGETS_DN.html Genes down-regulated in ALAB cells (breast cancer) upon reintroduction of SMARCA4 [GeneID=6597] expressed off adenoviral vector. 14673169 22/89 John Newman 0.000187273826346054 0.00032757191125704 1325 2088.36363636364 2182 1.70263427118818e-05 1127 1.44966827649099 1.51184634721318 1 1.84651334805302 1323 1127 1681 2738 2552 1634 1331 2288 3924 2192 2182 2148 M951 REACTOME_TRAF6_MEDIATED_INDUCTION_OF_NFKB_AND_MAP_KINASES_UPON_TLR7_8_OR_9_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF6_MEDIATED_INDUCTION_OF_NFKB_AND_MAP_KINASES_UPON_TLR7_8_OR_9_ACTIVATION.html Genes involved in TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation 60/132 Reactome 8.69067015349975e-06 2.245009941527e-05 1865 2563.36363636364 2183 7.90064044044003e-07 1643 1.24188473203316 -1.45214899130469 -1 2.110278109196 3761 1862 3260 1725 1643 2183 4602 2102 2345 2849 1865 2149 M1576 GERHOLD_ADIPOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GERHOLD_ADIPOGENESIS_DN.html Selected genes down-regulated during differentiation of 3T3-L1 cells (fibroblast) into adipocytes in response to adipogenic hormones. 12021175 63/116 John Newman 0.000455504552973474 0.000742174664545792 1215 2067 2183 4.14180810372784e-05 1215 1.50702632700164 1.45327209104746 1 1.72390843790084 1215 2579 1686 2183 2747 1555 1759 2370 2809 2373 1461 2150 M18215 BIOCARTA_TOB1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TOB1_PATHWAY.html Role of Tob in T-cell activation 8/22 BioCarta 0.00267274444361937 0.00392002518397507 2135 2208.90909090909 2184 0.000267596449895459 744 1.47577365446999 1.6680481608109 1 1.29826387214185 2135 2351 3867 1696 3473 2950 2184 1217 744 2389 1292 2151 M83 PID_CDC42_REG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CDC42_REG_PATHWAY.html Regulation of CDC42 activity 18832364 22/42 Pathway Interaction Database 1.26433791845457e-06 5.54746019276978e-06 3005 2125.36363636364 2184 1.14939876824451e-07 808 1.40089715361993 -1.71362113024032 -1 2.69136795140726 3001 962 2106 1590 808 2201 3640 3174 1154 2184 2559 2152 M1103 GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP.html Genes up-regulated in ME-A cells (breast cancer) undergoing apoptosis in response to doxorubicin [PubChem=31703]. 17160024 861/1799 Arthur Liberzon 2.36290005059431e-07 2.10466605212724e-06 2710 2199.36363636364 2185 2.36290030184269e-08 221 1.46900772714342 1.5523296716619 1 3.04823334785388 2708 914 4164 1035 221 4250 2172 2781 2185 528 3235 2153 M1571 YAMAZAKI_TCEB3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAMAZAKI_TCEB3_TARGETS_DN.html Genes down-regulated in embryonic stem cells from TCEB3 [GeneID=6924] knockout mice. 12604609 166/568 John Newman 1.17804440626267e-05 2.88614527577122e-05 4575 2731.90909090909 2185 1.07095519494551e-06 698 1.86390594796521 -1.6804801686701 -1 3.09291979909076 4571 2185 698 1089 1749 3345 4616 4531 1622 1672 3973 2154 M1805 WILLERT_WNT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/WILLERT_WNT_SIGNALING.html Genes up-regulated in NCCIT cell line (embryonic teratocarcinoma) after stimulation with WNT3A [GeneID=89780]. 12095419 24/43 Yujin Hoshida 0.0242855889346705 0.0317279456795478 1415 2761.63636363636 2187 0.00223253572235299 1415 1.60242934306602 1.80919869412679 1 0.877751759578267 1415 4395 2187 4089 3793 1809 2094 1689 3739 3370 1798 2155 M285 PID_HNF3A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HNF3A_PATHWAY.html FOXA1 transcription factor network 18832364 20/84 Pathway Interaction Database 1.50725724978334e-05 3.55396060881347e-05 2175 2314 2188 1.37024325123365e-06 1513 1.96158353557737 -1.53055366389552 -1 3.19018976075799 2174 2549 1618 2609 1834 1513 2188 4572 1633 2532 2232 2156 M15468 GENTILE_UV_RESPONSE_CLUSTER_D4 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D4.html Cluster d4: genes progressively down-regulated in WS1 cells (fibroblast) through 12 h after irradiation with high dose UV-C. 12907719 48/89 John Newman 5.06817132416428e-05 0.000101450024882673 610 2242.54545454545 2189 4.60753462192223e-06 343 1.32014182981845 1.36425562654179 1 1.92717202746224 608 4443 2189 3870 4620 343 558 1184 3639 2852 362 2157 M2540 KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION.html Gamma and UV responding genes. 15897889 90/185 Jessica Robertson 4.07670634391936e-05 8.37870435421322e-05 2195 2244.45454545455 2192 3.70616535383488e-06 1047 1.92631464191915 2.16856786661848 1 2.87057135492366 2192 3762 1047 2267 2143 2467 1442 3066 1857 2035 2411 2158 M13266 KEGG_RENAL_CELL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RENAL_CELL_CARCINOMA.html Renal cell carcinoma 41/78 KEGG 3.10365010908893e-06 1.00578868680434e-05 2125 2083.72727272727 2194 2.82150407961102e-07 1238 1.40169053964099 1.62251552498941 1 2.56049309523177 2124 1866 2453 1265 1238 2928 2247 2549 1676 2381 2194 2159 M1110 GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP.html Up-regulated genes from the set A (Fig. 5a): specific to cells expressing MLL-AF4 [GeneID=4297;4299] fusion protein alone. 17130830 138/360 Arthur Liberzon 0.00201344290382768 0.00298670257908722 1680 2177.36363636364 2194 0.000183207997628986 986 1.74846188962976 2.10856182562866 1 1.61362934178649 1676 2937 986 3101 3012 2194 2173 1541 2238 1787 2306 2160 M5002 DAZARD_UV_RESPONSE_CLUSTER_G24 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G24.html Cluster G24: genes induced in NHEK (normal keratinocyte) but not in SCC12B2 cells (squamous cell carcinoma) by UV-B radiation. 12771951 38/102 Arthur Liberzon 0.0168165900274259 0.0223489906036635 1320 2223.54545454545 2194 0.00154059337260328 1319 1.55783416532592 -1.70871188443003 -1 0.939982348338135 1319 2194 1713 1759 3331 2093 2426 1781 2612 2998 2233 2161 M16004 KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION.html Antigen processing and presentation 37/124 KEGG 0.0839184282471183 0.0965721401684667 2195 2761.36363636364 2195 0.00793650793650794 1759 1.75654817621114 -1.56271117742208 -1 0.651791571030475 2195 3599 1860 2193 4217 1759 2085 4489 3268 2522 2188 2162 M2290 CHANGOLKAR_H2AFY_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANGOLKAR_H2AFY_TARGETS_DN.html Genes down-regulated in liver tissue upon knockout of H2AFY [GeneID=9555]. 17242180 22/47 Arthur Liberzon 1.06634559329271e-06 4.93276944735402e-06 2855 2056.36363636364 2195 9.69405554684977e-08 428 1.8010670350469 2.21199405603679 1 3.49374161875653 2851 2695 2078 1945 747 2751 2576 3070 428 2195 1284 2163 M704 REACTOME_SIGNALING_BY_FGFR_MUTANTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR_MUTANTS.html Genes involved in Signaling by FGFR mutants 19/63 Reactome 3.18206423699582e-05 6.7715346844185e-05 1930 2206.90909090909 2196 2.89282751188814e-06 789 1.18872159540737 -1.27324957557198 -1 1.81160658835834 1926 2896 2873 2424 2067 1403 2196 789 2769 3527 1406 2164 M2650 CAIRO_HEPATOBLASTOMA_POOR_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_HEPATOBLASTOMA_POOR_SURVIVAL.html Genes whose expression classifies hepatoblastoma tumors as belonging to either rC1 or rC2 subtypes and whose expression predicts poor survival. 19061838 10/25 Yujin Hoshida 9.76991946201207e-06 2.47068767398751e-05 2200 2057.63636363636 2196 8.88178440840756e-07 943 2.31377639355519 2.30174979769662 1 3.89651201113685 2196 2484 1556 2328 1686 2687 2352 3514 943 1369 1519 2165 M1840 KEGG_GLUTATHIONE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLUTATHIONE_METABOLISM.html Glutathione metabolism 27/58 KEGG 0.000713605919880994 0.0011266702629927 1765 2433.09090909091 2198 6.48943177072974e-05 1765 1.15021075443093 -1.24325951960847 -1 1.23952155220083 1765 2198 2540 3825 2838 1878 1852 1799 3498 2635 1936 2166 M3389 LIU_TARGETS_OF_VMYB_VS_CMYB_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_TARGETS_OF_VMYB_VS_CMYB_UP.html Genes regulated in the opposite directions by v-MYB (UP) and c-MYB (DN) variants of CMYB [GeneID=4602] overexpressed in primary monocyte cultures off adenoviral vectors. 16205643 11/25 Arthur Liberzon 1.05555947222706e-05 2.62824212904145e-05 2990 2043.45454545455 2198 9.59604124393543e-07 188 1.27940682616745 1.32631697153372 1 2.14202789093619 2988 188 2198 1417 1711 3168 4026 2209 927 790 2856 2167 M13658 HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_DN.html Genes whose expression correlated with lower risk of late recurrence of hepatocellular carcinoma (HCC). 18923165 38/119 Yujin Hoshida 7.11040799306258e-05 0.00013711675660696 1410 2196.54545454545 2199 6.4642161928238e-06 1091 1.66624368917541 1.79686847636097 1 2.35273112488572 1410 3148 2377 3189 2304 1771 2082 1812 2779 2199 1091 2168 M11640 LEE_LIVER_CANCER_CIPROFIBRATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_CIPROFIBRATE_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) induced by ciprofibrate [PubChem=2763]. 15565109 33/117 Yujin Hoshida 8.94027621032134e-07 4.40527174779872e-06 4295 2635.36363636364 2200 8.12752713039893e-08 675 1.66167169189734 -1.4535729225421 -1 3.25317370555841 4294 1689 1239 2200 675 4268 4271 2573 2138 1214 4428 2169 M2039 GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_DN.html Down-regulated genes from the set E (Fig. 5a): specific signature shared by cells expressing either MLL-AF4 [GeneID=4297;4299] or AF4-MLL fusion proteins alone, and those expressing both fusion proteins. 17130830 8/35 Arthur Liberzon 4.23042673209382e-07 2.82649481163302e-06 2205 1869 2202 4.23042753743701e-08 198 1.15799145611875 1.218489754505 1 2.34865866695481 2397 198 4169 1459 423 3002 2205 223 2620 1661 2202 2170 M81 PID_CDC42_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CDC42_PATHWAY.html CDC42 signaling events 18832364 49/107 Pathway Interaction Database 1.10405094128694e-05 2.7344517499316e-05 4010 2480.27272727273 2203 1.00368771082715e-06 838 1.50461473061747 -1.27144047734728 -1 2.50961658732236 4006 1266 2170 838 1723 3772 3792 3569 953 2203 2991 2171 M2493 PEDRIOLI_MIR31_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PEDRIOLI_MIR31_TARGETS_UP.html Genes up-regulated in primary LEC cells (lymphatic endothelum) upon overexpression of MIR31 [GeneID=407035]. 20479124 133/454 Arthur Liberzon 3.24255001929563e-06 1.04001296306771e-05 4310 2410.27272727273 2203 2.94777708950525e-07 270 1.58145204540376 1.82178147553109 1 2.88046622532381 4310 270 858 1588 1256 2428 4494 3276 2203 1183 4647 2172 M656 REACTOME_SYNTHESIS_OF_PE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PE.html Genes involved in Synthesis of PE 4/12 Reactome 0.0176701851609134 0.0234103725371898 1830 2578.81818181818 2204 0.00178122839548819 1542 1.99449873445577 -1.99449873445577 -1 1.18877109262298 1830 3407 3949 3972 3517 1628 1542 1640 2017 2661 2204 2173 M18134 COLDREN_GEFITINIB_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/COLDREN_GEFITINIB_RESISTANCE_UP.html Genes up-regulated in NSCLC (non-small cell lung carcinoma) cell lines resistant to gefitinib [PubChem=123631] compared to the sensitive ones. 16877703 49/123 Arthur Liberzon 1.26284391998645e-06 5.54746019276978e-06 2100 2040.81818181818 2204 1.14804058625877e-07 806 1.43285421247909 1.59502236936409 1 2.75276303945491 2100 845 2284 2602 806 2995 2921 2159 1244 2204 2289 2174 M2154 DUTERTRE_ESTRADIOL_RESPONSE_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DUTERTRE_ESTRADIOL_RESPONSE_6HR_DN.html Genes down-regulated in MCF7 cells (breast cancer) at 6 h of estradiol [PubChem=5757] treatment. 20406972 64/150 Jessica Robertson 9.73858837394943e-06 2.46675811461227e-05 3650 2737.54545454545 2205 8.85330134850413e-07 998 1.45795045064294 -1.407867401064 -1 2.4556278855476 3646 1482 1154 1668 1682 3976 4654 4391 2205 998 4257 2175 M2045 MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_1 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_1.html Cluster 1: genes up-regulated in SW260 cells (colon cancer) by sodium butyrate, curcumin, sulindac and TSA [PubChem=5222465;969516;5352;5562]. 10969808 10/24 Arthur Liberzon 4.02235327830615e-05 8.28656255234052e-05 2115 2187.90909090909 2207 3.65675165689008e-06 145 3.28778015528931 3.28778015528931 1 4.90518265642182 2111 3487 2207 2308 3427 2460 1804 432 145 3497 2189 2176 M10748 YANG_BREAST_CANCER_ESR1_BULK_UP http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_BULK_UP.html Genes up-regulated in bulk samples from early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative samples. 16261164 15/39 Leona Saunders 4.78621651792335e-07 3.03067844198597e-06 3180 2060.81818181818 2209 4.35110687199129e-08 184 1.2055176025612 -1.41063891063226 -1 2.43170404093663 3177 184 2950 2286 431 2092 2898 2153 2209 2611 1678 2177 M2100 STAMBOLSKY_BOUND_BY_MUTATED_TP53 http://www.broadinstitute.org/gsea/msigdb/cards/STAMBOLSKY_BOUND_BY_MUTATED_TP53.html Gene promoters preferentially bound by a mutated form of TP53 [GeneID=7157] in SKBR3 cells (breast cancer). 20227041 12/32 Arthur Liberzon 0.00155028488555653 0.00232766259971737 1975 2243.72727272727 2210 0.0001410344010402 568 2.07828403928898 2.744704463792 1 2.00026806903662 1975 2873 2245 2139 3842 2210 2535 1091 568 3624 1579 2178 M2416 WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_36HR http://www.broadinstitute.org/gsea/msigdb/cards/WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_36HR.html Genes with promoters bound by PPARG [GeneID=5468] at 36 h time point of adipocyte differentiation of 3T3-L1 cells (preadipocyte). 19414603 17/37 Arthur Liberzon 3.28981653460493e-06 1.05085755154456e-05 3215 2316.72727272727 2210 2.99074677646543e-07 887 1.56584516157245 -0.947460208743181 -1 2.8494612235448 3212 2164 2488 2210 1263 3361 1572 2145 887 2808 3374 2179 M4359 SWEET_KRAS_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SWEET_KRAS_TARGETS_DN.html Genes upregulated in control vs KRAS [GeneID=3845] knockdown in a human cell line. 15608639 63/144 Aravind Subramanian 1.09550928108701e-06 5.01813928755984e-06 3190 2275 2212 9.95918024187124e-08 756 1.69422647989953 1.68039825959942 1 3.28187557629178 3189 1427 1161 1628 756 4048 2869 3191 2212 1297 3247 2180 M2294 BAKKER_FOXO3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BAKKER_FOXO3_TARGETS_UP.html Genes up-regulated in I/11 erythroblast cells upon expression of an activated form of FOXO3 [GeneID=2309]. 17353275 42/100 Arthur Liberzon 5.46814495265415e-06 1.55483781845494e-05 2665 2193.72727272727 2212 4.97105322171586e-07 1188 1.36456605805688 0.85347266507847 1 2.39831772643741 2661 1188 2212 2291 1470 2206 1559 2301 1852 2489 3902 2181 M13494 BIOCARTA_BIOPEPTIDES_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BIOPEPTIDES_PATHWAY.html Bioactive Peptide Induced Signaling Pathway 28/67 BioCarta 0.000274164412452513 0.00046430590413895 2215 2190.27272727273 2215 2.49271440759216e-05 1366 1.02765869428101 -1.31017661276076 -1 1.25207105553115 2215 1366 2698 1444 2635 1467 2294 1719 2863 3861 1531 2182 M208 MIZUKAMI_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MIZUKAMI_HYPOXIA_UP.html Genes up-regulated in DLD-1 cells (colon cancer) in response to hypoxia; might not be direct targets of HIF1A [GeneID=3091]. 16127434 8/20 Jessica Robertson 2.4660944458104e-06 8.52221133707046e-06 2400 2154.45454545455 2215 2.4660971825445e-07 197 1.88793571725539 1.80454774416773 1 3.49838095583574 2398 197 4535 1503 1180 2493 2215 3285 2182 1136 2575 2183 M19784 BIOCARTA_TCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCR_PATHWAY.html T Cell Receptor Signaling Pathway 27/73 BioCarta 9.31165313941093e-05 0.000173015093621251 3030 2261.72727272727 2216 8.4654975317886e-06 556 1.43641611296601 -1.24146137773203 -1 1.9751887951074 3030 1597 2216 556 2392 1910 3493 3817 1642 1728 2498 2184 M110 PID_IL1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL1_PATHWAY.html IL1-mediated signaling events 18832364 22/47 Pathway Interaction Database 5.17595464226155e-05 0.000103298651846838 2740 2206.54545454545 2216 4.70552401936552e-06 1597 1.23208853879005 -1.18591294281057 -1 1.79509794245323 1956 2075 3005 2222 2216 1597 2739 1625 2482 2740 1615 2185 M4389 RIZ_ERYTHROID_DIFFERENTIATION_12HR http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_12HR.html Selected genes down-regulated in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts) at 12 h time point. 17213805 25/63 Leona Saunders 3.22369078135829e-05 6.85089115711789e-05 1200 2238.90909090909 2216 2.93067092683584e-06 913 1.18401693421646 0.941660649021031 1 1.80224680495195 1199 2586 2419 2736 2071 1371 913 4212 2907 1998 2216 2186 M1871 BENPORATH_ES_1 http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_ES_1.html Set 'ES exp1': genes overexpressed in human embryonic stem cells according to 5 or more out of 20 profiling studies. 18443585 275/629 Jessica Robertson 1.69278327557209e-06 6.63242678037693e-06 1665 2022.81818181818 2216 1.53889507098219e-07 940 1.60348476633147 1.84885163276497 1 3.03510419757992 1665 2216 1061 1328 940 3404 2377 2940 2225 1227 2868 2187 M1504 RUAN_RESPONSE_TO_TROGLITAZONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TROGLITAZONE_UP.html Adipocyte abundant genes up-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to troglitazone [PubChem=5591]. 12732648 17/38 John Newman 0.000100610376698493 0.000185614261893361 3050 2288.72727272727 2216 9.14681619143467e-06 1209 1.76681484037395 -0.829479272836128 -1 2.40979875568446 3050 1209 1231 2123 2417 2072 3571 1634 2240 2216 3413 2188 M11650 BIOCARTA_NOS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NOS1_PATHWAY.html Nitric Oxide Signaling Pathway 10/27 BioCarta 0.00123621619943474 0.00189001928566107 1890 2488.54545454545 2217 0.000112446490601781 1287 1.03291754691504 1.22021190488854 1 1.02829486890623 1887 2485 2217 2140 2926 1287 1509 4171 3935 3476 1341 2189 M275 PID_ALPHA_SYNUCLEIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALPHA_SYNUCLEIN_PATHWAY.html Alpha-synuclein signaling 18832364 14/48 Pathway Interaction Database 6.68719214781979e-07 3.70404047336685e-06 2865 2158.72727272727 2217 6.07926743680138e-08 77 1.26274229680411 1.58188711172662 1 2.50691559044463 2863 1794 2234 2217 1949 3618 3516 77 1054 2503 1921 2190 M11585 NAGASHIMA_NRG1_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAGASHIMA_NRG1_SIGNALING_UP.html Genes up-regulated in MCF7 cells (breast cancer) after stimulation with NRG1 [GeneID=3084]. 17142811 133/284 Arthur Liberzon 2.35164312945786e-06 8.21581875658796e-06 1300 2193.72727272727 2218 2.13785967563677e-07 1105 1.65917713859796 1.71407673013384 1 3.08413075042 1912 2682 1153 1299 1105 3467 2897 3616 2218 1300 2482 2191 M957 REACTOME_NFKB_ACTIVATION_THROUGH_FADD_RIP1_PATHWAY_MEDIATED_BY_CASPASE_8_AND10 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NFKB_ACTIVATION_THROUGH_FADD_RIP1_PATHWAY_MEDIATED_BY_CASPASE_8_AND10.html Genes involved in NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 9/15 Reactome 0.000867961569778583 0.00135575597199415 2220 2300.36363636364 2219 8.68300767032182e-05 926 0.950545379205748 -0.932376359071278 -1 0.996423044223023 2219 1943 4063 2959 2882 1226 1141 1974 3402 2569 926 2192 M12678 BOYLAN_MULTIPLE_MYELOMA_D_CLUSTER_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_D_CLUSTER_DN.html Genes from cluster 4: down-regulated in group D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 26/61 Jessica Robertson 8.38216148742512e-06 2.18336902335042e-05 2410 2055.09090909091 2220 7.62017584022366e-07 766 1.69659455130391 1.91957134588115 1 2.89044409654541 1766 1124 2304 2406 1627 2154 2220 2800 766 3030 2409 2193 M11844 KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY.html Cytosolic DNA-sensing pathway 26/60 KEGG 0.000168260759942274 0.000296751946213585 2430 2045.90909090909 2221 1.52976027515779e-05 984 1.29182202269671 -1.24043695989319 -1 1.66572022529501 2426 1643 2717 2475 2527 984 1385 2221 2253 2072 1802 2194 M866 REACTOME_ROLE_OF_DCC_IN_REGULATING_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ROLE_OF_DCC_IN_REGULATING_APOPTOSIS.html Genes involved in Role of DCC in regulating apoptosis 8/16 Reactome 4.78341840369175e-05 9.63261651899422e-05 3055 2501.36363636364 2221 4.78352137172349e-06 178 2.00780554259921 2.32018261480462 1 2.94755730499641 3053 1228 4042 1118 2221 4524 3340 4003 178 1660 2148 2195 M1564 BURTON_ADIPOGENESIS_5 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_5.html Up-regulated at 48-96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 90/197 John Newman 0.000210556914462413 0.000364353656266937 845 2164 2223 1.91433699162323e-05 767 1.17750053968638 -0.968460947229933 -1 1.47994805396673 842 2223 3532 2633 2575 767 921 1820 2999 3935 1557 2196 M11816 KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY.html Fc epsilon RI signaling pathway 33/94 KEGG 0.000438334634109761 0.000716191107196075 1550 1885.09090909091 2224 3.98565448721005e-05 910 1.33364684793448 -1.48484951688359 -1 1.53312211597746 1546 2229 2303 1534 2742 910 2735 935 2447 2224 1131 2197 M10355 JI_RESPONSE_TO_FSH_UP http://www.broadinstitute.org/gsea/msigdb/cards/JI_RESPONSE_TO_FSH_UP.html Genes up-regulated in MCV152 cells (ovarian cancer) treated with follicle stimulating hormone (FSH). 15386376 84/208 John Newman 0.00069121151891242 0.00109352369264808 3075 2293.45454545455 2224 6.2857162199636e-05 1156 1.72461966421985 2.0965531165124 1 1.86670714215132 3074 2224 1156 1575 2833 4607 2523 1380 1716 1345 2795 2198 M2134 REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS.html Genes involved in Metabolism of lipids and lipoproteins 243/619 Reactome 3.1621354481576e-06 1.01980500413396e-05 3940 2595.36363636364 2226 2.87467272110224e-07 1243 1.40442619749996 -1.20675632193461 -1 2.56240490256501 3938 2530 2226 1653 1243 2181 3838 2910 2094 2005 3931 2199 M2597 GHANDHI_BYSTANDER_IRRADIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GHANDHI_BYSTANDER_IRRADIATION_UP.html Genes significantly (FDR < 10%) up-regulated in IMR-90 cells (fibroblast) in response to bystander irradiation. 19108712 43/108 Itai Pashtan 6.2256286194018e-06 1.72040678779681e-05 2670 2016.72727272727 2226 5.65967839722695e-07 1238 1.70326350501452 -1.92079810915957 -1 2.96624123703969 2668 2226 1238 2373 1514 1488 2621 1319 2765 1528 2444 2200 M2600 WARTERS_RESPONSE_TO_IR_SKIN http://www.broadinstitute.org/gsea/msigdb/cards/WARTERS_RESPONSE_TO_IR_SKIN.html Genes displaying an ionizing radiation response in the human skin cell samples. 19580510 46/132 Itai Pashtan 3.03192159219719e-06 9.88697604804179e-06 2230 2190.45454545455 2226 2.75629615512401e-07 940 1.05154130298497 1.23519180318899 1 1.92373018425931 2226 940 2073 1875 1228 3680 2884 2246 3107 2344 1492 2201 M7176 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_UP.html Genes up-regulated by RUNX1-RUNX1T1 [GeneID=861;862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing monocytes. 17898786 12/30 Arthur Liberzon 5.3405109599814e-05 0.000106220858906931 3245 2308 2227 4.85512782323368e-06 654 1.44719765192826 -2.08933947411099 -1 2.10209351735921 3241 654 1297 1910 2227 2998 1400 3098 2399 1595 4569 2202 M321 KEGG_CHRONIC_MYELOID_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CHRONIC_MYELOID_LEUKEMIA.html Chronic myeloid leukemia 39/90 KEGG 4.8151546209333e-05 9.69036935612458e-05 1770 2475.45454545455 2228 4.37750910342904e-06 1120 1.34076750926103 -1.07829355374615 -1 1.96704036454737 2923 2228 2813 1232 2201 1769 3284 4192 1120 3700 1768 2203 M2970 WILLIAMS_ESR1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WILLIAMS_ESR1_TARGETS_UP.html The 'ER-alpha profile': genes up-regulated in T47D cells (breast cancer, ESR2 [GeneID=2100] Tet-Off) upon activation of ESR1 [GeneID=2099] by estradiol (E2) [PubChem=5757]. 17700529 18/50 Jessica Robertson 0.000596766720609374 0.00095344318198961 1610 2057.09090909091 2228 5.42662417835755e-05 1037 1.54437943798481 1.50977027463451 1 1.70522464845505 1606 2637 1360 1622 2801 2228 2335 2121 2534 1037 2347 2204 M2081 KARLSSON_TGFB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KARLSSON_TGFB1_TARGETS_DN.html Genes down-regulated by TGFB1 [GeneID=7040] in MEF cells (embryonic fibroblast) via TGFB1R [GeneID=7046]. 15769904 169/385 Arthur Liberzon 2.01925783650902e-05 4.56671921905466e-05 1680 2150.18181818182 2228 1.83570579126689e-06 1368 1.35752455274444 1.49268815959572 1 2.15375484268489 1368 1677 2895 1676 1926 2390 2371 1891 2541 2689 2228 2205 M15411 BARIS_THYROID_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/BARIS_THYROID_CANCER_DN.html Genes down-regulated in oncocytic follicular carcinoma (FTC) vs mitochondrial-rich papillary carcinoma (PTC) types of thyroid cancer. 15806164 44/108 Arthur Liberzon 3.66385512722676e-06 1.14611649707507e-05 3115 2236.72727272727 2230 3.3307829354399e-07 1181 1.62038531735975 1.97890889253887 1 2.92639061705761 3114 1865 1668 1181 1299 3055 2511 2638 1644 2230 3399 2206 M2327 BILANGES_SERUM_SENSITIVE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_SERUM_SENSITIVE_GENES.html Genes translationally regulated in MEF cells (embryonic fibroblasts) in response to serum starvation but not by rapamycin (sirolimus) [PubChem=6610346]. 17562867 58/137 Arthur Liberzon 0.0288472826096577 0.0373214705435826 1870 2480.27272727273 2233 0.00265751205458909 1164 1.55760239679761 1.66407259057331 1 0.813048793600517 1866 2979 2233 3018 3416 1777 1164 2154 3127 3599 1950 2207 M2176 ROY_WOUND_BLOOD_VESSEL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROY_WOUND_BLOOD_VESSEL_DN.html Genes down-regulated in blood vessel cells from wound site. 17728400 26/64 Leona Saunders 9.61079428980428e-05 0.000178149454280154 3600 2390.72727272727 2236 8.73746742468334e-06 599 2.36884099337787 -1.75844998895805 -1 3.24635167345875 3596 2236 599 1167 2793 4515 3754 2014 683 1302 3639 2208 M2349 BIOCARTA_CCR5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CCR5_PATHWAY.html Pertussis toxin-insensitive CCR5 Signaling in Macrophage 12/27 BioCarta 0.000826275520317006 0.00129539213389277 2715 2237.09090909091 2237 7.51441832701166e-05 1569 2.00475979808181 -1.86651347387262 -1 2.11601352514312 2714 2518 1569 1967 2855 2453 2663 1659 1911 2237 2062 2209 M2440 LE_NEURONAL_DIFFERENTIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/LE_NEURONAL_DIFFERENTIATION_UP.html Genes up-regulated during neuronal differentiation of SH-SY5Y cells (neuroblastoma) in response to stimulation by tretinoin (all-trans retinoic acid, ATRA) [PubChem=444795] and BDNF [GeneID=627]. 19635812 9/34 Arthur Liberzon 1.95951486766901e-06 7.28752910309285e-06 2290 1922.63636363636 2238 1.95951659553549e-07 195 1.88072635052922 1.80533956620018 1 3.53174961413246 2288 195 4668 676 1064 2406 2528 3925 557 604 2238 2210 M13191 KEGG_PROSTATE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROSTATE_CANCER.html Prostate cancer 46/121 KEGG 3.09320225087206e-06 1.00397928952631e-05 1235 2562.72727272727 2239 2.81200599993286e-07 1231 1.4710271099762 -0.931344199485727 -1 2.68757192145593 3515 2191 2239 1231 1235 4275 2397 1723 1808 3688 3888 2211 M592 REACTOME_ACTIVATED_NOTCH1_TRANSMITS_SIGNAL_TO_THE_NUCLEUS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_NOTCH1_TRANSMITS_SIGNAL_TO_THE_NUCLEUS.html Genes involved in Activated NOTCH1 Transmits Signal to the Nucleus 12/38 Reactome 1.87691465141664e-05 4.28408283318966e-05 2430 2078.18181818182 2239 1.70630060397664e-06 160 3.0671270605586 3.0671270605586 1 4.897199315876 2427 2288 1609 1772 2680 4346 3943 333 160 2239 1063 2212 M1375 LASTOWSKA_COAMPLIFIED_WITH_MYCN http://www.broadinstitute.org/gsea/msigdb/cards/LASTOWSKA_COAMPLIFIED_WITH_MYCN.html Genes co-amplified within MYCN [GeneID=4613] in primary neuroblastoma tumors. 17533364 23/50 Leona Saunders 0.00064111561201331 0.00101908675640922 4570 2697 2239 5.83002290672842e-05 1431 1.57979068468331 -1.82320201289582 -1 1.72762602241833 4566 2239 2229 2162 2820 3775 4117 1842 1431 1792 2694 2213 M1599 LEE_AGING_CEREBELLUM_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_CEREBELLUM_UP.html Upregulated in the cerebellum of aged adult mice (30-month) vs young adult (5-month) 10888876 73/161 John Newman 0.000497970239461235 0.000803819683815138 2040 2375.81818181818 2239 4.52802718918681e-05 1118 1.77359381202637 -1.39307355752413 -1 2.00637361408388 2037 3232 1118 2179 2769 3116 2794 1989 3130 1531 2239 2214 M18155 KEGG_INSULIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_INSULIN_SIGNALING_PATHWAY.html Insulin signaling pathway 60/174 KEGG 7.63569884172268e-06 2.02151891368997e-05 1445 2237.63636363636 2242 6.94156849420248e-07 1371 1.23444507455118 1.28725820780789 1 2.11818513135861 1444 2390 2922 1371 1598 2289 2242 2637 2178 3442 2101 2215 M4500 DACOSTA_UV_RESPONSE_VIA_ERCC3_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_DN.html Genes down-regulated in fibroblasts expressing mutant forms of ERCC3 [GeneID=2071] after UV irradiation. 15608684 544/1296 Arthur Liberzon 5.1161982328623e-05 0.000102256771658131 770 2336.18181818182 2242 5.11631602635873e-06 769 1.48235273623239 1.69276441189766 1 2.1621071853067 769 4299 4260 2995 2242 1047 1600 1565 2634 3338 949 2216 M1703 HOWLIN_CITED1_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOWLIN_CITED1_TARGETS_1_DN.html Genes down-regulated in mammary glands from the CITED1 [GeneID=4435] knockout mice: homozygotic vs. heterozygotic animals. 16278680 29/75 Arthur Liberzon 3.71648487804104e-06 1.15563690368283e-05 3205 2371.90909090909 2244 3.37862832395983e-07 620 1.78040827275926 -2.13463162516877 -1 3.21305153732785 3202 620 1752 2244 1310 3524 3001 3234 1687 1536 3981 2217 M8066 BIOCARTA_IL22BP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL22BP_PATHWAY.html IL22 Soluble Receptor Signaling Pathway 9/17 BioCarta 7.32587309527567e-05 0.000140923814960845 2940 2399.63636363636 2245 7.32611461435628e-06 1315 0.955313269184956 -1.08547261716654 -1 1.34474624109351 2936 1315 3844 1744 2338 1909 2100 1999 2570 3396 2245 2218 M12570 DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN.html Genes down-regulated in T-PLL cells (T-cell prolymphocytic leukemia) bearing the inv(14)/t(14:14) chromosomal aberration. 17713554 209/534 Leona Saunders 5.68330181958671e-05 0.000112371106863221 1510 2423.18181818182 2245 5.16677149337551e-06 1507 1.38333612346471 1.63915617882237 1 1.99697247764473 1507 3472 3217 3072 2245 2077 2237 1560 2496 3012 1760 2219 M1540 VISALA_RESPONSE_TO_HEAT_SHOCK_AND_AGING_UP http://www.broadinstitute.org/gsea/msigdb/cards/VISALA_RESPONSE_TO_HEAT_SHOCK_AND_AGING_UP.html Genes up-regulated after heat shock in peripheral lympocytes from old donors, compared to those from the young ones. 12618007 12/30 John Newman 0.000238779353783841 0.000409111536318493 860 1908.09090909091 2246 2.1709570354103e-05 186 1.31243419947189 1.31243419947189 1 1.62540083518162 860 3344 2469 2792 2836 585 186 2192 2497 2246 982 2220 M7034 MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_UP.html Up-regulated 'cooperation response genes': responded synergystically to the combination of mutant TP53 and HRAS [GeneID=7157;3265] in YAMC cells (colon). 18500333 16/35 Jessica Robertson 1.39760447386858e-05 3.32551792934681e-05 2890 2174.63636363636 2246 1.27055759325093e-06 914 1.92646696517714 1.84750563561804 1 3.15339628655229 2890 1456 1019 2246 1811 2985 1134 3813 3270 914 2383 2221 M12208 TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_DN.html Genes down-regulated in ductal vs lobular carcinoma breast tumor cells. 17389037 6/11 Arthur Liberzon 3.82780133101763e-05 7.94730927653905e-05 2970 2293.90909090909 2247 3.82786726689974e-06 654 2.29391488917874 2.86730188718007 1 3.43761385507122 2968 1567 4118 2433 2152 3328 3364 1083 654 1319 2247 2222 M1330 MANTOVANI_VIRAL_GPCR_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/MANTOVANI_VIRAL_GPCR_SIGNALING_DN.html Down-regulated genes in the expression signature of direct and paracrine viral GPCR signaling in endothelial cells. 17906691 42/105 Jessica Robertson 7.01660552088295e-05 0.000135530970613592 2275 2321.45454545455 2248 6.37893574192436e-06 1456 1.72008554204338 1.75230294693179 1 2.43193203159129 2271 2769 1604 1794 2301 3503 2248 3864 1588 1456 2138 2223 M44 PID_HIF2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HIF2PATHWAY.html HIF-2-alpha transcription factor network 18832364 26/51 Pathway Interaction Database 1.3558200395691e-05 3.24324126513585e-05 2250 2236.72727272727 2250 1.23257126846711e-06 1546 1.81074643091823 1.81820075839599 1 2.9711768351199 2250 1546 1895 2745 1795 2556 2649 2885 1944 1651 2688 2224 M1388 SHIN_B_CELL_LYMPHOMA_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_5.html Cluster 5 of genes distinguishing among different B lymphocyte neoplasms. 19010892 10/25 Jessica Robertson 0.00111485370764269 0.00171848831382028 3245 2369.63636363636 2250 0.000101401732979191 788 1.72057375499324 -2.05238597663159 -1 1.73886015368746 3244 1977 1701 1461 2904 3031 2873 4470 788 1367 2250 2225 M1475 FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN.html Genes down-regulated in kidney biopsies from patients with acute transplant rejection compared to the biopsies from patients with well functioning kidneys more than 1-year post transplant. 15307835 377/974 Jean Junior 0.000135001697401291 0.000242011459075153 2195 2310.09090909091 2250 1.2273634764754e-05 1168 1.63979982340173 1.69788310785949 1 2.16749553903264 2194 2728 1168 2018 2488 3273 2707 1786 2250 2233 2566 2226 M13462 LUI_THYROID_CANCER_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_CLUSTER_5.html Cluster 5: genes with similar expression profiles across follicular thyroid carcinoma (FTC) samples. 15608688 10/14 Leona Saunders 0.00046875237023267 0.000760849881160475 1895 2473.45454545455 2251 4.26229342505477e-05 1747 1.63714665408047 -1.63714665408047 -1 1.86629622573508 1892 1747 1941 2251 2756 2033 3060 2886 3759 2705 2178 2227 M7257 REACTOME_NRIF_SIGNALS_CELL_DEATH_FROM_THE_NUCLEUS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NRIF_SIGNALS_CELL_DEATH_FROM_THE_NUCLEUS.html Genes involved in NRIF signals cell death from the nucleus 10/23 Reactome 1.21991615634074e-05 2.9689094560606e-05 3870 2579 2252 1.10902083719812e-06 851 1.49342102080557 -0.829466351138769 -1 2.47144340132441 3867 1890 2252 1992 1758 2397 3590 3579 851 1962 4231 2228 M17 PID_NOTCH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NOTCH_PATHWAY.html Notch signaling pathway 18832364 31/87 Pathway Interaction Database 2.48443162668944e-05 5.46574957871676e-05 4210 2528.63636363636 2253 2.25859971227179e-06 1133 1.61459945665878 -0.976655201832284 -1 2.51555135843752 4209 1444 2204 2253 1985 2964 4631 1133 1434 2515 3043 2229 M8599 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_UP.html Genes up-regulated in NIH3T3 cells (fibroblasts) transformed by activated KRAS [GeneID=3845] vs those reverted to normal cells upon over-expression of a dominant negative form of CDC25 [GeneID=5923]. 16607279 46/102 Lauren Kazmierski 2.20861258859982e-06 7.8703867605922e-06 2255 1980.09090909091 2253 2.00783164169257e-07 733 1.82760353679855 1.59060266508595 1 3.40966914808814 2253 2046 733 2399 1077 2736 1441 2318 2726 837 3215 2230 M971 REACTOME_ION_TRANSPORT_BY_P_TYPE_ATPASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ION_TRANSPORT_BY_P_TYPE_ATPASES.html Genes involved in Ion transport by P-type ATPases 15/39 Reactome 1.73239583734314e-05 3.99115383175514e-05 1885 2719.54545454545 2254 1.57491770844593e-06 1481 1.61413718060114 -1.86714671549002 -1 2.59539780060579 4256 1881 1626 1819 1884 4475 2742 2831 2254 1481 4666 2231 M2881 REACTOME_LYSOSOME_VESICLE_BIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LYSOSOME_VESICLE_BIOGENESIS.html Genes involved in Lysosome Vesicle Biogenesis 21/42 Reactome 5.89174315844578e-05 0.000116051737875061 3285 2387.36363636364 2255 5.35627359007045e-06 1130 1.19133088527436 -0.803349198196202 -1 1.7137001420814 3281 1130 2882 1670 2255 1283 2167 3647 1848 3163 2935 2232 M997 REACTOME_ION_CHANNEL_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ION_CHANNEL_TRANSPORT.html Genes involved in Ion channel transport 15/63 Reactome 1.73239583734314e-05 3.99115383175514e-05 1885 2720.54545454545 2255 1.57491770844593e-06 1482 1.61413718060114 -1.86714671549002 -1 2.59539780060579 4257 1882 1627 1820 1885 4476 2743 2832 2255 1482 4667 2233 M778 BIERIE_INFLAMMATORY_RESPONSE_TGFB1 http://www.broadinstitute.org/gsea/msigdb/cards/BIERIE_INFLAMMATORY_RESPONSE_TGFB1.html Inflammatory genes down-regulated in mammary carcinoma cells after stimulation with TGFB1 [GeneID=7040] for 1 hr. 18339861 2/10 Jessica Robertson 0.014856450623311 0.0199020376274543 2340 2511.2 2255 0.0016617192598691 1397 1.93332905988956 -1.93332905988956 -1 1.20214125282654 2340 2831 4456 NA 3716 1916 2093 1628 1397 2170 2565 2234 M663 REACTOME_THE_ACTIVATION_OF_ARYLSULFATASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THE_ACTIVATION_OF_ARYLSULFATASES.html Genes involved in The activation of arylsulfatases 6/10 Reactome 0.000139679142840907 0.000249727761675883 1945 2367.27272727273 2256 1.39687923235986e-05 372 3.40014050976233 3.40014050976233 1 4.47738153463197 1943 3691 3952 3178 3751 2256 1878 1458 372 3040 521 2235 M200 PID_ERA_GENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERA_GENOMIC_PATHWAY.html Validated nuclear estrogen receptor alpha network 18832364 37/121 Pathway Interaction Database 9.96435367978122e-06 2.51442979770893e-05 2965 2332.63636363636 2257 9.05854437375724e-07 610 1.24808260334423 -1.05577032590653 -1 2.09835475943998 2965 610 2679 2408 1691 1091 1999 4223 2257 3636 2100 2236 M1822 MATZUK_EARLY_ANTRAL_FOLLICLE http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_EARLY_ANTRAL_FOLLICLE.html Genes important for early anral follicle, based on mouse models with female fertility defects. 18989307 7/23 Jessica Robertson 0.000794506647413714 0.00124934837240962 955 2249.63636363636 2257 7.94790848796482e-05 802 1.43915231449737 1.43915231449737 1 1.52728604853192 953 2725 4490 2257 3690 849 814 1837 4054 2275 802 2237 M2592 ZEMBUTSU_SENSITIVITY_TO_MITOMYCIN http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_MITOMYCIN.html Top genes associated with chemosensitivity to mitomycin [PubChem=5746] across 85 tumor xenografts. 11809704 11/30 Arthur Liberzon 0.000488605004096178 0.000790881882277959 1575 2309.45454545455 2259 4.44285048809068e-05 1464 1.38882835685377 1.38882835685377 1 1.57468608700891 1571 1464 2098 3185 2765 2303 2259 2602 2987 2112 2058 2238 M13172 TURASHVILI_BREAST_NORMAL_DUCTAL_VS_LOBULAR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_NORMAL_DUCTAL_VS_LOBULAR_DN.html Genes down-regulated in normal ductal and normal lobular breast cells. 17389037 7/23 Arthur Liberzon 0.00077232233184699 0.00121568775513436 1955 2432.72727272727 2260 7.72590880016187e-05 960 1.21587111048506 -1.21587111048506 -1 1.29560274990809 1954 1947 4117 2612 3047 1742 2260 960 2913 3200 2008 2239 M1523 NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN.html Top 20 genes whose down-regulation correlated with gastrointestinal stromal tumors (GIST) and synovial sarcoma compared to other tumors. 11965276 14/32 John Newman 5.97156295199279e-05 0.000117475835403183 3845 2470.36363636364 2260 5.42884095189114e-06 940 2.16325305524375 -2.0550259978079 -1 3.10759785464067 3841 2243 940 2081 2260 2984 2418 3095 1925 1376 4011 2240 M2767 KANG_CISPLATIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_CISPLATIN_RESISTANCE_UP.html Genes up-regulated in gastric cancer cell lines resistant to cisplatin [PubChem=2767]. 14734480 12/30 Arthur Liberzon 0.000357196343881332 0.000592503386700149 2250 2184.72727272727 2260 3.24776683791919e-05 694 1.87787096307843 1.93923079934733 1 2.21526439808823 2352 3220 2249 2260 3268 2563 2096 803 694 2247 2280 2241 M948 REACTOME_IRAK2_MEDIATED_ACTIVATION_OF_TAK1_COMPLEX_UPON_TLR7_8_OR_9_STIMULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IRAK2_MEDIATED_ACTIVATION_OF_TAK1_COMPLEX_UPON_TLR7_8_OR_9_STIMULATION.html Genes involved in IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation 7/14 Reactome 0.000540144999870211 0.000868606544060333 1940 2359 2261 5.40276335280606e-05 722 1.25356437958013 -1.25356437958013 -1 1.40266616452504 1939 3748 4061 3519 3182 880 1725 912 3000 2261 722 2242 M2123 HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_UP.html Up-regulated genes in the cancer gene signature, representing a gene signature of cellular transformation. 20385360 189/397 Arthur Liberzon 1.8498738707153e-06 6.99647918381715e-06 1140 2117.63636363636 2264 1.68170493289712e-07 988 1.40590185135169 1.50456770629862 1 2.64918977747266 1139 2264 2518 3268 988 1813 1652 2610 2733 2385 1924 2243 M10431 GRUETZMANN_PANCREATIC_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRUETZMANN_PANCREATIC_CANCER_DN.html Genes down-regulated in pancreatic ductal adenocarcinoma (PDAC) identified in a meta analysis across four independent studies. 15897887 138/350 Leona Saunders 1.63733265325422e-06 6.49115128016012e-06 3655 2390.72727272727 2265 1.48848533802491e-07 927 1.85249232125282 2.1884584547511 1 3.51276179680127 3654 2265 1191 1222 927 3359 4594 2390 1696 1182 3818 2244 M15626 OUYANG_PROSTATE_CANCER_PROGRESSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/OUYANG_PROSTATE_CANCER_PROGRESSION_UP.html Genes up-regulated during prostate cancer progression in mice heterozygotic for both NKX3.1 and PTEN [GeneID=4824;5728]. 18381418 16/29 Jessica Robertson 0.000304547691426785 0.000511325862424191 815 1927.63636363636 2265 2.76899871245604e-05 433 1.20501576445553 -1.20501576445553 -1 1.44970535806332 813 2999 3075 2265 2664 433 609 1019 3234 3351 742 2245 M3782 NAKAYAMA_FRA2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_FRA2_TARGETS.html Genes down-regulated in ST1 cells (adult T-cell leukemia, ATL) after knockdown of FRA2 [GeneID=2355] by RNAi. 18071306 29/56 Jessica Robertson 2.11488069852944e-05 4.74632708491809e-05 1455 2327.54545454545 2267 1.92263729940927e-06 1455 1.09281683836302 1.13921593382904 1 1.72709564473943 1455 3150 3039 2980 1943 1591 1553 2267 3334 2783 1508 2246 M16651 RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN.html Genes down-regulated in poorly differentiated thyroid carcinoma (PDTC) compared to normal thyroid tissue. 17406368 490/1230 Arthur Liberzon 2.0968245304369e-06 7.59916453954163e-06 2855 2336.54545454545 2268 1.9062059353885e-07 1025 1.54434892738387 1.76594742459235 1 2.88981256871203 2852 2327 1405 1223 1054 4661 3387 2268 1883 1025 3617 2247 M19457 GRABARCZYK_BCL11B_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRABARCZYK_BCL11B_TARGETS_DN.html Genes down-regulated in Jurkat cells (transformed T lymphocytes) after knockdown of BCL11B [GeneID=64919] by RNAi. 17173069 25/97 Arthur Liberzon 5.37442285284313e-06 1.53388383485348e-05 3970 2603.81818181818 2272 4.8858508928821e-07 1452 1.06328528541844 -1.15238145028348 -1 1.87108648482341 3969 1452 2933 2254 1462 2213 2272 4047 2115 2484 3441 2248 M18806 TOOKER_GEMCITABINE_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TOOKER_GEMCITABINE_RESISTANCE_DN.html Down-regulated genes in Calu3 cells (non-small cell lung cancer, NSCLC) resistant to gemcitabine [PubChem=3461] which became up-regulated in response to bexarotene [PubChem=82146]. 17483357 86/171 Jessica Robertson 1.70030266028133e-05 3.93657028956439e-05 2275 2275.63636363636 2273 1.5457416376955e-06 1839 1.5325060599013 1.70836615421263 1 2.46749185975683 2273 1907 2310 1839 1872 3200 2396 2356 1889 2136 2854 2249 M13968 BIOCARTA_HIVNEF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HIVNEF_PATHWAY.html HIV-I Nef: negative effector of Fas and TNF 42/87 BioCarta 9.84325439933179e-06 2.48789051322917e-05 3580 2375.54545454545 2274 8.94845312760084e-07 461 1.92589617778619 -1.5149759057394 -1 3.24118151306894 3578 2274 1894 1269 1688 2562 3065 4603 461 2090 2647 2250 M4100 PROVENZANI_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PROVENZANI_METASTASIS_UP.html Genes up-regulated in polysomal and total RNA samples from SW480 cells (primary colorectal carcinoma, CRC) compared to the SW620 cells (lymph node metastasis from the same individual). 16531451 145/336 Arthur Liberzon 1.6010426137998e-06 6.42336103447421e-06 2275 2475.09090909091 2274 1.45549434450398e-07 913 1.34987495600039 1.73903587044973 1 2.56193055756312 2274 3386 1777 3313 913 4047 2847 2164 2611 1685 2209 2251 M3578 KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION.html Progesterone-mediated oocyte maturation 41/92 KEGG 1.9509775195665e-05 4.43154661012537e-05 1905 2683.72727272727 2275 1.7736316556412e-06 1397 1.0120129318591 -0.940319755931026 -1 1.6104169845723 1905 2275 2845 1807 1916 2085 1397 4486 3893 3758 3154 2252 M1585 FERRARI_RESPONSE_TO_FENRETINIDE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FERRARI_RESPONSE_TO_FENRETINIDE_DN.html Genes down-regulated in HUVEC cells (umbilical vein endothelium) by fenretinide [PubChem=1744]. 15958647 7/12 Arthur Liberzon 0.00121580694939123 0.00186063728440474 1750 2664.45454545455 2276 0.000121647264598433 1007 1.03938256623862 1.03938256623862 1 1.03731614183157 1748 3947 4518 2941 3916 1876 1007 1054 4357 2276 1669 2253 M12322 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_3.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 3. 12554760 11/24 Arthur Liberzon 8.49353385283104e-05 0.000160292789506106 3180 2169.54545454545 2276 7.72169252743609e-06 721 2.24045099515738 -2.72899692198977 -1 3.1079664560497 3179 3100 1332 2331 2359 2251 2791 721 1414 2111 2276 2254 M9174 ST_STAT3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_STAT3_PATHWAY.html STAT3 Pathway 8/19 Signaling Transduction KE 0.00671811966789948 0.00939111683217724 1660 2500.18181818182 2277 0.000673851641514229 1656 1.30554897145585 1.21396858145881 1 0.967446021955467 2461 1659 3886 2259 3198 3125 2177 1705 2277 1656 3099 2255 M885 GUTIERREZ_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP.html Genes exclusively up-regulated in B lymphocytes from CLL (chronic lymphocytic leukemia) patients but with a similiar expression pattern in the normal cells and in the cells from WM (Waldenstroem's macroblobulinemia) patients. 17252022 7/17 Arthur Liberzon 0.00029469543534548 0.00049620654330899 1850 2349.27272727273 2278 2.94734523070853e-05 187 2.06429082433848 2.09918686927983 1 2.49329997850344 1850 3035 4589 1470 2678 1918 2604 4072 187 2278 1161 2256 M229 PID_P38_ALPHA_BETA_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_ALPHA_BETA_DOWNSTREAM_PATHWAY.html Signaling mediated by p38-alpha and p38-beta 18832364 24/52 Pathway Interaction Database 0.000218308552755701 0.0003759624690236 2460 2222.54545454545 2279 1.98482017069714e-05 1022 1.88838863612757 2.01000625357558 1 2.36402944800544 2457 2279 1694 2420 2592 2132 1869 1939 1022 2872 3172 2257 M1806 BOCHKIS_FOXA2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BOCHKIS_FOXA2_TARGETS.html Direct targets of FOXA2 [GeneID=3170] in liver, according to a ChIP-chip analysis. 18660816 295/732 Jessica Robertson 1.13587903396069e-06 5.15768328792615e-06 4445 2496.09090909091 2279 1.03261783675026e-07 769 1.44388917050795 -1.2808062060931 -1 2.7906618349431 4443 1711 2115 1719 769 1498 4437 3417 2279 2332 2737 2258 M1482 IGLESIAS_E2F_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IGLESIAS_E2F_TARGETS_DN.html Genes down-regulated in pancreatic cells from mice with double knockout of E2F1 [GeneID=1869] and E2F2 [GeneID=1870] compared to wild type. 15146237 10/36 Kevin Vogelsang 0.0212502840319245 0.0278932299645933 3235 2602.90909090909 2280 0.00195076041383407 1661 2.19203091518536 -2.19203091518536 -1 1.2455380073313 3233 3431 1899 3764 3682 2156 2483 1661 2280 1969 2074 2259 M2201 PHESSE_TARGETS_OF_APC_AND_MBD2_UP http://www.broadinstitute.org/gsea/msigdb/cards/PHESSE_TARGETS_OF_APC_AND_MBD2_UP.html Genes up-regulated in small intestine upon loss of both APC and MBD2 [GeneID=324, 8932]. 18644872 7/31 Arthur Liberzon 4.15923969609568e-06 1.25824384867039e-05 4470 2484.18181818182 2281 4.15924748078987e-07 111 1.59862590456929 -0.940570615089736 -1 2.86340659391396 4470 384 4628 1508 1389 3823 4107 523 111 2281 4102 2260 M2148 SHEPARD_CRUSH_AND_BURN_MUTANT_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHEPARD_CRUSH_AND_BURN_MUTANT_DN.html Human orthologs of genes down-regulated in the crb ('crash and burn') zebrafish mutant that represents a loss-of-function mutation in BMYB [GeneID=4605]. 16150706 125/352 Jennifer Shepard 4.65969556153978e-07 2.97079366005108e-06 2115 2209.27272727273 2282 4.23608777134895e-08 425 1.67368185260377 1.81881558085913 1 3.38136179599971 2112 2683 1430 2423 425 3453 2282 2227 2821 1723 2723 2261 M972 MMS_MOUSE_LYMPH_HIGH_4HRS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MMS_MOUSE_LYMPH_HIGH_4HRS_UP.html Up-regulated at 4 hours following treatment of mouse lymphocytes (TK 3.7.2C) with a high dose of methyl methanesulfonate (MMS) 15515172 28/77 John Newman 1.58234026005592e-06 6.37457805738172e-06 3190 2306 2283 1.43849218013481e-07 727 2.18338708162263 3.25876632037262 1 4.1464973755932 3190 2810 2128 2575 906 3646 2283 1335 727 3589 2177 2262 M12595 FOSTER_TOLERANT_MACROPHAGE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FOSTER_TOLERANT_MACROPHAGE_UP.html Class T (tolerizeable) genes: induced during the first LPS stimulation and either not re-induced or induced to a much lesser degree in tolerant macrophages. 17538624 89/269 Jessica Robertson 3.05291665951378e-07 2.36072070403987e-06 3870 2389.63636363636 2283 2.77537916651261e-08 275 1.5531178502759 1.75364350451257 1 3.19445764137579 3866 1421 915 2069 275 3695 4662 2510 2283 523 4067 2263 M7494 REACTOME_TOLL_RECEPTOR_CASCADES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TOLL_RECEPTOR_CASCADES.html Genes involved in Toll Receptor Cascades 81/182 Reactome 2.03311413262015e-05 4.59583831425857e-05 3460 2587.54545454545 2284 1.84830265612806e-06 1928 1.29536920669655 -1.45017890152074 -1 2.05383641407228 3457 2044 2692 2182 1928 2214 4344 2284 2638 2432 2248 2264 M2306 SUMI_HNF4A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SUMI_HNF4A_TARGETS.html Genes up-regulated in HepG2 cells (hepatocellular carcinoma, HCC) upon expression of HNF4A [GeneID=3172] and down-regulated upon knockdown of HNF4A [GeneID=3172] in these cells by RNAi. 17403900 15/60 Arthur Liberzon 1.23089839044263e-05 2.99169598423972e-05 1580 2316.90909090909 2284 1.1190047976037e-06 1279 1.02886590374804 -0.918634450111119 -1 1.70140829278809 1578 2284 2531 3232 1762 1296 1279 3643 3796 2619 1466 2265 M3961 KYNG_DNA_DAMAGE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_UP.html Genes with GO annotation and up-regulated after DNA damage in cell lines from young donors. 15897889 152/392 Jessica Robertson 3.46133279881207e-05 7.2734553790284e-05 2775 2398.63636363636 2285 3.14671568936902e-06 1302 1.6517379738011 1.87865573514875 1 2.49849275930012 2774 2570 1302 1599 2095 4057 2311 2285 2200 2132 3060 2266 M7552 BIOCARTA_CARDIACEGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CARDIACEGF_PATHWAY.html Role of EGF Receptor Transactivation by GPCRs in Cardiac Hypertrophy 13/34 BioCarta 0.0121349810350865 0.0164538544937544 2700 2433.36363636364 2287 0.00110931253458217 1576 2.4947134188657 -2.4947134188657 -1 1.62655817766868 2700 2287 1839 1576 3276 2266 2704 2083 2777 3074 2185 2267 M2073 BAE_BRCA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BAE_BRCA1_TARGETS_DN.html Genes concordantly down-regulated in DU-145 and MCF-7 cells (lprostate, breast cancer) upon expression of BRCA1. 15520196 28/58 Arthur Liberzon 0.00257615742043927 0.00378666049942861 2600 2300.09090909091 2287 0.000234470818689568 1190 1.42143416983878 1.89097464388745 1 1.25827094237715 2599 2395 2230 1260 3685 3000 3556 1190 1908 2287 1191 2268 M10695 BROWNE_HCMV_INFECTION_8HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_8HR_UP.html Genes up-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 8 h time point that were not up-regulated at the previous time point, 6 h. 11711622 85/217 John Newman 1.99807962184357e-06 7.37244181729051e-06 2175 2163.90909090909 2288 1.81643766957979e-07 1026 1.58908072490048 1.80462573584471 1 2.98115629555676 2175 3306 1406 2566 1026 2946 2288 1338 2439 1414 2899 2269 M10462 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY.html Adipocytokine signaling pathway 32/102 KEGG 6.76600007837132e-05 0.000131612604264209 2290 2547.09090909091 2290 6.15109833871866e-06 1404 1.24481053692704 1.35161687451891 1 1.76576481345124 2290 1440 2090 1404 2288 2572 2342 4005 3720 3736 2131 2270 M7339 FURUKAWA_DUSP6_TARGETS_PCI35_DN http://www.broadinstitute.org/gsea/msigdb/cards/FURUKAWA_DUSP6_TARGETS_PCI35_DN.html Genes down-regulated in PCI-35 cells (pancreatic cancer, lack endogenous DUSP6 [GeneID=1848]) upon expression of DUSP6 off an adenoviral vector. 16532023 44/97 Arthur Liberzon 0.0839184282471183 0.0965721401684667 1040 2693.45454545455 2290 0.00793650793650794 1036 1.72841015352191 1.77739962856454 1 0.641350567297562 1036 4323 1940 3738 4661 2326 1628 2290 3260 2231 2195 2271 M7096 NIELSEN_SYNOVIAL_SARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_SYNOVIAL_SARCOMA_DN.html Top 20 negative significant genes associated with synovial sarcoma tumors. 11965276 13/30 Arthur Liberzon 2.39152339209194e-06 8.32591279000209e-06 3200 2171.18181818182 2291 2.17411453801451e-07 517 1.59603079014113 -1.55945791848897 -1 2.9633797340276 3198 517 1312 2359 1113 2988 2879 2181 2291 1283 3762 2272 M18615 KEGG_ALLOGRAFT_REJECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALLOGRAFT_REJECTION.html Allograft rejection 23/70 KEGG 0.0839184282471183 0.0965721401684667 2130 2399.27272727273 2292 0.00793650793650794 1631 1.91467826081909 -2.01689719116526 -1 0.710467932973614 2126 2867 1772 1929 3715 1631 2588 2738 2481 2292 2253 2273 M9267 TAGHAVI_NEOPLASTIC_TRANSFORMATION http://www.broadinstitute.org/gsea/msigdb/cards/TAGHAVI_NEOPLASTIC_TRANSFORMATION.html Genes that cooperate with MYC and TBX2 [GeneID=4609;6909] to transform MEF cells (embryo fibroblasts). 18762810 10/23 Jessica Robertson 8.27718988726102e-05 0.000156841535833826 4135 2762.09090909091 2292 7.52500120115206e-06 1393 1.37223277348957 -1.46722821967103 -1 1.90831062455743 4134 1393 2268 2130 2345 3841 4030 2292 2061 1968 3921 2274 M16830 NELSON_RESPONSE_TO_ANDROGEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/NELSON_RESPONSE_TO_ANDROGEN_DN.html Genes down-regulated in LNCaP cells (prostate cancer) in response to synthetic androgen R1881 [PubChem=13766]. 12185249 14/30 Broad Institute 0.000230603302941188 0.000395826768345204 4535 2808.36363636364 2292 2.09661343867345e-05 1577 1.88159618637157 -2.36582573889722 -1 2.34014705645244 4535 2207 1865 2292 2603 4270 4013 2185 1577 1896 3449 2275 M17668 BIOCARTA_AKAP13_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKAP13_PATHWAY.html Rho-Selective Guanine Exchange Factor AKAP13 Mediates Stress Fiber Formation 6/15 BioCarta 0.000707900583168094 0.00111841609329929 1785 2589.54545454545 2293 7.08126189778501e-05 948 0.681378109929211 0.681378109929211 1 0.735080662903369 1783 2293 3862 2628 4615 1522 1175 948 3648 4283 1728 2276 M1059 REACTOME_NOD1_2_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NOD1_2_SIGNALING_PATHWAY.html Genes involved in NOD1/2 Signaling Pathway 23/37 Reactome 0.00118219748950445 0.00181275439653726 1385 2026.45454545455 2294 0.000107530294220534 819 1.32682275639587 -1.29643619668403 -1 1.32967627865363 1382 2949 2715 2516 3154 819 1247 1153 3215 2294 847 2277 M1432 SANSOM_APC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_APC_TARGETS_DN.html Top genes down-regulated at day 5 of Cre-Lox induced APC [GeneID=324] knockout in the intestine. 15198980 241/653 Kevin Vogelsang 1.87697647435492e-09 3.71118639612959e-08 3895 2264.45454545455 2294 1.70634225086936e-10 228 1.69794022365565 1.90239913181553 1 4.61167761177737 3894 241 228 1162 638 4267 3911 3342 2294 427 4505 2278 M13606 AIYAR_COBRA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/AIYAR_COBRA1_TARGETS_DN.html Genes down-regulated in T47D cells (breast cancer) after COBRA1 [GeneID=25920] knockdown by RNAi. 17043641 29/55 Arthur Liberzon 0.000880555944851889 0.00137469920198994 2295 2487.63636363636 2295 8.00825988516958e-05 1317 1.60726895486099 1.57782987503471 1 1.68130273761758 2295 3313 2143 3470 2866 1928 1317 3953 1615 2338 2126 2279 M1409 PEART_HDAC_PROLIFERATION_CLUSTER_UP http://www.broadinstitute.org/gsea/msigdb/cards/PEART_HDAC_PROLIFERATION_CLUSTER_UP.html Cell proliferation genes up-regulated by histone deacetylase (HDAC) inhibitors SAHA and depsipeptide [PubChem=5311;5352062]. 15738394 45/88 Kate Stafford 6.13667639186769e-05 0.000120319939633021 1545 2646 2295 5.5789523408212e-06 1544 1.0727207280907 1.10720499685318 1 1.53693175923029 1544 3336 3276 3662 2266 2129 1550 1696 3709 3643 2295 2280 M2101 STAMBOLSKY_TARGETS_OF_MUTATED_TP53_UP http://www.broadinstitute.org/gsea/msigdb/cards/STAMBOLSKY_TARGETS_OF_MUTATED_TP53_UP.html Genes induced in SKBR3 cells (breast cancer) by mutated TP53 [GeneID=7157]. 20227041 26/63 Arthur Liberzon 5.33233169910784e-06 1.52547657765686e-05 3330 2290.63636363636 2295 4.84758602144426e-07 928 1.98893433065072 -1.47337937658806 -1 3.50170677134939 3330 2340 1534 2472 1459 2295 3305 3436 928 2076 2022 2281 M2252 CERIBELLI_PROMOTERS_INACTIVE_AND_BOUND_BY_NFY http://www.broadinstitute.org/gsea/msigdb/cards/CERIBELLI_PROMOTERS_INACTIVE_AND_BOUND_BY_NFY.html Transcriptionally inactive genes whose promoters (regions between -2 kb to +0.5 kb relative to trascription start sites) where bound by NF-Y transcription factor. 18212061 12/92 Arthur Liberzon 2.05637928350546e-05 4.63724413980106e-05 4135 2595 2296 1.86945318645577e-06 1084 2.18952814389747 1.56284015265574 1 3.46842764241074 4131 2173 2015 2296 1933 3150 3408 1408 1084 2979 3968 2282 M2219 WIERENGA_PML_INTERACTOME http://www.broadinstitute.org/gsea/msigdb/cards/WIERENGA_PML_INTERACTOME.html Proteins identified in complex with PML [GeneID=5371] in K562 cells (lymphoblast). 18779318 36/96 Arthur Liberzon 0.00101527842829632 0.0015732786755941 1550 2634.27272727273 2297 9.23406611161351e-05 986 2.00713056927645 2.2732540760474 1 2.0565917242462 1547 4326 2664 2950 4558 2007 2297 986 1539 3844 2259 2283 M727 REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES.html Genes involved in Metabolism of amino acids and derivatives 97/214 Reactome 8.56558593041302e-06 2.21758760607268e-05 1975 2326.09090909091 2298 7.78692661841773e-07 1637 1.52297637717634 -1.63189535381678 -1 2.59089564403694 1971 1906 2827 2298 1637 1956 3188 1991 2578 2925 2310 2284 M7362 HASLINGER_B_CLL_WITH_6Q21_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_6Q21_DELETION.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with deletions in the 6q21 region. 15459216 29/53 Kevin Vogelsang 0.0821344905348237 0.0965721401684667 765 2517 2298 0.00776103578249217 764 1.33590813205917 -1.45265131915637 -1 0.49570724628208 764 3057 2298 2590 3727 1788 2105 2025 3495 3627 2211 2285 M2526 BOSCO_ALLERGEN_INDUCED_TH2_ASSOCIATED_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/BOSCO_ALLERGEN_INDUCED_TH2_ASSOCIATED_MODULE.html Genes representing a co-expression network in atopic CD4 [GeneID=920] T lymphocyte responses. 19414752 85/248 Antony Bosco 3.42088172455331e-06 1.08312511900384e-05 2785 2241.81818181818 2299 3.10989731259278e-07 829 1.77661362179734 -1.44027836299457 -1 3.22447935565348 2783 2445 976 2299 1276 4364 3245 1732 2215 829 2496 2286 M9814 RODRIGUES_THYROID_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_DN.html Genes down-regulated in poorly differentiated thyroid carcinoma (PDTC) compared to anaplastic thyroid carcinoma (ATC). 17406368 60/154 Arthur Liberzon 2.57266545554547e-05 5.63078483170766e-05 4190 2667.18181818182 2300 2.33881412783434e-06 1752 1.70858044145253 -1.7972395147164 -1 2.65390559263191 4189 2300 1830 1924 1996 2709 4034 3280 1752 1939 3386 2287 M554 REACTOME_SPHINGOLIPID_DE_NOVO_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SPHINGOLIPID_DE_NOVO_BIOSYNTHESIS.html Genes involved in Sphingolipid de novo biosynthesis 22/37 Reactome 6.96149711434124e-05 0.000134688585787791 2445 2361.18181818182 2301 6.32883400720728e-06 1376 1.19441410307613 1.31418105707954 1 1.68989698196111 2444 1376 2260 2072 2299 2971 2580 2766 2301 2185 2719 2288 M2038 CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_UP.html Genes up-regulated in APL (acute promyeolocytic leukemia) blasts expressing PML-RARA fusion [GeneID=5371;5914] compared to normal promyeloblasts. 16990782 137/396 Leona Saunders 6.335360430494e-05 0.000123904419771682 2305 2542.81818181818 2301 5.75958443437476e-06 1418 1.79388703904552 2.03040904406762 1 2.56181701131639 2301 3628 1418 2390 2273 4173 3982 1729 2420 1582 2075 2289 M6117 GARCIA_TARGETS_OF_FLI1_AND_DAX1_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARCIA_TARGETS_OF_FLI1_AND_DAX1_UP.html Genes up-regulated in the A673 cells (Ewing sarcoma) after double knockdown of both FLI1 and DAX1 [GeneID=2313;190] by RNAi. 18591936 47/113 Jessica Robertson 0.0128759569806154 0.0174232556774946 2970 2512.72727272727 2302 0.00117744904655792 1212 1.74959778445608 1.9492772066329 1 1.1248416322104 2967 2302 1700 1212 3285 4160 3494 2195 2286 1228 2811 2290 M6822 ONDER_CDH1_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_1_DN.html Genes down-regulated in HMLE cells (mmortalized nontransformed mammary epithelial) by expression of a dominant-negative form of E-cadhedrin (CDH1) [GeneID=999]. 18483246 119/280 Jessica Robertson 1.62580172722633e-05 3.77340608904535e-05 2450 2187.72727272727 2303 1.47801249276196e-06 982 1.89785892395771 2.27659743578787 1 3.06850106530288 2448 2572 982 1712 1866 3827 2474 2323 1618 1940 2303 2291 M271 PID_PI3K_PLC_TRK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PI3K_PLC_TRK_PATHWAY.html Trk receptor signaling mediated by PI3K and PLC-gamma 18832364 34/60 Pathway Interaction Database 1.98144778908622e-06 7.32838542988004e-06 2735 2255 2305 1.80131779426858e-07 799 1.58542869235522 1.86127743360047 1 2.97581350029192 2733 2195 2272 799 1021 3454 2454 3465 1317 2305 2790 2292 M3334 SHIPP_DLBCL_CURED_VS_FATAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHIPP_DLBCL_CURED_VS_FATAL_UP.html Top 50 up-regulated markers for the diffused large B-cell lymphoma (DLBCL) that distinguished between cured and fatal/refractory clinical outcomes. 11786909 36/144 Jean Junior 1.04260052417536e-05 2.60150482230337e-05 3845 2677.90909090909 2305 9.47823150172082e-07 1206 2.00568024546889 2.29193852323867 1 3.361236022887 3844 2305 1590 1437 1707 4665 4610 2707 1206 2031 3355 2293 M1187 HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_DN.html Genes down-regulated in MCF7 cells (breast cancer, normal TP53 [GeneID=7157]) undergoing mitotic arrest and apoptosis after treatment with 100 nM docetaxel [PubChem=148124]. 17099726 36/85 Arthur Liberzon 7.64905885419562e-05 0.000146299958329635 3500 2502.54545454545 2306 6.95393164823339e-06 1109 1.57489456894287 -1.11298228036052 -1 2.20753932239285 3499 2306 1109 1560 2320 4376 3549 1937 1799 1688 3385 2294 M8804 GILMORE_CORE_NFKB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/GILMORE_CORE_NFKB_PATHWAY.html Genes encoding the NF-kB core signaling proteins. 17072321 6/14 Arthur Liberzon 0.000436486322815667 0.000713419919328293 2215 2493.45454545455 2308 4.36572080663133e-05 1566 0.974681658613903 -0.877741928686536 -1 1.12106589600492 2211 1566 4211 1962 2763 1715 3096 2308 2584 3053 1959 2295 M3026 CHUNG_BLISTER_CYTOTOXICITY_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHUNG_BLISTER_CYTOTOXICITY_UP.html Genes up-regulated in blister cells from patients with adverse drug reactions (ADR). 19029983 80/182 Jessica Robertson 7.62355876539466e-07 4.01259176310425e-06 2310 2429.36363636364 2308 6.9305103701388e-08 603 1.01033768565361 -0.909634412500928 -1 1.99298496171422 2308 1768 3385 3205 603 1293 2979 2233 3290 3914 1745 2296 M2831 BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_UP http://www.broadinstitute.org/gsea/msigdb/cards/BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_UP.html Genes up-regulated in pre B lymphocyte after induction of physiological DNA double-strand breaks (DSB) by RAG2 [GeneID=5897]; the changes depend on ATM [GeneID=472] but not NFKB signaling. 18849970 36/75 Jessica Robertson 1.21257539774068e-05 2.95967818648226e-05 3035 2479 2308 1.10234734650162e-06 1543 1.22342102093001 -1.31970698993003 -1 2.02522865608357 3034 1543 2308 3133 1755 2025 3015 3425 3169 1690 2172 2297 M7747 BIOCARTA_IL2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL2_PATHWAY.html IL 2 signaling pathway 16/41 BioCarta 0.00020611331866288 0.000357080454046044 1570 2347.45454545455 2309 1.87393301376637e-05 1288 1.00595511881772 -0.807309664100653 -1 1.26756024439561 1568 2750 3099 2309 2571 1288 1881 2033 3080 3341 1902 2298 M15009 SCHRAMM_INHBA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHRAMM_INHBA_TARGETS_DN.html Genes down-regulated in Kelly cells (neuroblastoma) by overexpressing INHBA [GeneID=3624] off a plasmid vector. 15580313 13/37 Arthur Liberzon 0.0351135999665226 0.0450627209760075 2245 2558.63636363636 2312 0.00324426276459933 1426 1.57053306006034 1.43385084768476 1 0.772805672970648 2243 2926 2218 3521 3443 1711 1426 2258 3006 3081 2312 2299 M19613 BIOCARTA_IGF1R_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IGF1R_PATHWAY.html Multiple antiapoptotic pathways from IGF-1R signaling lead to BAD phosphorylation 19/44 BioCarta 7.42083255457068e-05 0.000142341470940312 1805 2448.09090909091 2313 6.74643898083484e-06 1605 0.955503483089676 1.10477875710943 1 1.34349573278058 1805 2431 3352 1605 2313 2035 1859 3016 2617 3897 1999 2300 M235 PID_TCR_CALCIUM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCR_CALCIUM_PATHWAY.html Calcium signaling in the CD4+ TCR pathway 18832364 11/34 Pathway Interaction Database 0.000496793806147792 0.000802473552433145 810 1987.90909090909 2314 4.51732750274458e-05 508 1.43981924792019 1.43981924792019 1 1.62917505649554 810 3252 2573 2624 3628 523 508 2120 2314 2818 697 2301 M3835 BENPORATH_SOX2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_SOX2_TARGETS.html Set 'Sox2 targets': genes upregulated and identified by ChIP on chip as SOX2 [GeneID=6657] transcription factor targets in human embryonic stem cells. 18443585 540/1168 Jessica Robertson 2.29060577492805e-06 8.08266465460306e-06 2345 2534.90909090909 2314 2.29060813602514e-07 1144 1.4655459153784 1.70430692611481 1 2.72800438696243 2342 3626 4337 1726 1144 4207 2546 1258 2202 2182 2314 2302 M15164 FAELT_B_CLL_WITH_VH3_21_UP http://www.broadinstitute.org/gsea/msigdb/cards/FAELT_B_CLL_WITH_VH3_21_UP.html Genes up-regulated in samples from B-CLL (B-cell chronic lymphocytic leukemia) with the immunoglobulin heavy chain VH3-21 gene. 15817677 33/70 Kevin Vogelsang 7.42697095795338e-05 0.000142400924341119 875 2291.27272727273 2314 6.75201972419211e-06 873 1.30841316190141 1.30841316190141 1 1.83962136635323 873 3217 2928 4287 2314 1720 1248 1330 2978 2644 1665 2303 M18795 REACTOME_METAL_ION_SLC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METAL_ION_SLC_TRANSPORTERS.html Genes involved in Metal ion SLC transporters 11/24 Reactome 7.51577152870078e-05 0.000143926871203481 4015 2764.54545454545 2316 6.83275299932902e-06 657 1.6240289316772 2.03030651192408 1 2.28062737991901 4014 657 1893 1814 2316 4593 4403 3724 1562 1512 3922 2304 M9134 BIOCARTA_TRKA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TRKA_PATHWAY.html Trka Receptor Signaling Pathway 13/25 BioCarta 2.01288708299707e-05 4.55891197241387e-05 2635 2148 2318 1.82991409101515e-06 362 1.86860002753837 1.99463039541433 1 2.96509950594 2634 2318 1611 362 1923 3450 3072 3550 465 1746 2497 2305 M962 REACTOME_IRON_UPTAKE_AND_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IRON_UPTAKE_AND_TRANSPORT.html Genes involved in Iron uptake and transport 19/51 Reactome 0.000294535246480014 0.000496115084473525 2425 2226.81818181818 2318 2.67795169227606e-05 1559 1.39445545250817 -1.39919987901293 -1 1.68429755176507 1593 2013 2675 3092 2654 1559 1649 2100 2318 2421 2421 2306 M5793 CHANG_CORE_SERUM_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_CORE_SERUM_RESPONSE_DN.html Down-regulated genes in the canonical gene expression signature of the fibroblast core serum response (CSR) defined by the Stanford group. 14737219 135/325 Arthur Liberzon 1.70337535611398e-05 3.94173675000005e-05 1895 2433.81818181818 2318 1.54853504076087e-06 1465 1.51402942972528 1.5238887020486 1 2.43742736060284 1894 1526 1465 3343 1875 2734 2308 3371 2869 2318 3069 2307 M15068 NOUZOVA_TRETINOIN_AND_H4_ACETYLATION http://www.broadinstitute.org/gsea/msigdb/cards/NOUZOVA_TRETINOIN_AND_H4_ACETYLATION.html Genes whose CpG islands showed greatly increased histone H4 acetylation in NB4 cells (acute promyelocytic leukemia, APL) upon treatment with tretinoin [PubChem=444795]. 15302897 117/239 Kevin Vogelsang 7.69242677078654e-05 0.000147069407784193 1125 2752 2321 6.99335977644409e-06 1122 0.872934708541983 -0.896024182595708 -1 1.22287099241068 1122 4130 3643 4458 2321 1190 1643 2111 3710 4150 1794 2308 M13166 REACTOME_DOWNSTREAM_TCR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNSTREAM_TCR_SIGNALING.html Genes involved in Downstream TCR signaling 17/42 Reactome 1.83779266849654e-06 6.97587836865205e-06 3220 2271.63636363636 2322 1.67072200337944e-07 966 1.34814937801208 -1.26339700122371 -1 2.54099586553888 3220 1135 2322 966 981 2470 3316 4225 1715 2213 2425 2309 M738 REACTOME_PHASE1_FUNCTIONALIZATION_OF_COMPOUNDS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHASE1_FUNCTIONALIZATION_OF_COMPOUNDS.html Genes involved in Phase 1 - Functionalization of compounds 19/126 Reactome 2.93577220239983e-06 9.66083464918932e-06 2325 2111.36363636364 2323 2.66888738184055e-07 688 1.79139907354377 -1.61455236749861 -1 3.28383452403647 2323 1051 688 2318 1211 2348 3194 3747 2588 1113 2644 2310 M1548 KEEN_RESPONSE_TO_ROSIGLITAZONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KEEN_RESPONSE_TO_ROSIGLITAZONE_UP.html Genes up-regulated in aorta biopsies from mice treated with rosiglitazone [PubChem=77999]. 15054141 28/55 John Newman 0.00317485237775869 0.00460314302047563 1925 2701.27272727273 2323 0.000289040302910413 1232 1.45722848525043 1.86144332069863 1 1.24478828430567 1925 4147 2323 4351 4167 1925 1236 1232 3072 3184 2152 2311 M1680 SUZUKI_RESPONSE_TO_TSA http://www.broadinstitute.org/gsea/msigdb/cards/SUZUKI_RESPONSE_TO_TSA.html Genes up-regulated by TSA alone [PubChem=5562], with non-hypermethylated promoters, in RKO cells (colorectal cancer). 11992124 13/32 John Newman 2.42951794633919e-05 5.37268574636406e-05 2350 2567.09090909091 2323 2.20867706960055e-06 1798 1.44024554002839 0.704908310204565 1 2.24783377763921 3404 1798 1965 2323 1976 2044 2347 2347 2276 3087 4671 2312 M17641 FRASOR_RESPONSE_TO_ESTRADIOL_UP http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_RESPONSE_TO_ESTRADIOL_UP.html Genes up-regulated in MCF-7 cells (breast cancer) by estradiol (E2) [PubChem=5757]. 14973112 19/51 Arthur Liberzon 8.41374840819576e-06 2.19037916893363e-05 2825 1972.45454545455 2324 7.6488914419719e-07 837 2.02599315312383 1.95744797263515 1 3.45060097627671 2821 2513 1087 1077 1628 2799 2324 837 2610 1116 2885 2313 M13984 MARZEC_IL2_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARZEC_IL2_SIGNALING_UP.html Genes up-regulated by IL2 [GeneID=3558] in cells derived from CD4+ [GeneID=920] cutaneous T-cell lymphoma (CTCL). 18281483 71/169 Jessica Robertson 6.45072270638121e-07 3.62335367154678e-06 2325 2099.90909090909 2324 5.86429508893499e-08 544 1.31926258003902 1.38767103055108 1 2.6237374979156 2324 1769 1803 1481 544 2877 2575 3063 2679 1442 2542 2314 M1809 MATZUK_CUMULUS_EXPANSION http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_CUMULUS_EXPANSION.html Genes important for cumulus expansion, based on mouse models with female fertility defects. 18989307 5/10 Jessica Robertson 1.26363248914967e-05 3.05823083878495e-05 3315 2489.18181818182 2324 1.26363967465898e-06 997 1.65951696393654 -1.65951696393654 -1 2.73850453568989 3311 1759 4485 2324 1807 2869 3609 1255 2053 2912 997 2315 M10401 BIOCARTA_TEL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TEL_PATHWAY.html Telomeres, Telomerase, Cellular Aging, and Immortality 13/37 BioCarta 7.78909807659322e-05 0.000148763504199048 4160 2573 2326 7.08124896655685e-06 163 2.2526330832771 -1.34664192833354 -1 3.15155808868205 4160 1308 1970 716 2326 4201 4405 1462 163 3075 4517 2316 M10287 BIOCARTA_FMLP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FMLP_PATHWAY.html fMLP induced chemokine gene expression in HMC-1 cells 22/63 BioCarta 5.25811817449514e-05 0.000104804516230048 4450 2821.81818181818 2327 4.78022168231744e-06 1373 1.43862788845057 -1.1681851132404 -1 2.09271135286567 4448 1373 2157 1671 2220 4129 4199 2529 2327 1712 4275 2317 M5392 BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP.html Genes up-regulated in NIH3T3 cells (fibroblasts) after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins; the changes did not depend on expression of constitutively active (Q63L) form of RHOA [GeneID=387]. 17213802 19/41 Leona Saunders 0.001728688475502 0.00258311039419719 2745 2301.81818181818 2327 0.000157277119897157 1049 1.17174237011301 -1.1915334291303 -1 1.10838761430659 2745 1049 2257 2327 2994 1713 2197 2316 2823 2423 2476 2318 M3002 FRASOR_RESPONSE_TO_ESTRADIOL_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_RESPONSE_TO_ESTRADIOL_DN.html Genes down-regulated in MCF-7 cells (breast cancer) by estradiol (E2) [PubChem=5757]. 14973112 77/178 Arthur Liberzon 7.7905599510129e-05 0.000148763504199048 4230 2381.72727272727 2327 7.08257803742266e-06 643 1.80835131176461 1.89606658417202 1 2.52998335382753 4226 827 659 1091 2327 3377 4592 2398 1487 643 4572 2319 M1748 ZHENG_FOXP3_TARGETS_IN_T_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_IN_T_LYMPHOCYTE_UP.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are up-regulated only in mature (peripheral blood) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 10/14 Jessica Robertson 2.06178309668525e-05 4.64719364649692e-05 2010 2472.36363636364 2327 1.87436583585152e-06 1178 0.97836107428347 1.01781547803728 1 1.54948716523674 2010 2321 2688 3088 1936 1691 1178 2327 3749 3495 2713 2320 M7678 CHIANG_LIVER_CANCER_SUBCLASS_POLYSOMY7_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_POLYSOMY7_DN.html Marker genes down-regulated in the 'chromosome 7 polysomy' subclass of hepatocellular carcinoma (HCC); characterized by polysomy of chromosome 7 and by a lack of gains of chromosome 8q. 18701503 18/39 Yujin Hoshida 0.0132905636009297 0.0179428352157754 1460 2580.45454545455 2328 0.00121559452657465 673 1.71084518726485 1.82832150795293 1 1.09194633783328 1456 4521 2486 4132 4559 1880 673 1547 3028 2328 1775 2321 M18320 WINNEPENNINCKX_MELANOMA_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WINNEPENNINCKX_MELANOMA_METASTASIS_DN.html Genes from the 254-gene classifier which were down-regulated in melanoma patients with a reported distant metastasis within 4 years. 16595783 18/51 Arthur Liberzon 0.00880076050900925 0.0121152654950697 3800 2574.54545454545 2329 0.000803287730473213 1345 2.01466881001177 -1.11796346440559 -1 1.41146330890825 3799 1378 1345 1990 3228 3047 2806 2298 1652 2329 4448 2322 M9670 BIOCARTA_STRESS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STRESS_PATHWAY.html TNF/Stress Related Signaling 18/35 BioCarta 3.79472837118013e-05 7.88912916918815e-05 3170 2307.63636363636 2330 3.4498125701272e-06 1570 1.3481169872234 -1.38908458723246 -1 2.02183295778209 3170 1605 2580 1660 2122 2680 2795 2330 1570 2322 2550 2323 M9012 GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_DN.html Down-regulated genes from the set B (Fig. 5a): specific signature shared by cells expressing either AF4-MLL or MLL-AF4 [GeneID=4299;4297] fusion proteins. 17130830 6/11 Arthur Liberzon 0.000350594339964679 0.000582790023793716 3095 2469.63636363636 2331 3.50649664625579e-05 1320 1.76429605534337 -1.87641184836786 -1 2.08591325084908 3093 1321 4167 2027 2713 2512 3436 2183 2063 1320 2331 2324 M2780 REACTOME_SIGNALING_BY_ROBO_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ROBO_RECEPTOR.html Genes involved in Signaling by Robo receptor 13/36 Reactome 2.45650676927292e-05 5.41703092744136e-05 3065 2550.45454545455 2336 2.23321290809869e-06 1773 0.972641631123873 -1.16503189770351 -1 1.51676135148382 3065 2017 3002 2336 1982 2082 3512 3361 1773 3077 1848 2325 M2220 KEGG_FOLATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FOLATE_BIOSYNTHESIS.html Folate biosynthesis 5/12 KEGG 7.26984324286877e-05 0.00013996090976205 3495 2245.45454545455 2337 7.27008108161299e-06 565 1.24879375367669 -0.865277648940037 -1 1.75922309128634 3492 1668 3802 2548 2337 1191 565 3525 881 2881 1810 2326 M18008 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_RED_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_RED_DN.html Genes from the red module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 23/50 Arthur Liberzon 0.0115377851533191 0.0156804121892265 2195 2619.63636363636 2337 0.00105443113638569 1515 1.36889000050491 1.74083396608699 1 0.902981780966684 2193 3773 2158 4001 3300 2337 1562 1515 2806 2296 2875 2327 M9503 BIOCARTA_FAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FAS_PATHWAY.html FAS signaling pathway ( CD95 ) 17/35 BioCarta 9.04499819388361e-05 0.000168796740488007 1985 2054 2338 8.22306371634734e-06 544 1.16853457722509 -1.02768253029953 -1 1.61140874475059 1981 2479 2855 2338 2380 762 544 3562 1728 2799 1166 2328 M14981 REACTOME_GAP_JUNCTION_ASSEMBLY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAP_JUNCTION_ASSEMBLY.html Genes involved in Gap junction assembly 9/18 Reactome 0.00110621450608309 0.00170659075916021 1570 2279.90909090909 2340 0.000110676556193344 887 2.41060261599115 2.28939630864819 1 2.43888126821804 1566 1619 4103 2431 2922 2340 1624 3173 2032 887 2382 2329 M11105 NIELSEN_LEIOMYOSARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LEIOMYOSARCOMA_DN.html Top 20 negative significant genes associated with CNN1 [GeneID=1264] negative leiomyosarcoma tumors. 11965276 16/32 John Newman 8.1046354294973e-05 0.000153882988746452 1565 2454.09090909091 2340 7.36812183054858e-06 1565 0.952190550522595 0.982083821373205 1 1.32705282714792 1565 2455 2942 3052 2340 1978 2306 1878 3522 2738 2219 2330 M8834 WHITESIDE_CISPLATIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WHITESIDE_CISPLATIN_RESISTANCE_DN.html Genes down-regulated in NCI-H2170 cells (lung cancer) upon induction of resistance to cisplatin [PubChem=2767]. 14737109 23/64 John Newman 6.13474225214689e-05 0.000120319939633021 4045 2786.90909090909 2342 5.57719393390135e-06 290 2.11443030802842 2.45095652584475 1 3.02943255393581 4042 2240 1829 2276 2265 4365 3984 2342 290 2790 4233 2331 M68 PID_RHOA_REG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RHOA_REG_PATHWAY.html Regulation of RhoA activity 18832364 31/59 Pathway Interaction Database 4.20479263558215e-05 8.6079765357527e-05 2740 2401.72727272727 2344 3.82261182058793e-06 470 1.29279837425273 -1.33435264878347 -1 1.92097258215456 2740 470 1645 1687 2150 2344 3050 4487 3255 1677 2914 2332 M14387 DAIRKEE_TERT_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAIRKEE_TERT_TARGETS_DN.html Genes down-regulated in non-spontaneously immortalizing (NSI) primary breast cancer tumor cultures upon expression of TERT [GeneID=7015] off a retroviral vector. 17471242 80/295 Arthur Liberzon 5.50381836847085e-06 1.56159998283158e-05 2170 2326 2345 5.0034837614705e-07 1410 1.59619947931846 1.7039822271901 1 2.80432959549747 2168 2389 1896 2731 1473 3631 2345 3134 2448 1410 1961 2333 M2438 TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA.html Genes whose DNA methylation differed between primary ALL cells (acute lymphoblastic leukemia) and normal peripheral blood samples. 17363581 61/146 Jessica Robertson 2.82511139374921e-05 6.10349100558267e-05 3150 2620.81818181818 2345 2.56831606620952e-06 1045 1.81396887859385 2.19400355456064 1 2.79439033606315 3147 3390 1432 2345 2029 4169 4630 1045 2084 1226 3332 2334 M16120 BIOCARTA_SALMONELLA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SALMONELLA_PATHWAY.html How does salmonella hijack a cell 13/24 BioCarta 0.000810819769139587 0.00127329136668502 3095 2387.90909090909 2347 7.373806860425e-05 78 3.16989871765081 -1.31189359692459 -1 3.3544709595527 3094 2246 1732 1442 2851 3720 3341 1972 78 2347 3444 2335 M2186 PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_DN http://www.broadinstitute.org/gsea/msigdb/cards/PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_DN.html Genes down-regulated in ovarian tumors from mouse models for the BMP SMAD signaling (gonad specific double knockout of SMAD1 and SMAD5 [GeneID=4086, 4090]). 17967875 91/257 Arthur Liberzon 1.70028332864908e-06 6.64677658017817e-06 3160 2322.63636363636 2347 1.54571331156798e-07 943 1.44397675608201 -1.09982784422286 -1 2.73268921381189 3159 2413 2347 2690 943 3861 1780 1706 2068 1853 2729 2336 M16311 NAGASHIMA_EGF_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAGASHIMA_EGF_SIGNALING_UP.html Genes up-regulated in MCF7 cells (breast cancer) after stimulation with EGF [GeneID=1950]. 17142811 50/109 Arthur Liberzon 3.11645117656902e-07 2.39797868857183e-06 1745 2259.45454545455 2348 2.83313783457803e-08 278 1.63580735848739 1.51300522978606 1 3.36046732140553 1742 3051 1703 2455 278 2686 2348 3578 2780 1946 2287 2337 M2301 VANDESLUIS_COMMD1_TARGETS_GROUP_4_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_COMMD1_TARGETS_GROUP_4_UP.html Genes up-regulated in 9.5 days post coitus (dpc) embryos with COMMD1 [GeneID=150684] knockout and in normal 8.5 dpc embryos compared to normal 9.5 dpc embryos. 17371845 9/23 Arthur Liberzon 2.34852357085619e-06 8.21581875658796e-06 3050 2207.54545454545 2348 2.34852605286321e-07 597 2.97189889349878 2.99782451566277 1 5.52425931729187 3047 1066 4644 597 1158 3796 3441 2348 784 889 2513 2338 M1498 BRACHAT_RESPONSE_TO_METHOTREXATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BRACHAT_RESPONSE_TO_METHOTREXATE_DN.html Genes down-regulated in FL5.12 cells (pro-B lymphocyte) in response to methotrexate [PubChem=4112]. 12447701 26/59 John Newman 1.93487606751668e-05 4.40137342348698e-05 3280 2491.36363636364 2349 1.75899371340977e-06 1547 1.36316007940722 -1.43145400360395 -1 2.17067614473055 3276 2116 2349 2340 1913 3103 1547 2139 2600 2548 3474 2339 M2347 TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_TOP20_DN http://www.broadinstitute.org/gsea/msigdb/cards/TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_TOP20_DN.html Top 20 down-regulated genes in leukemic progenitor cells expressing activated fusion of ESWR1 and FLI1 [GeneID=2130, 2313] compared to normal hematopoetic progenitors. 17875932 13/32 Arthur Liberzon 0.000276160673800338 0.000467011518379064 960 1817.36363636364 2349 2.51086677885887e-05 614 1.3406809121143 1.3406809121143 1 1.63221210944435 956 2349 2708 2874 2899 896 710 1025 2592 2368 614 2340 M556 REACTOME_TERMINATION_OF_O_GLYCAN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TERMINATION_OF_O_GLYCAN_BIOSYNTHESIS.html Genes involved in Termination of O-glycan biosynthesis 4/22 Reactome 0.00472241233355057 0.00671192726570153 1830 2428.54545454545 2351 0.000473247798178297 1465 2.17126611361153 2.17126611361153 1 1.72473572891376 1826 1851 3929 2546 3145 2351 1499 3719 1465 2660 1723 2341 M14437 VALK_AML_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_5.html Top 40 genes from cluster 5 of acute myeloid leukemia (AML) expression profile; 96% of the samples are FAB M4 or M5 subtype. 15084694 21/69 Jessica Robertson 0.0807079349543271 0.0965721401684667 2130 2689.36363636364 2351 0.00762093949650225 1829 1.41534594819536 1.43922618816825 1 0.525183750156316 2128 3804 2599 4130 3554 2311 1829 2351 2838 2087 1952 2342 M13881 REACTOME_SIGNALLING_TO_ERKS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALLING_TO_ERKS.html Genes involved in Signalling to ERKs 24/46 Reactome 0.000100967468978372 0.000186053306973124 4425 2462.27272727273 2352 9.17928210071372e-06 753 1.5959169088297 -1.60157003095198 -1 2.17610865079825 4423 1692 1544 753 2420 3725 4317 2352 980 1491 3388 2343 M2974 NAGY_TFTC_COMPONENTS_HUMAN http://www.broadinstitute.org/gsea/msigdb/cards/NAGY_TFTC_COMPONENTS_HUMAN.html Composition of the 2 MDa human TFTC complex containing KAT2A [GeneID=2648]. 17694077 7/22 Arthur Liberzon 0.0032474380225104 0.00470256321801105 1335 2458.18181818182 2352 0.000325219344011489 447 0.827628317454924 -0.827628317454924 -1 0.704166133819318 1332 2352 4205 3704 3112 707 447 1429 4078 4499 1175 2344 M2213 WIERENGA_STAT5A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WIERENGA_STAT5A_TARGETS_DN.html Genes down-regulated in CD34+ [GeneID=947] cells by intermediate activity levels of STAT5A [GeneID=6776]; predominant long-term growth and self-renewal phenotype. 18779318 132/340 Arthur Liberzon 1.83358807959643e-06 6.97587836865205e-06 1545 2090.36363636364 2353 1.66689964345509e-07 732 1.66975644131027 1.86291871685079 1 3.14716179349537 1543 2444 732 3336 978 2554 1906 3045 3073 1030 2353 2345 M237 PID_VEGFR1_2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_VEGFR1_2_PATHWAY.html Signaling events mediated by VEGFR1 and VEGFR2 18832364 59/133 Pathway Interaction Database 2.60034177045382e-07 2.19949486215643e-06 2470 2333.72727272727 2354 2.36394734346127e-08 222 1.26934559865537 1.16501153002301 1 2.62504821855557 2468 2354 2178 850 222 1745 1850 4246 3424 3118 3216 2346 M12467 KEGG_ERBB_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ERBB_SIGNALING_PATHWAY.html ErbB signaling pathway 41/90 KEGG 8.44940464569974e-05 0.000159588513380689 2560 2198.09090909091 2355 7.68157197657744e-06 591 1.55951213782446 -1.50788951252934 -1 2.1644542985867 2558 2227 2369 591 2355 1994 3237 2505 934 3517 1892 2347 M17836 AMUNDSON_DNA_DAMAGE_RESPONSE_TP53 http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_DNA_DAMAGE_RESPONSE_TP53.html Genes discriminating TP53 [GeneID=7157] status across various genotoxic stress agents. 15824734 13/35 Leona Saunders 3.78358521870711e-06 1.17324558774667e-05 4005 2567.09090909091 2355 3.43962884161455e-07 1080 1.55474118244871 -1.14069905902401 -1 2.80206431466891 4004 1141 2138 1080 1316 3231 4100 4579 1121 2355 3173 2348 M3485 MONNIER_POSTRADIATION_TUMOR_ESCAPE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MONNIER_POSTRADIATION_TUMOR_ESCAPE_DN.html The postradiation tumor escape signature: genes down-regulated in tumors from irradiated stroma vs those from non-irradiated stroma. 18794119 285/596 Jessica Robertson 1.22054305016611e-06 5.44710926959846e-06 2965 2286.90909090909 2355 1.10958520664956e-07 33 1.34808433585604 1.4889932797005 1 2.59381197209565 2962 33 1799 889 790 4314 3213 3102 2355 1650 4049 2349 M9914 YAMASHITA_LIVER_CANCER_WITH_EPCAM_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_LIVER_CANCER_WITH_EPCAM_DN.html Down-regulated genes distinguishing hepatocellular carcinoma (HCC) samples positive for EPCAM [GeneID=4072] from the negative ones. 18316609 10/49 Yujin Hoshida 0.000119108216725114 0.000216249943267681 3110 2573 2355 1.08286059767743e-05 1282 1.35954651912202 1.32331208062022 1 1.82134624648224 3110 1395 2279 1869 2456 3967 3208 4411 1282 1971 2355 2350 M2021 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_2 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_2.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 2. 12554760 56/141 Arthur Liberzon 1.92328811689713e-07 1.8479836569521e-06 4235 2562.63636363636 2355 1.74844389548655e-08 157 2.08424083217896 -1.13499534135398 -1 4.36789268352324 4233 2355 1379 2757 157 3682 4632 1900 974 1694 4426 2351 M3879 LEE_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER.html Genes down-regulated in tumor compared to non-tumor liver samples from patients with hepatocellular carcinoma (HCC). 18519680 22/95 Leona Saunders 0.000267340277014118 0.000453897296408753 2880 2251.45454545455 2356 2.43066153890974e-05 1250 2.17813307506492 -2.31580997529558 -1 2.66161690058938 2879 2919 1471 2356 2627 1923 3232 1250 2395 1719 1995 2352 M15955 KEGG_SPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SPHINGOLIPID_METABOLISM.html Sphingolipid metabolism 23/46 KEGG 1.12307876465859e-05 2.77864154761887e-05 4550 3049.27272727273 2357 1.02098590718932e-06 1200 1.25180523356768 -1.23139858218795 -1 2.08475820898585 4546 1200 2061 2357 1727 4166 4607 4653 1990 1789 4446 2353 M11303 SABATES_COLORECTAL_ADENOMA_SIZE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SABATES_COLORECTAL_ADENOMA_SIZE_DN.html A selection of genes whose expression displayed significant negative correlation with size of colorectal adenoma. 18171984 6/21 Leona Saunders 0.00114501541827542 0.00176034850723052 2935 2472.90909090909 2358 0.000114560582360706 1089 2.96552240083366 -2.8619600031002 -1 2.98571039979055 2932 2136 4143 2358 2929 2389 1217 2333 1089 2053 3623 2354 M3898 ENK_UV_RESPONSE_KERATINOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ENK_UV_RESPONSE_KERATINOCYTE_DN.html Genes down-regulated in NHEK cells (normal epidermal keratinocytes) after UVB irradiation. 16434974 341/741 Lauren Kazmierski 0.000260747917141901 0.000443508072496169 1035 2238.72727272727 2359 2.37071660525679e-05 1034 1.63895730624875 1.79536771517774 1 2.00878380539881 1034 4354 2359 2951 2624 1438 1510 1796 2421 2869 1270 2355 M697 KONDO_COLON_CANCER_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_COLON_CANCER_HCP_WITH_H3K27ME3.html Genes with high histone H3 tri-methylation mark at K27 (H3K27me3) in SW48 cells (colon cancer), by ChIP-chip assay on a 12K CpG array (high-CpG-density promoters, HCP). 18488029 2/21 Jessica Robertson 0.00199747050112874 0.00296488652780782 1835 2464.7 2359.5 0.000222138446476159 769 1.01364828649144 1.01364828649144 1 0.936660535590735 1832 3010 4448 NA 3817 1266 769 3793 2552 2167 993 2356 M10579 BIOCARTA_EDG1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EDG1_PATHWAY.html Phospholipids as signalling intermediaries 24/51 BioCarta 0.0594812711236514 0.0746462872215936 1875 2791.81818181818 2360 0.00555937251088879 1871 1.169453797437 1.17109023851559 1 0.481751492882157 1871 3968 2763 2316 4570 1941 1875 1919 3763 3364 2360 2357 M4144 SAGIV_CD24_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SAGIV_CD24_TARGETS_UP.html Genes up-regulated in HT29 cells (colon cancer) after knockdown of CD24 [GeneID=100133941] by both RNAi and monoclonal antibodies. 18413748 15/39 Jessica Robertson 0.0386207353881557 0.049393222169459 1300 2522.81818181818 2360 0.00357416936561097 1298 1.22997909963867 1.22997909963867 1 0.587314549730901 1298 2481 2360 3392 3455 1901 1332 2166 3940 3264 2162 2358 M5443 HOFMANN_MYELODYSPLASTIC_SYNDROM_HIGH_RISK_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_HIGH_RISK_DN.html Genes down-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with high risk of myelodysplastic syndrome (MDS) compared with healthy controls. 12411319 13/43 Arthur Liberzon 1.44706079262429e-05 3.42298176387554e-05 3545 2181.27272727273 2360 1.31551846438663e-06 432 2.20346424168373 2.15026755812567 1 3.59670344324597 3545 1612 1076 758 1822 3519 2370 2495 432 2360 4005 2359 M16574 PACHER_TARGETS_OF_IGF1_AND_IGF2_UP http://www.broadinstitute.org/gsea/msigdb/cards/PACHER_TARGETS_OF_IGF1_AND_IGF2_UP.html Genes up-regulated in MCF7 cells (breast cancer) by IGF1 and IGF2 [GeneID=3479;3481]. 16774935 26/51 Arthur Liberzon 0.000175028469801923 0.00030776112926522 1950 2562.63636363636 2361 1.59129451215737e-05 1696 1.25049774400073 1.22530970265935 1 1.605204005221 1946 3966 2410 3475 2537 1904 1696 2361 3579 2074 2241 2360 M1422 MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_UP.html Up-regulated genes discriminating multiple myeloma samples by the ype of immunoglobulin light chain they produce: Ig lambda (IGLL) vs Ig kappa (IGLK). 12623842 30/77 Kate Stafford 2.42108614652108e-06 8.39284483788818e-06 4080 2350.36363636364 2363 2.20098982810477e-07 1090 1.59111259433043 -1.31042229728622 -1 2.95222563008658 4078 2363 1610 1357 1119 1509 2463 4142 1090 2865 3258 2361 M2392 JUBAN_TARGETS_OF_SPI1_AND_FLI1_UP http://www.broadinstitute.org/gsea/msigdb/cards/JUBAN_TARGETS_OF_SPI1_AND_FLI1_UP.html Genes up-regulated in 745A cells (erythroleukemia) upon knockdown of FLI1 [GeneID=2313] by RNAi and down-regulation of SPI1 [GeneID=6688] by HMBA [PubChem=3616]. 19289502 101/224 Arthur Liberzon 4.0824999891213e-05 8.3869333402115e-05 1950 2383.81818181818 2363 3.71143249936305e-06 1769 1.30469149352326 1.55018012298265 1 1.94403255762529 1949 2531 2522 2634 2144 2363 2065 1769 2590 3640 2015 2362 M5483 YANG_BREAST_CANCER_ESR1_BULK_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_BULK_DN.html Genes down-regulated in bulk samples from early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative samples. 16261164 15/44 Leona Saunders 0.000463816458219549 0.000753621332599448 3210 2221.63636363636 2364 4.21740246821065e-05 984 1.80404747615424 -1.77439614831438 -1 2.05929181927328 3207 3158 1570 2400 2752 1754 2895 1869 2364 1485 984 2363 M729 REACTOME_FATTY_ACYL_COA_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FATTY_ACYL_COA_BIOSYNTHESIS.html Genes involved in Fatty Acyl-CoA Biosynthesis 12/19 Reactome 2.60975065210016e-05 5.70396061368533e-05 4310 2570.45454545455 2365 2.37252873708105e-06 88 1.69576384267296 -0.624105792934294 -1 2.63052196653648 4308 2557 2314 2284 2000 2514 2213 2365 88 3614 4018 2364 M17300 KARAKAS_TGFB1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/KARAKAS_TGFB1_SIGNALING.html Genes up-regulated by TGFB1 [GeneID=7040] in MCF10A cells (breast cancer): both wild-type and those lacking p21 [GeneID=1026]. 16619041 10/28 Arthur Liberzon 7.24154542885091e-06 1.93797155223275e-05 4475 2636.54545454545 2365 6.58324478665035e-07 394 2.52612295693657 -1.96330631907268 -1 4.35150175097686 4471 1979 1110 2365 1575 4006 4091 3902 394 973 4136 2365 M12882 KEGG_TAURINE_AND_HYPOTAURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TAURINE_AND_HYPOTAURINE_METABOLISM.html Taurine and hypotaurine metabolism 5/12 KEGG 7.99286187799622e-05 0.000151883823034429 3635 2318.54545454545 2368 7.99314937883454e-06 322 1.35674270664261 0.622602471966362 1 1.89368714291269 3635 668 3790 1774 2368 2481 2115 1082 322 2880 4389 2366 M1780 MCGOWAN_RSP6_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCGOWAN_RSP6_TARGETS_UP.html Genes up-regulated by hemizygotic cre-lox knockout of RSP6 [GeneID=81492] in keratinocytes. 18641651 14/23 Jessica Robertson 0.000387925184982896 0.000640302013677298 2315 2554.27272727273 2370 3.527214587071e-05 1569 1.66104277200906 1.66104277200906 1 1.93902158389543 2315 2370 1948 2964 2716 1931 1569 2941 3942 3155 2246 2367 M4857 UROSEVIC_RESPONSE_TO_IMIQUIMOD http://www.broadinstitute.org/gsea/msigdb/cards/UROSEVIC_RESPONSE_TO_IMIQUIMOD.html Interferon cluster genes up-regulated in skin tumors treated with imiquimod [PubChem=57469]. 16077073 20/44 Jessica Robertson 2.06651241016842e-06 7.53593552844297e-06 3150 2375.63636363636 2370 1.87864941026846e-07 1045 1.48705307875458 1.55521112493106 1 2.7845719742166 3150 1652 1221 2370 1045 4497 2907 2865 2242 1200 2983 2368 M15055 MATTIOLI_MULTIPLE_MYELOMA_SUBGROUPS http://www.broadinstitute.org/gsea/msigdb/cards/MATTIOLI_MULTIPLE_MYELOMA_SUBGROUPS.html Genes differentially expressed in multiple myeloma (MM) patients: comparison of MGUS-like vs PCL-like samples; MGUS=monoclonal gammopathy of undetermined significance, PCL=plasma cell leukemia. 15735737 12/41 Leona Saunders 0.00165611184896274 0.00247940579049183 2200 2449.45454545455 2372 0.000150669077197084 773 0.780249617560086 0.734987834345966 1 0.743137695828396 2198 1310 3064 2372 2988 1623 773 3822 3855 3618 1321 2369 M544 REACTOME_SIGNALING_BY_ERBB4 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ERBB4.html Genes involved in Signaling by ERBB4 50/137 Reactome 7.95454339621517e-05 0.000151401260579465 2410 2344.45454545455 2373 7.23166456665753e-06 798 1.96191560598776 -1.77063283236988 -1 2.73935434242448 2407 4021 2710 2020 2333 798 2846 2373 1419 3287 1575 2370 M10783 HOFMANN_CELL_LYMPHOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_CELL_LYMPHOMA_UP.html Genes up-regulated in lymph nodes from patients with mantle cell lymphoma (MCL) compared to the non-malignant hyperplastic lymph nodes. 11468180 45/116 Kevin Vogelsang 8.86157293085458e-05 0.000166101323015938 2090 2574.81818181818 2373 8.0562999036835e-06 1433 1.00582728757771 -0.865525587297586 -1 1.38960572890485 2086 2109 3106 2635 2373 1433 2257 3663 3372 3019 2270 2371 M14371 NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN.html Down-regulated genes in peripheral zone of human pancreatic cancer growing in the pancreas of nude mice compared to that of the tumor from the central zone. 17699763 426/1057 Arthur Liberzon 1.26244367508445e-06 5.54746019276978e-06 2375 2062 2374 1.1476767268393e-07 561 1.74472941519998 1.90261068110058 1 3.35192974047438 2374 2441 678 592 805 4263 3382 2959 2007 561 2620 2372 M18983 GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_UP.html Genes up-regulated in quiescent (G0) CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients compared to the quiescent cells from normal donors. 17717066 74/198 Arthur Liberzon 3.7621193798625e-07 2.69293216693181e-06 1910 2251.54545454545 2374 3.42010911200498e-08 349 1.90288989521629 2.22181695674447 1 3.87409734920759 1906 2834 349 1847 1911 3622 3143 2374 2649 1184 2948 2373 M1467 BIOCARTA_CTLA4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CTLA4_PATHWAY.html The Co-Stimulatory Signal During T-cell Activation 8/29 BioCarta 0.000217902456726009 0.000375401070668411 960 2087.09090909091 2376 2.1792382634147e-05 958 1.35629626912282 1.71597743607958 1 1.69823723470182 1458 2376 3880 2421 2608 958 958 1321 3147 2392 1439 2374 M1306 GROSS_HIF1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HIF1A_TARGETS_UP.html Genes up-regulated in SEND cells (skin endothelium) at normal oxygen (normoxia) conditions after knockdown of HIF1A [GeneID=3091] by RNAi. 17704799 10/23 Jessica Robertson 0.00781533199787296 0.0108351022905422 1755 2296.72727272727 2376 0.000713021294161755 1679 1.26600544387154 1.26600544387154 1 0.909398601745073 1755 2521 2280 2415 3212 2417 1710 1679 2376 2709 2190 2375 M2496 PHONG_TNF_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PHONG_TNF_TARGETS_UP.html Genes up-regulated in Calu-6 cells (lung cancer) at 1 h time point after TNF [GeneID=7124] treatment. 20516219 55/104 Arthur Liberzon 8.83905789559944e-06 2.2770657118625e-05 2380 2397.54545454545 2376 8.03553946268707e-07 1097 1.67722351708113 1.64250951583813 1 2.84625460662412 2376 2580 1434 1097 1647 4571 3482 3197 2274 1170 2545 2376 M15196 TIEN_INTESTINE_PROBIOTICS_2HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_2HR_UP.html Genes up-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 2h. 16394013 34/79 Arthur Liberzon 0.0810043382543676 0.0965721401684667 1265 2557.72727272727 2377 0.00765003179850385 1262 1.80509799467362 1.64152859690558 1 0.669806654798001 1262 4450 2555 2991 4111 2032 1558 2609 2377 2308 1882 2377 M537 REACTOME_REGULATION_OF_KIT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_KIT_SIGNALING.html Genes involved in Regulation of KIT signaling 8/24 Reactome 0.00343527065165194 0.00495923545090604 790 2053.72727272727 2378 0.00034405927223845 787 1.23802772721823 1.23802772721823 1 1.04289936582765 787 2525 3921 2378 3441 835 1071 1278 2741 2394 1220 2378 M589 GOUYER_TATI_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GOUYER_TATI_TARGETS_UP.html Genes up-regulated in constitutively invasive HT-29 5M21 cells (colon cancer) vs those expressing functionally inactive TATI [GeneID=6690]. 18317448 6/14 Jessica Robertson 0.00307101383742694 0.00446502353154907 2480 2737.18181818182 2378 0.000307526611703367 1247 2.30618349282725 -2.30618349282725 -1 1.98113258979775 2476 3792 4317 2930 4160 2165 2378 1247 2243 2059 2342 2379 M2849 TIMOFEEVA_GROWTH_STRESS_VIA_STAT1_DN http://www.broadinstitute.org/gsea/msigdb/cards/TIMOFEEVA_GROWTH_STRESS_VIA_STAT1_DN.html Genes down-regulated in SK-NEP-1 cells (Wilm's tumor ) stably expressing inactivated forms of STAT1 [GeneID=6772] under growth stress (hypoxia or nutritional deprivation). 16799645 10/33 Arthur Liberzon 0.000287755751585049 0.000485218946357517 2510 2450.54545454545 2379 2.61630360341149e-05 1862 1.69379145427173 -1.69379145427173 -1 2.05182279018623 2510 1941 3269 2936 2649 1862 2019 1920 2379 3487 1984 2380 M4042 NIKOLSKY_BREAST_CANCER_10Q22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_10Q22_AMPLICON.html Genes within amplicon 10q22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 7/19 Jessica Robertson 1.98555820412316e-05 4.50354585891633e-05 4315 2619.90909090909 2380 1.98557594533248e-06 32 1.91180426906125 -0.730715279057165 -1 3.03736445915873 4312 2133 4353 1655 1951 2380 1863 3039 32 3203 3898 2381 M1700 BAFNA_MUC4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BAFNA_MUC4_TARGETS_DN.html Genes down-regulated in NIH3T3 cells (fibroblast) engineered to stably express MUC4 [GeneID=4585]. 19010895 3/7 Leona Saunders 0.0116872880742054 0.015865188851601 1640 2198.45454545455 2380 0.00117492136544507 566 3.36354643817181 3.36354643817181 1 2.21249217572366 1637 2380 4435 2772 3462 1297 666 2777 566 2466 1725 2382 M1917 ZHANG_TLX_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_UP.html Genes up-regulated in neural stem cells (NSC) at both 36 h and 60 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 97/204 Jessica Robertson 1.72983362477246e-05 3.99028054395766e-05 2520 2418.09090909091 2380 1.57258838763327e-06 1478 1.35604495788356 1.44882057300786 1 2.18045416459709 2520 1857 2125 1478 1882 3672 2334 3079 2393 2380 2879 2383 M11690 KORKOLA_CHORIOCARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_CHORIOCARCINOMA.html Genes predicting the choriocarcinoma (CC) of nonseminomatous male germ cell tumors (NSGCT). 15870693 3/12 Leona Saunders 0.00200415529998936 0.00297386692075685 1290 2248.45454545455 2381 0.000200596508487872 390 1.66940814073258 1.66940814073258 1 1.54181319037548 1290 2381 4254 2509 3025 1134 390 1956 3828 2459 1507 2384 M19141 WONG_IFNA2_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WONG_IFNA2_RESISTANCE_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) cell lines resistant to IFNA2 [GeneID=3440]. 15709204 19/37 Yujin Hoshida 2.83061994876336e-06 9.38068251761322e-06 1700 2205.72727272727 2382 2.57329417343104e-07 1199 1.11833588694698 1.22917813008287 1 2.0552588673572 1696 2593 2775 2382 1199 1577 1530 3527 2824 2425 1735 2385 M5457 YAMANAKA_GLIOBLASTOMA_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAMANAKA_GLIOBLASTOMA_SURVIVAL_UP.html Genes whose expression most strongly and consistently associated with the long term survival of patients with high grade glioma tumors. 16652150 13/17 Arthur Liberzon 3.84289479911453e-05 7.96653213708495e-05 3275 2589.63636363636 2382 3.49360175209416e-06 1840 1.31631517557102 -0.718208133976904 -1 1.97209813249935 3275 1973 1840 3237 2129 3994 2285 2418 2382 2364 2589 2386 M12242 PENG_GLUCOSE_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/PENG_GLUCOSE_DEPRIVATION_UP.html Genes up-regulated in BJAB cells (B-lymphoma) after glucose [PubChem=206] deprivation. 12101249 41/80 Broad Institute 5.14621676242789e-07 3.16887933623352e-06 4345 2363.45454545455 2383 4.67837996929625e-08 460 2.0466508958756 -1.47033433440914 -1 4.11390432486763 4342 1112 1773 1965 460 4280 2892 2936 471 2383 3384 2387 M1515 JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_DN.html Genes down-regulated in H460 cells (non-small cell lung carcinoma, NSCLC) after treatment with sodium butyrate [PubChem=5222465]. 15318170 40/171 John Newman 0.0149047533533939 0.0199610386436136 2070 2713.63636363636 2384 0.00136424542287107 1570 1.34620808177465 1.46643974074521 1 0.83643765712707 2068 3446 2356 3370 4669 2384 1570 1574 3466 2334 2613 2388 M1725 LEIN_LOCALIZED_TO_DISTAL_AND_PROXIMAL_DENDRITES http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_LOCALIZED_TO_DISTAL_AND_PROXIMAL_DENDRITES.html Transcripts showing subcellular localization to both distal and proximal dendrites in the adult mouse brain. 17151600 13/31 Jessica Robertson 2.30081399387525e-06 8.11257665560528e-06 3595 2684.18181818182 2384 2.09165127284228e-07 1095 1.52578194070085 -1.03688343546299 -1 2.83923453968582 3592 1143 1997 2215 1095 3665 2655 4304 2384 2359 4117 2389 M2046 MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_2 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_2.html Cluster 2: genes up-regulated in SW260 cells (colon cancer) by sodium butyrate, curcumin, sulindac and TSA [PubChem=5222465;969516;5352;5562]. 10969808 6/17 Arthur Liberzon 0.000111754723724847 0.00020384688025482 2810 2381.45454545455 2384 1.11760344225882e-05 832 1.65322424132831 -1.74677123228211 -1 2.23027944096138 2808 2254 4610 2325 2464 2070 2552 2568 832 1329 2384 2390 M2131 WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_UP.html Genes up-regulated in RS4;11 cells (MLL, mixed lineage leukemia) in response to SB216763 [PubChem=176158], an inhibitor of GSK3B [GeneID=2932]. 20541704 210/675 Arthur Liberzon 4.13103268167612e-06 1.25190142048799e-05 1840 2243 2384 3.75549130791874e-07 847 1.26109881942119 -1.08204933781157 -1 2.25985075768825 1839 2384 2872 3255 1350 847 1851 2787 2955 2688 1845 2391 M12050 STARK_HYPPOCAMPUS_22Q11_DELETION_UP http://www.broadinstitute.org/gsea/msigdb/cards/STARK_HYPPOCAMPUS_22Q11_DELETION_UP.html Genes up-regulated in hyppocampus of mice carrying a hemizygotic microdeletion in the 22q11.2 region. 18469815 37/98 Jessica Robertson 3.20097151381332e-06 1.02878960999514e-05 3355 2513.18181818182 2386 2.90997833744991e-07 1251 1.18124326341985 1.26503467823981 1 2.15355816085778 3352 1436 2214 2071 1251 4404 3101 2640 2386 1763 3027 2392 M4120 LOPEZ_MBD_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MBD_TARGETS.html Genes up-regulated in HeLa cells (cervical cancer) after simultaneus knockdown of all three MBD (methyl-CpG binding domain) proteins MeCP2, MBD1 and MBD2 [GeneID=4204;4152;8932] by RNAi. 18223687 701/1612 Jessica Robertson 2.87577409351329e-07 2.30751325380193e-06 2390 2463.72727272727 2387 2.8757744656668e-08 282 1.50769109058474 1.74975689250421 1 3.10647986844004 2387 2409 4312 1150 282 4149 2336 1687 2252 3471 2666 2393 M4023 FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP.html Genes up-regulated in kidney biopsies from patients with well functioning kidneys more than 1-year post transplant compared to the biopsies from normal living kidney donors. 15307835 429/962 Jean Junior 0.00182264638333932 0.00272003851984971 1340 2394.09090909091 2387 0.000165832559562839 1249 1.65780159786801 1.83832190535267 1 1.55457298880393 1340 3725 2129 2118 3000 2438 2387 1249 2442 3430 2077 2394 M9435 GRADE_COLON_VS_RECTAL_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_VS_RECTAL_CANCER_DN.html Genes down-regulated in rectal but up-regulated in colon carcinoma compared to normal mucosa samples. 17210682 49/101 Jessica Robertson 9.21532944266118e-05 0.000171633679524286 2760 2543.72727272727 2387 8.37792315976294e-06 1666 1.27739161581014 -0.946671047689648 -1 1.75814277351964 2757 2273 2180 1666 2387 3812 1953 2767 2931 2205 3050 2395 M7146 BIOCARTA_CLASSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CLASSIC_PATHWAY.html Classical Complement Pathway 8/17 BioCarta 0.00128966339959722 0.00196660028978606 2375 2718.27272727273 2388 0.000129041246575488 1751 1.30078668376319 1.41779207712256 1 1.28676336116268 2375 1751 3823 2206 2963 3167 3626 1913 3311 2388 2378 2396 M493 REACTOME_EXTRINSIC_PATHWAY_FOR_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EXTRINSIC_PATHWAY_FOR_APOPTOSIS.html Genes involved in Extrinsic Pathway for Apoptosis 9/17 Reactome 8.38628705456809e-05 0.000158524167558314 2655 2491.72727272727 2388 8.38660355552611e-06 456 1.68480531373144 1.54566373604572 1 2.34013901884482 2653 1510 3909 1647 2388 3523 3344 3952 456 1804 2223 2397 M14582 REACTOME_P75NTR_RECRUITS_SIGNALLING_COMPLEXES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P75NTR_RECRUITS_SIGNALLING_COMPLEXES.html Genes involved in p75NTR recruits signalling complexes 7/19 Reactome 9.2029772988757e-07 4.4922032940137e-06 3220 2013.63636363636 2388 9.2029811101435e-08 169 1.86239727997114 -1.56741886946991 -1 3.64037119658738 3219 1073 3975 741 723 3564 2667 2630 169 1001 2388 2398 M17406 BIOCARTA_CYTOKINE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CYTOKINE_PATHWAY.html Cytokine Network 8/34 BioCarta 0.000322527879588532 0.000538427375757698 2415 2343.54545454545 2389 3.22574700057623e-05 1470 1.8393950470483 -1.91984168325261 -1 2.19782087148668 2413 2524 3826 3338 2699 1857 1870 1738 1470 1655 2389 2399 M936 REACTOME_TRAF6_MEDIATED_IRF7_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF6_MEDIATED_IRF7_ACTIVATION.html Genes involved in TRAF6 mediated IRF7 activation 13/36 Reactome 0.000477662551873669 0.000773704361590049 2605 2463.45454545455 2389 4.34332993807117e-05 1657 0.901473375315268 -0.867814857284662 -1 1.02525402984764 2605 2021 2959 3140 2760 1835 1657 2389 3397 2352 1983 2400 M11190 KEGG_DORSO_VENTRAL_AXIS_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DORSO_VENTRAL_AXIS_FORMATION.html Dorso-ventral axis formation 12/28 KEGG 7.04737590689811e-06 1.89793123561635e-05 3420 2462.45454545455 2393 6.40672589293626e-07 923 1.89612398642599 2.19811134679622 1 3.27254908078323 3418 1701 2393 1295 1559 4393 3950 2460 923 2234 2761 2401 M11519 AMIT_SERUM_RESPONSE_40_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_40_MCF10A.html Genes whose expression peaked at 40 min after stimulation of MCF10A cells with serum. 17322878 20/49 Leona Saunders 4.49774802247357e-05 9.12400313130354e-05 3150 2231.18181818182 2394 4.08894543496072e-06 385 2.20229950012433 -1.77007936075703 -1 3.25204886207848 3149 2547 1689 1602 2180 2394 2648 3645 385 1548 2756 2402 M1749 KEGG_VEGF_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VEGF_SIGNALING_PATHWAY.html VEGF signaling pathway 32/89 KEGG 7.89205006567304e-05 0.000150456251455427 4050 2639.09090909091 2396 7.17484835549813e-06 1093 1.41364714686631 -1.6356343458861 -1 1.97523132129509 4049 1832 1985 1093 2330 3707 3854 3279 2396 1739 2766 2403 M5868 REACTOME_AMINE_LIGAND_BINDING_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINE_LIGAND_BINDING_RECEPTORS.html Genes involved in Amine ligand-binding receptors 8/45 Reactome 0.000417927612031938 0.000685477350361099 1690 2774.45454545455 2397 4.18006231412306e-05 847 2.22268393381506 2.22268393381506 1 2.5705992783143 1687 4008 4000 4417 3984 2236 3134 847 1798 2397 2011 2404 M12985 BIOCARTA_TALL1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TALL1_PATHWAY.html TACI and BCMA stimulation of B cell immune responses. 8/23 BioCarta 6.9501392216074e-05 0.000134579968563852 3695 2578 2399 6.95035660113437e-06 895 1.22887599767808 -0.829466351138769 -1 1.73881220384084 3692 895 3877 2554 2319 2083 2251 2788 3109 2391 2399 2405 M6929 KEGG_O_GLYCAN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_O_GLYCAN_BIOSYNTHESIS.html O-Glycan biosynthesis 13/33 KEGG 0.000286357640313984 0.000483035242084712 3465 2487.36363636364 2400 2.60359018320179e-05 1269 1.22758519529856 1.40970587806928 1 1.48794948826057 3463 1389 2346 1908 2648 4084 3857 2400 1460 1269 2537 2406 M12090 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_DN.html Genes down-regulated in erythroid lineage cells by RUNX1-RUNX1T1 [GeneID=861;862] fusion . 17898786 8/25 Arthur Liberzon 0.0390368352844769 0.049884540535331 1285 2620 2400 0.00397400275912994 1282 2.32760571675028 2.32760571675028 1 1.10777356695827 1282 3033 4137 4210 3667 2094 1596 1918 2810 2400 1673 2407 M12398 MAINA_HYPOXIA_VHL_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAINA_HYPOXIA_VHL_TARGETS_UP.html Genes up-regulated by hypoxia in RCC4 cells (renal cell carcinoma) engineered to stably express VHL [GeneID=7428] off a plasmid vector. 15824735 4/8 Leona Saunders 8.78162644388111e-05 0.000164998803191768 2425 2337.27272727273 2401 8.78197348951639e-06 1080 2.85994910682048 -2.85994910682048 -1 3.95420059525645 2421 1080 4265 1812 2401 2332 3252 2943 1149 1633 2422 2408 M1808 WEBER_METHYLATED_HCP_IN_SPERM_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_HCP_IN_SPERM_DN.html Unmethylated germline-specific genes with high-CpG-density promoters (HCP) in sperm. 17334365 8/45 Jessica Robertson 2.28357847097131e-07 2.06580091022617e-06 2405 2194.27272727273 2401 2.28357870563422e-08 46 2.01330192668381 -2.73533463431538 -1 4.18361653200114 2121 2705 4478 2401 3186 1912 3261 46 897 2405 725 2409 M19387 TCGA_GLIOBLASTOMA_MUTATED http://www.broadinstitute.org/gsea/msigdb/cards/TCGA_GLIOBLASTOMA_MUTATED.html Genes significantly mutated in 91 glioblastoma samples. 18772890 7/14 Arthur Liberzon 0.000140861513635762 0.000251745634209451 3175 2229.27272727273 2401 1.4087044331712e-05 60 2.69253397404501 -1.2594163797329 -1 3.54214944808279 3175 1397 4562 511 2508 3309 2401 794 60 2277 3528 2410 M1342 FUJIWARA_PARK2_HEPATOCYTE_PROLIFERATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/FUJIWARA_PARK2_HEPATOCYTE_PROLIFERATION_DN.html Genes commonly down-regulated in both non-tumorous and tumorous liver tissues of PARK2 [GeneID=5071] knockout mice. 18574468 8/15 Jessica Robertson 0.000139285337228921 0.000249118736738444 1450 2435.90909090909 2402 1.39294068181449e-05 519 1.56142303691353 -1.56142303691353 -1 2.05672222269336 1446 1945 4322 2768 2920 1124 1473 4027 3849 2402 519 2411 M180 PID_HIF1A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HIF1A_PATHWAY.html Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 18832364 17/30 Pathway Interaction Database 0.00179955092146478 0.00268642740298947 2465 2252.72727272727 2403 0.000163729509260227 450 2.01003824534377 2.84771044748265 1 1.88884389710873 2463 2344 2046 2559 3246 2323 2403 1115 450 3383 2448 2412 M8795 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_UP.html Genes up-regulated in transformed NIH3T3 cells (fibroblasts transformed by activated KRAS [GeneID=3845]) vs normal cells. 16607279 96/210 Lauren Kazmierski 7.52588383570108e-06 1.99922288288522e-05 1205 2130.36363636364 2403 6.84173598253767e-07 1033 1.68471366374569 1.63322201457088 1 2.89376740408626 1205 3229 1033 2891 1590 2457 1975 2403 2709 1435 2507 2413 M12825 YAGUE_PRETUMOR_DRUG_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAGUE_PRETUMOR_DRUG_RESISTANCE_UP.html Up-regulated genes common to all pretumorigenic cells with acquired drug resistance. 17283147 5/15 Jessica Robertson 0.00623244608443176 0.00873885169109731 2915 2479 2403 0.000624999491605038 1047 3.19864216869597 3.19864216869597 1 2.4068299493507 2647 1989 4500 2915 3681 1826 1047 2125 2403 2914 1222 2414 M13072 SMID_BREAST_CANCER_LUMINAL_A_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_LUMINAL_A_DN.html Genes down-regulated in the luminal A subtype of breast cancer. 18451135 17/24 Jessica Robertson 0.0569133893107357 0.0715770644954663 690 2302.36363636364 2407 0.00531285068130069 689 2.21662102864748 2.21662102864748 1 0.927901639942075 689 2752 1157 2225 4481 2532 1824 2746 2807 1706 2407 2415 M1970 MIKKELSEN_IPS_ICP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_ICP_WITH_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV8.1 cells (induced pluripotent cells, iPS). 18509334 30/120 Jessica Robertson 2.01863311475732e-06 7.41325609385014e-06 2690 2335 2407 1.83512269725247e-07 859 1.74983631951007 1.51136321704486 1 3.28120435867963 2690 1919 859 2360 1036 2953 2407 3667 2549 1032 4213 2416 M1398 ZEILSTRA_CD44_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZEILSTRA_CD44_TARGETS_UP.html Genes implicated in apoptosis that were up-regulated in duodenum of CD44 [GeneID=960] knockout mice. 18483247 8/12 Jessica Robertson 8.88793360160151e-05 0.000166395752525388 4110 2829.09090909091 2408 8.88828910074948e-06 826 1.90772483319166 -1.39703925928365 -1 2.63509046030361 4109 2131 4361 2363 2408 2726 4540 826 1469 1664 4523 2417 M5490 WELCSH_BRCA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WELCSH_BRCA1_TARGETS_UP.html Up-regulated by induction of exogenous BRCA1 in EcR-293 cells 12032322 185/395 John Newman 2.66803482135681e-06 8.9558819289957e-06 1980 2239.54545454545 2410 2.42548914273011e-07 1176 1.60604132349471 1.86420873002024 1 2.96337074769697 1978 2496 2435 2196 1176 2469 1856 1291 2410 3888 2440 2418 M17814 REACTOME_ACTIVATION_OF_BH3_ONLY_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_BH3_ONLY_PROTEINS.html Genes involved in Activation of BH3-only proteins 15/26 Reactome 1.33701477375148e-06 5.74793690807288e-06 3815 2572.72727272727 2411 1.21546871481954e-07 258 1.58336095049732 -0.842294349395756 -1 3.03298953498374 3811 1884 2331 2056 830 4253 3702 2411 258 3256 3508 2419 M1132 DARWICHE_SKIN_TUMOR_PROMOTER_DN http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_SKIN_TUMOR_PROMOTER_DN.html Genes down-regulated during skin tumor progression: epidermis treated with the carcinogen DMBA [PubChem=6001] followed by 20 weekly applications of the tumor promoter TPA [PubChem=4792], compared to the untreated skin. 17525749 131/344 Arthur Liberzon 8.59365245751722e-06 2.22362536807983e-05 4115 2863.27272727273 2412 7.8124418420679e-07 1446 1.59365522399972 -1.15406980006682 -1 2.71044701632352 4112 2412 2149 2271 1638 3709 4122 2037 1446 3235 4365 2420 M6162 BOWIE_RESPONSE_TO_EXTRACELLULAR_MATRIX http://www.broadinstitute.org/gsea/msigdb/cards/BOWIE_RESPONSE_TO_EXTRACELLULAR_MATRIX.html Genes up-regulated by growing HMEC-E6 cells (mammary epithelial cells damaged by expression of HPV-16 E6 [GeneID=1489078]) in extracellular matrix (ECM). 17016442 14/52 Arthur Liberzon 2.18901800018564e-07 2.0192398324547e-06 1915 2102.81818181818 2412 1.99001656181341e-08 176 1.1648517233976 1.1499186399393 1 2.42476299562536 1915 1137 2428 2412 176 2666 1911 3403 2546 2507 2030 2421 M17906 KEGG_VIBRIO_CHOLERAE_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VIBRIO_CHOLERAE_INFECTION.html Vibrio cholerae infection 30/73 KEGG 9.24400777197894e-06 2.36319805889216e-05 3800 2470.27272727273 2413 8.40367873989093e-07 393 2.20469883881577 -1.46075624948242 -1 3.72838780594666 3797 1641 1724 1631 1660 2619 4160 4283 393 2413 2852 2422 M19118 BIOCARTA_KERATINOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_KERATINOCYTE_PATHWAY.html Keratinocyte Differentiation 30/63 BioCarta 9.98662353441901e-05 0.000184459274269955 2415 2419.72727272727 2414 9.07916081223304e-06 1090 1.22697769905236 -1.28676735886407 -1 1.67471845457915 3117 1362 2961 1090 2414 2229 3597 3205 1842 2414 2386 2423 M8455 HOOI_ST7_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOOI_ST7_TARGETS_UP.html Genes up-regulated in PC-3 cells (prostate cancer) stably expressing ST7 [GeneID=7982] off a plasmid vector. 16474848 51/167 Leona Saunders 5.38070978142458e-05 0.00010692962695401 2930 2393 2415 4.89167398736587e-06 1058 1.22624138362718 -1.14102076016371 -1 1.77985401380038 2929 2149 3157 3834 2230 1058 2415 1259 2922 3018 1352 2424 M1726 LEIN_LOCALIZED_TO_PROXIMAL_DENDRITES http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_LOCALIZED_TO_PROXIMAL_DENDRITES.html Transcripts showing subcellular localization only to proximal dendrites in the adult mouse brain. 17151600 18/54 Jessica Robertson 5.47796066463007e-05 0.000108723946101044 3655 2412.81818181818 2415 4.98008824511477e-06 966 1.372498775525 -1.24295020200134 -1 1.9885166454787 3652 966 2614 1689 2232 4321 2798 2415 1464 1780 2610 2425 M10759 LOPEZ_MESOTHELIOMA_SURVIVAL_OVERALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_OVERALL_UP.html Top genes associated with favorable overall survival of mesothelioma patients after surgery. 16540645 2/12 Arthur Liberzon 0.16212052640664 0.182094148308129 1835 2951.6 2415 0.0194615761750273 1443 0.837231896236838 0.837231896236838 1 0.226372144872733 1831 2440 4586 NA 3706 1782 1443 2368 4322 4648 2390 2426 M266 PID_NCADHERIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NCADHERIN_PATHWAY.html N-cadherin signaling events 18832364 30/76 Pathway Interaction Database 2.86360245833783e-05 6.17526052451498e-05 3210 2295.27272727273 2416 2.60330884794544e-06 628 2.0155076641023 -1.60305661563782 -1 3.10111732409298 3209 1363 1930 1017 2031 2850 2658 3176 628 2416 3970 2427 M15 PID_LYSOPHOSPHOLIPID_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LYSOPHOSPHOLIPID_PATHWAY.html LPA receptor mediated events 18832364 50/103 Pathway Interaction Database 5.2502466784569e-06 1.50919893779846e-05 1780 2513.27272727273 2418 4.7729629164411e-07 1447 1.44123098707 1.25671240903733 1 2.53987772544153 1779 2418 2167 2188 1447 2832 2212 3493 3241 2991 2878 2428 M7778 EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_DN.html Genes down-regulated in Rh4 cells (alveolar rhabdomyosarcoma, ARMS) after knockdown of the PAX3-FOXO1 [GeneiD=5077;2308] fusion protein by RNAi for 72 hr. 17525748 21/71 Leona Saunders 0.000258837024136235 0.000440737752580813 4145 2349 2419 2.35334074686846e-05 378 2.22939902492305 3.11304492029223 1 2.73467476136319 4142 2077 1621 2692 2621 2419 2778 1022 378 1614 4475 2429 M687 LIN_NPAS4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIN_NPAS4_TARGETS_UP.html Genes up-regulated in neurons after NPAS4 [GeneID=266743] knockdown by RNAi. 18815592 104/291 Jessica Robertson 3.47008575629774e-06 1.09606456061272e-05 2420 2413.18181818182 2419 3.15462839065156e-07 1280 1.35885742973581 1.603486717305 1 2.46370762540228 2419 2974 2655 1829 1280 3310 2676 3369 2107 2200 1726 2430 M12294 KEGG_VIRAL_MYOCARDITIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VIRAL_MYOCARDITIS.html Viral myocarditis 41/116 KEGG 0.000107228684066041 0.000196202113835794 2820 1939.81818181818 2420 9.74853734382725e-06 415 2.52342673498404 3.0210489824643 1 3.41953655101359 2818 2420 837 896 2434 3657 2821 1229 415 1151 2660 2431 M1313 GROSS_HYPOXIA_VIA_ELK3_ONLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_ONLY_UP.html Genes specifically up-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of ELK3 [GeneID=2004] by RNAi. 17704799 28/48 Jessica Robertson 0.00124669652343671 0.00190542071390229 1295 2500.27272727273 2421 0.000113400323883101 1291 1.23869267809523 1.26739930962044 1 1.23155320943805 1291 3314 2184 3472 2928 1954 2421 1444 3480 3181 1834 2432 M17636 KEGG_RENIN_ANGIOTENSIN_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RENIN_ANGIOTENSIN_SYSTEM.html Renin-angiotensin system 9/30 KEGG 0.00565230542342458 0.00796592577869702 3400 2590.18181818182 2422 0.000566673395188777 1720 1.67665913960157 -1.55658184329167 -1 1.2862565043979 3399 2603 3807 3696 3169 2009 1720 1807 2422 1800 2060 2433 M19930 BILBAN_B_CLL_LPL_UP http://www.broadinstitute.org/gsea/msigdb/cards/BILBAN_B_CLL_LPL_UP.html Genes up-regulated in B-CLL (B-cell chronic leukemia) samples expressing high levels of LPL [GeneID=4023] compared with those expressing low levels of the gene. 16617321 57/156 Arthur Liberzon 2.89142034873361e-05 6.23070558170936e-05 3560 2670 2422 2.62859850077215e-06 1743 1.40501788635605 -1.51247386764194 -1 2.15980675863126 3556 3829 2422 3364 2032 1851 3390 1743 2135 2651 2397 2434 M2424 YANG_BCL3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BCL3_TARGETS_UP.html Genes up-regulated in neonatal cardiac myocytes upon knockdown of BCL3 [GeneID=602] by RNAi. 19451226 236/593 Arthur Liberzon 2.59313244427058e-07 2.19924948249389e-06 2425 2139.90909090909 2422 2.35739340902024e-08 219 1.58992702933306 -1.33149813712183 -1 3.28804926314874 2422 1411 340 1870 219 3931 2679 3268 2902 851 3646 2435 M16713 DIRMEIER_LMP1_RESPONSE_LATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/DIRMEIER_LMP1_RESPONSE_LATE_DN.html Cluster 4: genes down-regulated in B2264-19/3 cells (primary B lymphocytes) within 60-180 min after activation of LMP1 (an oncogene encoded by Epstein-Barr virus, EBV). 15674340 24/59 Arthur Liberzon 1.33427822407737e-06 5.74143963087839e-06 2425 2234 2423 1.21298093936781e-07 603 1.73779368674726 2.06684294027357 1 3.32912346166764 2423 2714 2546 2834 828 3308 2998 2193 603 2376 1751 2436 M9869 SASSON_RESPONSE_TO_FORSKOLIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/SASSON_RESPONSE_TO_FORSKOLIN_UP.html Genes up-regulated in primary granulosa cells in response to forskolin [PubChem=47936]. 15026540 74/158 Arthur Liberzon 5.83165728153278e-07 3.4235028683673e-06 2425 2114.45454545455 2423 5.3015080248744e-08 500 1.35729169658265 1.59660674996054 1 2.7115940341664 3075 1099 2423 1145 500 4412 2632 1469 2516 1565 2423 2437 M2231 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_UP.html Genes from the black module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 19/61 Arthur Liberzon 0.000860867108696606 0.00134602044422833 1620 2491.54545454545 2426 7.82912866757931e-05 1595 1.67140318533472 1.39063611675487 1 1.75398491566183 1616 3243 2381 3090 2861 2426 2321 2810 2060 3004 1595 2438 M1477 MARCINIAK_ER_STRESS_RESPONSE_VIA_CHOP http://www.broadinstitute.org/gsea/msigdb/cards/MARCINIAK_ER_STRESS_RESPONSE_VIA_CHOP.html Endoplasmic retuculum (ER) stress response (caused by tunicamycin [PubChem=5282055]) genes dependent on CHOP [GeneID=13198]. 15601821 19/36 Kevin Vogelsang 0.000151443126756734 0.0002690153495004 1275 2294.45454545455 2426 1.3768504797356e-05 634 1.24360345790429 1.24360345790429 1 1.62291773870321 1273 3127 2577 4129 4314 1361 634 657 3405 2426 1336 2439 M11636 GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN.html Genes down-regulated in quiescent (G0) CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients compared to the quiescent cells from normal donors. 17717066 39/82 Arthur Liberzon 0.000105090687021158 0.000192855416614301 3455 2146.90909090909 2427 9.55415521643321e-06 718 1.84818724091232 1.93657559134558 1 2.50955623755254 3454 718 846 999 2427 3877 3003 2432 1129 896 3835 2440 M5372 REACTOME_XENOBIOTICS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_XENOBIOTICS.html Genes involved in Xenobiotics 2/46 Reactome 0.0581921887616166 0.0731264672933589 2195 2750 2428 0.00663942179798626 1922 1.08861813587471 -1.08861813587471 -1 0.452006445069774 2191 2727 3978 NA 3787 2075 1922 1981 4018 2156 2665 2441 M4891 BIOCARTA_PML_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PML_PATHWAY.html Regulation of transcriptional activity by PML 11/26 BioCarta 0.000105924504933124 0.000194156247177443 4145 2601.54545454545 2429 9.62996411611476e-06 43 2.75409205457243 -2.35778447542164 -1 3.73669766054965 4141 1144 1468 1288 2429 4486 4356 2793 43 2096 4373 2442 M6206 HEDENFALK_BREAST_CANCER_BRCA1_VS_BRCA2 http://www.broadinstitute.org/gsea/msigdb/cards/HEDENFALK_BREAST_CANCER_BRCA1_VS_BRCA2.html Genes differentially expressed in hereditary breast cancer tumors with mutated BRCA1 [GeneID=672] compared to those with mutated BRCA2 [GeneID=675]. 11207349 118/254 John Newman 4.10856347325888e-06 1.24683044971305e-05 2370 2632.45454545455 2429 3.73506467830887e-07 1348 1.23656574166868 1.4286650461932 1 2.21668497928273 2367 3630 3252 1981 1348 3826 2429 1664 2920 3428 2112 2443 M7897 BIOCARTA_GLEEVEC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GLEEVEC_PATHWAY.html Inhibition of Cellular Proliferation by Gleevec 20/42 BioCarta 1.80563156849609e-05 4.13547875365233e-05 2200 2436.27272727273 2430 1.64149671657836e-06 1220 0.779777952467633 -0.786776931783407 -1 1.24942058540507 2199 2430 3471 1302 1899 1220 2514 2897 3549 3921 1397 2444 M16335 MELLMAN_TUT1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MELLMAN_TUT1_TARGETS_DN.html Genes down-regulated in HEK293 cells (embryo kidney) after knockdown of TUT1 [GeneID=64852] by RNAi. 18288197 34/77 Jessica Robertson 9.55971925537452e-06 2.42407166832711e-05 2430 2144.27272727273 2430 8.69069163248435e-07 816 1.378582461688 -1.09547501381668 -1 2.32576846440797 2430 2889 2407 2529 1679 816 1370 2872 2597 2759 1239 2445 M13863 BIOCARTA_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MAPK_PATHWAY.html MAPKinase Signaling Pathway 46/109 BioCarta 7.29195032777145e-05 0.000140328867498715 3905 2768.81818181818 2431 6.62926548395378e-06 1441 1.29041210750633 -1.30266625661705 -1 1.81731460398643 3904 1912 2799 1441 2308 2973 4392 3541 2431 2343 2413 2446 M9546 BIOCARTA_TID_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TID_PATHWAY.html Chaperones modulate interferon Signaling Pathway 17/35 BioCarta 6.10400733302532e-05 0.000119829821376442 3660 2415.18181818182 2432 5.54925154387781e-06 384 2.38771556313628 -1.7419834993325 -1 3.422526906347 3659 2432 1648 1438 2264 2581 2948 3907 384 2208 3098 2447 M1854 RIZ_ERYTHROID_DIFFERENTIATION_6HR http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_6HR.html Selected genes down-regulated in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts) at 6 h time point. 17213805 17/53 Leona Saunders 3.98679451241425e-05 8.22638444965794e-05 3850 2683.63636363636 2433 3.62442432919373e-06 1123 2.24545109870884 2.3930144656032 1 3.35268454329396 3850 2433 1392 2865 2136 4430 2244 3395 1123 1264 4388 2448 M19943 BIOCARTA_CERAMIDE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CERAMIDE_PATHWAY.html Ceramide Signaling Pathway 17/33 BioCarta 0.00235894335332958 0.00347938575816885 1755 2291 2434 0.000214679684244754 980 0.884978325772504 -0.85732969897828 -1 0.795282893073919 1753 2434 3392 2801 3068 1051 1169 1860 3313 3380 980 2449 M13108 LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN.html Genes down-regulated in Wilm's tumor samples compared to fetal kidney. 12057921 109/287 Kevin Vogelsang 0.0258158758611628 0.0335663691135985 630 2538.63636363636 2434 0.00237489855084923 627 1.95411030975576 2.15576803257476 1 1.05291663180912 627 4173 1041 3082 4562 2763 2434 2259 2606 1949 2429 2450 M6910 BIOCARTA_INFLAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INFLAM_PATHWAY.html Cytokines and Inflammatory Response 13/44 BioCarta 0.00015628036456781 0.000277082780312054 3305 2439.81818181818 2437 1.42083152078825e-05 1743 1.53221285968884 -1.57954450065084 -1 1.99236952266062 3302 1930 1816 2916 2510 1993 3010 2437 2783 1743 2398 2451 M19496 ZEMBUTSU_SENSITIVITY_TO_CISPLATIN http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_CISPLATIN.html Top genes associated with chemosensitivity to cisplatin [PubChem=2767] across 85 tumor xenografts. 11809704 16/28 Arthur Liberzon 0.0366589508735427 0.0469483038517138 2685 2455.45454545455 2437 0.0033894951119038 1410 1.88996477993025 -1.51508085930864 -1 0.917688563822414 2683 2055 1410 2437 3457 1764 3315 3593 2542 2129 1625 2452 M2357 RAFFEL_VEGFA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAFFEL_VEGFA_TARGETS_UP.html Genes up-regulated in hearts of E18.5 embryos upon knockout of VEGFA [GeneID=7422]. 18981216 9/14 Arthur Liberzon 0.0106082909987466 0.0144759614502407 1205 2460.09090909091 2437 0.00106592750010947 1108 1.59092149646835 1.59092149646835 1 1.06962854972004 1201 2437 4654 3045 3272 1596 1108 2963 3125 1829 1831 2453 M16955 ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN.html Genes whose promoters display lower levels of histone H3 trimethylation mark at K27 (H3K27me3) in hepatocellular carcinoma (HCC) compared to normal liver. 18413731 101/413 Jessica Robertson 1.8265263348324e-05 4.17924922120344e-05 2370 2102.81818181818 2438 1.66049227231553e-06 514 1.88753463817834 2.15024902286064 1 3.02119932825996 2368 2498 514 1652 2474 3427 2534 2438 1560 1120 2546 2454 M15935 PARK_TRETINOIN_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/PARK_TRETINOIN_RESPONSE.html Genes up-regulated in U937 cells (acute promyelocytic leukemia, APL) by tretinoin (ATRA) [PubChem=444795]. 12893766 7/18 Arthur Liberzon 7.01154761910221e-05 0.000135489122239641 1965 2773.54545454545 2438 7.01176885702674e-06 1779 1.72337297785526 1.72337297785526 1 2.43666443887174 1964 2438 4534 3230 2325 2149 3470 2417 2991 3212 1779 2455 M2191 SUBTIL_PROGESTIN_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SUBTIL_PROGESTIN_TARGETS.html Genes responding to progestin R5020 [PubChem=36709] treatment of T47D-MTVL cells (breast cancer). 18378698 30/62 Arthur Liberzon 0.000110918433467185 0.000202557980992684 1775 2422.72727272727 2438 1.00840023717005e-05 1394 1.41663196388979 1.51462537236403 1 1.91253145381757 1772 3420 2749 2759 2438 1394 1940 1615 3744 3332 1487 2456 M1262 REACTOME_GRB2_SOS_PROVIDES_LINKAGE_TO_MAPK_SIGNALING_FOR_INTERGRINS_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GRB2_SOS_PROVIDES_LINKAGE_TO_MAPK_SIGNALING_FOR_INTERGRINS_.html Genes involved in GRB2:SOS provides linkage to MAPK signaling for Intergrins 8/22 Reactome 0.0270605707311019 0.0351262699296243 2440 2575 2439 0.00273958549332309 1004 1.42813880638737 1.32354981713104 1 0.759213583952746 2439 3488 3996 2342 3421 1911 1004 2016 2857 2396 2455 2457 M12674 WANG_LMO4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_LMO4_TARGETS_DN.html Genes down-regulated in MCF7 cells (breast cancer) engineered to conditionally express LMO4 [GeneID=8543] by a Tet Off system. 17452977 256/560 Arthur Liberzon 0.000111461656912676 0.000203407404690011 1775 2580.27272727273 2439 1.0133391313642e-05 577 1.41878335017895 -1.08366481778809 -1 1.91449343493049 1774 4127 3430 4104 2439 577 1587 3278 1975 3790 1302 2458 M12299 SEMENZA_HIF1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SEMENZA_HIF1_TARGETS.html Genes that are transcriptionally regulated by HIF1A [GeneID=3091]. 11516994 35/68 John Newman 0.000138753419582972 0.000248262132174803 2460 2358 2439 1.26147428633929e-05 1338 1.78470100497201 -1.34692430681105 -1 2.35180208889484 2460 2615 1338 2303 2492 3193 2163 2439 2158 1977 2800 2459 M1851 QI_PLASMACYTOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/QI_PLASMACYTOMA_UP.html Up-regulated genes that best disciminate plasmablastic plasmacytoma from plasmacytic plasmacytoma tumors. 17363561 164/394 Jessica Robertson 6.83851397603009e-07 3.76560240795265e-06 2445 2295.81818181818 2441 6.21683281975025e-08 563 1.54691796923845 1.4948285164995 1 3.06704020971575 2441 1578 912 1931 563 3414 2726 3802 2701 1307 3879 2460 M1204 TERAMOTO_OPN_TARGETS_CLUSTER_8 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_8.html Cluster 8: genes showing sustained pattern of down-regulation after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 2/8 Arthur Liberzon 0.0678436943911679 0.0846420532260417 2500 2699 2441.5 0.00777569702465698 1407 2.17401461051923 -2.17401461051923 -1 0.85220505546094 2497 3072 4257 NA 3772 1714 1407 2386 3832 2163 1890 2461 M15807 BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN.html Top highly correlated genes negatively associated with poor survival of patients with suboptimally debulked ovarian tumors. 18593951 29/41 Jessica Robertson 0.000113654811042378 0.000206996580705153 3155 2587.27272727273 2443 1.03327893654398e-05 1221 1.52236362089037 -1.32740996270082 -1 2.05003658063578 3151 1920 1984 2212 2443 2571 4129 3427 1956 1221 3446 2462 M12101 REACTOME_P130CAS_LINKAGE_TO_MAPK_SIGNALING_FOR_INTEGRINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P130CAS_LINKAGE_TO_MAPK_SIGNALING_FOR_INTEGRINS.html Genes involved in p130Cas linkage to MAPK signaling for integrins 9/21 Reactome 0.000832166079583211 0.00130288347775708 1480 2137.63636363636 2444 8.32477869093636e-05 625 1.30565964997499 1.19510727166664 1 1.37692176307911 1480 2954 3994 2786 2876 1049 625 1450 2444 2566 1290 2463 M186 PID_PDGFRB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PDGFRB_PATHWAY.html PDGFR-beta signaling pathway 18832364 101/200 Pathway Interaction Database 3.45765505153973e-06 1.09329092925204e-05 2680 2299.81818181818 2446 3.14332771437693e-07 1279 1.51293719347753 1.95847325135369 1 2.74367401195703 2679 2685 2446 1301 1279 2911 2020 1746 2188 3279 2764 2464 M1071 REACTOME_TANDEM_PORE_DOMAIN_POTASSIUM_CHANNELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TANDEM_PORE_DOMAIN_POTASSIUM_CHANNELS.html Genes involved in Tandem pore domain potassium channels 3/12 Reactome 1.37295298881582e-07 1.50319105270817e-06 3865 2329.45454545455 2450 1.37295307364083e-08 83 1.76476810779318 -0.854885286868658 -1 3.75623391452754 3864 528 4092 385 100 4148 3975 3889 83 2450 2110 2465 M1663 SASSON_FSH_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/SASSON_FSH_RESPONSE.html Genes up-regulated in rFSH-17 cells (primary granulosa) after stimulation with FSH. 12832290 6/12 John Newman 0.0001060495385003 0.000194272141287101 2885 2540.63636363636 2451 1.06054599767319e-05 967 1.28541029817735 -1.42111778149162 -1 1.74389751747288 2885 2093 4420 1298 2451 2590 4491 3759 967 1325 1668 2466 M6370 KEGG_P53_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_P53_SIGNALING_PATHWAY.html p53 signaling pathway 47/91 KEGG 0.000288141144165743 0.00048569402933837 1880 2532.72727272727 2452 2.61980808971289e-05 1435 1.33127498876403 1.57829161180109 1 1.61247126739079 1877 4063 2084 3032 2650 3425 2452 1435 2397 2771 1674 2467 M18359 RODRIGUES_DCC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_DCC_TARGETS_UP.html Genes up-regulated in HCT8/S1 cells (colon cancer) which normally lack DCC [GeneID=9423] compared to those stably expressing wild type DCC off a plasmid vector. 17334389 3/7 Arthur Liberzon 0.000975229967841236 0.0015142238665686 1715 2510 2452 9.75658215440739e-05 978 3.13259805698275 3.13259805698275 1 3.22881942660597 1714 3818 4125 3304 3410 1327 978 1003 3840 2452 1639 2468 M2031 RAMPON_ENRICHED_LEARNING_ENVIRONMENT_EARLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAMPON_ENRICHED_LEARNING_ENVIRONMENT_EARLY_DN.html Genes down-regulated in the brain cortex of mice that were exposed to an enriched learning environment for one day. 11070096 7/16 Arthur Liberzon 0.0111813909241267 0.0152181231107923 2150 2835.81818181818 2452 0.0011238053170582 1590 1.69786698536991 -1.69786698536991 -1 1.12805564685944 2148 3787 4604 4060 3278 1903 1590 3096 2452 2279 1997 2469 M1333 RAHMAN_TP53_TARGETS_PHOSPHORYLATED http://www.broadinstitute.org/gsea/msigdb/cards/RAHMAN_TP53_TARGETS_PHOSPHORYLATED.html Proteins phosporylated in HCT116 cells (colon cancer) upon p53 [GeneID=7157] activation. 18438429 25/44 Jessica Robertson 0.000687902821076562 0.00108976085854117 1740 2225.36363636364 2453 6.2556182806371e-05 283 2.68775572186121 4.20907948130304 1 2.910664497331 1740 2773 1546 2453 3760 2821 2764 922 283 2987 2430 2470 M1697 TUOMISTO_TUMOR_SUPPRESSION_BY_COL13A1_DN http://www.broadinstitute.org/gsea/msigdb/cards/TUOMISTO_TUMOR_SUPPRESSION_BY_COL13A1_DN.html Genes down-regulated in small intestine tissue from transgenic mice expressing a mutant form of COL13A1 [GeneID=1305], compared to normal controls. 19074901 4/22 Leona Saunders 0.00014844377318066 0.000264310008882168 2455 2180 2453 1.48453690112215e-05 660 2.1699198025412 -2.20872783338527 -1 2.83785028414856 2453 1079 4433 1067 2520 1643 2480 4133 660 981 2531 2471 M1767 JI_CARCINOGENESIS_BY_KRAS_AND_STK11_DN http://www.broadinstitute.org/gsea/msigdb/cards/JI_CARCINOGENESIS_BY_KRAS_AND_STK11_DN.html Cluster B: genes down-regulated in primary lung tumors driven by KRAS [GeneID=3845] activation and loss of STK11 [GeneID=6794]; also up-regulated in human squamous cell carcinoma (SCC) vs adenocarcinoma subtype of NSCLC (non-small cell lung cancer). 17676035 11/30 Jessica Robertson 0.230763775665937 0.256550190455654 1140 2672.90909090909 2454 0.0235684731116199 1140 1.52540821965354 1.52540821965354 1 0.329432277242545 1140 3458 2053 3481 3773 1658 2388 2748 4139 2110 2454 2472 M1827 MATZUK_PREOVULATORY_FOLLICLE http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_PREOVULATORY_FOLLICLE.html Genes important for preovulatory follicle, based on mouse models with female fertility defects. 18989307 8/19 Jessica Robertson 0.000107488980592248 0.000196601624923994 4250 2853.54545454545 2454 1.07494180192648e-05 382 1.8717106354747 -2.21338196512368 -1 2.53578107807362 4246 382 4492 2163 2454 3787 4419 2379 1063 2407 3597 2473 M17040 CASTELLANO_HRAS_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_HRAS_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) isolated from HRAS [GeneID=3265] knockout mice. 16909116 3/10 Leona Saunders 0.000737186782464246 0.00116155254291441 4255 2614.45454545455 2455 7.3743144666051e-05 699 0.888362059395425 -0.490827793528663 -1 0.953041050381083 4255 909 4158 1828 2852 2424 2754 2257 699 2455 4168 2474 M1665 JIANG_AGING_CEREBRAL_CORTEX_DN http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_AGING_CEREBRAL_CORTEX_DN.html Down-regulated in the cerebral cortex of aged (22 months) BALB/c mice, compared to young (2 months) controls 11172053 50/114 John Newman 0.000122095991409551 0.000221331456767952 1390 2487.09090909091 2460 1.11002516401034e-05 829 1.20545631444512 1.17395801249041 1 1.6104712690073 1390 3594 3584 3217 2460 1441 829 2129 3213 3939 1562 2475 M128 PID_TNF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TNF_PATHWAY.html TNF receptor signaling pathway 18832364 30/60 Pathway Interaction Database 0.000122430031709167 0.000221851171148166 1520 2146.36363636364 2461 1.1130622315733e-05 901 1.4312652513143 -1.49491230347524 -1 1.91161568049668 1519 3234 2877 3400 2461 901 1662 1127 2574 2863 992 2476 M9695 HOLLMANN_APOPTOSIS_VIA_CD40_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLMANN_APOPTOSIS_VIA_CD40_UP.html Genes up-regulated in DLBCL (diffuse large B-cell lymphoma) cell lines sensitive to stimulation of CD40 [GeneID=958] relative to the resistant ones. 16585179 128/339 Arthur Liberzon 1.00328621730874e-05 2.52491901949986e-05 2465 2620.81818181818 2462 9.12082538832985e-07 1696 1.59682536120888 1.97042966624171 1 2.68362769717784 2462 3987 2064 2632 1696 4027 3221 1887 1988 2495 2370 2477 M6303 SCHEIDEREIT_IKK_INTERACTING_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/SCHEIDEREIT_IKK_INTERACTING_PROTEINS.html Genes encoding IkappaB kinase (IKK) interacting proteins. 17072322 42/88 Arthur Liberzon 6.95718116060587e-05 0.000134660681200327 3715 2693.36363636364 2463 6.32491016465297e-06 1884 1.40734977335791 -1.45853770565394 -1 1.99121177428808 3712 2111 2835 3059 2298 2423 4251 1884 2499 2092 2463 2478 M13965 GOUYER_TUMOR_INVASIVENESS http://www.broadinstitute.org/gsea/msigdb/cards/GOUYER_TUMOR_INVASIVENESS.html Genes up-regulated in constitutively invasive HT-29 5M21 cells (colon cancer) vs the parental non-invasive cells. 18317448 3/15 Jessica Robertson 0.0499907909176658 0.0632613681447967 2200 2819.72727272727 2463 0.00511523247846689 1697 1.71547697988609 -1.71547697988609 -1 0.751749466814553 2200 3353 4313 3390 3505 2034 1697 2043 3745 2463 2274 2479 M2605 ONKEN_UVEAL_MELANOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONKEN_UVEAL_MELANOMA_DN.html Genes down-regulated in uveal melanoma: class 2 vs class 1 tumors. 16651410 400/1035 Arthur Liberzon 2.98496656509508e-06 9.77467038716671e-06 2140 2655.27272727273 2464 2.71360965010393e-07 1221 1.33056038096817 1.55933118413277 1 2.4365914239763 2138 4015 3159 2195 1221 3825 2464 1650 2861 3915 1765 2480 M9642 GALLUZZI_PERMEABILIZE_MITOCHONDRIA http://www.broadinstitute.org/gsea/msigdb/cards/GALLUZZI_PERMEABILIZE_MITOCHONDRIA.html Proteins that permeabilize mitochondria. 16892093 29/69 Arthur Liberzon 0.000306451478192999 0.000513969802008731 2210 2077 2464 2.78631067293999e-05 610 1.66999906985847 -1.26371412920457 -1 2.00774055752099 2207 3022 2464 3110 2667 1024 944 2555 610 2782 1462 2481 M1879 PIONTEK_PKD1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PIONTEK_PKD1_TARGETS_UP.html Genes up-regulated during later stages of renal maturation (days P14-P16) in kidney specific knockout of PKD1 [GeneID=5310]. 17965720 19/67 Jessica Robertson 4.24872659569347e-05 8.69032423719755e-05 3825 2554.63636363636 2464 3.86255331908401e-06 852 1.75716870458164 1.75803963381675 1 2.60832588771826 3824 3093 1711 1277 2157 3659 4534 2607 852 1923 2464 2482 M7899 WEIGEL_OXIDATIVE_STRESS_BY_HNE_AND_TBH http://www.broadinstitute.org/gsea/msigdb/cards/WEIGEL_OXIDATIVE_STRESS_BY_HNE_AND_TBH.html Oxidative stress genes down-regulated in ARPE-19 cells (retinal pigmented epithelium) in response to HNE and tBH [PubChem=5283344;6410]. 12419474 52/117 John Newman 8.59292097487204e-08 1.08243085183469e-06 3475 2620.81818181818 2465 7.81174664590968e-09 41 1.2436430256006 1.16058492814362 1 2.71187150198672 3475 1267 2465 2270 41 4634 3646 1979 3166 2033 3853 2483 M1788 NIKOLSKY_BREAST_CANCER_16P13_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_16P13_AMPLICON.html Genes within amplicon 16p13 identified in a study of 191 breast tumor samples. 19010930 68/165 Jessica Robertson 0.00136160855642498 0.00206355035427149 1455 2442.72727272727 2466 0.00012385927314131 1314 1.82767048916183 -1.67649379210769 -1 1.79400519743295 1452 3177 2985 3641 2949 1314 1848 1433 2466 3473 2132 2484 M18761 SMITH_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SMITH_LIVER_CANCER.html Potential marker genes specifically up-regulated in the majority of hepatocellular carcinoma (HCC) tumors. 12591738 22/66 Yujin Hoshida 0.000144815205936153 0.000258614350235066 1745 2118.63636363636 2466 1.31658853899272e-05 1128 1.05895462085902 -1.08452480948043 -1 1.38857721087787 1741 1128 2607 2837 2497 1149 2466 1378 3496 2743 1263 2485 M564 REACTOME_MEMBRANE_BINDING_AND_TARGETTING_OF_GAG_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEMBRANE_BINDING_AND_TARGETTING_OF_GAG_PROTEINS.html Genes involved in Membrane binding and targetting of GAG proteins 6/17 Reactome 0.00011310158313581 0.000206143142191523 3245 2695.90909090909 2467 1.13107339933828e-05 2031 1.06530227316986 -0.891872242551638 -1 1.43524993204172 3243 2179 3930 3756 2467 2272 2290 2031 2935 2047 2505 2486 M14435 TIAN_TNF_SIGNALING_VIA_NFKB http://www.broadinstitute.org/gsea/msigdb/cards/TIAN_TNF_SIGNALING_VIA_NFKB.html Genes modulated in HeLa cells (cervical carcinoma) by TNF [GeneID=7124] via NFKB pathway. 15722553 12/31 Arthur Liberzon 0.000692322109868854 0.00109491103842236 4440 2484.36363636364 2467 6.29581885491973e-05 863 1.77953112927914 -1.87629578636319 -1 1.92578446662632 4439 1505 1660 1131 2834 3722 3077 2467 863 1602 4028 2487 M15837 CHANG_IMMORTALIZED_BY_HPV31_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_IMMORTALIZED_BY_HPV31_UP.html Genes up-regulated in normal keratinocytes immortalized by infection with the high risk HPV31 (human papilloma virus) strain. 10756030 45/128 John Newman 0.0518643712030538 0.0654555463122838 1535 2414.81818181818 2470 0.00482990907782026 1144 1.85861229056904 1.77217848646212 1 0.804413587763328 1533 2470 1144 3002 3574 2605 2333 2572 3082 1951 2297 2488 M8701 KRISHNAN_FURIN_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KRISHNAN_FURIN_TARGETS_DN.html Genes down-regulated in naive T lymphocytes lacking FURIN [GeneID=5045]: Cre-Lox knockout of FURIN in CD4+ [GeneID=920] cells. 18690214 3/23 Jessica Robertson 1.4752251233705e-06 6.06395169132821e-06 4100 2435.63636363636 2470 1.47522610270154e-07 185 1.7193143469092 -0.564703027248038 -1 3.27880590144776 4097 669 4508 1421 920 3511 4388 1998 185 2470 2625 2489 M859 REACTOME_JNK_C_JUN_KINASES_PHOSPHORYLATION_AND_ACTIVATION_MEDIATED_BY_ACTIVATED_HUMAN_TAK1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_JNK_C_JUN_KINASES_PHOSPHORYLATION_AND_ACTIVATION_MEDIATED_BY_ACTIVATED_HUMAN_TAK1.html Genes involved in JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 11/16 Reactome 0.000127379766022299 0.000229489267043635 1275 2181.63636363636 2472 1.15806492631908e-05 820 0.972386337092905 -0.972386337092905 -1 1.29350619024748 1274 3098 3125 3289 2472 820 1511 1397 3141 2822 1049 2490 M13337 ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN http://www.broadinstitute.org/gsea/msigdb/cards/ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN.html Hepatic graft versus host disease (GVHD), day 35: genes down-regulated in allogeneic vs syngeneic bone marrow transplant. 12663442 33/96 Arthur Liberzon 1.33294352823457e-06 5.74096817399557e-06 4435 2429.90909090909 2473 1.21176757803967e-07 827 1.92791405924011 -2.33609680369542 -1 3.69336570303815 4434 2473 1311 2203 827 3784 3455 2574 1177 988 3503 2491 M2065 HOFFMAN_CLOCK_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMAN_CLOCK_TARGETS_DN.html Genes down-regulated in MCF7 cells (breast cancer) upon knockdown of CLOCK [GeneID=9575] by RNAi that also belong to the highest confidence network (according to Ingenuity Pathway Analysis). 20124474 3/13 Jessica Robertson 0.0209522790004712 0.0275097728764943 1920 2650.63636363636 2473 0.00211524900135068 990 2.66138912218119 2.66138912218119 1 1.51808125317448 1920 3138 4617 3194 3469 1693 990 1681 3915 2473 2067 2492 M14577 HAHTOLA_SEZARY_SYNDROM_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_SEZARY_SYNDROM_UP.html Genes up-regulated in monocytes isolated from peripheral blood samples of Sezary syndrom patients compared to those from healthy normal donors. 16914566 54/196 Arthur Liberzon 9.06095702048974e-06 2.32528174140279e-05 2085 2789.72727272727 2474 8.23726758119544e-07 1653 1.6695400250392 -1.87013157498795 -1 2.82766229984719 2474 4439 2306 3936 1653 2103 2828 2082 3322 3463 2081 2493 M1284 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM6 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM6.html Cluster PAM6: genes changed exclusively in normal liver tissue adjacent to hepatocellular carcinoma (HCC) from mice deficient for TXNIP [GeneID=10628]. 16607285 33/57 Leona Saunders 1.46115007752525e-06 6.03255441698969e-06 3775 2628.36363636364 2474 1.32831913451119e-07 878 1.52657096595823 -1.29822414307428 -1 2.91249404895202 3773 3053 1550 3900 878 2146 3415 2474 3443 1844 2436 2494 M16284 INGA_TP53_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/INGA_TP53_TARGETS.html Genes whose promoters contain TP53 [GeneID=7157] response elements. 12446780 14/27 John Newman 0.0264825163301776 0.0344045110959835 1585 2621.27272727273 2474 0.00243697979813566 1391 1.50761119642938 1.50761119642938 1 0.806430763832495 1584 4198 2474 3265 3642 1846 1391 2416 3325 3152 1541 2495 M276 PID_FGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FGF_PATHWAY.html FGF signaling pathway 18832364 32/84 Pathway Interaction Database 2.51117625480295e-05 5.51164961592816e-05 4025 2699.36363636364 2475 2.28291356265953e-06 668 2.04814485855738 -1.83364538799937 -1 3.18829753931758 4022 2475 1497 668 1989 4226 4547 3389 774 2140 3966 2496 M2139 LU_EZH2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LU_EZH2_TARGETS_UP.html Genes up-regulated in SKOV3ip1 cells (ovarian cancer) upon knockdown of EZH2 [GeneID=2146] by RNAi. 20708159 205/459 Arthur Liberzon 6.74360325603446e-06 1.83297707991749e-05 2475 2531.90909090909 2475 6.13056720646936e-07 1499 1.44036942279828 -1.27398787070612 -1 2.49391777706162 2475 2569 3119 2895 1540 1499 2885 2186 2391 3940 2352 2497 M17395 KEGG_LIMONENE_AND_PINENE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LIMONENE_AND_PINENE_DEGRADATION.html Limonene and pinene degradation 6/14 KEGG 0.000117235164785932 0.000213014339738999 2560 2527.63636363636 2476 1.17241350082927e-05 1095 1.26808932975306 -1.59455292833059 -1 1.70185836599141 2556 1512 3804 3517 2476 2257 1996 1724 3834 3033 1095 2498 M1650 MCDOWELL_ACUTE_LUNG_INJURY_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCDOWELL_ACUTE_LUNG_INJURY_DN.html Genes down-regulated in the mouse model of acute lung injury induced by inhaling nickel sulfate [PubChem=24586]. 12540486 34/75 John Newman 0.00211745464386975 0.00313404689234796 1305 2363.63636363636 2477 0.000192681400063726 802 1.65760694407819 1.94606130715105 1 1.51710917710417 1302 2307 802 2732 3141 2697 2131 2477 4052 1555 2804 2499 M4625 AMIT_EGF_RESPONSE_20_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_20_MCF10A.html Genes whose expression peaked at 20 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 16/30 Leona Saunders 8.77505199839284e-05 0.000164941410607577 3525 2859.45454545455 2479 7.9776382044799e-06 1458 1.81187734459329 1.48925811567032 1 2.50522382961694 3524 1458 1974 2479 2366 4093 3460 3929 2266 2127 3778 2500 M1865 WANG_TUMOR_INVASIVENESS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_TUMOR_INVASIVENESS_UP.html Up-regulated genes in the subpopulation of invasive PyMT cells (breast cancer) compared to the general population of PyMT cells. 17440055 299/637 Jessica Robertson 0.0839184282471183 0.0965721401684667 1280 2748.18181818182 2479 0.00793650793650794 1276 1.57559009643911 1.74121974900837 1 0.584644564744076 1276 4356 3440 2861 3661 2402 1962 2126 2479 3596 2071 2501 M48 PID_MET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MET_PATHWAY.html Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met) 18832364 53/111 Pathway Interaction Database 3.97273950685708e-06 1.21357609707511e-05 4605 2740.45454545455 2480 3.61158789164655e-07 662 1.52272964842262 -1.21409172969678 -1 2.73620106807427 4584 1631 2480 714 1337 3456 4603 3635 662 2439 4604 2502 M17742 SMITH_TERT_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMITH_TERT_TARGETS_UP.html Genes consistently up-regulated in HMEC cells (primary mammary epithelium) upon expression of TERT [GeneID=7015] off a retroviral vector. 12717449 105/229 Broad Institute 6.85950649409637e-05 0.000133099989363708 1500 2223.18181818182 2480 6.23610943629988e-06 515 1.60526756715865 2.11568017615978 1 2.27420967501668 1499 4131 3097 2545 2781 2480 1680 515 1777 2491 1459 2503 M13 PID_ERBB4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB4_PATHWAY.html ErbB4 signaling events 18832364 25/81 Pathway Interaction Database 2.64007219115818e-06 8.88110429846893e-06 4075 2328.72727272727 2481 2.40006850848796e-07 507 1.72345552958075 -1.51407342589749 -1 3.18231033418066 4073 1042 1295 507 1172 2570 4139 4149 622 2481 3566 2504 M4282 BHATTACHARYA_EMBRYONIC_STEM_CELL http://www.broadinstitute.org/gsea/msigdb/cards/BHATTACHARYA_EMBRYONIC_STEM_CELL.html The 'stemnes' signature: genes up-regulated and common to 6 human embryonic stem cell lines tested. 15070671 81/195 Kate Stafford 9.29952004864461e-07 4.52518701432489e-06 2780 2575.72727272727 2481 8.45411270873164e-08 691 1.83774734714631 2.03811088742061 1 3.59005449986271 2778 3231 2105 1335 691 4289 4182 2481 1899 2433 2909 2505 M210 PID_IL8_CXCR2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL8_CXCR2_PATHWAY.html IL8- and CXCR2-mediated signaling events 18832364 25/67 Pathway Interaction Database 6.51933695329105e-05 0.000127290054013008 2535 2582.90909090909 2483 5.92684559190778e-06 2079 1.398630764973 1.16092879234564 1 1.99137341616733 2532 2201 2373 2666 2277 2322 2079 3741 2535 2483 3203 2506 M14279 DOUGLAS_BMI1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DOUGLAS_BMI1_TARGETS_DN.html Genes down-regulated in A4573 cells (Ewing's sarcoma, ESFT) after knockdown of BMI1 [GeneID=648] by RNAi. 18701473 231/491 Jessica Robertson 4.05304067948934e-07 2.78483117655235e-06 3100 2405.72727272727 2483 3.68458311470695e-08 364 1.48829385293195 1.85030408741771 1 3.02209230955627 3098 995 1765 2483 364 3935 3825 1802 1924 3126 3146 2507 M2304 VANDESLUIS_NORMAL_EMBRYOS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_NORMAL_EMBRYOS_DN.html Genes down-regulated in normal 9.5 days post coitus (dpc) embryos compared to normal 8.5 dpc and 9.5 dpc embryos. 17371845 14/62 Arthur Liberzon 0.000133145969168599 0.000239050579127991 2070 2672.90909090909 2483 1.21049116331503e-05 1366 1.88283226540011 1.55360029306264 1 2.49241637036029 2069 2817 1366 4345 2483 2670 2038 4577 3045 1904 2088 2508 M2494 PEDRIOLI_MIR31_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PEDRIOLI_MIR31_TARGETS_DN.html Genes down-regulated in primary LEC cells (lymphatic endothelum) upon overexpression of MIR31 [GeneID=407035]. 20479124 243/811 Arthur Liberzon 2.0714667398843e-05 4.66229257593555e-05 3425 2708.18181818182 2483 1.88316931324613e-06 522 1.72472777751854 -1.67913317608142 -1 2.73066326711136 3423 1524 522 1773 2020 4670 3890 3984 2483 879 4622 2509 M2110 KIM_ALL_DISORDERS_CALB1_CORR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_CALB1_CORR_UP.html Genes whose expression significantly and positively correlated with the density of CALB1-positive [GeneID=793] GABAergic interneurons in the BA9 brain region across all subjects with psychiatric disorders. 18762803 358/844 Jessica Robertson 0.000408478592142567 0.000671153815841539 895 2343.90909090909 2484 3.7141314085089e-05 892 1.39973438914518 1.5117821608193 1 1.62352622664391 892 4048 3423 2675 2729 1343 1138 2261 2484 2999 1791 2510 M2249 BRUINS_UVC_RESPONSE_MIDDLE http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_MIDDLE.html Middle response genes: differentially expressed in the period between 3 h and 12 h after UV-C irradiation of MEF cells (embryonic fibroblast). 18195040 70/136 Arthur Liberzon 1.40575747164854e-06 5.89211047597948e-06 3835 2546.27272727273 2484 1.27796215445563e-07 856 1.14650497981016 -0.940478291875241 -1 2.19166610044709 3835 1821 3530 2484 856 1356 2966 3372 2030 3333 2426 2511 M7465 CAFFAREL_RESPONSE_TO_THC_24HR_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_24HR_3_UP.html Genes up-regulated in EVSA-T cells (breast cancer) after treatment with 3 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 24 h. 18454173 8/23 Jessica Robertson 0.000563678041533271 0.00090396827605233 2460 2667.54545454545 2485 5.63821072417904e-05 903 1.0191952828403 1.0191952828403 1 1.13396446818868 2205 2459 4320 2459 2953 2485 1866 903 3841 3311 2541 2512 M19 PID_P73PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P73PATHWAY.html p73 transcription factor network 18832364 63/123 Pathway Interaction Database 0.0116577275064485 0.0158342351000631 2290 2658.63636363636 2486 0.00106545123769312 1519 1.66726234480742 2.20969636255681 1 1.09721793553207 2289 3309 1708 2486 3412 3664 3477 1519 1722 3285 2374 2513 M18788 REACTOME_PHASE_II_CONJUGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHASE_II_CONJUGATION.html Genes involved in Phase II conjugation 24/95 Reactome 6.19140218465167e-05 0.000121342160758167 2540 2306.27272727273 2486 5.6287058495652e-06 484 1.74233155924954 -1.3187079295027 -1 2.49397121355968 2539 484 1812 1305 2267 3763 4020 2486 742 2875 3076 2514 M16597 REACTOME_EGFR_DOWNREGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EGFR_DOWNREGULATION.html Genes involved in EGFR downregulation 17/36 Reactome 0.0641285202469997 0.0801563739336998 1530 2656.90909090909 2487 0.00600707764401178 1526 1.66727794458502 2.23802576183487 1 0.667978295184793 1526 3605 2838 2931 4635 2487 1751 2128 1692 3830 1803 2515 M966 REACTOME_N_GLYCAN_ANTENNAE_ELONGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_N_GLYCAN_ANTENNAE_ELONGATION.html Genes involved in N-Glycan antennae elongation 5/14 Reactome 8.83024833878618e-06 2.27604750910627e-05 2490 2501.63636363636 2488 8.83028342696097e-07 250 1.43118394457439 1.43118394457439 1 2.42882614221618 2488 1516 4064 2355 2955 2994 3581 250 3316 1865 2134 2516 M15130 MILI_PSEUDOPODIA_CHEMOTAXIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MILI_PSEUDOPODIA_CHEMOTAXIS_UP.html Transcripts enriched in pseudopodia of NIH/3T3 cells (fibroblast) in response to the chemotactic migration stimulus by lysophosphatidic acid (LPA) [PubChem=3988]. 18451862 36/95 Jessica Robertson 0.00835114212018323 0.0115403868991975 2020 2609.81818181818 2488 0.000762092030455545 1374 1.33466773913901 1.41065967383465 1 0.945359078855579 2017 3359 3204 3699 3219 2041 1374 2047 2488 3843 1417 2517 M17181 REACTOME_SIGNALLING_TO_P38_VIA_RIT_AND_RIN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALLING_TO_P38_VIA_RIT_AND_RIN.html Genes involved in Signalling to p38 via RIT and RIN 9/20 Reactome 0.000124188138684453 0.000224602708558606 2595 2218.36363636364 2489 1.24195079442573e-05 249 1.97425355069408 2.40668075596175 1 2.63297446766332 2594 2291 3943 1011 2489 3577 2959 2581 249 1806 902 2518 M17811 PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN http://www.broadinstitute.org/gsea/msigdb/cards/PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN.html Genes down-regulated in post-GC, BCL6 [GeneID=604] dependent B cell non-Hodgkin's lymphoma (B-NHL) vs MYC [GeneID=4609] driven pre-GC lymphoma. 18066064 119/276 Jessica Robertson 0.00109308487565852 0.00168770864162631 1580 2492.81818181818 2489 9.94207600323019e-05 1341 1.4357744807816 1.47696037288716 1 1.45515333214394 1577 3631 2489 3319 2900 1926 1341 1893 3239 3440 1666 2519 M11290 SOUCEK_MYC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SOUCEK_MYC_TARGETS.html Chemokine genes up-regulated within 2 hr of c-Myc [GeneID=4609] activation in a mouse model of Myc-induced pancreatic beta-cell tumorigenesis. 17906636 6/13 Jessica Robertson 8.791494728953e-05 0.000165051860175776 2490 2648.36363636364 2489 8.79184255502798e-06 1326 1.95079296976358 1.95952492470059 1 2.69709064101986 2298 2489 4527 2143 2402 3021 3540 2490 2046 1326 2850 2520 M10960 REACTOME_P2Y_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P2Y_RECEPTORS.html Genes involved in P2Y receptors 5/14 Reactome 0.0334728557557951 0.0430680401075387 1570 2638.63636363636 2490 0.00339880051991312 1502 3.2192329663136 3.2192329663136 1 1.60721152918601 1567 2490 4006 2997 4036 2036 1502 2158 3717 2889 1627 2521 M1559 MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_UP.html Cluster 9: genes up-regulated in SW260 cells (colon cancer) by sodium butyrate and TSA [PubChem=5222465;5562] with the same kinetics with which each alters the level of histone H4 acetylation. 10969808 53/120 John Newman 6.78164445283963e-06 1.84118110695287e-05 3170 2643.72727272727 2492 6.16515032526741e-07 1180 1.32309271553327 -1.05646938598271 -1 2.28992184448087 3035 1180 2227 2205 1541 4127 3498 3167 2492 2441 3168 2522 M2353 VANLOO_SP3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANLOO_SP3_TARGETS_UP.html Genes up-regulated in E12.5 hearts from mice with SP3 [GeneID=6670] knockout compared to the wild type organ. 17923686 4/10 Arthur Liberzon 7.00031403231373e-05 0.000135327852951411 3860 2819.09090909091 2493 7.00053456187553e-06 35 2.86710078966162 -2.21720595069278 -1 4.05431488770351 3857 2493 4652 1645 2323 4423 4409 3680 35 1647 1846 2523 M85 BIOCARTA_BAD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BAD_PATHWAY.html Regulation of BAD phosphorylation 18/40 BioCarta 6.22653680002873e-05 0.000121877825584522 950 1919.18181818182 2494 5.66064821199628e-06 103 1.06037227764666 1.19485739518135 1 1.51707409267549 946 2620 2927 2535 2494 452 103 1896 3062 3451 625 2524 M1268 KREPPEL_CD99_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KREPPEL_CD99_TARGETS_UP.html Genes up-regulated in ESFT cells (Ewing's sarcoma family of tumors) after knockdown of CD99 [GeneID=4267] by RNAi. 16314831 3/5 Arthur Liberzon 0.00515356795351124 0.0072937539807169 2400 2500.90909090909 2494 0.000516555877740987 23 2.98482897467722 2.98482897467722 1 2.33159523919211 2399 2494 4284 1692 3623 3120 3529 2705 23 2461 1180 2525 M16498 REACTOME_SEMA3A_PAK_DEPENDENT_AXON_REPULSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMA3A_PAK_DEPENDENT_AXON_REPULSION.html Genes involved in Sema3A PAK dependent Axon repulsion 9/35 Reactome 0.00432994097455164 0.00618223747920444 1585 2336.54545454545 2497 0.000433840095854018 638 1.66168138257401 1.64562634672515 1 1.34163406663948 1581 2128 4018 2665 3583 1148 638 2497 3735 2567 1142 2526 M1147 DARWICHE_PAPILLOMA_PROGRESSION_RISK http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_PROGRESSION_RISK.html Genes that classify progression risk of benign papilloma samples: low vs high risk. 17525749 36/112 Arthur Liberzon 7.36010132085535e-08 9.55386005250088e-07 3450 2327.90909090909 2497 6.69100142462508e-09 32 1.53295808593536 -1.20895191157001 -1 3.37313029856892 3450 951 1284 2497 32 3845 2831 4368 1903 1687 2759 2527 M12256 REACTOME_SIGNALLING_TO_RAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALLING_TO_RAS.html Genes involved in Signalling to RAS 20/36 Reactome 0.000145812947414603 0.000260098771063887 4145 2461.09090909091 2498 1.32566011446619e-05 620 1.56857450954592 -1.40265510746966 -1 2.0554021623541 4145 1497 1594 620 2498 3155 4463 3084 1240 1545 3231 2528 M2439 HUANG_GATA2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_GATA2_TARGETS_DN.html Genes down-regulated in G1ME cells (megakaryocyte/erythroid progenitor lacking GATA1 [GeneID=2623]) upon knockdown of GATA2 [GeneID=2624] by RNAi. 19620289 45/97 Arthur Liberzon 3.74909689371862e-05 7.80811913065131e-05 2500 2372.27272727273 2499 3.40832798628497e-06 961 2.07499654476197 2.21247499142948 1 3.11536754400002 2499 2537 961 3250 2117 2747 1622 2709 2175 1952 3526 2529 M15195 REACTOME_MAPK_TARGETS_NUCLEAR_EVENTS_MEDIATED_BY_MAP_KINASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MAPK_TARGETS_NUCLEAR_EVENTS_MEDIATED_BY_MAP_KINASES.html Genes involved in MAPK targets/ Nuclear events mediated by MAP kinases 22/37 Reactome 2.42754142914755e-06 8.40758251070616e-06 2870 2224.90909090909 2500 2.20685827978971e-07 976 1.24136890244559 1.11529343754363 1 2.30294889224355 2870 1126 2898 976 1122 2500 1535 3705 1430 2741 3571 2530 M18159 BIOCARTA_RB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RB_PATHWAY.html RB Tumor Suppressor/Checkpoint Signaling in response to DNA damage 14/23 BioCarta 0.0839184282471183 0.0965721401684667 3365 2860.90909090909 2501 0.00793650793650794 901 2.25803873048441 -1.45207462392387 -1 0.837876599357361 3363 2403 1586 1720 4015 4126 4331 2302 901 2501 4222 2531 M12012 ST_P38_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_P38_MAPK_PATHWAY.html p38 MAPK Pathway 28/52 Signaling Transduction KE 0.000108155293239178 0.000197743154162618 4445 2860.09090909091 2503 9.83278278920699e-06 2050 1.29630270808351 -1.68278974080115 -1 1.75503087243588 4445 3275 2852 2050 2436 4499 2957 2059 2503 2283 2102 2532 M7057 LOPEZ_MESOTHELIOMA_SURVIVAL_WORST_VS_BEST_DN http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_WORST_VS_BEST_DN.html Genes higher expressed in the best 25 mesothelioma survivors compared to the 25 worst ones. 16540645 3/8 Arthur Liberzon 0.000136833604466677 0.000245014241700744 2505 2799.27272727273 2503 1.36842030742808e-05 294 2.19346350803879 -3.54969511984073 -1 2.89503714703715 4386 1853 4140 2501 2503 3854 3746 1639 294 2453 3423 2533 M19476 GRAHAM_CML_DIVIDING_VS_NORMAL_DIVIDING_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_DIVIDING_VS_NORMAL_DIVIDING_UP.html Genes up-regulated in dividing CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients compared to the dividing cells from normal donors. 17717066 16/54 Arthur Liberzon 0.034943559641908 0.0448740807021049 635 2267.63636363636 2503 0.0032282952613544 632 1.15078548685743 -1.15078548685743 -1 0.567028576508025 632 2595 2309 2756 3547 1099 881 2503 4106 2728 1788 2534 M17794 ASGHARZADEH_NEUROBLASTOMA_POOR_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ASGHARZADEH_NEUROBLASTOMA_POOR_SURVIVAL_DN.html Down-regulated genes associated with poor survival prognosis of patients with metastatic neuroblastoma that lack MYCN [GeneID=4613] amplification. 16954472 37/116 Jessica Robertson 2.22670565687135e-06 7.92281147160148e-06 2525 2251.81818181818 2503 2.0242799187364e-07 984 1.71850064013943 1.89294090888817 1 3.20431015749148 2523 2503 2636 1178 1080 3249 3740 2359 984 2526 1992 2535 M2216 WIERENGA_STAT5A_TARGETS_GROUP2 http://www.broadinstitute.org/gsea/msigdb/cards/WIERENGA_STAT5A_TARGETS_GROUP2.html Genes up-regulated in a linear fashion in CD34+ [GeneID=947] cells upon increasing activity levels of STAT5A [GeneID=6776]; predominant long-term growth and self-renewal phenotype. 18779318 32/93 Arthur Liberzon 0.000622768514249345 0.000992616754344364 2180 2334.18181818182 2504 5.66313523034956e-05 1306 1.73085985370316 1.6899170430706 1 1.90006330603752 2179 2807 1306 1922 2811 2888 2323 2917 2504 1421 2598 2536 M94 PID_FAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FAS_PATHWAY.html FAS (CD95) signaling pathway 18832364 33/54 Pathway Interaction Database 6.94903530276586e-05 0.000134579968563852 2960 2674.81818181818 2505 6.31750437122163e-06 1579 0.944991437266776 -0.936358148252263 -1 1.33712648488471 2957 2505 3042 2054 2296 1579 2405 3868 3528 3097 2092 2537 M1457 GREENBAUM_E2A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GREENBAUM_E2A_TARGETS_DN.html Genes down-regulated in pre-B lymphocytes upon Cre-Lox knockout of E2A [GeneID=6929]. 15310760 21/36 Kevin Vogelsang 5.20067407058439e-05 0.000103747802021109 2915 2526.63636363636 2506 4.72799728691948e-06 492 1.1838475564172 1.22695960315394 1 1.72399761856814 2911 492 2506 1914 2217 4131 3534 1394 2402 2628 3664 2538 M4163 PALOMERO_GSI_SENSITIVITY_UP http://www.broadinstitute.org/gsea/msigdb/cards/PALOMERO_GSI_SENSITIVITY_UP.html Up-regulated genes associated with sensitivity and resistance to gamma-secretase (GSI) in T-cell acute lymphoblastic leukemia (T-ALL) cell lines. 17873882 4/9 Jessica Robertson 0.000301120377759577 0.000506182054952704 2685 2741 2507 3.01161188609667e-05 1813 1.11823243820124 -1.31223458353142 -1 1.34709467559572 2507 1813 4525 2599 2682 2398 1835 4441 2293 2685 2373 2539 M12784 RHEIN_ALL_GLUCOCORTICOID_THERAPY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RHEIN_ALL_GLUCOCORTICOID_THERAPY_UP.html Genes up-regulated in ALL (acute lymphoblastic leukemia) blasts after 1 week of treatment with glucocorticoids. 17330098 50/190 Arthur Liberzon 0.000158715377040051 0.000280974785345553 2110 2557.09090909091 2508 1.44297116778339e-05 1808 1.54662371618152 -1.82817182176423 -1 2.00768359375831 2109 3567 2040 3414 2514 1808 2508 2634 3129 1945 2460 2540 M930 REACTOME_TRANSPORT_OF_ORGANIC_ANIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_ORGANIC_ANIONS.html Genes involved in Transport of organic anions 5/16 Reactome 0.00395266057775443 0.00566773790310809 4060 2619.81818181818 2511 0.000395970881491655 1078 1.36743551445372 -1.37558340851903 -1 1.12292298906928 2511 2097 4057 3228 3115 2125 1078 2027 4059 1864 2657 2541 M1760 WANG_LSD1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_LSD1_TARGETS_DN.html Genes down-regulated after Cre-lox knockout of LSD1 [GeneID=23028] in pituitary. 17392792 14/76 Jessica Robertson 8.45507469591972e-05 0.00015963126520983 2515 2590.90909090909 2511 7.68672696378975e-06 963 1.83606138069787 1.51888604845655 1 2.54820023551219 2381 3247 2049 2515 2356 3380 3313 3880 963 2511 1905 2542 M8560 BIOCARTA_G2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_G2_PATHWAY.html Cell Cycle: G2/M Checkpoint 20/43 BioCarta 0.0102115630764206 0.0139752875514331 1680 2580.09090909091 2512 0.000932661052682966 1394 3.06400283704495 3.06400283704495 1 2.07714999696047 1680 3777 2521 2723 3933 2491 1948 1483 1394 3919 2512 2543 M268 PID_S1P_S1P2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P2_PATHWAY.html S1P2 pathway 18832364 15/36 Pathway Interaction Database 3.9060397139867e-05 8.09182232526157e-05 3400 2684.63636363636 2514 3.55100824215939e-06 1555 1.35247485380799 -1.54895457599267 -1 2.02292208785576 3398 1555 2035 1601 2130 3640 3939 2362 3752 2605 2514 2544 M1996 KYNG_WERNER_SYNDROM_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_WERNER_SYNDROM_UP.html Genes distinctly up-regulated in primary fibroblast cultures from Werner syndrom patients compared to those from normal young donors. 14527998 15/29 Arthur Liberzon 2.80289101860113e-06 9.30194568921026e-06 2575 2333.18181818182 2514 2.54808599055147e-07 327 2.29983694134419 2.8124462936748 1 4.22967894131775 2571 1742 2514 1781 1196 4676 4417 2785 327 2618 1038 2545 M1629 KYNG_RESPONSE_TO_H2O2_VIA_ERCC6 http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_RESPONSE_TO_H2O2_VIA_ERCC6.html Genes down-regulated in CS-B cells (Cockayne syndrome fibroblast, CS) with defficient ERCC6 [GeneID=2074] in response to hydrogen peroxide [PubChem=784]. 12606941 16/42 John Newman 6.9501218406898e-05 0.000134579968563852 1565 2497.45454545455 2515 6.31849219537961e-06 869 0.866414635241906 0.866414635241906 1 1.22594333646374 1564 2515 3298 3308 2297 1135 869 2995 3961 4589 941 2546 M6335 AUJLA_IL22_AND_IL17A_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/AUJLA_IL22_AND_IL17A_SIGNALING.html Genes changed in HBE cells (bronchial epithelium) after treatment with IL22 and IL17A [GeneID=50616;3605]. 18264110 3/19 Jessica Robertson 0.0853403083779276 0.0981361190328758 1815 2735.90909090909 2515 0.00888065244066432 1757 1.93332905988956 -1.93332905988956 -1 0.712458022843648 1811 2852 4483 2795 3664 1757 1943 2072 3734 2469 2515 2547 M587 REACTOME_DEGRADATION_OF_THE_EXTRACELLULAR_MATRIX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEGRADATION_OF_THE_EXTRACELLULAR_MATRIX.html Genes involved in Degradation of the extracellular matrix 15/70 Reactome 5.12527348202352e-05 0.000102330769223529 2645 2664 2516 4.65944807987697e-06 1983 1.60195510606783 -1.62962026985808 -1 2.3363710054269 2641 3159 1993 4416 2214 2265 2446 2642 3029 1983 2516 2548 M9904 KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY.html T cell receptor signaling pathway 56/137 KEGG 1.16463181603267e-05 2.86180633976356e-05 2520 2215.36363636364 2518 1.0587618012583e-06 899 1.3373751857443 -1.28351635814226 -1 2.22100552139155 2518 1722 2528 899 1742 1716 3796 2643 2566 2632 1607 2549 M8353 BIOCARTA_HCMV_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HCMV_PATHWAY.html Human Cytomegalovirus and Map Kinase Pathways 14/25 BioCarta 0.000247780232417767 0.000423140732182818 3425 2541.27272727273 2518 2.25280130597139e-05 1409 1.2253411642073 -1.28636146419916 -1 1.51098078191719 3425 2169 2725 1409 2614 2309 3497 2518 2576 2499 2213 2550 M1739 GAVIN_IL2_RESPONSIVE_FOXP3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_IL2_RESPONSIVE_FOXP3_TARGETS_UP.html FOXP3 [GeneID=50943] target genes up-regulated in T lymphocytes after stimulation with IL2 [GeneID=3558]. 17220874 6/28 Jessica Robertson 6.17953435445607e-06 1.71243630898765e-05 2830 2544.45454545455 2518 6.1795515385135e-07 1230 1.07585793918493 1.15088840676906 1 1.87440463943619 2827 1230 4437 2434 1543 2758 2587 2146 2518 3058 2451 2551 M19610 CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_UP.html Marker genes up-regulated in the 'unannotated' subclass of hepatocellular carcinoma (HCC) samples. 18701503 42/161 Yujin Hoshida 0.000189065117447583 0.000330458463394023 2285 2600.72727272727 2518 1.71892152191989e-05 1457 1.52360468884737 1.60526711837776 1 1.93856778678526 2284 2612 2490 2048 2553 2788 2518 4336 2478 1457 3044 2552 M1979 KEGG_GNRH_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GNRH_SIGNALING_PATHWAY.html GnRH signaling pathway 44/116 KEGG 6.32330102290251e-06 1.7416986422689e-05 3415 2481.72727272727 2519 5.74847199780258e-07 891 1.53487597859597 -1.62776412602047 -1 2.66999659264979 3414 1487 1671 891 1521 3591 2519 2775 2873 1907 4650 2553 M6564 HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_UP.html Genes up-regulated in lesional skin biopsies from mycosis fundoides patients compared to the normal skin samples. 16914566 120/264 Arthur Liberzon 0.000317362475615763 0.000530749664787817 3095 2442 2519 2.88552969273262e-05 1394 1.35076649520352 1.37633687103826 1 1.61705747744735 1394 4053 2519 3023 2674 1963 2037 1465 3093 3093 1548 2554 M760 REACTOME_INTEGRIN_ALPHAIIB_BETA3_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTEGRIN_ALPHAIIB_BETA3_SIGNALING.html Genes involved in Integrin alphaIIb beta3 signaling 20/42 Reactome 0.0216126722574467 0.0283609583305504 1570 2591.18181818182 2520 0.00198436006855044 1045 1.13587380630423 1.03558521058507 1 0.642418431756376 1570 3676 2520 3211 3881 1389 1045 1665 4119 3583 1844 2555 M36 PID_IL27_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL27_PATHWAY.html IL27-mediated signaling events 18832364 11/27 Pathway Interaction Database 0.0059533959795248 0.0083776617297457 2815 2439.72727272727 2523 0.000542687972691628 1902 1.38003233668041 -1.489573494923 -1 1.04765750168176 2696 2060 2083 2091 3163 2569 2813 2122 1902 2815 2523 2556 M278 PID_RAC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RAC1_PATHWAY.html RAC1 signaling pathway 18832364 37/83 Pathway Interaction Database 6.63659005410234e-06 1.80703434012339e-05 4615 2743.45454545455 2524 6.0332818857598e-07 674 1.52353062095524 -1.17751165646875 -1 2.6413541717157 4613 1595 2477 846 1535 3752 4324 4485 674 2524 3353 2557 M12899 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GLOBO_SERIES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GLOBO_SERIES.html Glycosphingolipid biosynthesis - globo series 5/15 KEGG 8.77035945727714e-05 0.00016491935961798 3125 2645.45454545455 2526 8.77070561292727e-06 1476 1.3223237205562 1.65338668212554 1 1.82836203288467 3121 1519 3797 2866 2400 3173 4349 2526 1476 1855 2018 2558 M16927 BOYLAN_MULTIPLE_MYELOMA_C_D_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_D_UP.html Genes up-regulated both in group C and D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 88/197 Jessica Robertson 3.69043715792456e-06 1.14906236026807e-05 2055 2726.63636363636 2526 3.35494849867456e-07 1307 1.6574616506956 1.7434255892473 1 2.99267447790598 2052 4498 2150 3585 1307 2744 1998 3649 2012 3472 2526 2559 M15147 BOYAULT_LIVER_CANCER_SUBCLASS_G12_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G12_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G12, defined by unsupervised clustering 17187432 25/64 Yujin Hoshida 1.20282224384235e-05 2.93869918386093e-05 2615 2360.09090909091 2526 1.0934807456105e-06 279 1.48414712741442 1.67554095373778 1 2.45850582146953 2612 3365 2526 3539 3730 1789 1353 279 1124 3438 2206 2560 M603 REACTOME_YAP1_AND_WWTR1_TAZ_STIMULATED_GENE_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_YAP1_AND_WWTR1_TAZ_STIMULATED_GENE_EXPRESSION.html Genes involved in YAP1- and WWTR1 (TAZ)-stimulated gene expression 9/30 Reactome 6.2164797677283e-05 0.000121731818602486 4150 2786.63636363636 2527 6.21665367536842e-06 909 1.70311475701087 1.68316535141225 1 2.43696952410332 4147 2091 3936 2125 2291 2405 2527 3482 909 2564 4176 2561 M4551 SANA_RESPONSE_TO_IFNG_UP http://www.broadinstitute.org/gsea/msigdb/cards/SANA_RESPONSE_TO_IFNG_UP.html Genes up-regulated in five primary endothelial cell types (lung, aortic, iliac, dermal, and colon) by IFNG [GeneID=3458]. 15749026 54/166 Yujin Hoshida 5.80068414192648e-06 1.62849910499712e-05 3540 2351.72727272727 2527 5.27336312409049e-07 582 1.73984964952515 -1.80059350019396 -1 3.0451198076466 3538 1343 966 2173 1488 3144 3424 2839 2527 582 3845 2562 M15343 REACTOME_ACTIVATED_TLR4_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_TLR4_SIGNALLING.html Genes involved in Activated TLR4 signalling 60/124 Reactome 2.98086868524651e-05 6.40456242964932e-05 3585 2748.90909090909 2528 2.70991734091284e-06 1933 1.1474867721755 -1.14743097484891 -1 1.75891428725195 3582 2270 3326 1933 2043 2097 4427 2818 2930 2528 2284 2563 M15473 SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_DN.html Selected genes down-regulated in peripheral blood monocytes (PBMC) of patients with hepatocellular carcinoma (HCC) compared to those with chronic hepatitis. 19074895 23/62 Arthur Liberzon 4.30303263626185e-06 1.29246056481187e-05 4610 2627 2528 3.91185550244489e-07 743 1.360638040988 1.31584834794811 1 2.43133513254873 4606 743 935 1618 1367 2528 4101 4275 3292 1110 4322 2564 M1975 MIKKELSEN_IPS_LCP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_LCP_WITH_H3K4ME3.html Table 2S. Genes in MEF, MCV6, MCV8.1 and ES cells by epigenetic mark of their promoter 18509334 101/284 Jessica Robertson 1.01909096389551e-06 4.79448552966058e-06 4565 2539.81818181818 2531 9.2644675996578e-08 515 1.72924738582268 -1.77589928561419 -1 3.36223010632074 4563 1250 515 1551 726 4208 3333 3668 2531 1433 4160 2565 M9740 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_DN.html Genes down-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 8 days after transduction. 16818636 88/354 Arthur Liberzon 8.88146564205974e-07 4.38551612209609e-06 3155 2520.09090909091 2532 8.07406293412358e-08 384 2.14885154288068 -2.05534739196157 -1 4.20849381685147 3152 2532 384 2122 673 4320 3536 3696 2363 796 4147 2566 M1115 GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_DN.html Down-regulated genes from the set C (Fig. 5a): specific to cells expressing AF4-MLL [GeneID=4299;4297] fusion protein alone. 17130830 14/26 Arthur Liberzon 0.000171883959942212 0.000302572590642075 1890 2481.36363636364 2532 1.56270355041533e-05 1241 1.16171468945547 1.17656094666426 1 1.49437305808398 2554 1305 2450 3448 2532 1886 1241 3959 3254 1890 2776 2567 M1448 NEMETH_INFLAMMATORY_RESPONSE_LPS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NEMETH_INFLAMMATORY_RESPONSE_LPS_UP.html Genes up-regulated in RAW 264.7 cells (macrophage) 3 hr after stimulation with bacterial lipopolysaccharide (LPS). 12766259 61/147 Kevin Vogelsang 4.09216037546704e-07 2.79255907977434e-06 2535 2293.63636363636 2533 3.72014648785354e-08 369 1.44198062852404 1.51342102656064 1 2.92741549061649 2533 2535 2186 2106 369 3300 2842 1442 2409 2589 2919 2568 M3004 CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_DN.html Genes down-regulated in type 2B (EDL) vs type 1 (soleus) myofibers. 21364395 12/45 Emmanuelle Fouilloux-Meugnier 0.0303418000445621 0.0391685055120711 2135 2451.09090909091 2534 0.00279713894767932 772 2.76841814768001 3.67306816721969 1 1.42385078893526 2133 3518 1763 3366 3431 2534 1867 1750 772 2981 2847 2569 M15171 SASAKI_ADULT_T_CELL_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/SASAKI_ADULT_T_CELL_LEUKEMIA.html Genes up-regulated in adult T-cell leukemia (ATL) cells compared to T lymphocytes from healthy controls. 15471956 116/286 Kate Stafford 3.04897779787863e-07 2.36072070403987e-06 1920 2372.72727272727 2536 2.77179838221476e-08 273 1.13154686438212 -1.11187402850559 -1 2.32736912147438 1917 2040 3025 2536 273 1899 2734 2657 3242 3534 2243 2570 M11835 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION.html Valine, leucine and isoleucine degradation 27/60 KEGG 0.00717424250028919 0.00998767093177515 2800 2313.63636363636 2537 0.000654340473986219 1353 2.10400761509146 -1.47347169510114 -1 1.5385544815486 2800 2864 2192 2748 3191 1353 1518 2537 1452 2634 2161 2571 M17523 ZHAN_MULTIPLE_MYELOMA_CD2_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD2_DN.html Top 50 down-regulated genes in cluster CD-2 of multiple myeloma samples with the charachteristic expression spike of CCND3 [GeneID=896]. 16728703 31/72 Kevin Vogelsang 0.000932432817832981 0.0014506574317282 1430 2281.63636363636 2537 8.48025680344419e-05 737 1.37155227284894 -1.2204658328016 -1 1.42301863674151 1429 3479 2537 4354 3404 737 1193 973 2695 2957 1340 2572 M220 PID_CASPASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CASPASE_PATHWAY.html Caspase cascade in apoptosis 18832364 42/81 Pathway Interaction Database 3.7356376174515e-05 7.78354729896742e-05 4500 2653.18181818182 2539 3.39609186429541e-06 473 2.09735497551656 -1.59215966163901 -1 3.14998556792584 4497 2539 1537 2145 2116 3204 3794 3838 473 1759 3283 2573 M1421 PEART_HDAC_PROLIFERATION_CLUSTER_DN http://www.broadinstitute.org/gsea/msigdb/cards/PEART_HDAC_PROLIFERATION_CLUSTER_DN.html Cell proliferation genes down-regulated by histone deacetylase (HDAC) inhibitors SAHA and depsipeptide [PubChem=5311;5352062]. 15738394 54/131 Kate Stafford 1.70247023182968e-08 2.7227902752061e-07 2540 2489.18181818182 2540 1.54770022273113e-09 3 1.56095309244497 2.0226168886919 1 3.74578541700707 2540 3267 2333 3409 3 4164 3599 1351 1678 2178 2859 2574 M7860 BIOCARTA_NGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NGF_PATHWAY.html Nerve growth factor pathway (NGF) 16/34 BioCarta 0.000224000306165414 0.000385198324657296 2750 2081.54545454545 2541 2.03657378865549e-05 800 1.30535075120239 -0.964540775494394 -1 1.62910897869441 2746 2283 2541 800 2598 1557 2556 1285 918 2719 2894 2575 M1524 RUAN_RESPONSE_TO_TNF_TROGLITAZONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TNF_TROGLITAZONE_DN.html Adipocyte abundant genes down-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to troglitazone [PubChem=5591] and TNF [GeneID=7124]. 12732648 30/67 John Newman 7.96443548312464e-06 2.09670475696191e-05 2090 2730.18181818182 2541 7.24042210554887e-07 1302 1.26484946561155 -1.0013654709166 -1 2.16302363537382 2088 3448 2071 3830 1607 1302 2541 4284 4010 3329 1522 2576 M7772 BIOCARTA_BARRESTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BARRESTIN_PATHWAY.html fl-arrestins in GPCR Desensitization 6/23 BioCarta 0.000163158674977185 0.000288404960748054 1715 2816.18181818182 2543 1.63170655554152e-05 1386 0.804644505039319 0.804644505039319 1 1.04118098314005 1715 3464 3874 3709 2543 1814 1386 1834 4218 4288 2133 2577 M649 REACTOME_PHOSPHOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHOSPHOLIPID_METABOLISM.html Genes involved in Phospholipid metabolism 101/208 Reactome 6.48166265810036e-06 1.77102456069145e-05 2545 2608.90909090909 2545 5.89243795865492e-07 1531 1.37299142449024 -1.23278411566902 -1 2.38475068012781 2545 2975 2752 2549 1531 2413 4079 2270 2156 2313 3115 2578 M1002 REACTOME_RIG_I_MDA5_MEDIATED_INDUCTION_OF_IFN_ALPHA_BETA_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RIG_I_MDA5_MEDIATED_INDUCTION_OF_IFN_ALPHA_BETA_PATHWAYS.html Genes involved in RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways 41/95 Reactome 0.000180713685782832 0.000316806708409409 1560 2231.90909090909 2545 1.64298665253944e-05 894 0.966550323982856 -0.960435192928054 -1 1.23626958646959 1556 2614 3368 3300 2545 894 1237 1428 3337 3169 1103 2579 M2891 ROETH_TERT_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROETH_TERT_TARGETS_DN.html Genes down-regulated in T lymphocytes overexpressing TERT [GeneID=7015] off a retrovirus vector. 15741219 2/14 Kevin Vogelsang 1.81383017349431e-07 1.78961007243281e-06 4430 2337.2 2545.5 2.01536702190628e-08 45 1.71981631118288 -2.28071318215885 -1 3.61294014745705 4426 218 4388 NA 179 3512 2635 2456 45 1083 4430 2580 M5931 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_1 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_1.html Amplification hot spot 1: colocolized fragile sites and cancer genes in the Xp22.3-p11.1 region. 16751803 2/18 Arthur Liberzon 0.00619804443843106 0.00869581923308023 2190 2745.9 2546 0.000690576115164783 568 0.479364056218788 0.479364056218788 1 0.361074877486247 2186 2906 4237 NA 3454 1391 568 1897 4370 4519 1931 2581 M2579 ST_DIFFERENTIATION_PATHWAY_IN_PC12_CELLS http://www.broadinstitute.org/gsea/msigdb/cards/ST_DIFFERENTIATION_PATHWAY_IN_PC12_CELLS.html Differentiation Pathway in PC12 Cells; this is a specific case of PAC1 Receptor Pathway. 32/73 Signaling Transduction KE 8.82434310760273e-05 0.000165535915941659 2675 2593.81818181818 2548 8.02245188874749e-06 1239 1.40136087209957 -1.26337740895641 -1 1.93681568113299 2675 3447 2548 1577 2370 2982 2484 2453 1239 3429 3328 2582 M2517 RAO_BOUND_BY_SALL4_ISOFORM_A http://www.broadinstitute.org/gsea/msigdb/cards/RAO_BOUND_BY_SALL4_ISOFORM_A.html Loci bound exclusively by SALL4 [GeneID=57167] isoform a in ES cells (embryonic stem). 20837710 96/360 Arthur Liberzon 7.09254051934839e-06 1.90790154269039e-05 1605 2373.09090909091 2548 6.44778489542335e-07 1260 1.40285589559454 1.42159391378099 1 2.42004339116435 1602 2628 2748 2698 1562 1437 2021 4260 2548 3340 1260 2583 M2590 SMIRNOV_RESPONSE_TO_IR_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_RESPONSE_TO_IR_6HR_DN.html Genes down-regulated in B lymphocytes at 6 h after exprosure to 10 Gy dose of ionizing radiation. 21844125 61/177 Itai Pashtan 0.000183912557132739 0.000322173548681874 1605 2716.81818181818 2548 1.67207212181738e-05 1601 1.53457510011352 1.69915352400424 1 1.95871141303947 1601 4571 1662 4622 2548 2624 2011 2211 3421 2591 2023 2584 M1074 REACTOME_NUCLEOTIDE_BINDING_DOMAIN_LEUCINE_RICH_REPEAT_CONTAINING_RECEPTOR_NLR_SIGNALING_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEOTIDE_BINDING_DOMAIN_LEUCINE_RICH_REPEAT_CONTAINING_RECEPTOR_NLR_SIGNALING_PATHWAYS.html Genes involved in Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways 33/56 Reactome 0.00088067584386978 0.00137469920198994 2415 2296.27272727273 2549 8.00935074957858e-05 932 1.30373317205464 -1.19927971137812 -1 1.36378553453893 2412 2712 2781 2706 2867 1380 2549 1395 3300 2225 932 2585 M242 PID_AURORA_A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AURORA_A_PATHWAY.html Aurora A signaling 18832364 26/47 Pathway Interaction Database 2.20985189332439e-05 4.94053720043803e-05 2550 2580.27272727273 2550 2.00897644646873e-06 974 2.010166036991 1.99870284204611 1 3.16408384028166 2550 3542 2454 3600 1955 3295 1872 974 1180 3808 3153 2586 M19828 PASTURAL_RIZ1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PASTURAL_RIZ1_TARGETS_UP.html Genes up-regulated in K562 (chronic myelogenous leukemia, CML) cells engineered to stably express RIZ1 [GeneID=7799]. 16953217 19/43 Aravind Subramanian 0.0063048023649685 0.00883501910354138 3470 2762.36363636364 2550 0.000574813056019964 1115 1.81645120859389 2.27741731691678 1 1.36363943469003 3466 2550 1505 1844 3446 4469 4593 1387 2214 1115 3797 2587 M7245 SEKI_INFLAMMATORY_RESPONSE_LPS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SEKI_INFLAMMATORY_RESPONSE_LPS_UP.html Genes up-regulated in hepatic stellar cells after stimulation with bacterial lipopolysacharide (LPS). 17952090 52/123 Jessica Robertson 0.000213840849833304 0.000369490494955334 1995 2432.90909090909 2550 1.94419670977675e-05 1050 1.66641751646212 1.64116643144663 1 2.09074252021043 1995 1183 1285 2175 2582 3669 3195 3833 2550 1050 3245 2588 M2420 WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_WITH_H4K20ME1_MARK http://www.broadinstitute.org/gsea/msigdb/cards/WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_WITH_H4K20ME1_MARK.html Genes with promoters bound by both PPARG and RXRA [GeneID=5468, 6256] at 8 (but not 0) day time point of adipocyte differentiation of 3T3-L1 cells (preadipocyte) and that were newly modified by H4K20me1. 19414603 108/219 Arthur Liberzon 2.60002969781335e-05 5.68536591878365e-05 3315 2560.18181818182 2550 2.36369129663314e-06 686 0.980170252541454 -0.797173926606606 -1 1.52097885719565 3313 1477 3533 2526 1998 686 2550 3733 2993 3889 1464 2589 M562 REACTOME_GRB2_EVENTS_IN_ERBB2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GRB2_EVENTS_IN_ERBB2_SIGNALING.html Genes involved in GRB2 events in ERBB2 signaling 11/28 Reactome 0.000187210613856991 0.00032757191125704 3435 2288.45454545455 2551 1.70205951436064e-05 172 2.7148271500137 -1.95322526380809 -1 3.45800805172093 3435 2642 1780 307 2551 1252 2249 4685 172 2821 3279 2590 M2909 REACTOME_PYRIMIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRIMIDINE_METABOLISM.html Genes involved in Pyrimidine metabolism 17/29 Reactome 9.70982506563489e-05 0.000179842846867846 2640 2546.45454545455 2551 8.8275033097871e-06 1453 1.67991807441459 2.43519131822848 1 2.29970200434885 2636 2551 1453 1911 2405 3913 3616 2758 1863 2214 2691 2591 M9096 IIZUKA_LIVER_CANCER_PROGRESSION_G2_G3_UP http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_G2_G3_UP.html Genes up-regulated during transition from G2 (moderately differentiated tumor, infected with HCV) to G3 (poorly differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 16/49 Yujin Hoshida 0.0121280404766762 0.0164492033787858 2035 2650 2552 0.00110867453455287 1792 0.981518619390424 1.1643984528918 1 0.63999616790009 2033 2552 2989 3388 3275 2462 2024 1792 3358 2733 2544 2592 M4779 IGARASHI_ATF4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IGARASHI_ATF4_TARGETS_DN.html Genes down-regulated in A549 cells (lung cancer) after knockdown of ATF4 [GeneID=468] by RNAi. 17297441 63/145 Leona Saunders 1.05371265654254e-05 2.62503854787792e-05 4660 2658.18181818182 2553 9.57925184946973e-07 1296 1.60920234751966 -1.79113725112156 -1 2.69449471402657 4659 2884 1393 1565 1710 3549 4192 2553 2126 1296 3313 2593 M10582 STAEGE_EWING_FAMILY_TUMOR http://www.broadinstitute.org/gsea/msigdb/cards/STAEGE_EWING_FAMILY_TUMOR.html Genes up-regulated in Ewing family tumors (EFT) compared with normal bone marrow samples. 15548687 12/44 Kevin Vogelsang 0.00359181024719142 0.00517247167127811 3020 2439.72727272727 2554 0.000327062529336045 739 2.06653110154171 2.08851853428154 1 1.72700967012119 3017 2753 2052 2366 3089 3336 2521 2813 739 1597 2554 2594 M211 PID_HEDGEHOG_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HEDGEHOG_2PATHWAY.html Signaling events mediated by the Hedgehog family 18832364 14/34 Pathway Interaction Database 6.93033110376632e-05 0.000134362977046955 2935 2554.18181818182 2555 6.30049948114093e-06 1373 1.19854634931848 -0.64662617794095 -1 1.69620394270328 2935 2555 2398 1837 2295 3479 3178 1373 1681 3144 3221 2595 M12403 WATANABE_COLON_CANCER_MSI_VS_MSS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_COLON_CANCER_MSI_VS_MSS_UP.html Up-regulated genes discriminating between MSI (microsatellite instability) and MSS (microsatellite stability) colon cancers. 17047040 16/42 Leona Saunders 2.08128082417766e-07 1.9505763884193e-06 4400 2685.36363636364 2556 1.89207365552227e-08 169 1.37016764015597 -1.16320270852065 -1 2.85967494342356 4399 1554 2556 885 169 4544 3900 2605 2298 2122 4507 2596 M19166 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_CHONDROITIN_SULFATE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_CHONDROITIN_SULFATE.html Glycosaminoglycan biosynthesis - chondroitin sulfate 9/24 KEGG 0.00744182442894915 0.0103386864138914 1160 2546.54545454545 2558 0.00074668638623888 580 1.67234500774904 1.67234500774904 1 1.2137314227217 1158 3192 3792 3819 3429 1414 580 2260 4011 2558 1799 2597 M2607 ELLWOOD_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELLWOOD_MYC_TARGETS_UP.html Genes up-regulated in transgenic mice expressing human MYC [GeneID=4609] in prostate. 14522256 9/17 Arthur Liberzon 0.000179312226630449 0.000314703031457036 2965 2513.54545454545 2559 1.79326697067381e-05 859 1.22422515440028 -1.58568256139937 -1 1.56714426220092 2963 2175 4552 2778 2559 2263 2599 1039 859 3419 2443 2598 M506 REACTOME_INSULIN_RECEPTOR_RECYCLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INSULIN_RECEPTOR_RECYCLING.html Genes involved in Insulin receptor recycling 9/27 Reactome 0.000267816089629115 0.000454540454908378 855 2058 2560 2.67848371560848e-05 370 1.09129128616542 -1.09129128616542 -1 1.33328172941036 855 2560 3916 3512 2655 450 370 969 2837 3397 1117 2599 M17037 PETRETTO_HEART_MASS_QTL_CIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_HEART_MASS_QTL_CIS_UP.html Up-regulated cis-regulated expression quantitative loci (cis-eQTL) in the heart that colocalize with previously mapped cardiac mass QTLs. 18443592 22/45 Jessica Robertson 1.27503581189254e-06 5.58394188273686e-06 3265 2618.27272727273 2561 1.159124137141e-07 810 1.13486444535394 -0.860442613918323 -1 2.17909180817701 3261 1873 2561 2249 810 3975 3610 2953 2344 2189 2976 2600 M7732 RAGHAVACHARI_PLATELET_SPECIFIC_GENES http://www.broadinstitute.org/gsea/msigdb/cards/RAGHAVACHARI_PLATELET_SPECIFIC_GENES.html Genes in this set correspond to the most abuntant transcripts that are also specific to platelets. 17353439 81/163 Arthur Liberzon 0.000821129465278206 0.00128818636568252 1540 2626.54545454545 2561 7.46760094935431e-05 1539 1.40610269581657 1.75699445768766 1 1.48537918879274 1539 3474 2113 3079 2854 2525 1838 2123 3318 3468 2561 2601 M3053 MULLIGHAN_MLL_SIGNATURE_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_MLL_SIGNATURE_2_UP.html The 'MLL signature 2': genes up-regulated in pediatric AML (acute myeloid leukemia) with rearranged MLL [GeneID=4297] compared to the AML cases with intact MLL and NPM1 [GeneID=4869]. 17597811 278/649 Arthur Liberzon 7.17668995217824e-07 3.85223013927918e-06 4420 2487.72727272727 2562 6.52426572119105e-08 583 1.33165206140047 -1.30658827793198 -1 2.635429186587 4416 1238 2095 2293 583 2809 3747 2562 2836 1913 2873 2602 M15346 LEE_LIVER_CANCER_E2F1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_E2F1_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) induced by overexpression of E2F1 [GeneID=1869]. 15565109 29/118 Yujin Hoshida 4.43740994266331e-06 1.32221120359448e-05 2940 2648.27272727273 2562 4.03401717542227e-07 1381 1.46695090429828 -1.60653643596572 -1 2.61600680129136 2940 2365 2054 2785 1381 2492 3907 3083 3223 2339 2562 2603 M12692 FINETTI_BREAST_CANCER_KINOME_GREEN http://www.broadinstitute.org/gsea/msigdb/cards/FINETTI_BREAST_CANCER_KINOME_GREEN.html Genes in the green cluster of protein kinases distinguishing between luminal A and basal breast cancer subtypes. 18245477 9/27 Jessica Robertson 0.0015960349314297 0.00239252069375546 2040 2467.27272727273 2562 0.000159718238885094 1127 1.36245709976542 1.25931928920589 1 1.30536816322402 2039 2673 4453 2923 2997 1741 2562 1352 3454 1819 1127 2604 M10941 PENG_RAPAMYCIN_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/PENG_RAPAMYCIN_RESPONSE_UP.html Genes up-regulated in BJUB cells (B-lymphoma) in response to rapamycin (sirolimus) [PubChem=6610346] treatment. 12101249 174/380 Broad Institute 4.3527151350043e-06 1.30247912660474e-05 3535 2718.90909090909 2563 3.95702158809545e-07 1372 1.44667139782415 -1.3162864337835 -1 2.58329552844586 3532 2218 1715 2019 1372 2892 4351 3452 2563 2493 3301 2605 M7182 KUROKAWA_LIVER_CANCER_EARLY_RECURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KUROKAWA_LIVER_CANCER_EARLY_RECURRENCE_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) with early recurrence. 15288478 17/42 Yujin Hoshida 0.0839184282471183 0.0965721401684667 2245 2919.72727272727 2563 0.00793650793650794 2219 1.82900941983845 -1.54586232795916 -1 0.678679320875594 2244 4159 2424 2239 4039 2273 2563 3896 3083 2219 2978 2606 M2468 KRIEG_KDM3A_TARGETS_NOT_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/KRIEG_KDM3A_TARGETS_NOT_HYPOXIA.html Genes not induced under hypoxia, but dependent on KDM3A [GeneID=55818] for hypoxic expression in RCC4 cells (renal carcinoma) expressing VHL [GeneID=7428]. 19858293 134/310 Arthur Liberzon 6.32488353913094e-07 3.5795174232328e-06 3300 2378.36363636364 2564 5.74989577954746e-08 535 1.27657789115683 -1.13040537988646 -1 2.54131326091783 3299 813 2881 1971 535 2023 2564 4006 2509 2946 2615 2607 M3362 MARKS_HDAC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARKS_HDAC_TARGETS_DN.html Genes whose transcription is down-regulated by histone deacetylase inhibitors. 17322921 11/23 Arthur Liberzon 0.000203061794154363 0.000352555601114244 4085 3041.09090909091 2565 1.84618672132623e-05 1515 1.54081952396203 -1.47336921805252 -1 1.94463891404453 4085 2086 1526 1747 2565 4381 4255 4606 2104 1515 4582 2608 M3169 RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_UP.html ES/PNET (Ewing sarcoma; primitive neuroectodermal tumors) markers up-regulated in neuroblastoma cell lines expressing ESWR1-FLI1 [GeneID=2130;2313] fusion protein. 14973077 26/73 Kevin Vogelsang 0.0108364667616787 0.0147787203856887 2565 2526.45454545455 2565 0.000990019508542075 1207 1.96403329153358 2.16191642288112 1 1.31403024960308 2565 2587 1207 1711 3257 3911 3898 1924 2330 1652 2749 2609 M2069 BILD_MYC_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/BILD_MYC_ONCOGENIC_SIGNATURE.html Genes selected in supervised analyses to discriminate cells expressing c-Myc [GeneID=4609] from control cells expressing GFP. 16273092 142/338 Arthur Liberzon 3.81602501043131e-06 1.1803229834245e-05 2020 2717.54545454545 2565 3.469119663236e-07 1318 1.51205923790118 1.85781870280154 1 2.72369628969279 2697 2909 2017 2314 1318 4443 3999 2019 2565 2148 3464 2610 M18491 STEIN_ESRRA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESRRA_TARGETS_UP.html Genes up-regulated by ESRRA [GeneID=2101] only. 18974123 287/727 Leona Saunders 2.11645985063209e-06 7.65704986603088e-06 2595 2315.72727272727 2568 1.92405626066071e-07 733 1.33538208017612 -1.31938152765186 -1 2.4971815151876 2591 2568 3492 3484 1057 733 2091 2297 2756 3284 1120 2611 M1063 REACTOME_THE_NLRP3_INFLAMMASOME http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THE_NLRP3_INFLAMMASOME.html Genes involved in The NLRP3 inflammasome 9/16 Reactome 0.0101039564946508 0.0138407106686828 2185 2695.09090909091 2570 0.00101501931178638 1208 1.46909369668235 -1.00423547851022 -1 0.998185210112856 2185 2723 4091 3640 3262 1548 1208 2464 3859 2570 2096 2612 M16227 REACTOME_CHOLESTEROL_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHOLESTEROL_BIOSYNTHESIS.html Genes involved in Cholesterol biosynthesis 9/24 Reactome 0.00671967877470984 0.00939111683217724 1820 2794.36363636364 2571 0.000674008501045753 1423 1.18996060869875 -1.18996060869875 -1 0.881792014035192 1817 2372 4099 3763 3672 2330 2793 1423 3362 2571 2536 2613 M14736 BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP.html Genes up-regulated in ALL (acute lymphoblastic leukemia) patients who developed t-ML (treatment related myeloid leukemia). 16341039 18/63 Arthur Liberzon 0.00604973176604061 0.0085055634730472 2255 2631.27272727273 2572 0.000551493829070077 2001 1.22317875853 -1.5540873452585 -1 0.925639362024537 2255 2784 2430 2839 3164 2345 3547 2001 2072 2935 2572 2614 M17387 XU_GH1_EXOGENOUS_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_GH1_EXOGENOUS_TARGETS_DN.html Genes down-regulated in MFCF-7 cells (breast cancer) by exogenous HG1 [GeneID=2688]. 15845533 91/268 John Newman 3.0289753886655e-05 6.49375977959839e-05 3865 2785.09090909091 2572 2.75365190237671e-06 1307 1.77294154384032 1.99727003698338 1 2.71374401788896 3865 2297 1307 2572 2050 3794 4103 2986 2147 1618 3897 2615 M18193 REACTOME_ACTIVATION_OF_KAINATE_RECEPTORS_UPON_GLUTAMATE_BINDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_KAINATE_RECEPTORS_UPON_GLUTAMATE_BINDING.html Genes involved in Activation of Kainate Receptors upon glutamate binding 13/38 Reactome 1.37896089137998e-05 3.29012766650031e-05 3200 2585.36363636364 2573 1.25360866798935e-06 1750 1.3405650448898 -1.14678688001092 -1 2.19662169854827 3200 1934 1810 3184 1804 3363 3638 2201 2982 1750 2573 2616 M1513 LEE_CALORIE_RESTRICTION_NEOCORTEX_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_CALORIE_RESTRICTION_NEOCORTEX_UP.html Up-regulated in the neocortex of aged (30-month) mice subjected to caloric restriction since young adulthood. 10888876 77/187 John Newman 0.00844585836353101 0.0116575235026528 1955 2631.81818181818 2573 0.000770768871086048 1452 1.59456261707781 1.7571196795826 1 1.12688896831099 1951 3592 1825 3553 4113 2724 2044 1452 2573 3096 2027 2617 M6890 HELLER_HDAC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_HDAC_TARGETS_DN.html Genes down-regulated in at least one of three multiple myeloma (MM) cell lines by TSA [PubChem=5562]. 18172295 189/493 Jessica Robertson 6.05288688904945e-06 1.68431282435188e-05 3205 2636.36363636364 2573 5.50263958408661e-07 1291 1.34121908301614 -1.31122038824198 -1 2.34025363707551 4453 3204 1657 2573 1504 1889 4171 2594 3203 1291 2461 2618 M1554 MEDINA_SMARCA4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MEDINA_SMARCA4_TARGETS.html Genes up-regulated in H1299 cells (lung cancer) by expression of SMARCA4 [GeneID=6597] off a plasmid vector. 15731117 30/89 John Newman 1.67130050872513e-06 6.57023002003858e-06 2030 2392.36363636364 2575 1.51936525307589e-07 936 1.20288449417832 1.40118776191741 1 2.27864009778277 2026 2073 2575 2832 936 2817 2302 2421 2781 2866 2687 2619 M17695 REACTOME_PACKAGING_OF_TELOMERE_ENDS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PACKAGING_OF_TELOMERE_ENDS.html Genes involved in Packaging Of Telomere Ends 32/64 Reactome 0.0512029717565553 0.0647079626891096 515 2666.54545454545 2576 0.00476681910750775 515 0.945985781753593 -0.945985781753593 -1 0.411150812571248 515 2946 2880 2496 3784 1768 2116 2576 4181 3737 2333 2620 M1184 HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_UP http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_UP.html Genes up-regulated in MCF7 cells (breast cancer, normal TP53 [GeneID=7157]) undergoing aberrant mitosis and necrosis after treatment wiht 4 nM docetaxel [PubChem=148124]. 17099726 21/109 Arthur Liberzon 0.00420321031125418 0.00600861608253114 2570 2779.36363636364 2576 0.0003828420273435 1540 1.63848276466116 -1.47223613170882 -1 1.33031285155081 2568 2119 1540 1887 3110 2576 4533 3725 3146 2083 3286 2621 M2474 LIU_IL13_MEMORY_MODEL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_IL13_MEMORY_MODEL_UP.html Genes up-regulated in BEAS-2B cells (bronchial epithelium) stimulated with IL13 [GeneID=3596] on days 1 to 3 and then rested for the next 3 days (repeated-stimulation or memory model) 20123980 13/35 Arthur Liberzon 0.000337150320450633 0.000562437309231637 2660 2453.81818181818 2577 3.06547272613202e-05 1475 1.28238344867552 1.51343483822776 1 1.52338828051046 2660 2556 2515 2885 2687 2577 1633 1475 2872 2369 2763 2622 M2527 BOSCO_TH1_CYTOTOXIC_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/BOSCO_TH1_CYTOTOXIC_MODULE.html Genes representing Th1 / cytotoxic module in sputum during asthma exacerbations. 20336062 67/233 Antony Bosco 0.000217346600819541 0.000374609511303227 2075 2338.90909090909 2577 1.97607342100282e-05 856 1.69094608069016 2.01666998988376 1 2.11782347624543 2075 2577 856 3135 2588 3283 3070 1817 2796 1090 2441 2623 M8139 HOEGERKORP_CD44_TARGETS_TEMPORAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOEGERKORP_CD44_TARGETS_TEMPORAL_UP.html Genes temporally up-regulated by CD44 [GeneID=960] stimulation of B lymphocytes. 12411303 9/15 Kevin Vogelsang 0.00112429038040303 0.00173075713619206 1555 2468.81818181818 2578 0.000112485959874384 1114 1.49500354049783 1.49500354049783 1 1.50920423394159 1553 3583 4392 3828 2927 1523 1383 1264 3012 2578 1114 2624 M12804 LE_EGR2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LE_EGR2_TARGETS_UP.html Genes up-regulated in P14 nerves of transgenic mice having hypomorhic (reduced function) allele of EGR2 [GeneID=1959]. 15695336 88/189 Kate Stafford 0.00172313287092879 0.00257563018601988 700 2431.81818181818 2580 0.000156771271192124 696 1.82445630996728 2.12640737962726 1 1.72664998559979 696 3500 783 1939 3983 2884 2409 2587 2876 2513 2580 2625 M10189 REACTOME_SIGNALING_BY_NOTCH http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH.html Genes involved in Signaling by NOTCH 50/129 Reactome 6.05995294578584e-05 0.000119014834467529 2120 2209.54545454545 2581 5.50919988644138e-06 501 1.84802259685363 2.22065949552543 1 2.6509386267539 2116 2983 1879 3241 2581 2805 2638 501 1266 2992 1303 2626 M17200 SA_B_CELL_RECEPTOR_COMPLEXES http://www.broadinstitute.org/gsea/msigdb/cards/SA_B_CELL_RECEPTOR_COMPLEXES.html Antigen binding to B cell receptors activates protein tyrosine kinases, such as the Src family, which ultimate activate MAP kinases. 14/37 SigmaAldrich 0.000476218322885649 0.000771767913003107 2585 2560.09090909091 2582 4.33019488838719e-05 1637 1.26670826066258 -1.51702154370172 -1 1.4411429653136 2582 2554 3243 1637 2758 1995 3672 1975 2748 3142 1855 2627 M17466 SANA_TNF_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/SANA_TNF_SIGNALING_UP.html Genes up-regulated in five primary endothelial cell types (lung, aortic, iliac, dermal, and colon) by TNF [GeneID=7124]. 15749026 73/173 Yujin Hoshida 1.92076937050387e-06 7.17189264556267e-06 3225 2596.63636363636 2583 1.74615549771405e-07 650 1.6326824169063 1.60645210931954 1 3.07010227765062 3222 1586 1145 1366 1009 4615 4663 3539 2583 650 4185 2628 M11911 KEGG_ABC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ABC_TRANSPORTERS.html ABC transporters 17/50 KEGG 0.000215083090455724 0.000371226284300377 2880 2392.09090909091 2585 1.95549200855843e-05 1207 1.90356310194675 2.39800838925277 1 2.38685694246019 2876 1695 1342 1988 2585 3872 2978 3573 1207 1259 2938 2629 M10209 SHEPARD_BMYB_MORPHOLINO_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHEPARD_BMYB_MORPHOLINO_UP.html Human orthologs of genes up-regulated in zebra fish after knockdown of BMYB [GeneID=4605] by morpholino. 16150706 140/302 Jennifer Shepard 4.489993618519e-07 2.90609255474862e-06 2690 2430.81818181818 2586 4.08181321353167e-08 409 1.55514232544932 1.63733207793854 1 3.14731088407511 2689 1716 2586 2174 409 3950 2536 2954 1759 2945 3021 2630 M19751 MORI_SMALL_PRE_BII_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_SMALL_PRE_BII_LYMPHOCYTE_UP.html Up-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Small Pre-BII stage. 18922927 62/144 Jessica Robertson 2.5739328479434e-06 8.72122149346547e-06 4030 3007.27272727273 2587 2.33994169033745e-07 1156 1.41017973682631 -1.1663680121573 -1 2.60792251520589 4027 2004 2339 1760 1156 3811 4402 4282 2587 2319 4393 2631 M12053 NIKOLSKY_BREAST_CANCER_22Q13_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_22Q13_AMPLICON.html Genes within amplicon 22q13 identified in a copy number alterations study of 191 breast tumor samples. 19010930 12/28 Jessica Robertson 0.0248530982657809 0.0324134757788614 2210 2918.81818181818 2590 0.00228530750755378 1697 0.979493192900792 -0.979493192900792 -1 0.533206450136663 2210 3978 2590 4355 3604 1767 1802 1697 4066 3619 2419 2632 M3256 HASLINGER_B_CLL_WITH_17P13_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_17P13_DELETION.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with deletions in the 17p13 region. 15459216 21/36 Kevin Vogelsang 0.000409327320339868 0.00067231259134687 2340 2467.18181818182 2590 3.72184998867429e-05 140 2.00322806690442 2.00322806690442 1 2.3229588917816 2338 2590 3066 2457 3206 3147 3361 830 140 3632 2372 2633 M264 PID_TOLL_ENDOGENOUS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TOLL_ENDOGENOUS_PATHWAY.html Endogenous TLR signaling 18832364 20/47 Pathway Interaction Database 0.000414356167090618 0.000680168571752279 3460 2752.18181818182 2592 3.76758390048723e-05 1925 1.55268480510534 -1.05167823200939 -1 1.79764195208934 3459 2592 2466 1925 2731 2379 3269 4055 1937 2531 2930 2634 M3069 LENAOUR_DENDRITIC_CELL_MATURATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/LENAOUR_DENDRITIC_CELL_MATURATION_DN.html Genes down-regulated during in vitro maturation of CD14+ [GeneID=929] monocytes (day 0) into immature (day 7) and mature dendritic cells (day 14). 11279020 91/235 Kevin Vogelsang 8.6174078510589e-06 2.22731236569564e-05 2800 2529.54545454545 2592 7.83403782332846e-07 808 1.58217174872307 1.66904191919605 1 2.6905001122306 2798 1679 808 2042 1641 4556 4501 2592 2811 1099 3298 2635 M5091 EINAV_INTERFERON_SIGNATURE_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/EINAV_INTERFERON_SIGNATURE_IN_CANCER.html A gene expression signature found in a subset of cancer patients suggestive of a deregulated immune or inflammatory response. 16007187 15/53 Leona Saunders 0.000220227865254515 0.000379128499846677 1380 2386.81818181818 2593 2.00227194492038e-05 926 0.938127049912638 -0.938127049912638 -1 1.17317039276587 1376 2846 3194 3711 2593 926 1176 2500 3150 3259 1524 2636 M225 BIOCARTA_MTA3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MTA3_PATHWAY.html Downregulated of MTA-3 in ER-negative Breast Tumors 12/43 BioCarta 0.00034421398502719 0.000572793584459308 3515 2271.63636363636 2595 3.12970775325208e-05 216 2.10290067176382 -1.64951492861646 -1 2.49201854007991 3513 1975 1265 1398 2692 2595 3353 3005 216 2236 2740 2637 M10735 REACTOME_PLATELET_AGGREGATION_PLUG_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_AGGREGATION_PLUG_FORMATION.html Genes involved in Platelet Aggregation (Plug Formation) 23/51 Reactome 0.0192831583151012 0.0254322769109384 1910 2959 2595 0.00176857092342887 1368 1.13587380630423 1.03558521058507 1 0.662071834566274 1910 4517 2595 4484 4070 1850 1368 1638 4146 3708 2263 2638 M8323 KRASNOSELSKAYA_ILF3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KRASNOSELSKAYA_ILF3_TARGETS_UP.html Up-regulated in GHOST(3)CXCR4 cells (osteosarcoma) upon ectopic expression of ILF3 [GeneID=3609]. 12036489 52/150 John Newman 0.000217363051906418 0.000374609511303227 4350 2928 2596 1.97622300589563e-05 1229 1.78261180962423 2.1808861138615 1 2.2326301132431 4347 2984 1229 1489 2589 3954 4516 2596 2417 1736 4351 2639 M11266 KEGG_LYSOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LYSOSOME.html Lysosome 75/155 KEGG 0.000223968672287109 0.000385198324657296 1335 2493.09090909091 2597 2.03628614937327e-05 1335 1.32890022466308 -1.25252089389016 -1 1.65849928521953 1335 2144 2644 3632 2597 1614 3243 2498 2639 2996 2082 2640 M3434 NIKOLSKY_BREAST_CANCER_17Q11_Q21_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_17Q11_Q21_AMPLICON.html Genes within amplicon 17q11-q21 identified in a copy number alterations study of 191 breast tumor samples. 19010930 67/185 Jessica Robertson 6.58302497369719e-07 3.66176210424019e-06 4455 2748.09090909091 2597 5.98456994866009e-08 551 1.71258012449162 -1.53698293272337 -1 3.40309720073227 4454 2068 1859 2504 551 3237 3780 3897 1955 2597 3327 2641 M9544 BOYLAN_MULTIPLE_MYELOMA_PCA3_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_PCA3_DN.html Top down-regulated genes from principal component 3 (PCA3) which captures variation among different plasma cell tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609]. 17483317 46/116 Arthur Liberzon 0.000405607658662155 0.000667138465598758 3550 2595.54545454545 2598 3.68802235167901e-05 1418 1.7075324397524 1.75595052884495 1 1.98216211968597 3547 1772 1438 2598 2726 3753 2338 2918 1749 1418 4294 2642 M18750 CAMPS_COLON_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAMPS_COLON_CANCER_COPY_NUMBER_UP.html Genes from chromosomal copy number gains in a panel of 51 primary colon carcinoma samples. 18316590 49/166 Jessica Robertson 2.48485780356361e-06 8.54295206713065e-06 2560 2775.54545454545 2599 2.25896419106116e-07 1133 1.68925275048972 1.85791824724279 1 3.12956578062114 4490 2690 2558 2833 1133 2599 3528 2540 1387 2556 4217 2643 M2170 FIGUEROA_AML_METHYLATION_CLUSTER_4_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_4_UP.html Cluster 4 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 69/172 Arthur Liberzon 0.000224940220439993 0.00038667273403588 1770 2398.27272727273 2599 2.04512020791217e-05 627 1.35696941374577 1.6101248362216 1 1.69270734739633 1768 4057 2941 4215 2599 1698 1480 771 2947 3278 627 2644 M2064 BIOCARTA_41BB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_41BB_PATHWAY.html The 4-1BB-dependent immune response 10/25 BioCarta 0.00357595631675265 0.00515122388573715 1725 2446.72727272727 2600 0.000325616551057327 1248 0.922463146828257 -0.922463146828257 -1 0.771509532782054 1724 2600 3199 3106 3088 1248 1272 1765 3870 3477 1565 2645 M705 REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION.html Genes involved in MHC class II antigen presentation 61/131 Reactome 4.64655525319158e-07 2.96645203221468e-06 2440 2272.63636363636 2600 4.22414203143375e-08 422 1.24921529866196 -1.30001535639943 -1 2.52409637563136 2440 1015 1926 2600 422 2694 1702 3442 2655 2928 3175 2646 M1709 HILLION_HMGA1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/HILLION_HMGA1_TARGETS.html Genes changed in Rat1a cells (fibroblasts) by overexpression of HMGA1 isoform a [GeneID=3159] off a plasmid vector. 19074878 61/175 Leona Saunders 5.16280765081888e-06 1.49062949178911e-05 3535 2701.81818181818 2601 4.69347251507105e-07 1442 1.58196065707745 -1.65419737811699 -1 2.79099438612214 3534 3334 2601 2460 1442 1755 2320 4097 2713 2590 2874 2647 M1850 MATTHEWS_AP1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MATTHEWS_AP1_TARGETS.html Known targets of AP1 that were down-regulated by overexpression of TAM67, a dominant-negative form of JUN [GeneID=3725]. 17363560 12/22 Jessica Robertson 1.72868210700064e-05 3.99028054395766e-05 3645 2678.18181818182 2601 1.57154153683819e-06 975 1.67252413479419 1.65997168346322 1 2.68933724834728 3643 975 1337 2601 1881 4590 3981 2559 2895 1600 3398 2648 M15226 LOPEZ_MESOTHELIOMA_SURVIVAL_WORST_VS_BEST_UP http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_WORST_VS_BEST_UP.html Genes higher expressed in the worst 25 mesothelioma survivors compared to the 25 best ones. 16540645 9/24 Arthur Liberzon 0.000201582626027049 0.00035037692342832 2005 2494.81818181818 2602 2.01600914361748e-05 726 2.91878371535146 2.91878371535146 1 3.68661343274495 2003 2602 4139 3046 2974 3201 2503 726 836 2572 2841 2649 M836 OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_UP http://www.broadinstitute.org/gsea/msigdb/cards/OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_UP.html Genes up-regulated in pirmary cultures of epithelial ovarian cancer (EOC): invasive (TOV) vs low malignant potential (LMP) tumors. 15940270 49/95 Leona Saunders 7.22836557058538e-07 3.87109955014435e-06 3810 2591.54545454545 2604 6.57124358686657e-08 586 1.33989618792118 -1.31139840494595 -1 2.65070552459574 3810 1270 2604 2701 586 2548 4167 3195 2932 2553 2141 2650 M8615 BIOCARTA_IL2RB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL2RB_PATHWAY.html IL-2 Receptor Beta Chain in T cell Activation 24/61 BioCarta 0.000156370742482836 0.000277138161601578 3385 2785 2606 1.42165325497846e-05 1588 0.854991552262021 -0.914442785823023 -1 1.11173688240841 3385 2366 3321 2389 2511 1588 2815 2606 3663 3986 2005 2651 M17749 DORN_ADENOVIRUS_INFECTION_12HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_12HR_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) 12 h after infection with adenovirus Ad12. 15681441 42/84 Arthur Liberzon 0.0012999481735346 0.00198099419225468 2610 2593.09090909091 2606 0.000118246993647796 988 1.95192407126675 2.44969128832593 1 1.92862140006943 2606 2770 988 2062 2938 4633 4205 1525 2370 1458 2969 2652 M15493 CHEN_HOXA5_TARGETS_9HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_HOXA5_TARGETS_9HR_DN.html Genes down-regulated 9 h after induction of HoxA5 [GeneID=3205] expression in a breast cancer cell line. 15757903 35/69 Arthur Liberzon 3.06002385718875e-06 9.9578276352684e-06 3200 2327.72727272727 2608 2.78184373949566e-07 139 1.3272709056586 1.40960664091327 1 2.42665602673329 3199 139 1397 1557 1232 4068 2844 4372 2608 587 3602 2653 M1985 KUROZUMI_RESPONSE_TO_ONCOCYTIC_VIRUS http://www.broadinstitute.org/gsea/msigdb/cards/KUROZUMI_RESPONSE_TO_ONCOCYTIC_VIRUS.html Inflammatory cytokines and their receptors modulated in brain tumors after treatment with an oncocytic virus, a potential anticancer therapy. 18042934 16/57 Jessica Robertson 0.000211892320237359 0.000366476771329398 4125 3022.54545454545 2608 1.92647937575462e-05 917 1.80702271168921 -1.9867567592285 -1 2.26949978042105 4123 2345 1024 2608 2576 3947 4242 4570 2348 917 4548 2654 M4741 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS.html Systemic lupus erythematosus 64/146 KEGG 0.0282284169542569 0.0365409839358144 1410 2638.54545454545 2609 0.00259975105192512 1406 1.27545957441831 -1.23150240088223 -1 0.670052956951883 1406 2609 2036 2456 3413 2190 3116 2645 3559 3067 2527 2655 M3910 RODRIGUES_THYROID_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_UP.html Genes up-regulated in poorly differentiated thyroid carcinoma (PDTC) compared to anaplastic thyroid carcinoma (ATC). 17406368 5/18 Arthur Liberzon 0.000101466886992587 0.00018690009137078 2625 2475.09090909091 2609 1.01471520278456e-05 524 0.939550478412604 -1.12604773508427 -1 1.28044450044504 2622 524 4151 1948 2441 2609 3335 3082 1821 2897 1796 2656 M661 REACTOME_SIGNALING_BY_FGFR1_MUTANTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR1_MUTANTS.html Genes involved in Signaling by FGFR1 mutants 13/51 Reactome 1.61382034748598e-05 3.75489679658358e-05 2610 2423.09090909091 2610 1.46712016896602e-06 312 1.05934269868508 -1.13265794971027 -1 1.71359606075716 2610 2871 2816 2152 2915 1975 3321 312 2453 3675 1554 2657 M1192 HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer, mutated TP53 [GeneID=7157]) undergoing mitotic arrest and apoptosis after treatment with 100 nM docetaxel [PubChem=148124]. 17099726 52/123 Arthur Liberzon 2.96533615937281e-05 6.37996567622635e-05 3760 2743.54545454545 2610 2.69579648118384e-06 1166 1.46074577767448 -1.16036105706992 -1 2.23998268418961 3759 2610 1166 1877 2040 2906 3945 3619 2426 1735 4096 2658 M673 REACTOME_SIGNALING_BY_FGFR1_FUSION_MUTANTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR1_FUSION_MUTANTS.html Genes involved in Signaling by FGFR1 fusion mutants 13/36 Reactome 1.61382034748598e-05 3.75489679658358e-05 2615 2424.09090909091 2611 1.46712016896602e-06 313 1.05934269868508 -1.13265794971027 -1 1.71359606075716 2611 2872 2817 2153 2916 1976 3322 313 2454 3676 1555 2659 M1076 REACTOME_AMYLOIDS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMYLOIDS.html Genes involved in Amyloids 52/136 Reactome 0.0839184282471183 0.0965721401684667 775 2593.81818181818 2611 0.00793650793650794 774 1.24620829298363 -1.24620829298363 -1 0.462422876410989 774 2805 2305 2764 3559 1854 2241 2611 3644 3818 2157 2660 M2102 STAMBOLSKY_TARGETS_OF_MUTATED_TP53_DN http://www.broadinstitute.org/gsea/msigdb/cards/STAMBOLSKY_TARGETS_OF_MUTATED_TP53_DN.html Genes repressed in SKBR3 cells (breast cancer) by mutated TP53 [GeneID=7157]. 20227041 45/125 Arthur Liberzon 1.93870620487564e-05 4.4079462765877e-05 4085 2623.09090909091 2611 1.76247571777174e-06 961 1.77149634022747 2.03536596968418 1 2.82048517795907 4081 2611 1291 1529 1914 4254 3132 3077 1721 961 4283 2661 M2183 WANG_ADIPOGENIC_GENES_REPRESSED_BY_SIRT1 http://www.broadinstitute.org/gsea/msigdb/cards/WANG_ADIPOGENIC_GENES_REPRESSED_BY_SIRT1.html Adipogenic genes (group 2) that are selectively repressed by SIRT1 [GeneID=23411] in mature 3T3-L1 adipocytes. 17954559 21/62 Arthur Liberzon 0.000246788873069863 0.00042190903290966 4640 2800.63636363636 2612 2.24378692176952e-05 1496 1.4528731630417 -1.20184244781857 -1 1.79222516055288 4638 1496 1667 2214 2612 4041 4076 2691 2248 1617 3507 2662 M8432 NIKOLSKY_BREAST_CANCER_12Q24_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_12Q24_AMPLICON.html Genes within amplicon 12q24 identified in a copy number alterations study of 191 breast tumor samples. 19010930 11/18 Jessica Robertson 0.00194717281372367 0.00289941271214144 2615 2603.63636363636 2613 0.000177172577557227 1507 0.732656923663614 -0.732656923663614 -1 0.679607979222707 1963 1507 3354 2613 3006 1707 2611 2654 3776 3566 1883 2663 M8655 DAIRKEE_CANCER_PRONE_RESPONSE_BPA http://www.broadinstitute.org/gsea/msigdb/cards/DAIRKEE_CANCER_PRONE_RESPONSE_BPA.html 'Cancer prone response profile' (CPRP): genes changed in response to bisphenol A [PubChem=6623] in epithelial cell cultures from patients at high risk of breast cancer. 18381411 42/87 Jessica Robertson 0.00142023660102008 0.00214201117231416 1230 2279.27272727273 2613 0.000129195843765927 1181 1.36931905675664 -1.09574131385174 -1 1.33598469403537 1227 2613 2402 2800 2964 1181 1540 3199 2675 2857 1614 2664 M4835 BIOCARTA_BCELLSURVIVAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BCELLSURVIVAL_PATHWAY.html B Cell Survival Pathway 17/27 BioCarta 2.66311003258446e-05 5.79782435361686e-05 2615 2731.36363636364 2615 2.42103842745381e-06 1896 1.10219589688071 -0.543815263671915 -1 1.70690493920472 2615 2454 2869 1896 2009 3316 3602 2812 2310 3827 2335 2665 M15181 BIOCARTA_PGC1A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PGC1A_PATHWAY.html Regulation of PGC-1a 15/30 BioCarta 0.000514191982848068 0.000828577589967691 1770 2410.63636363636 2615 4.67556546366246e-05 871 1.28484529712196 1.68084060234977 1 1.44729069947467 1770 3096 2653 4062 3245 1600 1674 871 2615 3252 1679 2666 M3721 ST_JNK_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_JNK_MAPK_PATHWAY.html JNK MAPK Pathway 29/52 Signaling Transduction KE 7.19722319284118e-06 1.9294157827033e-05 4560 2749.90909090909 2617 6.54295158037583e-07 895 1.59414084735382 -1.1138048952619 -1 2.74718820482058 4559 3480 2617 2277 1569 4327 2720 1744 895 2337 3724 2667 M2052 ZEMBUTSU_SENSITIVITY_TO_VINCRISTINE http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_VINCRISTINE.html Top genes associated with chemosensitivity to vincristine [PubChem=5978] across 85 tumor xenografts. 11809704 11/33 Arthur Liberzon 0.0256483904267255 0.0333671175845741 3070 2544.81818181818 2617 0.0023593074513678 499 2.75851949905224 2.72758752775443 1 1.4889567603376 3067 2289 1151 2512 3398 3817 3080 2617 499 2113 3450 2668 M1810 DAZARD_UV_RESPONSE_CLUSTER_G6 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G6.html Cluster G6: genes increasingly down-regulated in NHEK cells (normal keratinocyte) after UV-B irradiation. 12771951 92/252 John Newman 4.54468771465679e-05 9.19137101030717e-05 1985 2587 2619 4.13161963639782e-06 1385 1.44864867202045 1.55171926396939 1 2.13747064285746 1982 3665 2767 3605 2184 2277 1458 1385 2773 3742 2619 2669 M10778 CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY http://www.broadinstitute.org/gsea/msigdb/cards/CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY.html Genes down-regulated in T cell acute lymphocytic leukemia (T-ALL) patients refractory to chemotherapy treatment. 14684422 23/69 Arthur Liberzon 0.0436991795090319 0.0556149796793383 2115 2601.09090909091 2619 0.00405382911007861 1158 1.65422725433884 2.27628427375748 1 0.758737895112314 2114 2619 1158 1980 3974 3543 3168 1854 3165 1799 3238 2670 M1940 BIOCARTA_CHREBP2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CHREBP2_PATHWAY.html Regulation And Function Of ChREBP in Liver 24/64 BioCarta 0.000257595376307153 0.000438782963786013 1365 2390 2620 2.34205038897906e-05 961 1.39742003966036 1.39742003966036 1 1.7151203752639 1361 3366 2694 2275 2620 1873 1637 3087 2673 3743 961 2671 M11798 PARK_TRETINOIN_RESPONSE_AND_RARA_PLZF_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/PARK_TRETINOIN_RESPONSE_AND_RARA_PLZF_FUSION.html Genes up-regulated by tretinoin (ATRA) [PubChem=444795] in U937 cells (acute promyelocytic leukemia, APL) made resistant to the drug by expression of the PLZF-RARA fusion [GeneID=7704, 5914]. 12893766 15/41 Arthur Liberzon 0.00491016484474496 0.00696610126021038 1355 2409.27272727273 2620 0.000447378015774433 862 1.07118824008525 1.07118824008525 1 0.844573106246095 1352 2898 2059 3312 3475 881 862 2620 4118 3777 1148 2672 M14238 BALLIF_DEVELOPMENTAL_DISABILITY_P16_P12_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/BALLIF_DEVELOPMENTAL_DISABILITY_P16_P12_DELETION.html Candidate genes in the pericentromeric microdeletion in 16p11.2-p12.2 associated with developmental disabilities. 17704777 9/28 Leona Saunders 0.00696517438042323 0.00971971624379489 2795 2639.18181818182 2621 0.000698710231698248 1812 2.07387842183998 -2.39946101702775 -1 1.52547567586799 2795 2177 4292 2958 3207 2471 2823 1927 1948 1812 2621 2673 M16973 BIOCARTA_CBL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CBL_PATHWAY.html CBL mediated ligand-induced downregulation of EGF receptors 9/21 BioCarta 0.000811901706936481 0.00127456328264802 2450 2844.09090909091 2622 8.12198492528081e-05 2008 1.37910014193689 1.31897772660044 1 1.45918179234831 2446 2488 3821 2622 2869 2715 3459 2008 3857 2561 2439 2674 M127 PID_ERBB1_RECEPTOR_PROXIMAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB1_RECEPTOR_PROXIMAL_PATHWAY.html EGF receptor (ErbB1) signaling pathway 18832364 19/54 Pathway Interaction Database 7.35403740712172e-05 0.000141233685613821 3895 2488.54545454545 2622 6.68571204117375e-06 715 1.26520825794956 -1.64593997445518 -1 1.7805286178777 3895 1207 2804 715 2311 3818 3743 1700 1033 3526 2622 2675 M19488 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP.html Genes up-regulated in nasopharyngeal carcinoma (NPC) positive for LMP1 [GeneID=9260], a latent gene of Epstein-Barr virus (EBV). 16912175 222/643 Arthur Liberzon 7.97566710456217e-06 2.09848265311501e-05 4510 2719.72727272727 2623 7.25063274447331e-07 1121 1.53573840800322 -1.50048085740986 -1 2.62606515771354 4506 2799 1491 2560 1608 2461 4150 3944 2654 1121 2623 2676 M1140 DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN.html Genes down-regulated in squamous cell carcinoma (SCC) compared to normal skin. 17525749 127/323 Arthur Liberzon 6.85327965297547e-07 3.76930380913651e-06 3270 2561.18181818182 2623 6.23025617078194e-08 564 1.49381237531526 -0.98717194966646 -1 2.96151593781314 3268 2571 2247 2623 564 3983 3551 1599 1621 3319 2827 2677 M486 REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER.html Genes involved in RNA Polymerase III Transcription Initiation From Type 2 Promoter 11/27 Reactome 0.000724681311062504 0.00114300121966977 1065 2197.90909090909 2624 6.59018301509271e-05 557 0.830650140752728 -0.830650140752728 -1 0.893250294794142 1064 2624 3504 3309 3694 557 602 930 3232 3554 1107 2678 M13954 NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON.html Genes within amplicon 8q12-q22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 62/161 Jessica Robertson 2.47336791356604e-06 8.53475849997824e-06 2630 2351.54545454545 2628 2.24851881297676e-07 1109 1.3330764929803 -1.43145542825016 -1 2.46990487316727 2628 2803 2815 3452 1127 1109 2341 1753 3144 2983 1712 2679 M9583 SANA_RESPONSE_TO_IFNG_DN http://www.broadinstitute.org/gsea/msigdb/cards/SANA_RESPONSE_TO_IFNG_DN.html Genes down-regulated in five primary endothelial cell types (lung, aortic, iliac, dermal, and colon) by IFNG [GeneID=3458]. 15749026 75/144 Yujin Hoshida 0.00471074374256113 0.00669737414370191 2305 2724.18181818182 2629 0.00042916917736757 1326 2.05127032122649 2.05391645719097 1 1.63012441305965 1545 3881 2391 2629 3346 3566 3402 1326 2303 3275 2302 2680 M11572 BROWNE_HCMV_INFECTION_12HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_12HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 12 h time point that were not up-regulated at the previous time point, 10 h. 11711622 85/220 John Newman 1.21829700818941e-05 2.96722441807461e-05 3340 2684.81818181818 2629 1.10754886801974e-06 1713 1.51485761992453 -1.27783227965436 -1 2.50705508059662 3340 2629 1938 2261 1757 3959 4316 2678 1713 1847 3095 2681 M14275 FONTAINE_PAPILLARY_THYROID_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_PAPILLARY_THYROID_CARCINOMA_DN.html Genes down-regulated in papillary thyroid carcinoma (PTC) compared to other thyroid tumors. 17968324 36/137 Arthur Liberzon 1.04781634377393e-05 2.61173797176842e-05 3780 2556.63636363636 2629 9.5256484940775e-07 1139 1.5701969361743 -1.67208353731754 -1 2.63044910965561 3780 2158 1704 2774 1708 2629 3559 3561 2691 1139 2420 2682 M4319 BIOCARTA_IL12_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL12_PATHWAY.html IL12 and Stat4 Dependent Signaling Pathway in Th1 Development 13/29 BioCarta 0.000908924832663898 0.00141596468280021 3585 2638.45454545455 2630 8.26636881973366e-05 1040 1.60555708596672 1.66002343181684 1 1.67197377022125 3585 1560 1954 1040 2875 4530 2993 4626 1486 1744 2630 2683 M9526 ST_T_CELL_SIGNAL_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/ST_T_CELL_SIGNAL_TRANSDUCTION.html T Cell Signal Transduction 30/72 Signaling Transduction KE 6.70024513046322e-05 0.000130550306367362 3840 2885.45454545455 2631 6.09131745413623e-06 2052 1.76949064892908 1.82266359184979 1 2.51230045883306 3839 2394 2321 2631 2284 3713 3438 2052 2305 2862 3901 2684 M2837 BARIS_THYROID_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/BARIS_THYROID_CANCER_UP.html Genes up-regulated in oncocytic follicular carcinoma (FTC) vs mitochondrial-rich papillary carcinoma (PTC) types of thyroid cancer. 15806164 16/39 Arthur Liberzon 0.000270844662315553 0.000459015583222669 2085 2649.72727272727 2631 2.46252738252595e-05 1559 0.806227419709195 0.922363848853738 1 0.983751932340583 2085 3156 3325 3200 2631 2143 1621 1559 3490 3801 2136 2685 M11720 BEIER_GLIOMA_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/BEIER_GLIOMA_STEM_CELL_DN.html Genes down-regulated in cancer stem cells derived from glyoblastoma tumors: CD133+ [GeneID=8842] vs. CD133- cells. 17483311 47/103 Jessica Robertson 1.34344553419121e-05 3.22014617556011e-05 3175 2792.09090909091 2631 1.22132158009669e-06 1749 1.6638225494059 -1.21809039125668 -1 2.73198324904089 3171 2631 2476 3295 1790 1749 3432 4380 2414 2772 2603 2686 M16088 LIAN_LIPA_TARGETS_3M http://www.broadinstitute.org/gsea/msigdb/cards/LIAN_LIPA_TARGETS_3M.html Genes up-regulated at 3 months of age in lungs from LIPA [GeneID=3988] knockout mice, which display pulmonary pathology. 16127159 35/122 John Newman 1.05455231114963e-06 4.89755414276232e-06 4210 2730 2632 9.58684378764675e-08 741 1.82137948810031 1.64804761238616 1 3.53521564309414 4206 2112 943 2097 741 4470 4134 2883 2632 1312 4500 2687 M9538 GRADE_COLON_VS_RECTAL_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_VS_RECTAL_CANCER_UP.html Genes up-regulated in rectal but down-regulated in colon carcinoma compared to normal mucosa samples. 17210682 19/52 Jessica Robertson 0.0839184282471183 0.0965721401684667 1660 2719.81818181818 2632 0.00793650793650794 1163 0.94539380397646 1.1296693934995 1 0.350801486474432 1660 2662 2632 3902 4403 1949 1163 2623 3492 3533 1899 2688 M601 REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS.html Genes involved in Antigen Activates B Cell Receptor Leading to Generation of Second Messengers 16/47 Reactome 0.00357393023523166 0.0051498884016899 2770 2655.81818181818 2635 0.000325431761172835 2011 1.47916457452035 1.38758142967629 1 1.23717217121972 2768 2480 2301 2011 3087 3153 2228 2635 2604 2723 3224 2689 M9990 REACTOME_APOPTOTIC_CLEAVAGE_OF_CELL_ADHESION_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOTIC_CLEAVAGE_OF_CELL_ADHESION_PROTEINS.html Genes involved in Apoptotic cleavage of cell adhesion proteins 8/19 Reactome 0.00025089714198402 0.000427839886221659 4625 2985 2638 2.50925473705212e-05 131 2.92506049554915 2.80738789924457 1 3.60179386613099 4624 2178 3980 1657 2638 4356 4576 1688 131 2395 4612 2690 M18377 MELLMAN_TUT1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MELLMAN_TUT1_TARGETS_UP.html Genes up-regulated in HEK293 cells (embryo kidney) after knockdown of TUT1 [GeneID=64852] by RNAi. 18288197 12/26 Jessica Robertson 0.00132604038046988 0.00201878662211886 2475 2543.81818181818 2638 0.000120621847328828 1689 1.32552321723627 -1.19672850543099 -1 1.30572219858751 2473 1801 2638 3091 2940 2001 3348 2324 2702 2975 1689 2691 M1785 POS_HISTAMINE_RESPONSE_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/POS_HISTAMINE_RESPONSE_NETWORK.html Genes corresponding to the histamine [PubChem=774] response network. 18339882 27/55 Jessica Robertson 0.0354966241002181 0.0455219432221188 1730 2732.81818181818 2639 0.00328023971841285 1418 1.22763137899929 1.2825567923034 1 0.602099529237634 1729 4026 2796 4157 3883 1418 1573 1789 3947 2639 2104 2692 M3582 ALONSO_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ALONSO_METASTASIS_UP.html Up-regulated genes in melanoma tumous that developed metastatic disease compared to primary melanoma that did not. 17409456 160/333 Jessica Robertson 1.83849974077791e-06 6.97587836865205e-06 2375 2824.81818181818 2639 1.67136479743663e-07 983 1.54116513085307 1.80589347637973 1 2.90479251767458 2371 3915 2367 2639 983 4308 3775 2517 2432 2774 2992 2693 M1912 ZHANG_TLX_TARGETS_36HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_36HR_UP.html Genes up-regulated in neural stem cells (NSC) at 36 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 179/403 Jessica Robertson 1.88604513093156e-06 7.09880119160265e-06 2535 2431.90909090909 2639 1.71458795257022e-07 994 1.26281707874255 1.27802151005108 1 2.37665959880963 2534 1676 2639 1841 994 3028 1707 3386 2688 3015 3243 2694 M1347 SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN.html Genes down-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 6 h. 18794802 354/839 Jessica Robertson 2.47884408187802e-06 8.53480041710536e-06 2835 2569.27272727273 2641 2.25349715901211e-07 1130 1.65235888595057 1.84470348255378 1 3.06146539176959 2831 3698 1809 1850 1130 4599 2970 2712 1929 2093 2641 2695 M1145 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 1. 12554760 52/114 Arthur Liberzon 2.75710457834313e-06 9.19375517427172e-06 2610 2619.18181818182 2641 2.5064618487578e-07 1189 1.56248740489702 1.24923413123622 1 2.87650559509653 2609 2981 1597 2099 1189 3265 2695 4616 2641 1464 3655 2696 M14958 PRAMOONJAGO_SOX4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PRAMOONJAGO_SOX4_TARGETS_UP.html Genes up-regulated in ACC3 cells (adenoid cystic carcinoma) after knockdown of SOX4 [GeneID=6659] by RNAi. 16636670 33/71 Leona Saunders 0.00206252504735674 0.00305660732824594 1850 2562.45454545455 2642 0.000187678293619834 1477 1.15336777859383 1.28522144910082 1 1.06018991470674 1846 2196 2758 3404 3016 2192 1477 3142 2875 2642 2639 2697 M17043 CHANDRAN_METASTASIS_TOP50_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANDRAN_METASTASIS_TOP50_DN.html Top 50 genes down-regulated in metastatic vs primary prostate cancer tumors. 17430594 36/61 Arthur Liberzon 2.79115166382416e-07 2.28659732459441e-06 2715 2475 2643 2.53741092539919e-08 237 1.24014833634162 1.56674368187201 1 2.55702150596447 2715 857 2662 2329 237 3558 2902 4526 2358 2438 2643 2698 M18120 GEORGES_TARGETS_OF_MIR192_AND_MIR215 http://www.broadinstitute.org/gsea/msigdb/cards/GEORGES_TARGETS_OF_MIR192_AND_MIR215.html Genes down-regulated in HCT116 cells (colon cancer) by expression of MIR192 or MIR215 [GeneID=406967;406997] at 24 h. 19074876 513/1300 Jessica Robertson 1.48288736974625e-07 1.58989032256369e-06 2315 2696.63636363636 2646 1.48288746869923e-08 117 1.42825196706135 1.63290507998341 1 3.02725978470062 2312 2605 4347 2511 117 4271 3095 2719 2646 1909 3131 2699 M2538 KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES http://www.broadinstitute.org/gsea/msigdb/cards/KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES.html Genes indentified by RNAi screen as regulating infection of THP-1 cells (macrophage) with Mycobacterium tuberculosis. 20211141 175/569 Arthur Liberzon 1.11927796070013e-05 2.77070075216101e-05 2650 2684.36363636364 2646 1.01753059564506e-06 1725 1.46989350424126 1.72813099699633 1 2.44863051771919 2646 3356 2022 3029 1725 4221 2404 2114 2598 2692 2721 2700 M16121 KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS.html Fc gamma R-mediated phagocytosis 39/116 KEGG 1.32184384666151e-05 3.17323784090975e-05 1785 2669.09090909091 2647 1.20168344442721e-06 1782 1.49082904458581 -1.44182132455612 -1 2.4514021739469 3506 2860 2711 2306 1785 2914 4474 1784 1782 2647 2591 2701 M213 PID_AR_NONGENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AR_NONGENOMIC_PATHWAY.html Nongenotropic Androgen signaling 18832364 20/48 Pathway Interaction Database 3.36249615855992e-05 7.09439756821783e-05 3180 2788.27272727273 2647 3.0568614111799e-06 1809 1.09764520361477 -1.40096049318392 -1 1.6646905398904 3178 2997 2944 1809 2087 2604 3924 2276 2647 3581 2624 2702 M4406 GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP.html Genes up-regulated in quiescent vs dividing CD34+ [GeneID=8842] cells isolated from peripheral blood of normal donors. 17717066 58/142 Arthur Liberzon 0.000702658280637708 0.00111088282829565 2945 2613.36363636364 2647 6.38984366505814e-05 1013 1.82852284615545 -1.71720305822952 -1 1.97459895324282 2945 2045 1013 1597 2835 2647 3978 4641 2315 1532 3199 2703 M13519 KEGG_GRAFT_VERSUS_HOST_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GRAFT_VERSUS_HOST_DISEASE.html Graft-versus-host disease 22/73 KEGG 0.0839184282471183 0.0965721401684667 2695 2542.72727272727 2648 0.00793650793650794 1599 1.88093876279346 -2.01689719116526 -1 0.697948424096856 2695 2748 1599 1800 3632 2010 3071 3765 2292 1710 2648 2704 M2486 GUILLAUMOND_KLF10_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GUILLAUMOND_KLF10_TARGETS_DN.html Genes down-regulated in the liver tissue from 10 week old male mice with KLF10 [GeneID=7071] compared to wild-type littermates. 20385766 24/42 Arthur Liberzon 0.00144434130179599 0.0021769647282779 2005 2802.18181818182 2650 0.000131390037403843 2002 1.89579997767271 -1.24487529398605 -1 1.84477778083723 2002 2713 2650 2476 2966 3049 3331 4558 2407 2379 2293 2705 M15040 CONRAD_GERMLINE_STEM_CELL http://www.broadinstitute.org/gsea/msigdb/cards/CONRAD_GERMLINE_STEM_CELL.html Genes enriched in pluripotent adult germline stem cells. 18849962 7/17 Jessica Robertson 0.00172112156290489 0.00257344468531344 2655 2695.27272727273 2651 0.000172245603451234 1122 1.33376964821091 1.73121157404058 1 1.26244802449434 2651 2322 4504 2730 3028 3356 2605 1122 1592 3210 2528 2706 M2245 BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_C http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_C.html Category C genes: p53-independent genes whose expression in the absence of S389 phosphorylation is dissimilar to loss of TP53 [GeneID=7157] in MEF (embryonic fibroblast) cells in response to UV-C irradiation. 18195040 72/201 Arthur Liberzon 2.91165426924012e-06 9.60845908849239e-06 3400 2549.45454545455 2651 2.64696192978287e-07 1207 1.41520786743199 -1.36409759257353 -1 2.59545532552093 3397 2651 1917 2514 1207 2727 2683 3223 2194 1978 3553 2707 M1776 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_DN.html All common down-regulated stress response genes (Human Environmental Stress Response, H-ESR). 15897889 8/24 Jessica Robertson 0.000587030658411608 0.000939168885393238 2820 2389.36363636364 2652 5.87185788337122e-05 801 3.0221855636555 3.0221855636555 1 3.34417941572956 2820 1752 4447 1776 2846 3228 2652 911 801 3313 1737 2708 M1361 DAZARD_RESPONSE_TO_UV_SCC_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_RESPONSE_TO_UV_SCC_UP.html Genes up-regulated in SCC12B2 cells (squamous cell carcinoma) by UV-B irradiation. 12771951 97/186 John Newman 0.000352312708316871 0.000585231248200233 2565 2773.81818181818 2653 3.20335582800505e-05 1652 1.45590212132469 -1.08858430625091 -1 1.7203354424487 2563 3013 2507 2310 2698 1652 2236 4519 2653 3129 3232 2709 M862 BIOCARTA_P38MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P38MAPK_PATHWAY.html p38 MAPK Signaling Pathway 30/62 BioCarta 2.71385304892845e-05 5.89847652471183e-05 4515 2945.36363636364 2654 2.46716956979267e-06 1909 1.31322966336134 1.2188429789614 1 2.03013226730886 4511 1917 2654 2007 2013 3329 4379 3886 1909 2415 3379 2710 M14940 BILBAN_B_CLL_LPL_DN http://www.broadinstitute.org/gsea/msigdb/cards/BILBAN_B_CLL_LPL_DN.html Genes down-regulated in B-CLL (B-cell chronic leukemia) samples expressing high levels of LPL [GeneID=4023] compared with those expressing low levels of the gene. 16617321 31/81 Arthur Liberzon 7.85400179306582e-06 2.06995795288563e-05 3895 3033.72727272727 2654 7.14002711999887e-07 1605 1.45628080442097 -1.47631072311953 -1 2.49335908832716 3891 2654 2512 2305 1605 4456 4165 3324 2418 1678 4363 2711 M4377 KEGG_GALACTOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GALACTOSE_METABOLISM.html Galactose metabolism 12/39 KEGG 0.0839184282471183 0.0965721401684667 3920 2866.54545454545 2655 0.00793650793650794 1107 1.8035433721743 -1.64796075831339 -1 0.669229790549296 3920 2599 2416 2655 3998 2381 2253 3571 1107 2958 3674 2712 M10837 NIKOLSKY_BREAST_CANCER_20Q11_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_20Q11_AMPLICON.html Genes within amplicon 20q11 identified in a copy number alterations study of 191 breast tumor samples. 19010930 24/52 Jessica Robertson 7.98767860874006e-07 4.11774058972012e-06 3530 2445.54545454545 2655 7.26152864443484e-08 536 1.7988740447679 -1.30444516373872 -1 3.54105942787655 3526 2655 1850 2879 624 4189 3363 1626 536 1937 3716 2713 M14933 KEGG_STEROID_HORMONE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STEROID_HORMONE_BIOSYNTHESIS.html Steroid hormone biosynthesis 14/88 KEGG 0.00136443243183625 0.00206716145347064 4605 2417.81818181818 2656 0.000124116307601384 278 2.53280681303457 -1.51171894179712 -1 2.48545007293305 4605 2870 1653 1548 3467 2656 2969 1056 278 2498 2996 2714 M11619 VETTER_TARGETS_OF_PRKCA_AND_ETS1_DN http://www.broadinstitute.org/gsea/msigdb/cards/VETTER_TARGETS_OF_PRKCA_AND_ETS1_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer) after knockdown of PRKCA and ETS1 [GeneID=5578;2113] by RNAi. 15531915 12/27 Leona Saunders 0.000211940258280552 0.000366476771329398 3345 2945.27272727273 2656 1.92691526012173e-05 2109 1.79704724017809 -1.54592121811673 -1 2.2569712547553 3341 4283 2196 3011 2577 2226 2656 4633 3122 2244 2109 2715 M1280 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4.html Cluster PAM4: genes down-regulated in hepatocellular carcinoma (HCC) vs normal liver tissue from mice deficient for TXNIP [GeneID=10628]. 16607285 134/403 Leona Saunders 9.97612519528678e-07 4.72749354697327e-06 2660 2361.27272727273 2656 9.0692088355143e-08 717 1.42450112636051 1.63097042329632 1 2.77288435664239 2656 1766 1218 2684 717 3494 2872 2598 2822 2040 3107 2716 M16424 BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_UP.html Genes up-regulated in the invasive ductal carcinoma (IDC) compared to the invasive lobular carcinoma (ILC), the two major pathological types of breast cancer. 18490921 23/48 Jessica Robertson 4.86939944514853e-06 1.41726744099168e-05 4665 2887.09090909091 2656 4.42673656630215e-07 1260 1.92187566086311 -1.41130299318212 -1 3.4060910538349 4661 2656 1857 2012 1423 2929 3452 4530 1260 2297 4681 2717 M6921 NUTT_GBM_VS_AO_GLIOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NUTT_GBM_VS_AO_GLIOMA_UP.html Top 50 marker genes for glioblastoma multiforme (GBM), a class of high grade glioma. 12670911 51/110 Arthur Liberzon 0.00557783676013574 0.00786334027015525 2125 2555.90909090909 2657 0.00050836628178344 1225 1.65194595358795 1.57720039494865 1 1.27069674868255 2125 3080 2874 2638 3156 2026 1225 1666 2657 3807 2861 2718 M7955 SIG_INSULIN_RECEPTOR_PATHWAY_IN_CARDIAC_MYOCYTES http://www.broadinstitute.org/gsea/msigdb/cards/SIG_INSULIN_RECEPTOR_PATHWAY_IN_CARDIAC_MYOCYTES.html Genes related to the insulin receptor pathway 36/82 Signaling Gateway 0.0146975055801075 0.0197060117735004 1540 2694.36363636364 2658 0.00134514756978307 1538 1.35267144981949 1.69917762545635 1 0.843214669544073 1538 4184 3218 3035 3366 2013 2127 1571 2658 3839 2089 2719 M599 ST_PAC1_RECEPTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_PAC1_RECEPTOR_PATHWAY.html PAC1 Receptor Pathway 4/9 Signaling Transduction KE 8.9299793618909e-06 2.29670050986942e-05 2660 2510 2659 8.930015247133e-07 308 1.74000588620404 -2.49872111272945 -1 2.95042493389791 3748 1669 3889 2322 1687 2659 4003 1534 308 2659 3132 2720 M844 ONDER_CDH1_TARGETS_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_3_UP.html Genes up-regulated in HMLE cells (immortalized nontransformed mammary epithelial) cells after loss of function of E-cadhedrin (CDH1) [GeneID=999], which was achieved either by RNAi knockdown or by expression of a dominan-negative form of CDH1. 18483246 11/28 Jessica Robertson 0.0160177339046006 0.0213357308348376 1665 2613.63636363636 2660 0.00146686894477924 793 2.32018261480462 2.32018261480462 1 1.41706549031346 1664 4286 2660 3394 4162 2271 2154 3114 793 2832 1420 2721 M710 REACTOME_VEGF_LIGAND_RECEPTOR_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_VEGF_LIGAND_RECEPTOR_INTERACTIONS.html Genes involved in VEGF ligand-receptor interactions 4/10 Reactome 0.02428684190195 0.0317279456795478 2160 2828.63636363636 2663 0.00245564307904326 1088 1.01399533154882 1.01399533154882 1 0.555429285706208 2159 3528 3963 4543 3679 1434 1088 1721 4295 2663 2042 2722 M2384 SCHMIDT_POR_TARGETS_IN_LIMB_BUD_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHMIDT_POR_TARGETS_IN_LIMB_BUD_DN.html Genes down-regulated in E12.5 forelimb buds with POR [GeneID=5447] knockout. 19273610 11/35 Arthur Liberzon 6.5386007356582e-05 0.000127559879464173 3140 2621.27272727273 2663 5.9443591608405e-06 1903 1.52089282666911 1.24457170851517 1 2.16493914922035 3140 2126 1966 2663 2278 3638 3201 1903 3024 2115 2780 2723 M8809 BIOCARTA_PTDINS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PTDINS_PATHWAY.html Phosphoinositides and their downstream targets. 25/42 BioCarta 0.00030573076052936 0.000513128346647773 4515 3051.63636363636 2665 2.77975687046267e-05 1758 1.70045627973845 -1.72071175249467 -1 2.04479975087744 4513 2200 1968 2176 2665 3115 4488 3761 1758 2479 4445 2724 M616 REACTOME_SIGNALING_BY_NOTCH1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH1.html Genes involved in Signaling by NOTCH1 33/86 Reactome 0.000306100452990508 0.00051356488460921 1890 2369.09090909091 2666 2.78311864595847e-05 1106 1.77622467103981 1.90429080868328 1 2.13567150946092 1889 3052 2437 2963 2666 3097 2803 1228 1106 3465 1354 2725 M1740 GAVIN_IL2_RESPONSIVE_FOXP3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_IL2_RESPONSIVE_FOXP3_TARGETS_DN.html FOXP3 [GeneID=50943] target genes down-regulated in T lymphocytes after stimulation with IL2 [GeneID=3558]. 17220874 2/8 Jessica Robertson 0.115314057035443 0.131667073895733 2225 3020.8 2666.5 0.0135213719606022 1763 0.717773725536766 0.717773725536766 1 0.23101885006271 2224 3011 4438 NA 3651 1894 1763 2212 4096 4597 2322 2726 M9378 ST_INTERLEUKIN_4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_INTERLEUKIN_4_PATHWAY.html Interleukin 4 (IL-4) Pathway 16/32 Signaling Transduction KE 0.0806881831203091 0.0965721401684667 2190 2668.45454545455 2667 0.00761900113586771 1281 0.88452272728963 -0.935708120705795 -1 0.328214428885736 2187 2667 2935 2718 3614 1281 2183 2531 3949 3343 1945 2727 M888 REACTOME_ORGANIC_CATION_ANION_ZWITTERION_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ORGANIC_CATION_ANION_ZWITTERION_TRANSPORT.html Genes involved in Organic cation/anion/zwitterion transport 4/14 Reactome 8.17543873760602e-05 0.000155164463039375 2170 2646.36363636364 2667 8.17573952327365e-06 561 2.99609723536049 -2.99609723536049 -1 4.17166871125941 2169 3301 4045 3758 3852 1505 3046 561 2521 2667 1685 2728 M5407 BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_24HR_DN.html Genes down-regulated in A172 cells (glioma, does not express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 24 h. 15980968 10/20 John Newman 5.34290843166591e-05 0.000106223457406816 3115 2509.72727272727 2668 4.85730744879192e-06 777 1.01306381590082 -1.1935805048464 -1 1.47149850817203 3111 777 2859 1790 2228 2880 2481 3502 2668 1972 3339 2729 M2642 KEGG_TGF_BETA_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TGF_BETA_SIGNALING_PATHWAY.html TGF-beta signaling pathway 37/94 KEGG 0.0227019226876808 0.0297154217079531 2300 2813.18181818182 2669 0.00208542057224363 1897 1.58701749758092 1.62096834923383 1 0.88581932428684 2300 3668 2392 3251 3383 3244 2609 2669 1897 2949 2583 2730 M16431 DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP.html Genes up-regulated in T-PLL cells (T-cell prolymphocytic leukemia) bearing the inv(14)/t(14:14) chromosomal aberration. 17713554 264/702 Leona Saunders 1.48584214958893e-06 6.07483098661735e-06 4365 2796.81818181818 2669 1.35076650282009e-07 885 1.56715544797917 1.8049668541887 1 2.98818644662557 4363 2263 1680 2669 885 3174 3580 3963 2009 1830 4349 2731 M1761 TESAR_ALK_TARGETS_EPISC_3D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_ALK_TARGETS_EPISC_3D_UP.html Genes up-regulated in EpiSC cells (mouse epiblast embryonic stem cells) after treatment with the ALK [GeneID=238] inhibitor SB-431542 [PubChem=4521392]. 17597760 3/11 Jessica Robertson 0.00856232509947298 0.0118052066117736 2675 2810.54545454545 2669 0.000859549615650022 1572 1.53003930582573 1.53003930582573 1 1.07823218113291 2671 1572 4444 2084 3241 2669 2147 3770 3716 2467 2135 2732 M11028 ROVERSI_GLIOMA_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROVERSI_GLIOMA_COPY_NUMBER_UP.html Genes in the most frequently gained loci in a panel of glioma cell lines. 16247447 56/137 Arthur Liberzon 1.02008153501315e-06 4.79448552966058e-06 4035 2756.27272727273 2670 9.27347279998319e-08 729 1.29635016643248 -1.08243753539964 -1 2.52053442027428 4035 1021 2670 2911 729 2648 4395 4498 1935 1693 3784 2733 M9112 LU_AGING_BRAIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/LU_AGING_BRAIN_DN.html Age down-regulated genes in the human frontal cortex. 15190254 115/295 John Newman 0.000311368012334993 0.000521842097926244 1040 2340.18181818182 2670 2.83101899334893e-05 1037 1.54147002795612 1.74562141713361 1 1.84949812367974 1037 3952 2770 3328 2670 1234 1058 1365 2759 3508 2061 2734 M1593 MULLIGAN_NTF3_SIGNALING_VIA_INSR_AND_IGF1R_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGAN_NTF3_SIGNALING_VIA_INSR_AND_IGF1R_UP.html Genes similarly up-regulated in 3T3-L1 cells (fibroblasts able to differentiate to adipocytes) upon stimulation of INSR or IGFR1 by NTF3 [GeneID=3643;3480;4908]. 12213819 20/39 John Newman 4.92921404528244e-05 9.90493010986e-05 2220 2821.72727272727 2671 4.48120408212981e-06 1647 1.86697389946778 2.57199085383406 1 2.73254725805034 2216 3368 2649 3994 2206 2347 1647 3103 3250 3588 2671 2735 M14194 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_30 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_30.html Amplification hot spot 30: colocolized fragile sites and cancer genes in the 12q21-q24.3 region. 16751803 4/10 Arthur Liberzon 0.00380683070802683 0.0054703491866954 2865 2411.09090909091 2672 0.000381336785657361 171 2.31609665433819 2.31609665433819 1 1.91498616452203 2864 1812 4229 2510 3108 2746 2063 2676 171 2672 1671 2736 M206 PID_PDGFRA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PDGFRA_PATHWAY.html PDGFR-alpha signaling pathway 18832364 21/35 Pathway Interaction Database 6.5874209429673e-07 3.66176210424019e-06 2710 2646.90909090909 2674 5.98856628675263e-08 552 1.30944845116951 1.36690606545999 1 2.60202737041376 2710 3316 2442 2057 552 2927 2674 4009 2455 2625 3349 2737 M1603 ZHOU_TNF_SIGNALING_30MIN http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_TNF_SIGNALING_30MIN.html Genes up-regulated in HeLa cells (cervical carcinoma) at 30 min after stimulation with TNF [GeneID=7124]. 12673210 45/102 John Newman 2.3681666923128e-05 5.25188316146606e-05 2955 2693.72727272727 2674 2.15290198597858e-06 1902 1.68327807234042 1.98984980853481 1 2.63321860692319 2952 3596 2139 2674 1971 3641 3042 1902 2118 3020 2576 2738 M2063 HOFFMAN_CLOCK_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMAN_CLOCK_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) upon knockdown of CLOCK [GeneID=9575] by RNAi that also belong to the highest confidence network (according to Ingenuity Pathway Analysis). 20124474 9/23 Jessica Robertson 0.000105111552290423 0.000192855416614301 3880 2845.18181818182 2674 1.05116524418716e-05 606 2.05234924012608 -1.39703925928365 -1 2.7867770773155 3877 3102 4616 1051 2660 4655 4112 606 2116 1828 2674 2739 M7871 ST_GRANULE_CELL_SURVIVAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GRANULE_CELL_SURVIVAL_PATHWAY.html Granule Cell Survival Pathway is a specific case of more general PAC1 Receptor Pathway. 25/47 Signaling Transduction KE 0.00013488094970419 0.000241887535520028 3100 2953.54545454545 2676 1.22626563546082e-05 1509 1.72155148571282 1.77853389171147 1 2.27569526753145 3099 3930 2560 2676 2487 3556 2087 4630 1509 2480 3475 2740 M8565 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN.html Genes from the grey module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 39/102 Arthur Liberzon 0.000320325164541563 0.000535131451351787 2095 2913.81818181818 2676 2.91247103769978e-05 2092 1.27285574447605 1.4598518637834 1 1.52212601409074 2092 2633 2209 3579 2676 3382 2668 3183 3540 2648 3442 2741 M6161 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_GRANULOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_GRANULOCYTE_DN.html Genes down-regulated by RUNX1-RUNX1T1 [GeneID=861;862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing granulocytes. 17898786 5/10 Arthur Liberzon 0.00883791559358706 0.0121592696628153 2680 2729.63636363636 2677 0.000887326254216144 924 1.16192560962764 1.16192560962764 1 0.813368466691651 2045 2677 4135 4052 3717 1337 924 2677 4263 2895 1304 2742 M1266 SHANK_TAL1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHANK_TAL1_TARGETS_DN.html Genes down-regulated in preleukemic thymocytes from transgenic mice which overexpress TAL1 [GeneID=6886] in thymus. 16407836 4/16 Leona Saunders 0.00819201461349556 0.0113338590135342 1885 2758.18181818182 2677 0.000822237132783254 1106 1.11245022040216 -1.11245022040216 -1 0.791149117055643 1884 3525 4281 4055 4066 1426 1106 1461 3990 2677 1869 2743 M10456 OKAMOTO_LIVER_CANCER_MULTICENTRIC_OCCURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/OKAMOTO_LIVER_CANCER_MULTICENTRIC_OCCURRENCE_UP.html Genes up-regulated in both the patients in the multicentric hepatocellular carcinoma (HCC) group and those with multicentric recurrence. 16788756 17/52 Yujin Hoshida 0.000321672181045269 0.000537190249600189 2340 2536.81818181818 2677 2.92472021684949e-05 1043 1.32290553232405 1.80275852179103 1 1.58117092238263 2336 2015 2726 2445 2677 3083 2946 3483 1043 2220 2931 2744 M1673 WESTON_VEGFA_TARGETS_3HR http://www.broadinstitute.org/gsea/msigdb/cards/WESTON_VEGFA_TARGETS_3HR.html Genes up-regulated in MMEC cells (myometrial endothelium) at 3 h after VEGFA [GeneID=7422] stimulation. 12200464 47/110 John Newman 1.63440250016724e-05 3.78961410973957e-05 2680 2396.90909090909 2678 1.48583149312441e-06 509 2.04909920439966 1.9913066190319 1 3.31163553617791 2680 1272 509 1868 2147 3376 3000 3994 2678 1229 3613 2745 M1751 ZHENG_FOXP3_TARGETS_IN_T_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_IN_T_LYMPHOCYTE_DN.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are down-regulated only in mature (peripheral blood) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 21/62 Jessica Robertson 0.0839184282471183 0.0965721401684667 3275 2617.27272727273 2678 0.00793650793650794 1005 1.90014671415761 -1.5127602226148 -1 0.705075800960173 3274 2508 1956 1994 3688 3758 2678 2805 1005 2085 3039 2746 M32 PID_HDAC_CLASSIII_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HDAC_CLASSIII_PATHWAY.html Signaling events mediated by HDAC Class III 18832364 24/49 Pathway Interaction Database 9.75342476046692e-05 0.000180507695211485 4505 2794 2679 8.86714290290129e-06 961 1.53726972939405 -1.08774793588858 -1 2.10352491162668 4501 2118 2270 2113 2406 2679 3401 3006 961 3366 3913 2747 M10153 CLAUS_PGR_POSITIVE_MENINGIOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/CLAUS_PGR_POSITIVE_MENINGIOMA_UP.html Genes up-regulated in meningioma samples positive for PGR [GeneID=5241] compared to those without the receptor. 18172325 4/18 Jessica Robertson 0.00186821844745655 0.00278538709665332 1645 2693 2680 0.000186979091640397 1642 1.51445457825204 -1.51445457825204 -1 1.41444432964945 3036 2567 4452 2734 3015 1686 2110 1645 4056 2680 1642 2748 M2367 PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_DN http://www.broadinstitute.org/gsea/msigdb/cards/PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_DN.html Genes down-regulated in HEK-293 cells (fibroblast) upon knockdown of CTBP1 but not of SATB1 [GeneID=1487, 6304] by RNAi. 19103759 274/815 Arthur Liberzon 1.22610322698869e-06 5.45840142947162e-06 3225 2812.09090909091 2680 1.11463991847331e-07 794 1.31914061598532 1.35386687621126 1 2.53768849072839 3224 1902 2680 2045 794 4435 2596 3968 2860 2229 4200 2749 M9440 DUTTA_APOPTOSIS_VIA_NFKB http://www.broadinstitute.org/gsea/msigdb/cards/DUTTA_APOPTOSIS_VIA_NFKB.html NF-kB target genes involved in the regulation of programmed cell death. 17072329 21/51 Arthur Liberzon 0.0011818105361971 0.00181275422999006 3460 2797.36363636364 2681 0.000107495078804411 573 2.11583788360977 2.54548620623624 1 2.12038832776513 3458 2591 1565 2147 2913 4597 4274 2681 573 2626 3346 2750 M8213 LEE_INTRATHYMIC_T_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/LEE_INTRATHYMIC_T_PROGENITOR.html Genes enriched in the intrathymic T progenitor (ITTP) cells compared to all other T lymphocyte differentiation stages. 15210650 23/63 Arthur Liberzon 1.39144798147101e-05 3.31317339490506e-05 2675 2825.63636363636 2681 1.26496071102583e-06 1809 1.31488910232522 -1.46930996522626 -1 2.15309265817467 3954 2894 2286 2710 1809 2672 3990 2673 2622 2791 2681 2751 M14857 REACTOME_SPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SPHINGOLIPID_METABOLISM.html Genes involved in Sphingolipid metabolism 41/73 Reactome 6.22665367499655e-06 1.72040678779681e-05 2385 3109.90909090909 2682 5.66061027122398e-07 1515 1.29495594603002 -1.06323129357113 -1 2.25517174249418 3892 2538 2385 2682 1515 4660 3811 4458 2040 2382 3846 2752 M11782 SMID_BREAST_CANCER_RELAPSE_IN_LIVER_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_LIVER_DN.html Genes down-regulated in liver relapse of breast cancer. 18451135 4/14 Jessica Robertson 9.83275420382001e-05 0.000181760497826827 2355 2648.63636363636 2682 9.83318930466432e-06 597 3.27108383437009 -3.27108383437009 -1 4.4724000323702 2355 2964 4470 2864 4561 2224 4544 597 795 2682 1079 2753 M8916 TIEN_INTESTINE_PROBIOTICS_2HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_2HR_DN.html Genes down-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 2h. 16394013 52/139 Arthur Liberzon 0.0591304066572171 0.0742457356901713 2065 2968.81818181818 2683 0.00552565275041496 1777 1.61474842320649 1.9985967449786 1 0.666567908620162 2065 4575 2605 3720 3957 2683 2930 2443 2525 3377 1777 2754 M813 REACTOME_SYNTHESIS_SECRETION_AND_DEACYLATION_OF_GHRELIN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_SECRETION_AND_DEACYLATION_OF_GHRELIN.html Genes involved in Synthesis, Secretion, and Deacylation of Ghrelin 10/20 Reactome 0.00300400735464098 0.00437574711341238 2165 2785.72727272727 2684 0.000273465187146189 1787 1.55783136887986 2.08601645983635 1 1.34325362928725 2161 3323 2684 3827 3064 2450 1787 4168 2319 2696 2164 2755 M8716 HEDVAT_ELF4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HEDVAT_ELF4_TARGETS_UP.html Genes up-regulated in HEL cells (erythroleukemia) upon expression of ELF4 [GeneID=2000]. 14625302 8/21 Kevin Vogelsang 0.000304141309329003 0.000510826586206347 3555 2676.09090909091 2684 3.04182943220083e-05 1666 2.79219436914713 -2.58897046937271 -1 3.35960827375288 3552 2957 4384 1835 2684 2343 2961 2293 1816 1666 2946 2756 M14631 KEGG_COLORECTAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_COLORECTAL_CANCER.html Colorectal cancer 42/82 KEGG 0.000289776591412812 0.000488275119511125 3705 2974.36363636364 2686 2.63467969863146e-05 1225 1.44243187558118 -0.943679792991882 -1 1.74589344297473 3702 2471 2648 1640 2651 4671 3265 2686 1225 3543 4216 2757 M17987 CAFFAREL_RESPONSE_TO_THC_8HR_5_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_8HR_5_UP.html Genes up-regulated in EVSA-T cells (breast cancer) treated with 5 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 8 h. 18454173 14/32 Jessica Robertson 0.000266612011080828 0.000452824894499732 3815 2922.18181818182 2687 2.42403933225014e-05 1669 1.46235628936838 -1.29606589290116 -1 1.7875070731575 3814 1700 1669 2687 2626 2662 3623 3638 3723 1893 4109 2758 M3397 KEGG_BUTANOATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BUTANOATE_METABOLISM.html Butanoate metabolism 16/48 KEGG 2.78935829228288e-05 6.03899837904882e-05 3585 2575.72727272727 2688 2.53581241719019e-06 962 2.05019287963845 -1.75715300670922 -1 3.16174695078032 3584 2369 2169 2970 2023 2731 2688 3455 962 2116 3266 2759 M15693 GENTILE_UV_RESPONSE_CLUSTER_D8 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D8.html Cluster d8: genes progressively down-regulated in WS1 cells (fibroblast) through 18 h after irradiation with high dose UV-C. 12907719 29/67 John Newman 0.000340425049781285 0.000567496187575631 2690 2902.18181818182 2690 3.09525216464926e-05 2340 1.15776003753908 0.973974378546252 1 1.37369803727466 2526 2585 2690 3008 2688 3466 2365 3870 3535 2340 2851 2760 M8467 JISON_SICKLE_CELL_DISEASE_UP http://www.broadinstitute.org/gsea/msigdb/cards/JISON_SICKLE_CELL_DISEASE_UP.html Genes up-regulated in peripheral blood mononuclear cells (PBMC) from sickle cell disease patients compared to those from healthy subjects. 15031206 166/378 Jessica Robertson 0.000104564864658102 0.000192077991292774 4445 3077.09090909091 2690 9.50634862753513e-06 1845 1.6398765920641 -1.30975394409022 -1 2.22775368674024 4442 2443 1845 2115 2425 3299 4606 3000 2690 2601 4382 2761 M8817 ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN.html Genes whose promoters display lower histone H3 trimethylation mark at K9 (H3K9me3) in hepatocellular carcinoma (HCC) compared to normal liver. 18413731 75/203 Jessica Robertson 0.000573035055766307 0.000917404260786101 2080 2589.09090909091 2691 5.21076699030416e-05 1365 1.52064129292507 -1.18429247179273 -1 1.6883155867107 2076 2332 1365 2422 2795 2357 3562 3135 2763 2691 2982 2762 M1493 NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON.html Genes within amplicon 11q12-q14 identified in a copy number alterations study of 191 breast tumor samples. 19010930 75/230 Jessica Robertson 2.05456148202268e-07 1.93870664292301e-06 2695 2473.27272727273 2692 1.86778333990589e-08 167 1.39897803799189 -1.12843989302591 -1 2.92116064064346 2692 3075 2554 3977 167 1448 2866 2750 2392 2997 2288 2763 M1702 CHEN_NEUROBLASTOMA_COPY_NUMBER_GAINS http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_NEUROBLASTOMA_COPY_NUMBER_GAINS.html High-grade amplification (copy number, CN >= 5) detected in primary neuroblastoma samples. 18923524 19/69 Jessica Robertson 4.51891942300491e-05 9.1520361246926e-05 1325 2346.45454545455 2692 4.10819295157472e-06 93 1.89060598614963 1.34423879548777 1 2.79086262715055 1321 3154 2063 3570 4284 377 93 2692 4094 3006 1157 2764 M12718 BIOCARTA_P35ALZHEIMERS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P35ALZHEIMERS_PATHWAY.html Deregulation of CDK5 in Alzheimers Disease 10/19 BioCarta 0.000561354499037515 0.000901167243059196 4015 2951.54545454545 2693 5.10452532797779e-05 891 1.19206777735673 -1.39703925928365 -1 1.3268910056806 4012 891 2536 2419 2789 4596 2693 2449 3741 1958 4383 2765 M2222 ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_DN.html Genes down-regulated in K562 cells (lymphoblast) by MYC [GeneID=4609] in the presence of CKN1B [GeneID=1027]. 18838534 89/188 Arthur Liberzon 4.59822193257966e-06 1.36116664409781e-05 3750 2510.63636363636 2693 4.18021049395953e-07 566 1.3503036709368 -1.25837117833129 -1 2.40176615115814 3747 566 1734 1873 1393 2693 4660 3586 2775 1346 3244 2766 M3634 REACTOME_CASPASE_MEDIATED_CLEAVAGE_OF_CYTOSKELETAL_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CASPASE_MEDIATED_CLEAVAGE_OF_CYTOSKELETAL_PROTEINS.html Genes involved in Caspase-mediated cleavage of cytoskeletal proteins 10/20 Reactome 8.37191242735859e-05 0.000158316310066999 3455 2669.18181818182 2694 7.61111911847459e-06 482 1.61653297265562 1.2941311702676 1 2.24564768859201 3452 1889 2241 1742 2352 3278 3329 3862 482 2694 4040 2767 M2383 SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP.html Genes up-regulated in E12.5 forelimb buds with POR [GeneID=5447] knockout. 19273610 15/31 Arthur Liberzon 0.000228019418554255 0.000391534992797816 2770 2745.18181818182 2696 2.07311868272803e-05 1834 1.38312153930156 -1.5478069449589 -1 1.72258623112939 2767 2845 2696 4286 2602 1834 2120 2263 3461 2620 2703 2768 M11079 KEGG_N_GLYCAN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_N_GLYCAN_BIOSYNTHESIS.html N-Glycan biosynthesis 30/50 KEGG 6.7110109086462e-05 0.000130705723682112 3025 2832.09090909091 2697 6.1011051218722e-06 1520 0.930065556962721 -0.703584052156912 -1 1.32031965888369 3023 1726 3513 2697 2285 1520 2512 4671 3476 3328 2402 2769 M9044 HEIDENBLAD_AMPLIFIED_IN_PANCREATIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLIFIED_IN_PANCREATIC_CANCER.html Genes amplified and up-regulated more than twofold in at least two out of 10 pancreatic cancer cell lines studied. 15688027 20/53 Leona Saunders 0.0116843642509883 0.015865188851601 2715 2525.54545454545 2697 0.00106789874188061 1501 1.8096536065264 2.00175356179408 1 1.19036395543091 2712 2697 2794 2144 3273 3718 1687 2296 1849 3110 1501 2770 M2382 LIU_TOPBP1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LIU_TOPBP1_TARGETS.html Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of TOPBP1 [GeneID=11073]. 19289498 11/22 Arthur Liberzon 2.68513560723691e-05 5.84147885585522e-05 3280 2370.81818181818 2699 2.44106216391963e-06 696 3.66116277704589 -1.76355639142255 -1 5.66546437456882 3278 1226 1573 2699 2012 4353 2922 1667 696 2839 2814 2771 M19230 EPPERT_LSC_R http://www.broadinstitute.org/gsea/msigdb/cards/EPPERT_LSC_R.html Genes up-regulated in functionally defined leukemic stem cells (LSC) from acute myeloid leukemia (AML) patients. 21873988 30/67 Kolja Eppert 1.29529939425701e-07 1.4496433896277e-06 2870 2653 2699 1.17754497320062e-08 81 1.37714249238085 1.40414265985086 1 2.93911905199761 2699 2693 2587 2870 81 3470 2439 4604 1801 2868 3071 2772 M197 PID_HIV_NEF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HIV_NEF_PATHWAY.html HIV-1 Nef: Negative effector of Fas and TNF-alpha 18832364 24/52 Pathway Interaction Database 0.000572966244002853 0.000917404260786101 2015 2445.63636363636 2700 5.21014110277884e-05 1196 1.100193836343 -1.26278368174146 -1 1.2215072747186 2014 2893 3050 3529 2794 1196 1348 2089 2700 3367 1922 2773 M9634 SESTO_RESPONSE_TO_UV_C4 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C4.html Cluster 4: genes changed in primary keratinocytes by UVB irradiation. 11867738 13/37 John Newman 0.00243794143454794 0.00359025567639587 3450 2625.36363636364 2701 0.00022187702280014 1180 1.9631429469159 -2.50372636140233 -1 1.75439655902894 3449 2701 2110 2709 3570 2848 4421 1180 1623 2358 1910 2774 M4085 KEGG_PRIMARY_IMMUNODEFICIENCY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRIMARY_IMMUNODEFICIENCY.html Primary immunodeficiency 11/48 KEGG 3.23251745500001e-05 6.86342401183961e-05 2955 2478.81818181818 2702 2.93869541109111e-06 1062 1.30550770862824 -1.10027284490258 -1 1.98679473662519 2954 1062 1481 2996 2072 2430 3110 3712 3237 1511 2702 2775 M755 REACTOME_REGULATION_OF_INSULIN_LIKE_GROWTH_FACTOR_IGF_ACTIVITY_BY_INSULIN_LIKE_GROWTH_FACTOR_BINDING_PROTEINS_IGFBPS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_INSULIN_LIKE_GROWTH_FACTOR_IGF_ACTIVITY_BY_INSULIN_LIKE_GROWTH_FACTOR_BINDING_PROTEINS_IGFBPS.html Genes involved in Regulation of Insulin-like Growth Factor (IGF) Activity by Insulin-like Growth Factor Binding Proteins (IGFBPs) 11/52 Reactome 4.52133240048301e-05 9.1520361246926e-05 3965 2725.90909090909 2702 4.11038665760797e-06 257 2.59515416598934 -1.86878612719616 -1 3.83089804426676 3964 3859 1619 2702 2182 4009 4128 1040 257 2100 4125 2776 M13324 BIOCARTA_HIF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HIF_PATHWAY.html Hypoxia-Inducible Factor in the Cardiovascular System 13/24 BioCarta 0.0234370881940259 0.0306520221259295 1995 2904.63636363636 2703 0.00215368701977541 1476 1.57315385748746 1.57315385748746 1 0.870331298703409 1991 4676 2259 4307 4097 1825 1476 2703 4032 3073 1512 2777 M19336 ST_TYPE_I_INTERFERON_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_TYPE_I_INTERFERON_PATHWAY.html Type I Interferon (alpha/beta IFN) Pathway 6/14 Signaling Transduction KE 0.0296202491552376 0.0382581277677628 2705 2695.27272727273 2703 0.0030022630059701 1136 1.29693279574384 1.29693279574384 1 0.671879271582569 2603 2252 3888 2703 3938 1960 1136 2704 3831 3037 1596 2778 M3737 PUIFFE_INVASION_INHIBITED_BY_ASCITES_UP http://www.broadinstitute.org/gsea/msigdb/cards/PUIFFE_INVASION_INHIBITED_BY_ASCITES_UP.html Genes up-regulated in OV-90 cells (ovarian cancer) exposed to ascites which inhibited invasion. 17971902 67/157 Arthur Liberzon 0.0839184282471183 0.0965721401684667 1725 2901 2703 0.00793650793650794 1723 1.61462029297449 1.59547473171889 1 0.599127260711131 1723 4436 2721 3490 4049 2703 2399 2475 3174 2596 2145 2779 M1695 TUOMISTO_TUMOR_SUPPRESSION_BY_COL13A1_UP http://www.broadinstitute.org/gsea/msigdb/cards/TUOMISTO_TUMOR_SUPPRESSION_BY_COL13A1_UP.html Genes up-regulated in small intestine tissue from transgenic mice expressing a mutant form of COL13A1 [GeneID=1305], compared to normal controls. 19074901 11/40 Leona Saunders 0.000178551669396206 0.00031360311948674 2485 2848.18181818182 2703 1.62332874790568e-05 2482 1.26243636185314 1.28677900236423 1 1.61676052020473 3128 2703 2484 2527 2540 3206 2613 2482 3385 2836 3426 2780 M6444 NUYTTEN_NIPP1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NUYTTEN_NIPP1_TARGETS_UP.html Genes up-regulated in PC3 cells (prostate cancer) after knockdown of NIPP1 [GeneID=5511] by RNAi. 17724462 475/1265 Jessica Robertson 4.34118478814557e-06 1.29985890845049e-05 2875 2793.45454545455 2704 3.94653941316433e-07 1371 1.48873881487971 1.76533452798472 1 2.65889048234165 2875 3561 2185 3272 1371 4052 3244 2604 2490 2370 2704 2781 M106 PID_HNF3B_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HNF3B_PATHWAY.html FOXA2 and FOXA3 transcription factor networks 18832364 18/64 Pathway Interaction Database 0.000365317886641064 0.00060511828094734 4045 2857.27272727273 2705 3.32162330083612e-05 2075 1.49976601388212 -1.8993409418927 -1 1.76421030136306 4043 2664 2525 3410 2705 2802 3545 2075 2195 2323 3143 2782 M10541 YANG_BREAST_CANCER_ESR1_LASER_UP http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_LASER_UP.html Genes up-regulated in laser microdissected (LCM) samples of early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative ones. 16261164 23/49 Leona Saunders 3.78737505483795e-05 7.87733666532207e-05 2730 2378 2706 3.44312750669372e-06 1201 0.976983900911103 -0.915468165998854 -1 1.46545962605013 2728 1292 3234 2827 2121 1201 1846 2706 3023 3323 1857 2783 M2637 UEDA_CENTRAL_CLOCK http://www.broadinstitute.org/gsea/msigdb/cards/UEDA_CENTRAL_CLOCK.html Molecular timetable composed of 96 time-indicating genes (103 probes) in the central (suprachiasmatic nucleus (SCN)) clock. 15273285 78/147 Kate Stafford 0.0102206223209256 0.0139836018090094 1995 2766.18181818182 2707 0.000933492344467361 1526 1.43355499551106 1.5052354935857 1 0.97170081219404 1993 3921 2504 3737 3252 2342 2071 1526 3533 2842 2707 2784 M204 PID_RHODOPSIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RHODOPSIN_PATHWAY.html Visual signal transduction: Rods 18832364 9/35 Pathway Interaction Database 3.84386025649788e-05 7.96653213708495e-05 3815 2993.36363636364 2708 3.84392674679407e-06 1803 1.24322285371 -1.29699678068498 -1 1.8625915080612 3813 2026 3904 2473 2154 3991 2095 2708 3847 1803 4113 2785 M12921 BLALOCK_ALZHEIMERS_DISEASE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BLALOCK_ALZHEIMERS_DISEASE_UP.html Genes up-regulated in brain from patients with Alzheimer's disease. 14769913 1155/2922 John Newman 6.52750113260042e-07 3.63831479011075e-06 2710 2887.36363636364 2709 6.52750304997341e-08 584 1.51035348032196 1.76088884206217 1 3.00278939149275 2709 3983 4407 2589 584 4518 2955 1967 2533 2288 3228 2786 M2419 WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D http://www.broadinstitute.org/gsea/msigdb/cards/WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D.html Genes with promoters bound by PPARG [GeneID=5468] at 8 day time point of adipocyte differentiation of 3T3-L1 cells (preadipocyte). 19414603 464/1046 Arthur Liberzon 2.84416085338373e-07 2.29907642774426e-06 3040 2705.90909090909 2709 2.58560111007002e-08 246 1.47514146895553 1.84485031146852 1 3.04027167536183 3040 2709 2613 2854 246 4539 2825 2530 2445 3573 2391 2787 M1454 NUMATA_CSF3_SIGNALING_VIA_STAT3 http://www.broadinstitute.org/gsea/msigdb/cards/NUMATA_CSF3_SIGNALING_VIA_STAT3.html Target genes for STAT3 [GeneID=20848] in CSF3 [GeneID=12985] signaling during myeloblast differentiation to neutrophils. 15664994 10/36 Kevin Vogelsang 0.00743331985668176 0.0103299338221859 2420 2785.36363636364 2713 0.000678050442928555 1426 1.13302446670286 -1.18471591046119 -1 0.82246315582105 2417 3253 2820 4137 4597 1646 1455 1426 3867 2713 2308 2788 M1495 PETROVA_PROX1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PETROVA_PROX1_TARGETS_UP.html Genes specific to LEC (lymphatic endothelium cells) induced in BEC (blood endothelium cells) by expression of PROX1 [GeneID=5629] off adenovirus vector. 12198161 21/37 Kevin Vogelsang 0.151145915258414 0.170749700795788 785 2739.09090909091 2713 0.0147866759356796 782 1.0279733863198 1.0279733863198 1 0.288442162824452 782 3604 1589 3320 4686 1930 1299 2713 4310 3633 2264 2789 M861 REACTOME_THROMBIN_SIGNALLING_THROUGH_PROTEINASE_ACTIVATED_RECEPTORS_PARS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THROMBIN_SIGNALLING_THROUGH_PROTEINASE_ACTIVATED_RECEPTORS_PARS.html Genes involved in Thrombin signalling through proteinase activated receptors (PARs) 12/35 Reactome 0.000386950184596986 0.000639368323350309 3405 2524.27272727273 2714 3.51834782412763e-05 656 1.66178116344971 1.5126378828211 1 1.94026850361484 3403 656 1079 1950 2714 3430 3066 4125 2010 855 4479 2790 M19977 SU_SALIVARY_GLAND http://www.broadinstitute.org/gsea/msigdb/cards/SU_SALIVARY_GLAND.html Genes up-regulated specifically in human salivary gland tissue. 11904358 10/35 John Newman 0.0155082237245298 0.0206923509035155 2765 2500.81818181818 2714 0.0014198759424994 998 2.19249428587712 -2.92755107005774 -1 1.34973604893988 2763 3029 2155 2371 3318 2573 2944 1791 998 2714 2853 2791 M2111 KIM_ALL_DISORDERS_CALB1_CORR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_CALB1_CORR_DN.html Genes whose expression significantly and negatively correlated with the density of CALB1-positive [GeneID=793] GABAergic interneurons in the BA9 brain region across all subjects with psychiatric disorders. 18762803 20/82 Jessica Robertson 0.000126369048738355 0.000228019007465511 3260 2849.18181818182 2714 1.14887552745935e-05 1739 1.15181032070967 -1.18253669869159 -1 1.53335816213711 3259 1739 2183 3449 2470 2550 3489 3595 3876 2017 2714 2792 M18667 DITTMER_PTHLH_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DITTMER_PTHLH_TARGETS_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer) after knockdown of PTHLH [GeneID=5744] by RNAi. 16551631 60/141 Leona Saunders 5.5326370910067e-05 0.000109669785991782 2120 2624.54545454545 2716 5.0297965750926e-06 485 2.24352092407606 2.96676992407413 1 3.24739426703956 2117 4438 2072 3436 4326 2835 2716 485 1178 3651 1616 2793 M585 REACTOME_PRE_NOTCH_TRANSCRIPTION_AND_TRANSLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PRE_NOTCH_TRANSCRIPTION_AND_TRANSLATION.html Genes involved in Pre-NOTCH Transcription and Translation 12/31 Reactome 0.000535755380757159 0.00086184336224787 2720 2464.27272727273 2717 4.87168995616468e-05 285 2.43255211581551 3.0027535408805 1 2.72490386409268 2717 3162 2012 4223 3171 2740 2471 878 285 2962 2486 2794 M4086 KEGG_PROPANOATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROPANOATE_METABOLISM.html Propanoate metabolism 16/36 KEGG 0.00115979292350499 0.00178073055030943 2850 2456.54545454545 2718 0.000105491344832237 738 1.94943431221353 -1.47335858464781 -1 1.95914268629893 2848 2596 2452 2793 2911 2133 1613 3435 738 2718 2785 2795 M852 REACTOME_TAK1_ACTIVATES_NFKB_BY_PHOSPHORYLATION_AND_ACTIVATION_OF_IKKS_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TAK1_ACTIVATES_NFKB_BY_PHOSPHORYLATION_AND_ACTIVATION_OF_IKKS_COMPLEX.html Genes involved in TAK1 activates NFkB by phosphorylation and activation of IKKs complex 13/27 Reactome 0.000615905378553007 0.000982680491623899 1095 2043.54545454545 2718 5.60070793800328e-05 569 1.12829022928227 -1.12829022928227 -1 1.24039033141219 1094 2718 3160 2883 2806 569 1096 1157 3121 3078 797 2796 M2514 FOSTER_KDM1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FOSTER_KDM1A_TARGETS_DN.html Genes down-regulated in ES cells (embryonic stem) heterozygotic for KDM1A [GeneID=23028] loss of function mutant compared to the homozygotic loss of the gene. 20713442 168/326 Arthur Liberzon 8.0982457391074e-06 2.12396737148495e-05 2725 2874.81818181818 2721 7.3620686809745e-07 1615 1.26355488424112 1.27158620982677 1 2.15821845576243 2721 2184 3241 3240 1615 3435 1764 4241 2703 2490 3989 2797 M1924 MIKKELSEN_DEDIFFERENTIATED_STATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_DEDIFFERENTIATED_STATE_UP.html Genes up-regulated in partially reprogrammed and pluripotent cell populations (induced, iPS; and embryonic stem cells, ES) compared to parental lineage-commited cell lines. 18509334 3/8 Jessica Robertson 1.36438086015202e-06 5.83074605080017e-06 4435 2499.63636363636 2722 1.36438169784355e-07 390 1.86341544237943 -1.68867518373136 -1 3.56521355532682 4432 530 4549 390 889 3895 2722 4517 829 1400 3343 2798 M17961 NIKOLSKY_BREAST_CANCER_14Q22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_14Q22_AMPLICON.html Genes within amplicon 14q22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 7/21 Jessica Robertson 0.00170116472897854 0.00254522922094299 1985 2931.36363636364 2724 0.000170246841644209 1120 1.45439287043331 1.45439287043331 1 1.37916643583428 1984 2724 4354 3761 4075 2158 2560 1120 4009 3204 2296 2799 M1476 ZHAN_EARLY_DIFFERENTIATION_GENES_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_EARLY_DIFFERENTIATION_GENES_DN.html B lymphocyte early differentiation genes (EDG): top genes down-regulated in tonsil B lymphocytes (TBC) compared to the tonsil plasma cells (TPC). 12393520 26/58 Arthur Liberzon 8.1107448912606e-06 2.12396737148495e-05 3450 3242.90909090909 2725 7.37343163028742e-07 1617 1.67992448312192 1.52374049358825 1 2.86939971482644 3448 2426 2676 2534 1617 4565 4580 4459 2725 2551 4091 2800 M17609 WU_ALZHEIMER_DISEASE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WU_ALZHEIMER_DISEASE_UP.html Genes up-regulated in brain endothelial cells from patients with Alzheimer disease. 16116430 19/45 Jessica Robertson 0.0648735804708285 0.0810660261563474 2730 2855.63636363636 2726 0.00607904291783595 1173 1.87328333046735 2.43177271573242 1 0.747156534800967 2726 2553 1173 1673 4022 4407 4140 3245 2120 1924 3429 2801 M10066 BIOCARTA_GCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GCR_PATHWAY.html Corticosteroids and cardioprotection 13/35 BioCarta 0.00275541741426304 0.00403622569654161 2005 2763.18181818182 2727 0.000250806775867114 1017 0.825744892813226 0.920150371615191 1 0.722592994437619 2001 3554 2727 3125 4569 1535 1355 2522 4323 3667 1017 2802 M15154 MARTIN_INTERACT_WITH_HDAC http://www.broadinstitute.org/gsea/msigdb/cards/MARTIN_INTERACT_WITH_HDAC.html Interaction partners of class IIa histone deacetylases (HDAC). 17694086 29/63 Leona Saunders 0.124424745977931 0.141758900960998 1025 2800 2728 0.0120068065684873 1022 1.12739328372779 1.22142141476313 1 0.349639727333325 1022 3641 2728 4424 4133 1423 1238 2426 4080 3626 2059 2803 M1291 THEODOROU_MAMMARY_TUMORIGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/THEODOROU_MAMMARY_TUMORIGENESIS.html Candidate mammary tumorigenesis genes from the common insertion sites (CIS) of MMTV virus that induced breast tumors in mice. 17468756 14/53 Leona Saunders 0.00040798994602691 0.000670586070530376 3250 2513.81818181818 2728 3.70968752183885e-05 750 1.67083370911005 -0.860272498984592 -1 1.93819381910592 3247 2167 1039 1500 2728 4527 4224 3293 750 1375 2802 2804 M8941 HEDENFALK_BREAST_CANCER_BRACX_DN http://www.broadinstitute.org/gsea/msigdb/cards/HEDENFALK_BREAST_CANCER_BRACX_DN.html Down-regulated genes distinguishing between two groups of non-BRCA1/BRCA2 [GeneID=672;675] breast tumors (BRACx): group A vs group B. 12610208 12/27 John Newman 0.0839184282471183 0.0965721401684667 2600 2901.18181818182 2728 0.00793650793650794 1507 1.5408276132167 -1.5408276132167 -1 0.571745463016169 2600 4527 3355 4429 3888 1507 1819 2039 2728 2968 2053 2805 M1689 YANG_MUC2_TARGETS_DUODENUM_6MO_UP http://www.broadinstitute.org/gsea/msigdb/cards/YANG_MUC2_TARGETS_DUODENUM_6MO_UP.html Genes up-regulated in duodenum of 6 month old MUC2 [GeneID=4583] knockout mice. 18794118 4/16 Jessica Robertson 0.0594020442305706 0.0745668307700118 2020 2745.27272727273 2728 0.00610523512764692 1638 1.70012605474307 -1.70012605474307 -1 0.7006470948403 2019 3170 4426 3346 3522 1914 1776 2728 3844 1638 1815 2806 M1299 GROSS_ELK3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_ELK3_TARGETS_DN.html Genes down-regulated in SEND cells (skin endothelium) at normal oxygen (normoxia) conditions after knockdown of ELK3 [GeneID=2004] by RNAi. 17704799 23/58 Jessica Robertson 0.00460721824175291 0.0065641303377483 1975 2537.90909090909 2730 0.000419717728686023 1320 1.67736366739001 1.71672651092195 1 1.33833539533786 1972 3339 1819 3244 3906 2730 3198 1320 3010 1793 1586 2807 M1929 MEISSNER_ES_ICP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_ES_ICP_WITH_H3K4ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in ES cells (embryonic stem). 18600261 23/56 Jessica Robertson 1.57792754572223e-05 3.6933908487784e-05 4565 3162.72727272727 2730 1.43448987578195e-06 1854 1.70577251974802 -1.24130690711095 -1 2.76373520225704 4561 2546 2244 3294 1854 3465 4633 2636 2730 2300 4527 2808 M15821 AMIT_SERUM_RESPONSE_120_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_120_MCF10A.html Genes whose expression peaked at 120 min after stimulation of MCF10A cells with serum. 17322878 54/127 Leona Saunders 2.44452432747153e-05 5.39822855727218e-05 2260 2972.63636363636 2731 2.22231953651192e-06 1979 1.65154104232521 1.74238235117412 1 2.5763654296924 2257 4061 2079 4481 1979 3521 2692 2133 3301 3464 2731 2809 M3019 ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_UP.html Genes up-regulated in 3 out of 4 NSCLC cell lines (non-small cell lung cancer) after treatment with azacitidine [PubChem=9444] and TSA [PubChem=5562]. 17043644 143/350 Leona Saunders 1.61875245910311e-05 3.76391827059604e-05 3630 2788 2732 1.47160397268265e-06 1560 1.54056650539199 1.80607024586025 1 2.49143832499383 3628 2732 1560 2351 1863 4135 4204 1677 2835 1590 4093 2810 M18519 WEST_ADRENOCORTICAL_CARCINOMA_VS_ADENOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_CARCINOMA_VS_ADENOMA_DN.html Down-regulated genes in pediatric adrenocortical carcinoma (ACC) compared to the adenoma (ACA) tumors. 17234769 15/38 Jessica Robertson 0.000414400612964737 0.000680168571752279 3255 2692.45454545455 2732 3.76798810615854e-05 1437 2.09529985548873 -1.63932899732493 -1 2.42586190772486 3251 2082 1437 2030 2732 3889 2746 3376 2820 2616 2638 2811 M14985 BASAKI_YBX1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BASAKI_YBX1_TARGETS_UP.html Genes up-regulated in SKOC-3 cells (ovarian cancer) after YB-1 (YBX1) [GeneID=4904] knockdown by RNAi. 17072343 198/437 Arthur Liberzon 0.0839184282471183 0.0965721401684667 790 2793 2733 0.00793650793650794 790 1.53803941494879 1.74148732824179 1 0.570710863362707 790 4253 1709 2593 4012 3072 2689 2629 3016 3227 2733 2812 M17670 REACTOME_RAS_ACTIVATION_UOPN_CA2_INFUX_THROUGH_NMDA_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RAS_ACTIVATION_UOPN_CA2_INFUX_THROUGH_NMDA_RECEPTOR.html Genes involved in Ras activation uopn Ca2+ infux through NMDA receptor 10/23 Reactome 0.00196381344457666 0.00292233401120553 3390 2739.27272727273 2735 0.000178688056518709 1617 1.69424190733097 -2.30123737971674 -1 1.56945033771124 3389 1617 2591 1664 3007 2735 2931 3551 1981 2697 3969 2813 M3710 WALLACE_PROSTATE_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WALLACE_PROSTATE_CANCER_UP.html Genes up-regulated in prostate tumor vs normal tissue samples. 18245496 16/27 Jessica Robertson 1.72478427826392e-05 3.98341011727192e-05 3395 2780.90909090909 2736 1.56799800054348e-06 1811 1.29576954888041 -1.29576954888041 -1 2.08388872129939 3393 2402 3129 3051 1880 2918 4493 2144 2633 2736 1811 2814 M18201 GOTTWEIN_TARGETS_OF_KSHV_MIR_K12_11 http://www.broadinstitute.org/gsea/msigdb/cards/GOTTWEIN_TARGETS_OF_KSHV_MIR_K12_11.html Genes down-regulated in BJAB cell line (B lymphocyte) after expression of the viral microRNA miR-K12-11 which functions as an ortholog of cellular MIR155 [GeneID=406947]. 18075594 42/94 Jessica Robertson 0.0839184282471183 0.0965721401684667 2145 2648.18181818182 2737 0.00793650793650794 1913 1.28312320847086 1.36533978712096 1 0.476120667995679 2145 3082 2766 3006 3885 2339 1913 2737 2819 2487 1951 2815 M987 REACTOME_NFKB_AND_MAP_KINASES_ACTIVATION_MEDIATED_BY_TLR4_SIGNALING_REPERTOIRE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NFKB_AND_MAP_KINASES_ACTIVATION_MEDIATED_BY_TLR4_SIGNALING_REPERTOIRE.html Genes involved in NFkB and MAP kinases activation mediated by TLR4 signaling repertoire 48/99 Reactome 3.49622032447979e-05 7.32377668328667e-05 4505 2900.81818181818 2738 3.17843262485155e-06 1538 1.21343414297899 -1.26846389136818 -1 1.8341666678575 4502 2151 3291 1538 2100 3282 4012 3251 2530 2514 2738 2816 M14091 KEGG_OLFACTORY_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OLFACTORY_TRANSDUCTION.html Olfactory transduction 35/833 KEGG 0.0839184282471183 0.0965721401684667 1940 2729 2741 0.00793650793650794 1940 1.38611372955728 1.57179867536728 1 0.51433672983465 1940 3054 2380 2654 3625 2396 2309 2741 3077 2775 3068 2817 M12993 KLEIN_PRIMARY_EFFUSION_LYMPHOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KLEIN_PRIMARY_EFFUSION_LYMPHOMA_UP.html Genes up-regulated in AIDS-related primary effusion lymphoma (PEL) samples compared to other tumor subtypes and normal B lymphocytes. 12531789 41/72 Kate Stafford 3.69360529608677e-05 7.70624862754346e-05 2870 2818.45454545455 2741 3.35787937264401e-06 1697 1.52263158393108 1.45452235392343 1 2.28922968871986 2866 3394 2219 2524 2113 4077 2718 3762 2892 1697 2741 2818 M18122 DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_UP.html Genes exclusively up-regulated in fibroblasts expressing the XP/CS mutant form of ERCC3 [GeneID=2071] after high dose UVC irradiation. 15608684 22/42 Arthur Liberzon 0.000217106244220897 0.000374442348332397 4440 2970.36363636364 2742 1.97388792942314e-05 987 2.52172978311909 2.99091924799972 1 3.15851624441924 4436 2477 1790 3779 2587 3742 3376 2280 987 2742 4478 2819 M16649 ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_DN.html Genes commonly down-regulated in CD-1 and CD-2 clusters of multiple myeloma samples and which were higher expressed in the CD-1 group. 16728703 55/92 Kevin Vogelsang 0.000440315057440464 0.000718925560685022 2555 2791.81818181818 2743 4.00366552917669e-05 1658 1.38781913737447 -1.213770653873 -1 1.59455746704697 2553 3565 1658 3151 2743 2320 3503 3430 3277 2232 2278 2820 M13319 ABE_VEGFA_TARGETS_2HR http://www.broadinstitute.org/gsea/msigdb/cards/ABE_VEGFA_TARGETS_2HR.html Genes up-regulated in HUVEC cells (endothelium) at 2 h after VEGFA [GeneID=7422] stimulation. 12197474 22/49 John Newman 4.97816894128596e-05 9.99044953270493e-05 3990 2944 2744 4.5257105373307e-06 1129 1.37900428862599 -1.31465442263466 -1 2.0164613899697 3986 1129 2030 2033 2209 3614 3883 3918 2347 2744 4491 2821 M814 REACTOME_PURINE_SALVAGE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_SALVAGE.html Genes involved in Purine salvage 8/15 Reactome 0.000980235558770312 0.00152149182788926 2300 2377.45454545455 2745 9.80668215182225e-05 202 0.815342712365755 0.798898249357147 1 0.839767141089449 2299 202 4017 2868 2898 1133 999 3837 2745 3302 1852 2822 M16740 GRADE_COLON_AND_RECTAL_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_AND_RECTAL_CANCER_UP.html Up-regulated genes in both rectal and colon carcinoma compared to normal mucosa samples. 17210682 232/477 Jessica Robertson 1.48119093716543e-06 6.07122739761261e-06 2225 2908.54545454545 2745 1.34653812218702e-07 882 1.48733885312333 1.79998682170637 1 2.83613560426408 2222 3914 2745 2765 882 4493 3934 2414 2619 2645 3361 2823 M699 KEGG_FATTY_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FATTY_ACID_METABOLISM.html Fatty acid metabolism 22/56 KEGG 0.000753698468896718 0.00118677117783939 1405 2330.45454545455 2746 6.85415275025376e-05 598 0.985068548019619 -0.985068548019619 -1 1.05342967970824 1403 2746 3109 3598 3306 598 983 1294 3879 3955 764 2824 M5839 COLLIS_PRKDC_REGULATORS http://www.broadinstitute.org/gsea/msigdb/cards/COLLIS_PRKDC_REGULATORS.html Proteins that regulate activity of PRKDC [GeneID=5591]. 15592499 10/24 Jessica Robertson 0.00045452450916597 0.000740835426070168 2635 2740.72727272727 2746 4.13289492756092e-05 1512 2.38236779657299 -2.38236779657299 -1 2.72590681264681 2635 2822 3150 4220 2746 1866 1512 3317 2024 3491 2365 2825 M19818 KEGG_NON_SMALL_CELL_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NON_SMALL_CELL_LUNG_CANCER.html Non-small cell lung cancer 28/64 KEGG 0.000133387015222965 0.000239391632836007 4260 2961.36363636364 2747 1.2126827565981e-05 890 1.56808648609329 -1.36283995326233 -1 2.07541388370465 4259 2451 2074 2015 2484 3816 4391 3282 890 2747 4166 2826 M2318 KASLER_HDAC7_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/KASLER_HDAC7_TARGETS_1_DN.html Genes down-regulated in DO11.10 cells (hybridoma) by expression of transciptionally activating form of HDAC7 [GeneID=51564] and up-regulated by its transcriptionally repressing form. 17470548 16/28 Arthur Liberzon 0.000455785730347348 0.000742374672369715 4145 2932.36363636364 2748 4.14436532095191e-05 1669 1.43404786798631 1.59084948097555 1 1.64036601970722 4144 2242 2348 2929 2748 3182 4519 1895 1669 2130 4450 2827 M7 PID_FCER1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FCER1_PATHWAY.html Fc-epsilon receptor I signaling in mast cells 18832364 34/97 Pathway Interaction Database 0.00135989442637952 0.00206161930831912 2750 2573.18181818182 2749 0.00012370325011745 1449 1.20161095514911 -1.13229856947084 -1 1.17965612920521 2411 2692 2996 1449 2948 1823 3356 2749 2749 3132 2000 2828 M288 PID_HES_HEY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HES_HEY_PATHWAY.html Notch-mediated HES/HEY network 18832364 28/75 Pathway Interaction Database 0.0250723078703735 0.0326630065834224 3100 2654.81818181818 2749 0.00230569893349682 1727 1.55132367428445 -1.92559189962699 -1 0.842605066715043 3100 2839 2533 3352 3393 2029 2887 1727 2489 2749 2105 2829 M7094 MARKEY_RB1_ACUTE_LOF_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARKEY_RB1_ACUTE_LOF_DN.html Genes down-regulated in adult fibroblasts with inactivated RB1 [GeneID=5925] by Cre-lox: acute loss of function (LOF) of RB1. 17452985 175/446 Arthur Liberzon 1.61542055714871e-06 6.45892553822427e-06 3660 2441.27272727273 2749 1.46856522120389e-07 546 1.4782614990944 -1.45555652804995 -1 2.80429993594399 3657 546 1177 1751 917 2749 4514 3678 2786 2137 2942 2830 M11078 YANG_BREAST_CANCER_ESR1_LASER_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_LASER_DN.html Genes down-regulated in laser microdissected (LCM) samples of early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative ones. 16261164 28/75 Leona Saunders 0.000517335799557659 0.000833357015031691 1815 2556.72727272727 2750 4.70415902272339e-05 1529 1.75697083332705 1.71385452344008 1 1.97750374467101 1815 2918 2473 4211 2774 2901 1529 1713 2805 2750 2235 2831 M2184 KAPOSI_LIVER_CANCER_MET_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAPOSI_LIVER_CANCER_MET_DN.html Selected down-regulated MET [GeneID=4233] target genes from a classifier of hepatocellular carcinoma (HCC) cases; associated with poor survival. 16710476 4/10 Yujin Hoshida 0.145684161281741 0.165057055069206 2440 3122.18181818182 2751 0.0156221206319187 2262 2.34985618113092 -2.34985618113092 -1 0.67200182079736 2436 3526 4565 3408 4112 2401 2368 2262 3829 2686 2751 2832 M5410 KEGG_ARACHIDONIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ARACHIDONIC_ACID_METABOLISM.html Arachidonic acid metabolism 18/108 KEGG 2.78627931182863e-06 9.26650451045347e-06 3560 2543.81818181818 2752 2.53298440057403e-07 1193 1.90705416346897 -2.25745374407883 -1 3.50845945471691 3557 2782 1248 3333 1193 2392 2752 2199 2865 1772 3889 2833 M1492 BRUNO_HEMATOPOIESIS http://www.broadinstitute.org/gsea/msigdb/cards/BRUNO_HEMATOPOIESIS.html Genes that are rapidly down-regulated as multipotential cells of the FDCP-mix hematopoiesis model undergo differentiation and loose their self-renewal and proliferation properties. 14701746 42/112 Kevin Vogelsang 0.000690554713463457 0.00109285355869293 3925 2994.09090909091 2752 6.27974150864863e-05 1826 1.31985764525044 -0.980651396416121 -1 1.42872614291052 3923 1826 1887 2146 2832 2542 4207 4352 2752 2488 3980 2834 M11749 HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP.html Genes up-regulated in SCLC (small cell lung cancer) cells with acquired resistance to ABT-737 [PubChem=11228183], an inhibitor of the BCL2 [GeneID=596] family proteins. 18381439 30/114 Jessica Robertson 0.000506615064341566 0.000817492490187527 2720 2806.36363636364 2752 4.60665240971059e-05 1429 1.86183580957436 2.10642920044868 1 2.1012120284008 2720 3708 2492 2752 2771 4124 3612 1481 2450 3331 1429 2835 M1897 RASHI_RESPONSE_TO_IONIZING_RADIATION_1 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_1.html Cluster 1: ATM [GeneID=472] dependent genes induced at 30 min after ionizing radiation treatment. 16314843 38/89 Arthur Liberzon 0.000464544519435859 0.000754542675243131 4365 2858.27272727273 2753 4.22402400076899e-05 1479 1.72970510385295 -1.46676239131684 -1 1.97409568150765 4365 2391 1479 1530 2753 3880 4651 2861 1741 1505 4285 2836 M13678 JEON_SMAD6_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JEON_SMAD6_TARGETS_DN.html Genes down-regulated in H1299 cells (lung cancer) upon knockdown of SMAD6 [GeneID=4091] by RNAi. 19047146 13/32 Jessica Robertson 0.0292042833931692 0.0377520750290733 2755 2667.27272727273 2753 0.00269084746864924 1269 2.4533759915105 -1.15270499606842 -1 1.2761635026824 2753 2848 1269 2935 3418 3829 2501 2383 2133 2356 2915 2837 M16061 STANELLE_E2F1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/STANELLE_E2F1_TARGETS.html Genes up-regulated by induction of E2F1 expression in Saos2 (osteosarcoma) cells. 11937641 24/59 Yujin Hoshida 0.00128415439320086 0.00195960951968544 4390 2960.09090909091 2753 0.000116809506875832 1200 2.01861032418084 -1.42858385109945 -1 1.99798953661782 4389 2507 1779 2753 2935 3789 4555 2597 1200 2377 3680 2838 M2080 KARLSSON_TGFB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KARLSSON_TGFB1_TARGETS_UP.html Genes up-regulated by TGFB1 [GeneID=7040] in MEF cells (embryonic fibroblast) via TGFB1R [GeneID=7046]. 15769904 96/201 Arthur Liberzon 0.0839184282471183 0.0965721401684667 1275 3006.45454545455 2753 0.00793650793650794 1275 1.90737988047273 2.115085406093 1 0.707759767681326 1275 4565 2733 3809 4247 3082 2651 2205 2059 3692 2753 2839 M5669 KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY.html Natural killer cell mediated cytotoxicity 56/188 KEGG 0.000307247050059862 0.000515119741173708 4545 3144.81818181818 2755 2.793545162574e-05 1604 1.66410587636586 1.70464945658694 1 2.00006513501404 4542 2630 1823 1604 2669 3123 4645 4341 2755 2303 4158 2840 M18719 BIOCARTA_HER2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HER2_PATHWAY.html Role of ERBB2 in Signal Transduction and Oncology 14/37 BioCarta 0.000859079140307731 0.00134367318140255 2755 2796.63636363636 2755 7.81286169158118e-05 1732 1.30144740246592 -1.17576261174134 -1 1.36611072107163 2755 2669 2830 1898 2860 1732 4071 3734 2714 3141 2359 2841 M1012 REACTOME_IL_2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_2_SIGNALING.html Genes involved in Interleukin-2 signaling 23/57 Reactome 0.00056354308014747 0.00090396827605233 2310 2682.54545454545 2755 5.12443169861409e-05 1687 1.04240865633176 -0.898097348203399 -1 1.15979184515069 2307 2398 2984 2017 2790 1687 3685 2755 3440 3322 2123 2842 M1154 RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_MAPK1_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_MAPK1_DN.html Apoptotic genes dependent on MAPK1 [GeneID=5594] and down-regulated in AML12 cells (hepatocytes) after stimulation with TGFB1 [GeneID=7040]. 16909112 6/8 Arthur Liberzon 0.00042373935019517 0.000694523468000897 3600 2798.18181818182 2755 4.23820171652533e-05 1398 0.987344895897694 -1.00336215359225 -1 1.13983847808103 3598 1398 4190 2688 2755 2494 1912 2616 3106 3051 2972 2843 M2331 BILANGES_RAPAMYCIN_SENSITIVE_VIA_TSC1_AND_TSC2 http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_RAPAMYCIN_SENSITIVE_VIA_TSC1_AND_TSC2.html Genes translationally repressed by rapamycin (sirolimus) [PubChem=6610346] in MEF cells (embryonic fibroblast) lacking either TSC1 or TSC2 [GeneID=7248, 7249] but not in the wild type cells. 17562867 52/145 Arthur Liberzon 0.00527250504231797 0.00745083191444573 4610 3018.81818181818 2755 0.000480471241105459 1350 1.8767064578744 -0.761001963534026 -1 1.45963890440866 4610 3475 2583 2428 3868 2755 2701 1350 1356 3638 4443 2844 M6705 BIOCARTA_TH1TH2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TH1TH2_PATHWAY.html Th1/Th2 Differentiation 5/21 BioCarta 0.013826002568612 0.0186334909509681 2285 2894 2757 0.00139127846999225 2285 2.54304047385828 -2.54304047385828 -1 1.60784713958902 2285 2757 3878 3179 3313 2538 3149 2693 2699 2885 2458 2845 M7561 KEGG_MTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MTOR_SIGNALING_PATHWAY.html mTOR signaling pathway 34/78 KEGG 0.0143004486665479 0.0192176376402189 1300 2313 2758 0.00130856902921304 964 1.14706931799794 1.2935365641158 1 0.719618161335419 1300 2888 2924 2758 3307 1370 964 1867 3149 3523 1393 2846 M1658 LEE_AGING_MUSCLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_MUSCLE_UP.html Upregulated in the gastrocnemius muscle of aged adult mice (30-month) vs young adult (5-month) 10464095 43/85 John Newman 0.00866589839517619 0.0119423591307634 4200 2910.45454545455 2758 0.000790929381458475 1336 2.07059817242617 -1.641142296772 -1 1.45537196799798 4200 4097 2160 2670 3226 1336 2192 3905 2528 2943 2758 2847 M2464 DELACROIX_RAR_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DELACROIX_RAR_TARGETS_UP.html Genes bound by RARG [GeneID=5916] and up-regulated by tretinoin (all-trans retinoic acid, ATRA) [PubChem=444795] in MEF cells (embryonic fibroblast). 19884340 40/85 Arthur Liberzon 1.63596542344093e-06 6.49115128016012e-06 4155 2699.63636363636 2758 1.48724239998169e-07 925 1.4378367424383 -1.59571140827482 -1 2.72647714659008 4153 2155 1421 2079 925 3715 4064 3123 2758 934 4369 2848 M776 REACTOME_PROTEIN_FOLDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROTEIN_FOLDING.html Genes involved in Protein folding 32/70 Reactome 0.000476302348357872 0.000771767913003107 2900 2448.09090909091 2759 4.33095908719418e-05 659 1.95016754702627 2.64980734022438 1 2.21871944005302 2899 3600 1989 1935 2759 3531 2925 955 659 3013 2664 2849 M7534 YOSHIOKA_LIVER_CANCER_EARLY_RECURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/YOSHIOKA_LIVER_CANCER_EARLY_RECURRENCE_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) samples from patients with early recurrence (within 2 years after surgery) after resection. 19167881 46/124 Yujin Hoshida 8.11331966486997e-06 2.12396737148495e-05 2030 2527.54545454545 2763 7.37577235083049e-07 1150 1.01881732121986 1.05041695489942 1 1.74019377606063 2029 3114 3256 4146 1619 1723 1150 2771 3665 2763 1567 2850 M2505 RATTENBACHER_BOUND_BY_CELF1 http://www.broadinstitute.org/gsea/msigdb/cards/RATTENBACHER_BOUND_BY_CELF1.html Transcripts bound by CELF1 [GeneID=10658] in HeLa cells (cervical carcinoma). 20547756 287/748 Arthur Liberzon 3.47556093616442e-05 7.29764615851793e-05 3665 2970.18181818182 2763 3.15965076755027e-06 1460 1.55737779840414 -1.38447925267184 -1 2.35493844529117 3663 2763 1785 2672 2096 4434 2912 4436 2077 1460 4374 2851 M1519 KEGG_ENDOCYTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ENDOCYTOSIS.html Endocytosis 112/231 KEGG 0.000381664049188199 0.000631078946540544 4575 3044.90909090909 2764 3.47027525227105e-05 2041 1.3534442027757 -0.988008649129744 -1 1.58306310058068 4574 2764 2497 2304 2712 2360 3979 3014 2957 2041 4292 2852 M269 PID_RAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RAS_PATHWAY.html Regulation of Ras family activation 18832364 17/38 Pathway Interaction Database 3.68082433701846e-06 1.14830687329376e-05 3305 2580 2764 3.34620954129758e-07 1304 1.66145569617414 -2.05224412042316 -1 3.0000595018444 3301 2868 1617 2088 1304 2863 3860 2764 3035 2212 2468 2853 M2082 WANG_METASTASIS_OF_BREAST_CANCER_ESR1_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_METASTASIS_OF_BREAST_CANCER_ESR1_UP.html Genes whose expression in primary ER(+) [GeneID=2099] breast cancer tumors positively correlates with developing distant metastases. 15721472 18/41 Arthur Liberzon 0.00674211004702943 0.0094196564342218 1205 2661.36363636364 2764 0.000614805542928093 1203 1.05518540161294 -1.05518540161294 -1 0.781411770260759 1203 3552 2764 4172 3181 1251 1584 1740 4332 3460 2036 2854 M1937 MEISSNER_NPC_ICP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_ICP_WITH_H3_UNMETHYLATED.html Genes with intermediate-CpG-density promoters (ICP) that have no histone H3 methylation marks in neural precursor cells (NPC). 18600261 12/45 Jessica Robertson 1.3859535674751e-06 5.85372787868602e-06 2845 2471.45454545455 2769 1.25995858236124e-07 847 1.50604445372074 1.44581657848135 1 2.88052652282689 2843 1702 1718 2221 847 2829 2769 3270 3123 2250 3614 2855 M2279 MAEKAWA_ATF2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MAEKAWA_ATF2_TARGETS.html Genes down-regulated in MEF cells (embryonic fibroblast) upon knockout of ATF2 [GeneID=1386]. 17189429 6/46 Arthur Liberzon 0.00700204340290369 0.0097624443278806 2520 2933 2770 0.000702420461826878 2041 1.28664157875262 1.28664157875262 1 0.945514638375553 2517 2253 4640 3623 3209 2601 2770 3246 2041 3065 2298 2856 M12461 FINAK_BREAST_CANCER_SDPP_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/FINAK_BREAST_CANCER_SDPP_SIGNATURE.html Genes in the stroma-derived prognostic predictor of breast cancer disease outcome. 18438415 8/33 Arthur Liberzon 0.00270160648321597 0.00395987737890211 1970 2683.45454545455 2772 0.000270489651883593 1565 1.38726839941037 0.993895293855945 1 1.21817669390348 1970 1565 4543 2776 3061 2824 2772 2675 2854 2409 2069 2857 M2503 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_OLD http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_OLD.html Human environmental stress response (H-ESR) genes not changed in primary fibroblasts from old donors in response to gamma radiation. 15897889 19/42 Jessica Robertson 5.01120303109322e-06 1.45402460704042e-05 2760 2562.45454545455 2773 4.55564949613264e-07 1431 1.50902367602083 1.73666302557686 1 2.66827040954565 2756 3059 2773 3196 1431 2859 2254 1604 2899 3532 1824 2858 M13276 MARZEC_IL2_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARZEC_IL2_SIGNALING_DN.html Genes down-regulated by IL2 [GeneID=3558] in cells derived from CD4+ [GeneID=920] cutaneous T-cell lymphoma (CTCL). 18281483 29/59 Jessica Robertson 0.00140614760214219 0.00212349586324148 1745 2503.18181818182 2774 0.000127913377970635 1067 1.53980427580964 1.50783968786494 1 1.50444174526758 1744 3601 2100 3310 3151 3130 2053 1067 2774 2785 1820 2859 M6840 XU_HGF_SIGNALING_NOT_VIA_AKT1_6HR http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_SIGNALING_NOT_VIA_AKT1_6HR.html Genes changed similarly in DU-145 cells (prostate cancer) in the absence and presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 6 h. 17099727 24/48 Arthur Liberzon 0.0152949311323677 0.0204368540879027 3280 2733.81818181818 2775 0.00140021016382737 1242 1.61436794646466 -1.12060342216897 -1 0.997015859667576 3279 2775 1242 2131 3315 4341 3411 2223 2581 1935 2839 2860 M9070 BIOCARTA_CREB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CREB_PATHWAY.html Transcription factor CREB and its extracellular signals 22/45 BioCarta 0.00141651077465687 0.00213707968127562 1775 2440.09090909091 2776 0.000128856694941272 1129 1.0221586443731 0.96487702422613 1 0.997649474170887 1775 2776 3046 1940 2962 1174 1129 3758 3110 3657 1514 2861 M2390 WANG_THOC1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_THOC1_TARGETS_UP.html Genes up-regulated in testis tissue expressing hypomorphic allele of THOC1 [GeneID=9984]. 19307311 3/13 Arthur Liberzon 0.0765897756730953 0.0944224385172651 2780 3117.90909090909 2776 0.00793650793650794 2099 2.42311679412468 -2.42311679412468 -1 0.907790417470928 2776 3695 4661 3344 4108 2665 3386 2493 2099 2476 2594 2862 M6714 HAHTOLA_MYCOSIS_FUNGOIDES_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_UP.html Genes up-regulated in monocytes isolated from peripheral blood samples of patients with mucosis fungoides compared to those from normal healthy donors. 16914566 23/56 Arthur Liberzon 0.0163311515584338 0.0217284997736572 1420 2715.18181818182 2777 0.00149578698543746 1420 1.68605996583813 -2.13022354882986 -1 1.02488880294571 1420 2777 2224 3073 3675 1999 3468 1602 3401 3709 2519 2863 M1641 BURTON_ADIPOGENESIS_PEAK_AT_8HR http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_PEAK_AT_8HR.html Cluster 3: genes maximally expressed at 8 hr time point during differentiation of 3T3-L1 fibroblasts into adipocytes in response to adipogenic hormones. 12137940 35/78 John Newman 0.000106416057509295 0.000194867387842343 4040 3079.81818181818 2777 9.67465502746621e-06 1977 1.19909515190134 -0.98921572543949 -1 1.62621266637213 4036 2230 2493 2755 2432 1977 4099 4326 3222 2777 3531 2864 M1813 MATZUK_IMPLANTATION_AND_UTERINE http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_IMPLANTATION_AND_UTERINE.html Genes important for implantation and uterine, based on mouse models with female fertility defects. 18989307 9/32 Jessica Robertson 0.000148221066064759 0.000264092743566335 3625 2935.27272727273 2777 1.48230953260907e-05 1794 1.52616044951244 -1.58899354685301 -1 1.99613238081426 3624 2373 4487 2777 2519 3392 4226 1794 2354 1821 2921 2865 M884 REACTOME_RNA_POL_I_PROMOTER_OPENING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_I_PROMOTER_OPENING.html Genes involved in RNA Polymerase I Promoter Opening 37/75 Reactome 0.0632707282668206 0.0792109625055627 550 2836.18181818182 2778 0.00592428809693384 549 0.924522875029702 -0.924522875029702 -1 0.372142193854239 549 3149 2914 2725 3844 2076 2581 2778 4206 3858 2518 2866 M1602 HEIDENBLAD_AMPLICON_12P11_12_DN http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLICON_12P11_12_DN.html Down-regulated genes whose expression is associated with amplification of the 12p11-12 chromosome in pancreatic cancer cell lines. 15688027 20/38 Arthur Liberzon 0.00221786772121418 0.00327852622763711 1785 2447.90909090909 2779 0.000201827887502472 950 1.03516763110848 -1.20972927895294 -1 0.94002131812764 1781 2779 2956 3349 3280 950 1422 2003 3854 3586 967 2867 M19655 LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_DN.html Genes down-regulated in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of congenic D.B. Chr 3 (DB, small HSC population) vs parental D2 strain (huge HSC population). 17220891 26/56 Leona Saunders 7.09864988620206e-05 0.000136946370385932 905 2269.54545454545 2779 6.45352631434337e-06 408 0.959487479130093 1.02446073893085 1 1.35498285106235 902 3737 2779 4304 3543 564 418 1204 4079 3027 408 2868 M5522 ROZANOV_MMP14_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROZANOV_MMP14_TARGETS_DN.html Genes down-regulated in HT1080 cells (fibrosarcoma) over-expressing MMP14 [GeneID=4323] compared to those with knockdown of the gene by RNAi. 18519667 15/48 Jessica Robertson 0.00415275096850886 0.00594010715458868 3170 2766.09090909091 2779 0.000378237321610809 1302 1.41989980534227 -0.931001163991426 -1 1.15542628727334 3166 3516 2118 2779 3179 4410 4357 1302 1772 1989 1839 2869 M13831 BOYAULT_LIVER_CANCER_SUBCLASS_G123_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G123_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G123, defined by unsupervised clustering. 17187432 22/69 Yujin Hoshida 0.000959301360663256 0.00149047950134881 2780 2834 2779 8.72472650717968e-05 977 1.89739579670583 -1.89739579670583 -1 1.96043707657187 2779 3999 2443 3647 4283 2284 2274 977 3343 3247 1898 2870 M10550 AMIT_DELAYED_EARLY_GENES http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_DELAYED_EARLY_GENES.html Delayed early genes (DEG) which are coordinately down-regulated in multiple epithelial tumor types. 17322878 9/21 Arthur Liberzon 0.000162511613509095 0.000287369592793818 2525 3006.09090909091 2780 1.62523499243477e-05 2486 0.776617700349939 0.776617700349939 1 1.00535869575816 2521 2956 4335 2667 2542 2874 2486 2780 3860 3411 2635 2871 M17294 BIOCARTA_RAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAS_PATHWAY.html Ras Signaling Pathway 19/44 BioCarta 0.0039522925847973 0.00566773790310809 2040 2646.72727272727 2781 0.000359946434043248 1219 0.851376358426876 -0.874600619590574 -1 0.699140891248757 2036 2781 3389 2544 3101 1219 1589 3294 3612 3898 1651 2872 M494 REACTOME_PTM_GAMMA_CARBOXYLATION_HYPUSINE_FORMATION_AND_ARYLSULFATASE_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PTM_GAMMA_CARBOXYLATION_HYPUSINE_FORMATION_AND_ARYLSULFATASE_ACTIVATION.html Genes involved in PTM: gamma carboxylation, hypusine formation and arylsulfatase activation 12/27 Reactome 0.0478270458610567 0.0606871207432742 2785 2800.45454545455 2782 0.00444541577428439 1400 1.6229347243098 -1.0832724893101 -1 0.721898983722956 2782 3555 2275 3564 3482 3517 3227 2168 1400 2238 2597 2873 M10570 BIOCARTA_RNA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RNA_PATHWAY.html Double Stranded RNA Induced Gene Expression 8/17 BioCarta 5.00073260840505e-05 0.000100228541501224 4345 2578.18181818182 2783 5.00084514493904e-06 39 2.26393729069891 -0.616521354713752 -1 3.30929878909662 4343 1469 3827 1969 2236 2783 3090 731 39 3293 4580 2874 M1075 REACTOME_INWARDLY_RECTIFYING_K_CHANNELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INWARDLY_RECTIFYING_K_CHANNELS.html Genes involved in Inwardly rectifying K+ channels 9/39 Reactome 0.00102843485782647 0.00159313908885119 2450 2664.72727272727 2783 0.000102891112328302 1242 1.54055228733625 1.37246841373087 1 1.57544782271103 2450 1705 4093 2783 2906 2198 2138 3226 2812 1242 3759 2875 M12458 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_WS http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_WS.html Human environmental stress response genes not changed in primary fibroblasts from Werner syndrom (WS) patients in response to gamma radiation. 15897889 19/47 Jessica Robertson 8.20237126079887e-07 4.19610390044798e-06 3260 2786.72727272727 2783 7.45670392630183e-08 632 1.44154094950428 1.61205601947989 1 2.83333998145093 3258 2778 2783 3822 632 4011 2329 2124 3235 3007 2675 2876 M837 REACTOME_CREB_PHOSPHORYLATION_THROUGH_THE_ACTIVATION_OF_RAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CREB_PHOSPHORYLATION_THROUGH_THE_ACTIVATION_OF_RAS.html Genes involved in CREB phosphorylation through the activation of Ras 16/35 Reactome 0.000546398130583707 0.000878059547296039 3040 2535.81818181818 2784 4.96848984318613e-05 643 1.23920793954726 -1.4891046573039 -1 1.38447281224456 3038 643 3038 1528 2784 2596 2459 2840 2272 3345 3351 2877 M2583 TOMIDA_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TOMIDA_METASTASIS_DN.html Down-regulated genes associated with the acquision of metastatic potential in LNM35 cells (large cell lung cancer). 17260014 20/37 Arthur Liberzon 0.00161037269745993 0.00241247009600296 4085 2750.63636363636 2785 0.000146504789062893 1078 2.15357597916167 -1.82047111091365 -1 2.06049921851721 4084 2401 1247 2414 2985 2785 4106 3104 1078 2012 4041 2878 M4339 HANN_RESISTANCE_TO_BCL2_INHIBITOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/HANN_RESISTANCE_TO_BCL2_INHIBITOR_DN.html Genes down-regulated in SCLC (small cell lung cancer) cells with acquired resistance to ABT-737 [PubChem=11228183], an inhibitor of the BCL2 [GeneID=596] family proteins. 18381439 22/76 Jessica Robertson 1.52616829222332e-06 6.19188278559174e-06 4600 2550.45454545455 2786 1.38742668267901e-07 895 2.48554768093919 -2.30660823595593 -1 4.73180792542809 4596 3545 1323 1558 895 2977 3219 2786 948 1720 4488 2879 M15315 BERNARD_PPAPDC1B_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERNARD_PPAPDC1B_TARGETS_UP.html Genes up-regulated in ZR-75-1 cells (breast cancer, amplified 8p11-12 region) upon knockdown of PPAPDC1B [GeneID=84513] by RNAi. 18757432 29/63 Jessica Robertson 0.0206661098477029 0.0271492544845348 1955 2780.90909090909 2786 0.00189662116823736 1235 1.42006042899059 -1.38030218816673 -1 0.812989555918913 1955 4659 3229 3859 3537 1235 1931 3629 2282 2786 1488 2880 M7934 KEGG_PYRUVATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PYRUVATE_METABOLISM.html Pyruvate metabolism 21/49 KEGG 7.96949779186665e-05 0.000151562770506035 955 2021.72727272727 2788 7.24526045589653e-06 545 1.52645148307265 -1.52645148307265 -1 2.13107261352471 955 3649 2814 3154 2957 713 801 545 2788 3158 705 2881 M1171 RASHI_NFKB1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_NFKB1_TARGETS.html Known and putative targets of NFKB1 [GeneID=4790] identified among the ATM [GeneID=472] dependent, late responders to ionizing radiation. 16314843 16/29 Arthur Liberzon 0.0338900315004538 0.0435928321743416 3370 2675.18181818182 2788 0.00312942150456964 1677 1.17765015072501 -1.54512411047005 -1 0.585681077307698 3368 1741 2788 1677 3529 2931 2953 1777 2738 2732 3193 2882 M4333 LUI_THYROID_CANCER_CLUSTER_4 http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_CLUSTER_4.html Cluster 4: genes with similar expression profiles across follicular thyroid carcinoma (FTC) samples. 15608688 5/15 Leona Saunders 0.0148330608250477 0.0198763863386256 3625 2875.81818181818 2788 0.0014933009922848 1853 1.90269090729449 -1.90269090729449 -1 1.18348004344201 3623 2137 4235 2645 3326 3446 2436 3274 1853 1871 2788 2883 M13014 ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN.html Genes down-regulated in liver tumor compared to the normal adjacent tissue. 18413731 153/408 Jessica Robertson 2.38570163073022e-06 8.31181995658126e-06 4385 2869.54545454545 2789 2.16882201619314e-07 1112 1.59597848325547 -1.57501804192006 -1 2.96371181996486 4384 2972 1396 2789 1112 2618 4609 4402 2428 1767 3088 2884 M1117 CAIRO_PML_TARGETS_BOUND_BY_MYC_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_PML_TARGETS_BOUND_BY_MYC_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) after knockout of PML [GeneID=5371] and whose promoters were bound by MYC [GeneID=4609]. 15735755 15/27 Lauren Kazmierski 0.0987594076949696 0.113095450747465 1885 2987.18181818182 2790 0.00940846345446287 1883 1.67037150469693 1.67037150469693 1 0.577933825190566 1883 4465 2790 4097 3879 2055 2307 2098 4041 3258 1986 2885 M1678 BURTON_ADIPOGENESIS_6 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_6.html Strongly up-regulated at 96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 142/254 John Newman 1.02328170350398e-06 4.80470747757479e-06 4595 2634.09090909091 2791 9.30256526783008e-08 731 1.57797702030634 -1.31954307157679 -1 3.06757687581609 4591 2710 1124 3001 731 2240 2889 3390 2791 1581 3927 2886 M7330 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE.html Glycosaminoglycan biosynthesis - heparan sulfate 14/28 KEGG 2.63447171752567e-05 5.74726930555182e-05 2815 2575 2792 2.39500296864973e-06 1256 1.2579593810446 0.699829037860187 1 1.94987546221598 2812 1655 2792 3447 2005 2685 1601 2999 1256 3716 3357 2887 M175 PID_ERBB2_ERBB3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB2_ERBB3_PATHWAY.html ErbB2/ErbB3 signaling events 18832364 33/65 Pathway Interaction Database 4.1120323474793e-05 8.44020305750679e-05 2795 2633.81818181818 2793 3.7382810979254e-06 1303 1.3495536551902 1.66386076116751 1 2.00952220712699 2793 3216 2936 1303 2146 3671 3012 1864 1637 3760 2634 2888 M10546 REACTOME_CREB_PHOSPHORYLATION_THROUGH_THE_ACTIVATION_OF_CAMKII http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CREB_PHOSPHORYLATION_THROUGH_THE_ACTIVATION_OF_CAMKII.html Genes involved in CREB phosphorylation through the activation of CaMKII 9/19 Reactome 0.0930090266939625 0.106666739864882 1670 2782.45454545455 2793 0.00971478176318251 1483 1.08724643494519 1.08724643494519 1 0.386278502089338 1669 2793 4031 3354 3596 1483 1664 2696 3963 3402 1956 2889 M13453 DER_IFN_BETA_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_BETA_RESPONSE_UP.html Genes up-regulated in HT1080 (fibrosarcoma) cells by treatment with interferon beta for 6 h. 9861020 95/237 Yujin Hoshida 2.98487213843677e-07 2.3381051686704e-06 2795 2563.18181818182 2793 2.71352049401125e-08 266 1.54536264531978 1.83669310993518 1 3.18086819471712 2262 2734 2795 2114 266 3876 2849 2682 2874 2793 2950 2890 M91 PID_TCPTP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCPTP_PATHWAY.html Signaling events mediated by TCPTP 18832364 31/71 Pathway Interaction Database 5.91702214498682e-06 1.65239366933303e-05 3240 2686 2794 5.37912550836937e-07 1282 1.26081469138473 -1.01279917602805 -1 2.20378779071983 3239 1282 1931 1440 1498 4577 3922 3375 2794 2037 3451 2891 M923 REACTOME_RAP1_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RAP1_SIGNALLING.html Genes involved in Rap1 signalling 12/20 Reactome 0.0378495880475742 0.0484201937185184 2105 2897.81818181818 2794 0.00350153592558077 2103 1.251588684192 1.44312760062565 1 0.601586207423246 2103 3428 2344 2843 3453 2732 2152 2794 3937 3615 2475 2892 M18850 JIANG_VHL_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_VHL_TARGETS.html Genes up-regulated in 786-0 cells (renal carcinoma, RCC) upon expression of VHL [GeneID=7428] off a retroviral vector under normoxia (normal oxygen) condition. 12692265 103/212 John Newman 0.000234723965190781 0.000402604868551977 2795 2879.81818181818 2794 2.13408192971297e-05 2146 1.22009395802232 1.28611188345058 1 1.51414609419704 2794 2711 3463 2798 2605 4083 2235 2523 3266 2146 3054 2893 M8232 KEGG_LONG_TERM_DEPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LONG_TERM_DEPRESSION.html Long-term depression 17/94 KEGG 5.51623948037882e-07 3.30551127941881e-06 2860 2614 2795 5.01476442137367e-08 484 1.79980535714224 1.94111124603023 1 3.60566756340616 2856 1789 1642 1970 484 3597 2630 4662 2813 2795 3516 2894 M855 REACTOME_MAP_KINASE_ACTIVATION_IN_TLR_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MAP_KINASE_ACTIVATION_IN_TLR_CASCADE.html Genes involved in MAP kinase activation in TLR cascade 36/56 Reactome 5.61468916514929e-06 1.58592124339298e-05 4425 2792.36363636364 2795 5.10427590420475e-07 1481 1.23541366850653 -1.28989245328223 -1 2.16744162111187 4424 1831 3095 1487 1481 4390 3260 2795 2119 2437 3397 2895 M9152 BIOCARTA_CCR3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CCR3_PATHWAY.html CCR3 signaling in Eosinophils 17/52 BioCarta 0.00299230275285186 0.00436140923790476 4320 2934.27272727273 2796 0.000272398223931186 1893 1.61129366553776 -1.37913949276254 -1 1.39019146413251 4317 2367 2124 1893 3063 3412 3617 2273 2645 2796 3770 2896 M16523 REACTOME_GENERATION_OF_SECOND_MESSENGER_MOLECULES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GENERATION_OF_SECOND_MESSENGER_MOLECULES.html Genes involved in Generation of second messenger molecules 9/33 Reactome 3.48139394657334e-05 7.29924475778195e-05 3155 2501.90909090909 2796 3.48144848824307e-06 733 1.87369217458755 1.46255404177595 1 2.83317784502339 3154 1317 3973 1243 2126 3139 2796 3749 733 1240 4051 2897 M205 WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP.html Top up-regulated genes in pediatric adrenocortical tumors (ACT) compared to the normal tissue. 17234769 9/28 Arthur Liberzon 0.33296556889208 0.364210237121449 1725 3144.81818181818 2796 0.0396825396825397 1725 1.54032697607964 -0.684163046089497 -1 0.24697225960175 1725 2796 4105 2570 4074 2712 2565 3914 4002 3406 2724 2898 M19131 MAHADEVAN_RESPONSE_TO_MP470_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAHADEVAN_RESPONSE_TO_MP470_DN.html Bottom genes down-regulated in the GIST (gastrointestinal stromal tumor) cell line sensitive to imatinib [PubChem=5291] after treatment with MP470, a protein kinase inhibitor. 17325667 16/26 Arthur Liberzon 0.000202860936226325 0.000352468056046184 1705 2817.72727272727 2796 1.84436040318457e-05 1702 1.13894846398161 1.04723388071348 1 1.43749002063621 1702 3320 2824 3031 2564 2796 2571 2397 4151 2731 2908 2899 M4361 KEGG_PROXIMAL_TUBULE_BICARBONATE_RECLAMATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROXIMAL_TUBULE_BICARBONATE_RECLAMATION.html Proximal tubule bicarbonate reclamation 11/32 KEGG 0.00119100301648292 0.00182446555581528 3680 2634.09090909091 2797 0.000108331661176347 1009 2.18163489825259 -2.6080460448397 -1 2.18409659883386 3677 1843 1009 1991 2917 3541 4270 1745 3091 2094 2797 2900 M1777 ZHANG_GATA6_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_GATA6_TARGETS_UP.html Genes up-regulated after cre-lox knockout of GATA6 [GeneID=2627] in airway epithelium. 18536717 9/29 Jessica Robertson 0.0228121475020828 0.0298513608474616 2800 2720.90909090909 2799 0.00230497651282241 1331 2.69740034450088 2.91008466931297 1 1.50364292877032 2799 3165 4449 2641 3426 2602 3192 1701 1331 1818 2806 2901 M79 PID_TRAIL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TRAIL_PATHWAY.html TRAIL signaling pathway 18832364 17/31 Pathway Interaction Database 0.00017440224894119 0.000306775127078985 4100 2934.72727272727 2800 1.58560069087258e-05 1477 1.14492890798452 -0.862593478297117 -1 1.47027358521606 4098 1928 2581 1477 2536 2893 4104 4349 1720 2800 3796 2902 M2075 WHITFIELD_CELL_CYCLE_S http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_S.html Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the S phase of cell cycle. 12058064 123/285 Jessica Robertson 0.000357932673258522 0.000593514687505107 2730 2834.18181818182 2800 3.25446291800228e-05 1319 1.66843807055672 1.95352319055726 1 1.96775142161138 2730 2800 1319 2858 2703 4191 3212 2934 2628 2291 3510 2903 M234 PID_IL2_STAT5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL2_STAT5_PATHWAY.html IL2 signaling events mediated by STAT5 18832364 17/46 Pathway Interaction Database 0.0787516126854735 0.0965721401684667 3050 2908.18181818182 2801 0.00742913796829916 2144 1.15277913503639 -0.98349848356306 -1 0.427754691028389 3046 3286 2633 2719 3551 2144 2974 2721 3568 2801 2547 2904 M18227 BOYLAN_MULTIPLE_MYELOMA_PCA3_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_PCA3_UP.html Top up-regulated genes from principal component 3 (PCA3) which captures variation among different plasma cell tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609]. 17483317 42/124 Arthur Liberzon 3.42582643129288e-05 7.21502141889368e-05 2095 2830.45454545455 2801 3.11443616292164e-06 1762 1.27643324352021 1.25549536837694 1 1.93242450112691 3353 2071 2282 2094 2091 3761 2962 4048 2801 1762 3910 2905 M1636 YIH_RESPONSE_TO_ARSENITE_C3 http://www.broadinstitute.org/gsea/msigdb/cards/YIH_RESPONSE_TO_ARSENITE_C3.html Genes in cluster 3: delayed up-regulation in HFW cells (fibroblast) by sodium arsenite [PubChem=26435]. 12016162 18/51 John Newman 2.50218582423862e-05 5.49449052126624e-05 1675 2767.81818181818 2802 2.27474025771111e-06 1672 1.22054891551097 1.22054891551097 1 1.90060311569617 1672 4034 2802 4238 1988 2108 2161 2878 3646 2939 1980 2906 M4345 LIAN_LIPA_TARGETS_6M http://www.broadinstitute.org/gsea/msigdb/cards/LIAN_LIPA_TARGETS_6M.html Genes up-regulated at 6 months of age in lungs from LIPA [GeneID=3988] knockout mice, which display pulmonary pathology. 16127159 39/156 John Newman 1.90518379455499e-06 7.14787130607259e-06 3365 2748.36363636364 2804 1.73198676766556e-07 971 1.74255050506006 1.53176337652999 1 3.27762672198003 3365 2583 971 2611 1001 4037 3674 3359 2804 1559 4268 2907 M134 PID_TCR_RAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCR_RAS_PATHWAY.html Ras signaling in the CD4+ TCR pathway 18832364 5/17 Pathway Interaction Database 0.0456725716243132 0.058047645953765 2365 2946.81818181818 2805 0.00466393492890751 1472 0.676971934891053 -0.676971934891053 -1 0.305903226592205 2364 3201 3897 2805 3491 1472 2317 2321 4342 4299 1906 2908 M6349 SU_PLACENTA http://www.broadinstitute.org/gsea/msigdb/cards/SU_PLACENTA.html Genes up-regulated specifically in human placenta. 11904358 9/52 John Newman 3.91010519516811e-05 8.0930887564301e-05 3045 2593.18181818182 2805 3.91017399702379e-06 981 1.68133588223128 0.932254345198116 1 2.51476394705727 3041 981 4421 2872 2162 2939 2805 2179 1369 1816 3940 2909 M2561 HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_UP.html Genes distinguishing vincristine [PubChem=5978] resistant and sensitive ALL (B- and T-lineage ALL); here - genes up-regulated in the drug resistant samples. 15295046 18/41 Arthur Liberzon 0.000827643934726176 0.00129666983554893 1195 2533.36363636364 2805 7.52686781765366e-05 789 1.11979168458904 1.11979168458904 1 1.18175904114689 1191 3895 2805 3981 4612 871 815 1375 4072 3461 789 2910 M1798 JONES_TCOF1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/JONES_TCOF1_TARGETS.html Genes up-regulated in E8.5 embryos with heterozygous knockout of TCOF1 [GeneID=6949] compared to wild type. 18246078 2/5 Jessica Robertson 3.45687940025941e-05 7.26888289515353e-05 4070 2591.4 2806 3.84103612510449e-06 75 1.77039860477271 -1.76355639142255 -1 2.67816087381455 4069 912 4482 NA 2153 4397 4130 1152 75 1085 3459 2911 M19654 TOOKER_GEMCITABINE_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TOOKER_GEMCITABINE_RESISTANCE_UP.html Up-regulated genes in Calu3 cells (non-small cell lung cancer, NSCLC) resistant to gemcitabine [PubChem=3461] which became down-regulated in response to bexarotene [PubChem=82146]. 17483357 51/134 Jessica Robertson 9.27525223357667e-06 2.36860119708666e-05 4520 2925.18181818182 2806 8.43208303499192e-07 1662 1.27728311143899 -0.938819188048901 -1 2.15956291901312 4519 2768 2806 3236 1662 2446 2840 3322 2326 2004 4248 2912 M4470 BIOCARTA_EXTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EXTRINSIC_PATHWAY.html Extrinsic Prothrombin Activation Pathway 5/13 BioCarta 0.00115848791688667 0.0017793098585811 4310 2823.45454545455 2807 0.000115909230279129 955 1.36374780604345 -1.38236163270123 -1 1.37071219094016 4306 1472 3834 1811 2931 4496 2759 2807 955 1154 4533 2913 M477 BIOCARTA_GABA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GABA_PATHWAY.html Gamma-aminobutyric Acid Receptor Life Cycle 4/14 BioCarta 0.000560855553618741 0.000900674819827766 2750 3163.90909090909 2807 5.60997155447915e-05 1909 0.80259106418141 0.80259106418141 1 0.893433995700897 2748 1991 3838 2446 2807 3634 4467 1909 3978 4270 2715 2914 M607 REACTOME_PRE_NOTCH_EXPRESSION_AND_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PRE_NOTCH_EXPRESSION_AND_PROCESSING.html Genes involved in Pre-NOTCH Expression and Processing 20/53 Reactome 0.0109802097906176 0.0149616932476982 3240 2710.18181818182 2807 0.00100321800697229 1483 1.71020571831175 -1.05286553061093 -1 1.14086709596275 3240 3283 1891 4293 3386 2807 2122 1497 1483 2533 3277 2915 M12480 LINDSTEDT_DENDRITIC_CELL_MATURATION_B http://www.broadinstitute.org/gsea/msigdb/cards/LINDSTEDT_DENDRITIC_CELL_MATURATION_B.html Maturation of monocyte-derived dendritic cells (DC) in response to inflammatory stimuli: genes up-regulated both at 8 hr and 48 hr after the stimulation (cluster B). 12356685 30/83 Arthur Liberzon 0.0023097378878199 0.0034100289043239 1820 2611.18181818182 2808 0.000210196946153191 1458 1.4028760469976 -1.43145702608203 -1 1.2651740890369 1818 2808 3188 3121 3024 1458 1681 2435 3296 3650 2244 2916 M10395 DAIRKEE_TERT_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAIRKEE_TERT_TARGETS_UP.html Genes up-regulated in non-spontaneously immortalizing (NSI) primary breast cancer tumor cultures upon expression of TERT [GeneID=7015] off a retroviral vector. 17471242 275/574 Arthur Liberzon 7.08048899410958e-07 3.8227912014599e-06 2280 2613.09090909091 2809 6.43681024808916e-08 580 1.576911444257 1.9554827314628 1 3.12273440951982 2278 2442 3239 2349 580 4581 2870 2846 1739 3011 2809 2917 M19757 SHARMA_PILOCYTIC_ASTROCYTOMA_LOCATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHARMA_PILOCYTIC_ASTROCYTOMA_LOCATION_DN.html Genes down-regulated in pilocytic astrocytoma (PA) from supratentorial regions compared to the infratentorial PA tumors. 17283119 5/8 Jessica Robertson 0.000562654416010804 0.000902944723776242 2410 2644.18181818182 2809 5.62796927793519e-05 902 0.895999966395805 -0.603402446253122 -1 0.997057560583081 2408 902 4498 1818 2809 3045 4010 1513 3719 2913 1451 2918 M9577 MOOTHA_MITOCHONDRIA http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_MITOCHONDRIA.html Mitochondrial genes 12808457 286/573 Vamsi Mootha 0.000622571773109294 0.000992616754344364 1165 2857.09090909091 2810 5.66134566149215e-05 1161 1.17944036718978 -0.894839018284972 -1 1.29473877250737 1161 4421 3767 4277 2810 1330 1632 2667 3055 4225 2083 2919 M17770 BIOCARTA_CELLCYCLE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CELLCYCLE_PATHWAY.html Cyclins and Cell Cycle Regulation 11/30 BioCarta 0.514011397665828 0.550424453716195 2610 3229.09090909091 2812 0.0634920634920635 2306 1.45207462392387 -1.45207462392387 -1 0.137630445666578 2306 4082 2609 3478 4509 2496 2606 3746 4103 2812 2773 2920 M2036 BAUS_TFF2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BAUS_TFF2_TARGETS_DN.html Genes down-regulated in pyloric atrium with knockout of TFF2 [GeneID=7032]. 16121031 6/14 Arthur Liberzon 0.000569332688226429 0.000912100163086854 2835 2757.09090909091 2812 5.69478603712445e-05 1667 1.64733005006998 -1.45954608065557 -1 1.83049007394895 2832 1667 4607 2998 2812 1882 2419 3535 3349 2067 2160 2921 M1423 ABBUD_LIF_SIGNALING_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/ABBUD_LIF_SIGNALING_1_DN.html Genes down-regulated in AtT20 cells (pituitary cancer) after treatment with LIF [GeneID=3976]. 14576184 19/42 Kevin Vogelsang 6.78789153299104e-06 1.84181005927018e-05 3915 2640.90909090909 2814 6.17082952407057e-07 795 1.52041885080481 1.52181591581476 1 2.63135850496076 3915 1738 1883 3187 1542 3570 4281 795 2814 1117 4208 2922 M569 REACTOME_SHC1_EVENTS_IN_ERBB4_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC1_EVENTS_IN_ERBB4_SIGNALING.html Genes involved in SHC1 events in ERBB4 signaling 12/30 Reactome 0.0010413463437188 0.00161260706102653 3140 2249.81818181818 2815 9.47126891545364e-05 182 2.7148271500137 -1.95322526380809 -1 2.77108708732273 3136 2818 1923 309 2891 1012 2109 4592 182 2961 2815 2923 M2568 ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION http://www.broadinstitute.org/gsea/msigdb/cards/ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION.html Genes up-regulated in lung tissue upon LPS aspiration with mechanical ventilation (MV) compared to control (PBS aspiration without MV). 16116230 75/218 Jernej Godec 7.55157406938144e-07 3.99660067652382e-06 2815 2443.27272727273 2815 6.86506969225991e-08 599 1.31611395880455 -1.33468786862572 -1 2.59699136231345 2815 1256 1114 1833 599 3833 3240 4377 3196 803 3810 2924 M6659 FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP.html Genes up-regulated in monocyte-derived dendritic cells (MDDC) after stimulation with galecin-1 (lectin, LGALS1) [GeneID=3956] compared to that with bacterial lipopolysaccharide (LPS). 16785517 375/844 Arthur Liberzon 2.55596393975876e-07 2.19144534472488e-06 3300 2534.27272727273 2816 2.3236038515556e-08 215 1.36449002848747 1.47663582931975 1 2.82260418772756 3296 993 1762 2052 215 3998 2968 4667 2816 1125 3985 2925 M6384 LANDIS_ERBB2_BREAST_TUMORS_65_UP http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_TUMORS_65_UP.html Up-regulated genes from the 65 most significantly changed (p<0.01) genes identified by two analytical methods in the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 16/32 Leona Saunders 1.74313412017405e-05 4.01391964969808e-05 4195 2970.09090909091 2816 1.58467993796925e-06 1323 1.53762299177523 -1.85538774639387 -1 2.47098101268397 4191 2816 2250 2965 1887 4481 4568 2041 1323 1573 4576 2926 M906 REACTOME_AMINO_ACID_SYNTHESIS_AND_INTERCONVERSION_TRANSAMINATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINO_ACID_SYNTHESIS_AND_INTERCONVERSION_TRANSAMINATION.html Genes involved in Amino acid synthesis and interconversion (transamination) 13/20 Reactome 1.41837995819228e-05 3.36533087801975e-05 3485 2781.36363636364 2819 1.28944463893457e-06 1817 1.15946526881797 -1.14790721355347 -1 1.8957156534737 3483 1933 2937 2819 1817 2776 1955 3466 3033 2351 4025 2927 M119 PID_ERB_GENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERB_GENOMIC_PATHWAY.html Validated nuclear estrogen receptor beta network 18832364 12/50 Pathway Interaction Database 0.0131778991392503 0.0178061232314092 2025 3012.63636363636 2820 0.00120522750045276 1544 0.754618724154057 0.754618724154057 1 0.482551367832053 2023 2820 3280 4066 3780 2495 2809 1544 3591 4298 2433 2928 M524 REACTOME_ABCA_TRANSPORTERS_IN_LIPID_HOMEOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ABCA_TRANSPORTERS_IN_LIPID_HOMEOSTASIS.html Genes involved in ABCA transporters in lipid homeostasis 11/26 Reactome 0.0538926961917585 0.0678874124609086 4485 2868.09090909091 2820 0.00502363796416267 1053 2.8532357030446 -1.85517396161664 -1 1.2183669117281 4484 2520 1992 2398 3504 2698 3525 3235 1053 2820 3320 2929 M238 PID_THROMBIN_PAR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_THROMBIN_PAR1_PATHWAY.html PAR1-mediated thrombin signaling events 18832364 28/67 Pathway Interaction Database 5.33626414710608e-05 0.000106181459844327 3955 2922 2822 4.85126689688182e-06 2042 1.33816932558039 -1.22299984543175 -1 1.94380574864306 3953 2741 2042 2105 2225 3089 2822 4092 3371 2748 2954 2930 M19304 TESAR_ALK_TARGETS_HUMAN_ES_5D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_ALK_TARGETS_HUMAN_ES_5D_UP.html Genes up-regulated in hES cells (human embryonic stem cells) after treatment with the ALK [GeneID=238] inhibitor SB-431542 [PubChem=4521392]. 17597760 2/9 Jessica Robertson 0.000601491631012755 0.000960664547691128 3235 2692.2 2822 6.68502764956671e-05 768 1.53003930582573 1.53003930582573 1 1.6875583101267 3232 797 4360 NA 2843 3504 2801 3842 768 2164 2611 2931 M2460 KANG_GLIS3_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KANG_GLIS3_TARGETS.html Genes downregulated in the postnatal day 3 pancreata with impaired function of GLIS3 [GeneID=169792]. 19805515 12/49 Arthur Liberzon 0.0588028167444751 0.0738541943887993 2360 2861.27272727273 2822 0.00549418010391088 1209 1.33900934515671 1.19861489060981 1 0.553866792204516 2359 4003 2099 4468 3516 2822 1209 2504 3778 1603 3113 2932 M932 REACTOME_SYNTHESIS_SECRETION_AND_INACTIVATION_OF_GLP1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_SECRETION_AND_INACTIVATION_OF_GLP1.html Genes involved in Synthesis, Secretion, and Inactivation of Glucagon-like Peptide-1 (GLP-1) 11/25 Reactome 0.00179361263926416 0.00267841581503883 2295 2791.54545454545 2823 0.000163188782205844 2048 1.65839300501905 2.23685891404513 1 1.55918723770726 2293 2704 2415 3150 2999 2966 2314 3160 3835 2823 2048 2933 M17535 CAMPS_COLON_CANCER_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAMPS_COLON_CANCER_COPY_NUMBER_DN.html Genes from chromosomal copy number losses in a panel of 51 primary colon carcinoma samples. 18316590 55/215 Jessica Robertson 0.00463120501716375 0.00659429556682751 1755 2809.81818181818 2823 0.000421907542213939 1752 1.46610470068233 -1.12275935836038 -1 1.16870893894028 1752 2767 2069 2238 3124 2324 3224 4518 3138 2931 2823 2934 M2174 FIGUEROA_AML_METHYLATION_CLUSTER_5_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_5_DN.html Cluster 5 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 18/119 Arthur Liberzon 0.0134725236314193 0.0181727823076657 2980 2685.45454545455 2823 0.00123234018366661 1662 1.92056158292757 2.1033164080843 1 1.22191535133681 2976 3187 1723 2823 3293 3663 2506 1662 2246 2941 2520 2935 M832 REACTOME_ZINC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ZINC_TRANSPORTERS.html Genes involved in Zinc transporters 5/15 Reactome 0.0765897756730953 0.0944224385172651 3055 2802.72727272727 2824 0.00793650793650794 1810 2.21671639187365 2.21671639187365 1 0.830465086661121 3052 1811 4027 2824 4397 3219 2128 2501 1810 2891 2170 2936 M1056 REACTOME_VOLTAGE_GATED_POTASSIUM_CHANNELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_VOLTAGE_GATED_POTASSIUM_CHANNELS.html Genes involved in Voltage gated Potassium channels 10/43 Reactome 0.00410664503271229 0.00587595072466864 2410 2685.72727272727 2824 0.000374030074787598 972 1.33655289157383 1.37599127584369 1 1.08990779267084 2409 2824 2243 3453 3107 2743 2032 2962 3306 972 3492 2937 M14030 WEST_ADRENOCORTICAL_CARCINOMA_VS_ADENOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_CARCINOMA_VS_ADENOMA_UP.html Up-regulated genes in pediatric adrenocortical carcinoma (ACC) compared to the adenoma (ACA) tumors. 17234769 8/26 Jessica Robertson 0.0772580682013027 0.0951962418068115 2620 3081.18181818182 2825 0.00800832917257716 1126 1.41472256045833 1.41472256045833 1 0.528175146544548 2616 2825 4495 4285 3652 2652 1126 2243 3928 3314 2757 2938 M4000 TSUDA_ALVEOLAR_SOFT_PART_SARCOMA http://www.broadinstitute.org/gsea/msigdb/cards/TSUDA_ALVEOLAR_SOFT_PART_SARCOMA.html Protein kinase genes most significantly up-regulated in ASPS (alveolar soft part sarcoma) tumors compared to four other types of primitive sarcomas. 17283122 9/18 Jessica Robertson 8.44445490314181e-07 4.25034540022798e-06 2825 2479.81818181818 2825 8.44445811204035e-08 688 1.56333885494882 1.29387738153287 1 3.0695455252983 2825 1467 4499 1282 688 3210 2983 4078 1259 1823 3164 2939 M2113 KIM_ALL_DISORDERS_DURATION_CORR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_DURATION_CORR_DN.html Genes whose expression in brain significantly and negatively correlated with the duration of all psychiatric disorders studied. 18762803 97/208 Jessica Robertson 0.000490816110194783 0.000793912424015448 2035 2978.27272727273 2825 4.46296040558541e-05 1373 1.03718920172102 -0.799640760455274 -1 1.17535967642649 2032 3918 3725 4566 2767 1373 2209 2825 3271 4143 1932 2940 M252 PID_IL8_CXCR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL8_CXCR1_PATHWAY.html IL8- and CXCR1-mediated signaling events 18832364 18/52 Pathway Interaction Database 3.03770399907414e-05 6.50579567626207e-05 3170 2808.54545454545 2826 2.7615872215714e-06 2054 1.12578893661625 1.01971421124269 1 1.72285221473651 3168 2897 2448 2485 2054 2826 2203 2577 2969 3452 3815 2941 M1015 REACTOME_INHIBITION_OF_REPLICATION_INITIATION_OF_DAMAGED_DNA_BY_RB1_E2F1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INHIBITION_OF_REPLICATION_INITIATION_OF_DAMAGED_DNA_BY_RB1_E2F1.html Genes involved in Inhibition of replication initiation of damaged DNA by RB1/E2F1 6/13 Reactome 0.0765897756730953 0.0944224385172651 2470 2957.63636363636 2826 0.00793650793650794 2231 1.8818988242565 -1.8818988242565 -1 0.705029869992099 2469 2527 4072 2928 4200 2246 2826 2744 3243 3048 2231 2942 M10336 OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_DN http://www.broadinstitute.org/gsea/msigdb/cards/OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_DN.html Genes down-regulated in epithelial ovarian cancer (EOC) biopsies: invasive (TOV) vs low malignant potential (LMP) tumors. 15940270 11/15 Leona Saunders 0.0108818170627267 0.0148362510200574 2365 2829.63636363636 2826 0.000994183389163236 1593 1.76568178483752 -1.76568178483752 -1 1.18023478613593 2365 4111 3053 3832 3258 2112 4001 1593 2163 2826 1812 2943 M917 BIOCARTA_COMP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_COMP_PATHWAY.html Complement Pathway 12/24 BioCarta 0.00248399245216111 0.00365692385511372 2670 2786.54545454545 2828 0.000226072867120416 1631 1.30078668376319 1.41779207712256 1 1.15867117670388 2666 1745 1631 2828 3034 3136 3757 2222 3880 2959 2794 2944 M1160 MARKS_ACETYLATED_NON_HISTONE_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/MARKS_ACETYLATED_NON_HISTONE_PROTEINS.html Non-histone proteins that are acetylated. 17322921 11/27 Leona Saunders 0.0013355902049396 0.00203002779771228 4495 2781.72727272727 2828 0.000121491064860619 202 3.72033399346286 -1.8818988242565 -1 3.6614792113773 4495 2625 1915 2230 2941 3679 3422 2303 202 2828 3959 2945 M10024 WENDT_COHESIN_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WENDT_COHESIN_TARGETS_UP.html Cohesin targets identified by ChIP-chip which were up-regulated after knockdown of CTCF and RAD21 [GeneID=10664;5885] by RNAi. 18235444 21/49 Jessica Robertson 0.00409707319939477 0.00586583715623707 1340 2671.63636363636 2828 0.000373156650547672 1109 1.96572711309629 1.96572711309629 1 1.6035128808332 1336 4674 2828 3369 4095 1480 1338 2118 3874 3167 1109 2946 M1016 REACTOME_SYNTHESIS_OF_VERY_LONG_CHAIN_FATTY_ACYL_COAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_VERY_LONG_CHAIN_FATTY_ACYL_COAS.html Genes involved in Synthesis of very long-chain fatty acyl-CoAs 9/15 Reactome 0.000235352310275374 0.000403534916191146 4590 2689.90909090909 2829 2.35377239810841e-05 58 1.69576384267296 -0.624105792934294 -1 2.10383497606192 4588 1620 4074 1688 2622 3140 2829 2218 58 3404 3348 2947 M1214 PATTERSON_DOCETAXEL_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/PATTERSON_DOCETAXEL_RESISTANCE.html Genes up-regulated in DU145-RD cells (prostate cancer) resistant to docetaxel [PubChem=148124] vs the parental, docetaxel-sensitive cells. 16652143 27/80 Arthur Liberzon 0.0176028732978581 0.0233409915885012 3695 2920.09090909091 2829 0.00161321068065046 1673 1.8009019683022 -2.1413552731492 -1 1.07423111667823 3691 2235 1673 1975 3338 2772 3966 3757 2829 2636 3249 2948 M14772 NOJIMA_SFRP2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NOJIMA_SFRP2_TARGETS_UP.html Cellular proliferation, growth, apoptosis and Wnt signaling genes up-regulated in SNU638 cells (gastric cancer) by overexpression of SFRP2 [GeneID=6423] off a plasmid vector. 17297461 23/48 Arthur Liberzon 5.50027349765657e-05 0.000109120582599571 3170 2915.81818181818 2830 5.00037365104109e-06 1531 1.63865768948337 1.77305731785626 1 2.3731882606034 3169 3840 1705 1531 2235 4233 4482 2969 2785 2295 2830 2949 M16858 OSMAN_BLADDER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/OSMAN_BLADDER_CANCER_DN.html Genes down-regulated in blood samples from bladder cancer patients. 16740760 300/764 Leona Saunders 0.000690226661394301 0.00109270342408571 2240 2662.27272727273 2831 6.27675734410714e-05 443 1.20051748367452 -1.06533182136645 -1 1.2995683874262 2239 3875 3749 3281 2831 443 1857 2601 3272 4179 958 2950 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 0.00699893779985249 0.00976126442132235 1315 2645.72727272727 2833 0.000702107931753298 631 2.02769529075671 2.02769529075671 1 1.49013188382675 1313 3258 4480 4123 3403 1205 631 2833 3923 2683 1251 2951 M19618 ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_UP http://www.broadinstitute.org/gsea/msigdb/cards/ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_UP.html Hepatic graft versus host disease (GVHD), day 35: genes up-regulated in allogeneic vs syngeneic bone marrow transplant. 12663442 86/220 Arthur Liberzon 3.32963159581342e-05 7.04090869042494e-05 2995 2669.18181818182 2833 3.0269836271092e-06 1178 1.55321348880154 -1.43741961005921 -1 2.3574722166351 2995 1818 1178 2036 2081 3852 2901 4018 2833 1648 4001 2952 M5053 EHRLICH_ICF_SYNDROM_UP http://www.broadinstitute.org/gsea/msigdb/cards/EHRLICH_ICF_SYNDROM_UP.html Up-regulated in B lymphocytes from patients with ICF syndrom caused by mutations in DNMT3B [GeneID=1789] compared to normals. 11741835 11/23 John Newman 5.11720293508999e-05 0.000102256771658131 2625 2885.54545454545 2834 4.65211087743149e-06 1950 1.65714317446686 1.5052269096367 1 2.41705032637329 2621 3099 2011 4048 2212 1950 2054 4528 3427 2834 2957 2953 M7102 BILD_CTNNB1_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/BILD_CTNNB1_ONCOGENIC_SIGNATURE.html Genes selected in supervised analyses to discriminate cells expressing activated beta-catenin (CTNNB1) [GeneID=1499] oncogene from control cells expressing GFP. 16273092 42/126 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2560 2896.63636363636 2834 0.00793650793650794 1763 1.60128121181502 1.64221423623043 1 0.59417760956763 2560 3212 2834 2845 4046 1763 2080 3915 2734 3234 2640 2954 M4090 BOYAULT_LIVER_CANCER_SUBCLASS_G3_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G3_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G3, defined by unsupervised clustering. 17187432 27/77 Yujin Hoshida 1.22755152924927e-05 2.98510973848576e-05 2835 2721 2835 1.11596216251804e-06 1197 1.45108156892814 1.54601636977927 1 2.40012284055597 2835 1197 1290 2361 1761 3899 4261 3488 3221 1733 3885 2955 M11756 WOTTON_RUNX_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WOTTON_RUNX_TARGETS_UP.html Common target genes up-regulated by all three Runx family members (RUNX1, RUNX2, and RUNX3 [GeneID=861;860;864]) in MEF cells (embryonic fibroblasts). 18560354 15/31 Jessica Robertson 0.00153573494499276 0.00230655575392182 2380 2651.72727272727 2836 0.000139709821003874 1698 1.30280478963579 1.6018728072311 1 1.25578318155265 2377 1698 2513 2836 2979 2876 3125 1797 2784 3261 2923 2956 M3624 KEGG_GLYCOSAMINOGLYCAN_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_DEGRADATION.html Glycosaminoglycan degradation 12/28 KEGG 0.0869272450955402 0.0999364746118011 2675 3021.27272727273 2837 0.00823316700699306 1883 1.5167945681009 1.5167945681009 1 0.554582104912441 2674 2671 3061 4213 3566 2334 1883 2665 3722 3608 2837 2957 M2333 KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION.html Pathogenic Escherichia coli infection 52/116 KEGG 5.49511152673673e-06 1.56061167359323e-05 4610 2573.90909090909 2837 4.9955684112302e-07 440 2.06667699137858 -1.91887596607327 -1 3.63110943085687 4609 2837 1384 558 1472 3668 4047 3321 440 2764 3213 2958 M838 REACTOME_UNBLOCKING_OF_NMDA_RECEPTOR_GLUTAMATE_BINDING_AND_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_UNBLOCKING_OF_NMDA_RECEPTOR_GLUTAMATE_BINDING_AND_ACTIVATION.html Genes involved in Unblocking of NMDA receptor, glutamate binding and activation 7/19 Reactome 0.0509621599563828 0.0644383922168403 1560 2588.45454545455 2838 0.00521700467152153 1185 1.08724643494519 1.08724643494519 1 0.473267014849408 1557 2212 4028 2838 3528 1335 1185 2894 3945 3197 1754 2959 M13746 ZHAN_MULTIPLE_MYELOMA_HP_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_HP_UP.html Top 50 up-regulated genes in cluster HP of multiple myeloma samples characterized by a hyperploid signature. 16728703 34/96 Kevin Vogelsang 0.00554994809942842 0.00782637881249521 2235 2518.90909090909 2839 0.000505818056588234 1809 1.57282212053877 2.0299147321174 1 1.21101012274665 2231 3055 2864 3028 3155 2849 2839 1934 1809 1928 2016 2960 M11763 MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP.html Genes commonly up-regulated in SK-N-BE cells (neuroblastoma) after RNAi knockdown of CCND1 and CDK4 [GeneID=595;1019]. 18413728 63/136 Jessica Robertson 0.000723006123860531 0.00114112721334134 4470 2960.81818181818 2839 6.57494401232981e-05 1382 1.59526743284082 2.0222315159266 1 1.7159068641806 4468 1822 1382 1964 2839 3095 4364 3849 2698 1543 4545 2961 M711 REACTOME_ENOS_ACTIVATION_AND_REGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENOS_ACTIVATION_AND_REGULATION.html Genes involved in eNOS activation and regulation 14/31 Reactome 3.63299816638875e-06 1.13874444198647e-05 2840 2625.27272727273 2840 3.30273105981878e-07 1297 1.31162921625412 1.67659527049527 1 2.3701255277572 2840 2952 2409 2481 1297 2872 2332 3028 3207 3145 2315 2962 M4235 GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_DN.html Genes down-regulated in quiescent CD34+ [GeneID=8842] cells isolated from peripheral blood of normal donors compared to the dividing cells from CML (chronic myeloid leukemia) patients. 17717066 78/196 Arthur Liberzon 0.000238960064968213 0.000409271514781084 3460 2877.81818181818 2841 2.17260022118785e-05 1206 1.54838339201918 1.58252528577563 1 1.91751901691228 3460 2331 1206 1976 2607 4401 3417 3085 2618 2841 3714 2963 M6244 OHM_EMBRYONIC_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/OHM_EMBRYONIC_CARCINOMA_UP.html Genes with a high basal transcription state in undifferentiated embryonic carcinoma cells. 17211412 7/14 Leona Saunders 0.000312837702105641 0.000523743291199368 2345 2575.45454545455 2841 3.12881751175893e-05 100 5.05471798239466 5.05471798239466 1 6.06187153990093 2343 2827 4300 2925 4530 2841 2906 796 100 3202 1560 2964 M1336 RANKIN_ANGIOGENIC_TARGETS_OF_VHL_HIF2A_UP http://www.broadinstitute.org/gsea/msigdb/cards/RANKIN_ANGIOGENIC_TARGETS_OF_VHL_HIF2A_UP.html Angiogenic genes up-regulated in hepatocytes after knockout of VHL and HIF2A [GeneID=7428;2034]. 18490920 5/13 Jessica Robertson 0.000661455990232041 0.00105034997296759 4020 2530.90909090909 2841 6.61652958563595e-05 1016 2.04016502500758 -2.07017297238887 -1 2.22129557972693 4018 1323 4321 1813 2841 3086 3023 1318 1016 1166 3915 2965 M114 CHEOK_RESPONSE_TO_HD_MTX_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_HD_MTX_UP.html Genes specifically up-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by high-dose methotrexate (HDMTX) [PubChem=4112]. 12704389 11/79 Jean Junior 0.0487431387403657 0.0617492155007715 2410 2773.81818181818 2841 0.00453252939374269 1858 1.96402083131008 1.85515690801605 1 0.868208457222481 2406 2875 1858 2841 3487 2993 2270 3269 3757 2107 2649 2966 M897 REACTOME_BIOSYNTHESIS_OF_THE_N_GLYCAN_PRECURSOR_DOLICHOL_LIPID_LINKED_OLIGOSACCHARIDE_LLO_AND_TRANSFER_TO_A_NASCENT_PROTEIN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BIOSYNTHESIS_OF_THE_N_GLYCAN_PRECURSOR_DOLICHOL_LIPID_LINKED_OLIGOSACCHARIDE_LLO_AND_TRANSFER_TO_A_NASCENT_PROTEIN.html Genes involved in Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein 18/32 Reactome 0.00317676755836532 0.00460449513717906 1290 2570.45454545455 2842 0.000289214914432065 845 0.591521019712331 -0.591521019712331 -1 0.505259300836345 1286 2842 3596 3991 3073 845 922 2132 3700 4416 1472 2967 M9251 SILIGAN_TARGETS_OF_EWS_FLI1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/SILIGAN_TARGETS_OF_EWS_FLI1_FUSION_UP.html Genes bound by EWSR1-FLT1 [GeneID=2130;2321] fusion and up-regulated in STA-ET-7.2 cells (Ewing's sarcoma) after knockdown of EWSR1-FLT1 by RNAi. 15735734 10/24 Arthur Liberzon 0.000733697113939959 0.00115644287787509 3555 2975 2842 6.67219922972617e-05 1197 1.6957349376499 -1.67739227679168 -1 1.82038312572263 3555 2823 1957 3576 2842 2967 1197 4193 2732 2704 4179 2968 M19251 TIEN_INTESTINE_PROBIOTICS_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_6HR_UP.html Genes up-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 6h. 16394013 47/131 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2815 2903.09090909091 2843 0.00793650793650794 1193 2.56643359454185 -1.66133768761767 -1 0.952310792633759 2811 4022 2818 1982 4322 3358 2935 2513 1193 3137 2843 2969 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 0.0839184282471183 0.0965721401684667 3430 2662.27272727273 2843 0.00793650793650794 295 2.96177939451234 -0.895654950647659 -1 1.09900933712187 3430 2641 1413 2184 3659 3573 2843 2569 295 2970 3708 2970 M19232 EPPERT_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/EPPERT_PROGENITOR.html Genes up-regulated in human hematopoietic lineage committed progenitor cells versus hematopoietic stem cells (HSC) and mature cells. 21873988 78/189 Kolja Eppert 0.0308341784228848 0.0397712524331512 2210 2927.45454545455 2843 0.00284318277228706 1754 1.32401141429424 -0.900727795682544 -1 0.677754814690695 2209 3879 2366 3536 3599 3411 2792 1754 3043 2843 2770 2971 M11262 MORI_IMMATURE_B_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_IMMATURE_B_LYMPHOCYTE_UP.html Up-regulated genes in the B lymphocyte developmental signature based on expression profiling of lymphomas from the Emu-myc transgenic mice: the immature B stage. 18922927 43/84 Jessica Robertson 3.98557336734982e-05 8.22638444965794e-05 2905 2771 2844 3.62331415708644e-06 1913 1.49851473210911 -1.45514383662803 -1 2.23743335216131 2901 1913 2289 2844 2135 2464 3231 3901 3245 2542 3016 2972 M1525 ZHENG_RESPONSE_TO_ARSENITE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_RESPONSE_TO_ARSENITE_DN.html Down-regulated in HEK293 cells (kidney epithelium) by treatment with sodium arsenite [PubChem=26435]. 12679051 10/29 John Newman 0.232850105696956 0.258012673278774 2845 3009.81818181818 2845 0.0238095238095238 2127 1.53561774604294 -1.53561774604294 -1 0.330251457745051 2845 2127 2807 3297 3991 2304 2994 2544 3878 3493 2828 2973 M11837 RODWELL_AGING_KIDNEY_NO_BLOOD_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODWELL_AGING_KIDNEY_NO_BLOOD_DN.html Genes whose expression decreases with age in normal kidney, excluding those with higher expression in blood. 15562319 84/251 John Newman 0.000146286213712273 0.00026084368244129 4305 2984.72727272727 2845 1.32996310667626e-05 1473 1.64323932918027 -1.62185076127664 -1 2.15249416883025 4304 2533 2104 1473 2499 3702 3891 3778 1700 2845 4003 2974 M8334 ZEMBUTSU_SENSITIVITY_TO_DOXORUBICIN http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_DOXORUBICIN.html Top genes associated with chemosensitivity to doxorubicin [PubChem=31703] across 85 tumor xenografts. 11809704 12/24 Arthur Liberzon 0.131939688154985 0.150174733712475 2255 2784.18181818182 2845 0.0127807223896124 1886 1.7089385501971 1.7089385501971 1 0.51434936626015 2252 1886 2596 2918 3966 2962 2845 2188 3838 2978 2197 2975 M14050 KORKOLA_CHORIOCARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_CHORIOCARCINOMA_UP.html Genes from the 12p region that were up-regulated in choriocarcinoma cells compared to normal testis. 16424014 5/17 Arthur Liberzon 0.0001215721401556 0.000220467124136665 2745 2831.45454545455 2846 1.21578791571104e-05 1108 1.85815754819823 -0.58371703941372 -1 2.48362435249382 2744 3349 4108 3575 2485 2846 2455 2550 1108 2894 3032 2976 M0 BROWNE_HCMV_INFECTION_30MIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_30MIN_DN.html Genes down-regulated in primary fibroblast cell culture at 30 min time point after infection with HCMV (AD169 strain). 11711622 95/317 Arthur Liberzon 8.13182062526981e-06 2.12762207984446e-05 4385 2957.09090909091 2846 7.39259152993489e-07 1620 1.40025462582023 1.55891840483771 1 2.39132667484492 4385 2042 1797 2530 1620 3302 3959 3432 2846 2794 3821 2977 M1036 REACTOME_INNATE_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INNATE_IMMUNE_SYSTEM.html Genes involved in Innate Immune System 150/416 Reactome 1.79345388210517e-05 4.11563412906212e-05 2790 2628.27272727273 2847 1.63042591147387e-06 1485 1.26920751481793 -1.31329003091989 -1 2.03459167438975 2790 2973 2847 3215 1896 1485 3475 2210 3195 3072 1753 2978 M1883 BOYAULT_LIVER_CANCER_SUBCLASS_G1_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G1_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G1, defined by unsupervised clustering 17187432 26/75 Yujin Hoshida 0.000105621891720114 0.000193715923522682 2995 2843.45454545455 2849 9.6024511784362e-06 1929 1.7528626569618 -1.39141777902826 -1 2.37888118291249 2991 3602 2849 3477 2428 1929 2830 2924 2716 3032 2500 2979 M892 REACTOME_SYNTHESIS_OF_SUBSTRATES_IN_N_GLYCAN_BIOSYTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_SUBSTRATES_IN_N_GLYCAN_BIOSYTHESIS.html Genes involved in Synthesis of substrates in N-glycan biosythesis 6/18 Reactome 0.0133131890491591 0.0179682038837441 2360 2981.27272727273 2850 0.00133936265577439 1621 0.413279055215559 -0.413279055215559 -1 0.263682517027115 2356 2850 4047 3465 3302 1621 2198 2319 4209 4413 2014 2980 M12948 CHUANG_OXIDATIVE_STRESS_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHUANG_OXIDATIVE_STRESS_RESPONSE_DN.html Genes down-regulated in MCF7 cells (breast cancer) after treatment with the oxydants: hydrogen peroxyde, menadione, and t-butyl hydroperoxyde [PubChem=784;4055;6410]. 12414654 17/38 John Newman 0.000809143053228058 0.00127151051221552 4620 3132.36363636364 2850 7.35855275577815e-05 1296 1.45370789100649 -1.05518540161294 -1 1.53867526124122 4616 2478 1296 1748 2850 3982 4658 4128 2342 2217 4141 2981 M1589 ZHENG_RESPONSE_TO_ARSENITE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_RESPONSE_TO_ARSENITE_UP.html Up-regulated in HEK293 cells (kidney epithelium) by treatment with sodium arsenite [PubChem=26435]. 12679051 18/33 John Newman 0.0876145793398271 0.100677272875534 1775 2821.18181818182 2850 0.00830106049806034 1773 0.777976880611034 -0.764739268283389 -1 0.283537796414467 1773 2079 3043 2186 3568 2270 2850 2698 3800 3878 2888 2982 M921 REACTOME_IL_RECEPTOR_SHC_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_RECEPTOR_SHC_SIGNALING.html Genes involved in Interleukin receptor SHC signaling 15/37 Reactome 0.0113330684748366 0.0154156048978474 2840 3165.90909090909 2853 0.00103562492068785 2504 0.977612485639954 -0.984139914792292 -1 0.647520664121802 2839 2844 2987 2853 3266 2504 4642 2816 4021 3255 2798 2983 M13123 LEE_LIVER_CANCER_HEPATOBLAST http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_HEPATOBLAST.html Fig.5, Supplementary Fig.2 Genes overexpressed in human hepatocellular carcinoma with hepatoblast property 16532004 9/21 Yujin Hoshida 7.58944278593627e-05 0.000145218982829307 3445 3003 2853 7.5897019967838e-06 1650 2.29906434438922 2.10174250022254 1 3.22531918682249 3441 3520 4567 2005 2350 3925 2774 2853 1650 1824 4124 2984 M3412 BIOCARTA_CACAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CACAM_PATHWAY.html Ca++/ Calmodulin-dependent Protein Kinase Activation 9/15 BioCarta 0.0148281415631735 0.0198754780792423 1735 2960.63636363636 2854 0.00149280240623778 1600 0.99055872784057 0.99055872784057 1 0.616137992880459 1735 2792 3820 4348 3937 1974 2854 1600 3889 3394 2224 2985 M12517 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_DN.html Genes from the blue module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 42/73 Arthur Liberzon 0.0013814635204481 0.00209093606486427 2905 2859.45454545455 2855 0.000125666523382957 2121 1.30293816417916 -1.17740284715648 -1 1.27621141991539 2902 2303 2386 2564 2954 3515 2121 2718 3407 2855 3729 2986 M1035 REACTOME_MYD88_MAL_CASCADE_INITIATED_ON_PLASMA_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MYD88_MAL_CASCADE_INITIATED_ON_PLASMA_MEMBRANE.html Genes involved in MyD88:Mal cascade initiated on plasma membrane 55/113 Reactome 9.18394596018721e-05 0.000171117179997762 3175 2756 2856 8.3493903348525e-06 1836 1.21438738694784 -1.23947676436058 -1 1.67200767367995 3172 2856 3344 2189 2386 1836 4223 2078 3030 3233 1969 2987 M1869 VILIMAS_NOTCH1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VILIMAS_NOTCH1_TARGETS_UP.html Genes up-regulated in bone marrow progenitors by constitutively active NOTCH1 [GeneID=4851]. 17173050 22/80 Jessica Robertson 1.7781553800572e-05 4.0825262670005e-05 3210 2871.27272727273 2856 1.61651795654924e-06 1894 1.43199551082978 1.57436428942018 1 2.2973835882978 3208 2120 2013 2478 1894 4315 4036 3458 2856 2193 3013 2988 M1440 WANG_TARGETS_OF_MLL_CBP_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_TARGETS_OF_MLL_CBP_FUSION_UP.html Top 50 genes up-regulated in granulocyte/macrophage progenitors (GMP) upon expression of MLL-CBP fusion [GeneID=4297;1387]. 15635450 26/77 Kevin Vogelsang 9.08938794852693e-05 0.00016949013898447 2650 2831.36363636364 2857 8.26342136540585e-06 2048 1.68846592032997 1.6061312552883 1 2.32729505908605 2648 3839 2048 3098 2383 3762 2857 2315 2900 2075 3220 2989 M6355 BIOCARTA_ECM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ECM_PATHWAY.html Erk and PI-3 Kinase Are Necessary for Collagen Binding in Corneal Epithelia 23/51 BioCarta 0.000591156388664202 0.000945446702143498 2860 2966.72727272727 2858 5.375593605204e-05 1446 1.39727785867889 -1.29921474997334 -1 1.54467079800211 2858 2161 2663 1446 2799 3532 3346 4547 2142 3706 3434 2990 M156 PID_ECADHERIN_NASCENT_AJ_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ECADHERIN_NASCENT_AJ_PATHWAY.html E-cadherin signaling in the nascent adherens junction 18832364 36/73 Pathway Interaction Database 4.27804240910374e-07 2.82882663468366e-06 4425 2534.27272727273 2859 3.88913021908819e-08 392 1.2513177617835 -1.02007214481409 -1 2.53778091434927 4422 1280 2539 1148 392 3057 4477 3224 1274 2859 3205 2991 M1452 NEMETH_INFLAMMATORY_RESPONSE_LPS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NEMETH_INFLAMMATORY_RESPONSE_LPS_DN.html Genes down-regulated in RAW 264.7 cells (macrophage) 3 hr after stimulation with bacterial lipopolysaccharide (LPS). 12766259 29/60 Kevin Vogelsang 0.0839184282471183 0.0965721401684667 2280 2911.90909090909 2859 0.00793650793650794 2033 1.73768026129272 1.756375823289 1 0.644790369408338 2276 4233 2033 2058 3592 3819 2859 2271 3143 2784 2963 2992 M2169 FIGUEROA_AML_METHYLATION_CLUSTER_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_3_DN.html Cluster 3 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 48/108 Arthur Liberzon 0.00520285239880231 0.00735906016926882 2860 2810.81818181818 2859 0.000474108880831036 1681 1.41586935239467 1.68872406789281 1 1.10400097043021 2859 2581 1907 1681 3146 3605 2275 3803 3014 2853 3195 2993 M13103 KEGG_AUTOIMMUNE_THYROID_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AUTOIMMUNE_THYROID_DISEASE.html Autoimmune thyroid disease 24/87 KEGG 0.0839184282471183 0.0965721401684667 2505 2883.27272727273 2861 0.00793650793650794 1833 1.73087988766555 -1.74463954602475 -1 0.642266996419034 2505 3282 2254 2574 4131 1833 2861 3829 3192 2870 2385 2994 M2178 FIGUEROA_AML_METHYLATION_CLUSTER_6_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_6_DN.html Cluster 6 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 10/107 Arthur Liberzon 0.126746994252748 0.144334487258415 2780 3381.72727272727 2861 0.0122453132660188 1898 0.381600743476907 0.53180953743361 1 0.11725551600755 2780 4344 2861 4588 4677 2230 1898 2176 4522 4667 2456 2995 M286 PID_TGFBR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TGFBR_PATHWAY.html TGF-beta receptor signaling 18832364 43/85 Pathway Interaction Database 0.000157154996918167 0.000278422803613811 4180 3015.45454545455 2862 1.42878385695564e-05 1366 1.86237074912483 1.90699354811519 1 2.42025462327263 4180 4139 2425 1600 2512 2862 4085 3356 1366 2541 4104 2996 M1418 KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_UP http://www.broadinstitute.org/gsea/msigdb/cards/KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_UP.html Up-regulated genes predicting response of patients with hepatocellular carcinoma (HCC) to combination chemotherapy with 5-fluorouracil (5-FU) [PubChem=3385] and IFN1@ [GeneID=3438]. 15447987 12/15 Yujin Hoshida 0.0365885586659454 0.0468837806695708 2865 3034.81818181818 2862 0.00338287503750562 1800 1.09316291097368 -1.09316291097368 -1 0.531033262330739 2862 3429 2742 4134 3571 2369 2573 1800 3890 3620 2393 2997 M10850 CHUNG_BLISTER_CYTOTOXICITY_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHUNG_BLISTER_CYTOTOXICITY_DN.html Genes down-regulated in blister cells from patients with adverse drug reactions (ADR). 19029983 46/120 Jessica Robertson 0.0839184282471183 0.0965721401684667 1590 2972.36363636364 2862 0.00793650793650794 1587 1.33454571808858 -1.39293767363052 -1 0.495201703674846 1587 4098 2862 3611 3699 2117 2542 2575 3631 3884 2090 2998 M6787 SCIBETTA_KDM5B_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCIBETTA_KDM5B_TARGETS_DN.html Genes down-regulated in HB2 cells (mammary epithelium) upon expression of KDM5B [GeneID=10765] off an adenoviral vector. 17709396 55/109 Leona Saunders 0.000157684697339023 0.000279255665809019 3580 3227.63636363636 2863 1.43360000456584e-05 1793 1.74353280563867 1.85298454627098 1 2.26499137973587 3577 3957 1793 2716 2513 4603 3967 2863 2368 2585 4562 2999 M9719 CAVARD_LIVER_CANCER_MALIGNANT_VS_BENIGN http://www.broadinstitute.org/gsea/msigdb/cards/CAVARD_LIVER_CANCER_MALIGNANT_VS_BENIGN.html Genes identified by subtractive hybridization comparing malignant and benign components of a hepatocellular carcinoma (HCC) in a pre-existing liver adenoma in a morphologically normal liver. 16314847 35/108 Arthur Liberzon 0.000866006974238898 0.00135315394507618 3700 2406.54545454545 2864 7.87589142549343e-05 753 2.62933038433943 3.41056024050109 1 2.75703574616213 3699 2916 995 1094 2864 3892 4502 1329 753 1310 3118 3000 M1911 OKUMURA_INFLAMMATORY_RESPONSE_LPS http://www.broadinstitute.org/gsea/msigdb/cards/OKUMURA_INFLAMMATORY_RESPONSE_LPS.html Genes up-regulated in mast cells (MC) after stimulation with a bacterial lipopolysaccharide (LPS). 12855579 125/375 Kate Stafford 2.843623425436e-05 6.13782559723311e-05 4100 3121 2864 2.58514561957204e-06 1541 1.70420899877209 1.91356204032258 1 2.62378936502915 4100 3988 1541 3474 2030 2702 4536 2864 2539 2143 4414 3001 M3206 SANCHEZ_MDM2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SANCHEZ_MDM2_TARGETS.html Genes up-regulated in BJ cells (forskin fibroblasts) upon overexpression of the most abundant alternative splicing forms of MDM2 [GeneID=4193], HDM2-A and HDM2-B, off a retroviral vector. 16331255 25/48 Arthur Liberzon 0.232850105696956 0.258012673278774 1310 2937.36363636364 2866 0.0238095238095238 1306 1.19902720028303 -1.09061206483159 -1 0.257863964639012 1306 2866 2406 2392 3860 2522 2916 3895 3904 3434 2810 3002 M1792 WILSON_PROTEASES_AT_TUMOR_BONE_INTERFACE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WILSON_PROTEASES_AT_TUMOR_BONE_INTERFACE_UP.html Protease genes up-regulated at tumor-bone interface compared to the tumor alone area. 18632634 15/35 Jessica Robertson 0.0278588950871783 0.0360825821941728 1960 2891.81818181818 2866 0.00256527816282086 835 1.61727154504754 1.61727154504754 1 0.852862357539053 1958 4401 2866 4320 3866 1500 835 2809 4124 3265 1866 3003 M2221 ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP.html Genes up-regulated in K562 cells (lymphoblast) by MYC [GeneID=4609] in the presence of CKN1B [GeneID=1027]. 18838534 51/112 Arthur Liberzon 0.000350367967536863 0.000582620403079396 4070 3071.81818181818 2866 3.1856707176487e-05 1927 1.40756251803811 -1.12532068477704 -1 1.66421505819745 4066 2335 2508 3624 2695 2866 3448 3495 1927 2649 4177 3004 M1908 BIOCARTA_FCER1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FCER1_PATHWAY.html Fc Epsilon Receptor I Signaling in Mast Cells 24/61 BioCarta 0.00468630473753705 0.0066666739526711 2675 2822 2867 0.00042693791702563 1852 1.41717024892412 -1.15099536242409 -1 1.12724491834781 2672 3281 2624 1852 3127 2027 3708 3426 2867 2871 2587 3005 M2601 WARTERS_IR_RESPONSE_5GY http://www.broadinstitute.org/gsea/msigdb/cards/WARTERS_IR_RESPONSE_5GY.html Genes up-regulated in the human skin cells at 4 h after exprosure to 5 Gy dose of ionizing radiation. 19580510 30/90 Itai Pashtan 0.00131018035075499 0.00199528928295024 3935 3007.81818181818 2867 0.000119178296560823 1858 1.45358982006829 -0.961897974985679 -1 1.4345772616159 3934 2809 2176 2619 2939 3071 4475 2742 1858 2867 3596 3006 M8023 MARKS_HDAC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARKS_HDAC_TARGETS_UP.html Genes whose transcription is up-regulated by histone deacetylase inhibitors. 17322921 31/53 Arthur Liberzon 0.00089407330300173 0.00139468292205929 4655 3051.63636363636 2870 8.13124416849324e-05 878 1.83575365623178 1.98632897149204 1 1.91610606423073 4655 2310 1760 1845 2870 3778 4296 4574 878 2038 4564 3007 M19622 LEONARD_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/LEONARD_HYPOXIA.html Genes up-regulated in HK-2 cells kidney tubular epithelium) under hypoxia and down-regulated on re-oxygenation. 12885785 42/105 John Newman 0.0421598782195615 0.0537727788069856 2140 2702.90909090909 2870 0.00390819780512459 1121 1.51800849520391 1.39357761485651 1 0.704376376121985 2139 3703 1121 3167 3556 2651 1826 3607 3332 1760 2870 3008 M117 PID_CONE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CONE_PATHWAY.html Visual signal transduction: Cones 18832364 8/34 Pathway Interaction Database 1.03371750800899e-05 2.58071403437939e-05 4295 3130.81818181818 2871 1.03372231661396e-06 1733 1.18553093251262 -1.29699678068498 -1 1.98829202700936 4295 2375 3896 2871 1733 3879 3755 2729 3852 2393 2661 3009 M8410 REACTOME_ERKS_ARE_INACTIVATED http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ERKS_ARE_INACTIVATED.html Genes involved in ERKs are inactivated 9/15 Reactome 4.61322986670655e-06 1.36389233174096e-05 4240 3067.45454545455 2871 4.61323944358494e-07 1435 0.992887117504749 0.782284569364124 1 1.76571904607607 4236 1465 3964 2234 1435 4136 2871 3949 2506 2565 4381 3010 M609 CHOI_ATL_CHRONIC_VS_ACUTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHOI_ATL_CHRONIC_VS_ACUTE_DN.html Genes down-regulated in adult T-cell leukemia (ATL), chronic vs acute clinical condition. 16909099 17/34 Arthur Liberzon 0.0273640065305364 0.0355004802331377 3410 2808.90909090909 2871 0.0025191284046903 1562 1.0059376826776 -1.10642920540228 -1 0.533074819494959 2438 2786 3140 3406 3407 1562 1892 2871 3487 3833 2076 3011 M1939 MEISSNER_BRAIN_ICP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_ICP_WITH_H3K4ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in brain. 18600261 26/57 Jessica Robertson 2.89197282121593e-05 6.23070558170936e-05 4550 3028.72727272727 2871 2.62910076168688e-06 1778 1.42095539951945 -1.04521517801702 -1 2.18430605434059 4547 1778 2326 3340 2033 3623 3790 2207 2871 2550 4251 3012 M12434 DONATO_CELL_CYCLE_TRETINOIN http://www.broadinstitute.org/gsea/msigdb/cards/DONATO_CELL_CYCLE_TRETINOIN.html Genes involved in cell cycle regulation which were up-regulated in MCF-7 cells (breast cancer) by tretinoin (retinoic acid) [PubChem=444795]. 17234770 3/6 Jessica Robertson 0.00138933755998011 0.00210149638672267 3435 3058.18181818182 2873 0.000139020694154344 1087 0.86525486839667 -0.86525486839667 -1 0.84681420404156 3431 2379 4496 2873 3274 2860 3823 1087 2799 4609 2009 3013 M17812 TARTE_PLASMA_CELL_VS_B_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TARTE_PLASMA_CELL_VS_B_LYMPHOCYTE_DN.html Genes down-regulated in plasma cells compared with B lymphocytes. 12663452 16/64 Kate Stafford 0.000908771480669376 0.00141596468280021 3135 2898.81818181818 2874 8.26497355784382e-05 2080 1.36697112236058 -1.02297143676282 -1 1.42351827959574 3132 2080 2761 2744 2874 3341 2661 3036 3278 2734 3246 3014 M2136 QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2 http://www.broadinstitute.org/gsea/msigdb/cards/QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2.html Genes up-regulated by hypoxia in TRAMP-C cells (prostatic cancer) expressing HIF1A and FOXA2 [GeneID=3091,3170] off plasmid vectors. 20609350 34/57 Arthur Liberzon 0.0839184282471183 0.0965721401684667 975 2865.72727272727 2875 0.00793650793650794 974 1.5069606894358 1.64629992666069 1 0.55917867104489 974 4511 2501 4480 4223 1932 1352 2875 3561 3135 1979 3015 M16189 BERENJENO_TRANSFORMED_BY_RHOA_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_UP.html Genes up-regulated in NIH3T3 cells (fibroblasts) transformed by expression of contitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector. 17213802 395/796 Leona Saunders 0.0839184282471183 0.0965721401684667 1210 2964.90909090909 2877 0.00793650793650794 1206 1.61818242476537 1.92557364832448 1 0.600449039136589 1206 4353 1783 2816 3613 3738 3312 2877 2776 2770 3370 3016 M8179 BIOCARTA_RAB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAB_PATHWAY.html Rab GTPases Mark Targets In The Endocytotic Machinery 15/29 BioCarta 0.000640470903068924 0.00101840741492398 2880 2413.36363636364 2878 5.82415849997782e-05 392 3.35550790197514 4.09310155748499 1 3.6698684102188 2878 3609 1409 3063 3552 3438 3473 910 392 1982 1841 3017 M860 REACTOME_SHC_MEDIATED_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC_MEDIATED_CASCADE.html Genes involved in SHC-mediated cascade 6/33 Reactome 0.00083776256535223 0.00131120754216451 2215 2838.90909090909 2878 8.38078563780649e-05 1668 1.83561607901882 -1.83561607901882 -1 1.93394709199592 2213 3299 4040 3464 2878 1668 2225 2455 3863 3044 2079 3018 M14787 CLAUS_PGR_POSITIVE_MENINGIOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/CLAUS_PGR_POSITIVE_MENINGIOMA_DN.html Genes down-regulated in meningioma samples positive for PGR [GeneID=5241] compared to those without the receptor. 18172325 11/16 Jessica Robertson 0.0839184282471183 0.0965721401684667 2430 2858.36363636364 2881 0.00793650793650794 2031 1.31612393934252 1.75715606095418 1 0.488366047069588 2428 3001 2031 3284 3673 2894 3058 2761 2594 2837 2881 3019 M7577 ACEVEDO_LIVER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) compared to normal liver samples. 18413731 344/821 Jessica Robertson 1.45855045485111e-06 6.02713177374981e-06 4510 2799.90909090909 2881 1.32595583803464e-07 876 1.58067904671463 -1.64550742129743 -1 3.01595071819447 4509 3173 1738 2480 876 2881 4063 3652 2575 1419 3433 3020 M1860 ZHOU_PANCREATIC_EXOCRINE_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_PANCREATIC_EXOCRINE_PROGENITOR.html Transcription factors expressed in progenitors of exocrine pancreatic cells. 18754011 4/14 Jessica Robertson 0.00783123351976614 0.0108539367860468 2060 2851.18181818182 2881 0.000785896887853598 1282 1.85836770731583 -1.85836770731583 -1 1.33439263441368 2058 2881 4510 3231 3311 1625 3202 2647 3932 2684 1282 3021 M2376 IKEDA_MIR1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR1_TARGETS_DN.html Genes down-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-1 microRNA. 19188439 5/11 Arthur Liberzon 0.0153074454094962 0.0204477449227193 2265 2858 2881 0.00154139221799648 1609 1.08192913689702 1.08192913689702 1 0.668096013015396 2265 2879 4658 3042 3479 3146 2881 1609 2304 2919 2256 3022 M1150 RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_SMAD4_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_SMAD4_UP.html Apoptotic genes dependent on SMAD4 [GeneID=4089] and up-regulated in AML12 cells (hepatocytes) after stimulation with TGFB1 [GeneID=7040]. 16909112 3/7 Arthur Liberzon 0.0534943305751909 0.0674399873756644 1915 2943.18181818182 2882 0.00548274642756503 1288 0.983865201326097 -0.983865201326097 -1 0.421155374633424 1911 2882 4188 3386 4578 1569 1288 1916 4113 4494 2050 3023 M16807 FIRESTEIN_CTNNB1_PATHWAY_AND_PROLIFERATION http://www.broadinstitute.org/gsea/msigdb/cards/FIRESTEIN_CTNNB1_PATHWAY_AND_PROLIFERATION.html Genes required for both proliferation and CTNNB1 [GeneID=1499] activity in DLD-1 cell (colon cancer with APC [GeneID=324] deletions). 18794900 4/14 Jessica Robertson 0.0370361607413063 0.0474054764364276 2775 3148.81818181818 2884 0.00376682943007054 916 0.258499474883887 0.288582115942073 1 0.125118964316585 2775 2678 4509 3531 3609 2048 916 2770 4305 4612 2884 3024 M8873 ST_FAS_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_FAS_SIGNALING_PATHWAY.html Fas Signaling Pathway 48/100 Signaling Transduction KE 2.03825006351438e-05 4.60078988325066e-05 3180 2730.36363636364 2886 1.85297177062137e-06 971 1.48500915873573 -0.960419034161657 -1 2.35426088617749 3176 2886 2630 2902 1931 4480 2997 971 1507 2851 3703 3025 M3993 PARK_APL_PATHOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PARK_APL_PATHOGENESIS_UP.html Genes up-regulated in U937 cells (acute promyelocytic leukemia, APL) expressing RARA [GeneID=5914] fused with either PML or PLZF [GeneID=5371;7704]. 12893766 7/18 Arthur Liberzon 0.0185333501875119 0.0244847135547451 2345 2898.36363636364 2886 0.0018689757494282 1157 2.90883983979762 2.90883983979762 1 1.71302183185478 2341 3134 4533 3152 4603 2789 2886 1652 1157 3211 2424 3026 M1481 ABBUD_LIF_SIGNALING_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/ABBUD_LIF_SIGNALING_2_DN.html Genes down-regulated in GH3 cells (pituitary cancer) after treatment with LIF [GeneID=3976]. 14576184 4/16 Kevin Vogelsang 0.00452896997017876 0.00645657233959771 2890 2887.18181818182 2888 0.000453822673890484 668 2.06185949520096 -0.673151626945309 -1 1.65052471273308 2888 3693 4391 2242 3138 3587 4545 2272 668 2679 1656 3027 M122 PID_IL2_1PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL2_1PATHWAY.html IL2-mediated signaling events 18832364 38/87 Pathway Interaction Database 0.0010059213116214 0.00156032680114462 2890 2931.90909090909 2889 9.14892318785757e-05 1414 1.06649313638511 -1.07322939245367 -1 1.09417395702395 3530 2157 3059 1414 2886 2594 3709 2889 3406 3887 2720 3028 M2295 BAKKER_FOXO3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BAKKER_FOXO3_TARGETS_DN.html Genes down-regulated in I/11 erythroblast cells upon expression of an activated form of FOXO3 [GeneID=2309]. 17353275 113/308 Arthur Liberzon 4.92294639584688e-05 9.8965794984721e-05 4630 3116.27272727273 2889 4.47550596382975e-06 2205 1.28044725889302 -1.24784257203612 -1 1.87426440326479 4630 2573 2378 2889 2205 2301 3986 4086 3204 3755 2272 3029 M14032 ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN.html Genes down-regulated in macrophage by live P.gingivalis. 18025224 256/706 Arthur Liberzon 8.74307864947705e-06 2.25606093344986e-05 2895 3026 2891 7.94828490524755e-07 1644 1.39954398417214 -1.18867870945265 -1 2.3770903352167 2891 3820 3359 3868 1644 1841 4418 2843 2411 4036 2155 3030 M1578 BOQUEST_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOQUEST_STEM_CELL_DN.html Genes down-regulated in freshly isolated CD31- [GeneID=5175] (stromal stem cells from adipose tissue) versus the CD31+ (non-stem) counterparts. 15635089 148/359 Arthur Liberzon 4.54179932627536e-14 2.17172159621697e-12 1845 2570.81818181818 2891 4.12890847843223e-15 93 1.77792070221108 1.82230212674377 1 7.57965094003579 1845 2649 93 2004 3238 3644 2891 3630 3933 635 3717 3031 M19666 TIEN_INTESTINE_PROBIOTICS_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_24HR_DN.html Genes down-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 24h. 16394013 149/389 Arthur Liberzon 2.90797997788376e-05 6.26231350016696e-05 2640 2825.36363636364 2893 2.64365310594409e-06 1655 1.5676151430024 1.73040344970953 1 2.408493574354 2637 4050 3257 2240 2035 3397 2893 3032 1655 2809 3074 3032 M17915 KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP.html Genes up-regulated in HL-60 cells (acute promyelocytic leukemia, APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 24 h. 18701491 477/1166 Jessica Robertson 1.70542333840897e-06 6.65967813648703e-06 3010 2892.36363636364 2893 1.55038605494696e-07 945 1.30751499556784 1.48133229823112 1 2.47403631469253 3007 2762 3055 2893 945 4414 3437 2650 2746 2386 3521 3033 M1994 KYNG_NORMAL_AGING_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_NORMAL_AGING_UP.html Genes distinctly up-regulated in primary fibroblast cultures from normal old donors compared to those from normal young donors. 14527998 17/32 Arthur Liberzon 7.05932295420549e-05 0.000136299906730148 4680 2918.27272727273 2893 6.41777225704375e-06 1241 1.3726652802728 -0.940987196327815 -1 1.93950130319312 4677 1878 2893 2255 2303 2106 3268 3659 1241 3390 4431 3034 M546 REACTOME_O_LINKED_GLYCOSYLATION_OF_MUCINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_O_LINKED_GLYCOSYLATION_OF_MUCINS.html Genes involved in O-linked glycosylation of mucins 20/61 Reactome 0.00105320492453154 0.00162935565412836 4190 3093.09090909091 2894 9.57917693631848e-05 1784 1.15502646464765 -0.900347051226012 -1 1.1770677992848 4186 1784 2499 2770 2894 4585 3695 3230 2307 2010 4064 3035 M16 PID_INSULIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INSULIN_PATHWAY.html Insulin Pathway 18832364 29/68 Pathway Interaction Database 0.000154884797643191 0.000274816418688373 3215 2984.54545454545 2896 1.40814275405077e-05 2360 1.39083813128062 -1.09900854199957 -1 1.81035025691044 3215 3274 2777 2671 2507 3779 2896 2360 2717 3269 3365 3036 M806 REACTOME_POST_TRANSLATIONAL_MODIFICATION_SYNTHESIS_OF_GPI_ANCHORED_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POST_TRANSLATIONAL_MODIFICATION_SYNTHESIS_OF_GPI_ANCHORED_PROTEINS.html Genes involved in Post-translational modification: synthesis of GPI-anchored proteins 15/27 Reactome 3.47932634367027e-05 7.29817513269421e-05 4545 3095.72727272727 2896 3.16307397350126e-06 1405 1.20432442994265 -0.616207050567385 -1 1.82106636018484 4543 2436 2896 2290 2098 3423 4601 2310 1405 3769 4282 3037 M17681 BIOCARTA_IL3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL3_PATHWAY.html IL 3 signaling pathway 11/29 BioCarta 0.00728823655249229 0.0101403433743999 2040 2796.63636363636 2900 0.000664772168690153 1534 0.726012215025612 -0.726012215025612 -1 0.529147636908663 2038 2900 3428 2582 3194 1534 3054 1694 4289 4274 1776 3038 M1718 SIG_IL4RECEPTOR_IN_B_LYPHOCYTES http://www.broadinstitute.org/gsea/msigdb/cards/SIG_IL4RECEPTOR_IN_B_LYPHOCYTES.html Genes related to IL4 rceptor signaling in B lymphocytes 18/36 Signaling Gateway 0.0172923546296061 0.0229617381111744 2495 2911.09090909091 2900 0.00158452637224833 1452 0.894189262103748 -0.92133125177008 -1 0.535705853694933 2493 3285 3250 2900 3335 1452 2602 2672 3877 3871 2285 3039 M9367 BIOCARTA_ERYTH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERYTH_PATHWAY.html Erythrocyte Differentiation Pathway 7/15 BioCarta 0.00100810299356292 0.00156319345725872 2905 2921 2902 0.000100856060800137 1877 1.377541285852 1.61683686105435 1 1.41289396639582 2998 2706 3832 3513 2903 2842 1877 2902 3580 2256 2722 3040 M18799 REACTOME_DIABETES_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DIABETES_PATHWAYS.html Genes involved in Diabetes pathways 87/214 Reactome 0.00110640689849098 0.00170659075916021 2645 3125.90909090909 2902 0.000100633065102711 2459 1.54662394111131 1.84099256378688 1 1.56476730439897 2643 4313 3429 3495 2902 2989 2694 2772 2712 3977 2459 3041 M13656 NAKAMURA_LUNG_CANCER_DIFFERENTIATION_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_LUNG_CANCER_DIFFERENTIATION_MARKERS.html 14 candidate differentiation markers in lung adenocarcinoma cells, noncancerous lung cells and peripheral blood cells. 16491115 7/27 Arthur Liberzon 0.0104311472988622 0.0142549886971328 2165 2921.36363636364 2902 0.00104804372158099 1511 1.5182933605918 1.5182933605918 1 1.02450582477584 2163 3327 4217 3153 3887 2486 2292 1511 3931 2266 2902 3042 M1502 SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP.html Up-regulated in murine dorsal skin cells at 6 h after treatment with the phorbol ester carcinogen TPA [PubChem=4792]. 12640676 23/82 John Newman 0.00427482212785797 0.00610912366305046 2260 2840.09090909091 2902 0.000389377382329926 2108 1.44845475356369 1.34411899665765 1 1.17221138629644 2258 2657 2336 3095 3113 2902 2108 3768 3504 2298 3202 3043 M2197 THILLAINADESAN_ZNF217_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/THILLAINADESAN_ZNF217_TARGETS_UP.html Genes bound and activated by ZNF217 [GeneID=7764] in MCF7 cells (breast cancer). 18625718 27/58 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3220 3117.45454545455 2903 0.00793650793650794 2488 1.28065342417664 -1.1882348487556 -1 0.475204220265139 3216 3645 2524 3705 4577 2668 2903 2488 3336 2640 2590 3044 M12363 REACTOME_REMOVAL_OF_THE_FLAP_INTERMEDIATE_FROM_THE_C_STRAND http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REMOVAL_OF_THE_FLAP_INTERMEDIATE_FROM_THE_C_STRAND.html Genes involved in Removal of the Flap Intermediate from the C-strand 6/11 Reactome 0.136789362651113 0.155430396067681 2180 3016.54545454545 2904 0.0146019957517235 1295 0.71112730430769 -0.71112730430769 -1 0.210148992319018 2180 2904 4094 3202 4255 1821 1295 2454 4174 4453 2350 3045 M10911 KEGG_CYSTEINE_AND_METHIONINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CYSTEINE_AND_METHIONINE_METABOLISM.html Cysteine and methionine metabolism 14/39 KEGG 0.00112153663847949 0.00172822120615418 4000 2864.81818181818 2905 0.000102009890394597 1565 1.4942358607793 -1.59593511277129 -1 1.50877707233079 3996 1793 2403 3225 2905 4510 3635 2116 1565 1886 3479 3046 M1358 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX4_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX4_UP.html Early prostate development genes (up-regulated at 6 hr dihydrotestosterone [PubChem=10635]) which are also up-regulated in localized vs metastatic prostate cancers. 18794802 5/15 Jessica Robertson 0.0102828170525832 0.0140604845953909 2010 2872.09090909091 2905 0.00103307105994939 1410 2.20851549522936 2.20851549522936 1 1.49506686154269 2006 3870 4328 3841 4098 1410 1568 1505 4091 2905 1971 3047 M2835 PIEPOLI_LGI1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PIEPOLI_LGI1_TARGETS_DN.html Down-regulated genes in U87 cells (glioblastoma multiforme, GBM) engineered to stably express LGI1 [GeneID=9211]. 16533756 9/35 Arthur Liberzon 0.0149801474866452 0.0200448232788176 2910 3165.36363636364 2906 0.00150820982442034 1605 3.07897679076637 -3.07897679076637 -1 1.91100921184563 2906 4410 4120 3766 4517 2642 2880 1605 2027 3408 2538 3048 M2618 ZWANG_TRANSIENTLY_UP_BY_1ST_EGF_PULSE_ONLY http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_TRANSIENTLY_UP_BY_1ST_EGF_PULSE_ONLY.html Genes transiently induced only by the first pulse of EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 910/2790 Yaara Zwang 7.10248374878224e-07 3.82994693288764e-06 3000 2353.54545454545 2906 7.10248601882066e-08 394 1.55928073461439 1.70150440258532 1 3.0873576674415 2999 394 4686 693 608 4279 3184 2906 2054 538 3548 3049 M3115 KEGG_LONG_TERM_POTENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LONG_TERM_POTENTIATION.html Long-term potentiation 27/89 KEGG 0.0839184282471183 0.0965721401684667 1495 2560.81818181818 2907 0.00793650793650794 1307 1.41153156698083 1.32337408856612 1 0.52376837108226 1494 3121 2907 2110 3635 1307 1392 3650 3042 3536 1975 3050 M1877 REACTOME_GOLGI_ASSOCIATED_VESICLE_BIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GOLGI_ASSOCIATED_VESICLE_BIOGENESIS.html Genes involved in Golgi Associated Vesicle Biogenesis 39/88 Reactome 0.000593656150208648 0.00094879697130891 3080 2839.63636363636 2907 5.39833095570968e-05 1364 1.18394033050227 -0.939604137385403 -1 1.30816436930697 3076 3569 3225 2712 2800 1364 2771 2907 3230 3701 1881 3051 M2253 NIKOLSKY_BREAST_CANCER_17P11_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_17P11_AMPLICON.html Genes within amplicon 17p11 identified in a copy number alterations study of 191 breast tumor samples. 19010930 5/10 Jessica Robertson 0.0480871700225698 0.0610006710140124 4185 3141.54545454545 2907 0.0049160577914421 1364 1.81414720560134 -1.81414720560134 -1 0.805468257556326 4182 1951 4355 2775 3500 4187 2864 2663 1364 2907 3809 3052 M1543 HU_GENOTOXIN_ACTION_DIRECT_VS_INDIRECT_24HR http://www.broadinstitute.org/gsea/msigdb/cards/HU_GENOTOXIN_ACTION_DIRECT_VS_INDIRECT_24HR.html Genes discriminating between direct (cisplatin, MMS, mitomycin C [PubChem=2767;4156;5746]) and indirect (paclitaxel, hydroxyurea, etoposide [PubChem=4666;3657;36462]) acting genotoxins at 24 h time point. 15120960 56/114 John Newman 0.0839184282471183 0.0965721401684667 1730 2969.27272727273 2907 0.00793650793650794 1601 1.31886634268632 -1.32874997666459 -1 0.489383653881054 1728 3566 2685 2907 4052 1601 2640 3967 3659 3541 2316 3053 M1014 REACTOME_IL_6_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_6_SIGNALING.html Genes involved in Interleukin-6 signaling 5/11 Reactome 0.00490580911997361 0.006962029538521 3005 2783.45454545455 2908 0.000491667302287845 1355 1.22285542253572 1.22285542253572 1 0.964267851014131 3004 1987 4070 2220 3244 3339 2908 1355 2562 2893 3036 3054 M249 PID_PI3KCI_AKT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PI3KCI_AKT_PATHWAY.html Class I PI3K signaling events mediated by Akt 18832364 27/49 Pathway Interaction Database 0.0011350614846934 0.00174619110875683 2230 3315.63636363636 2909 0.000103240684391298 2133 0.717867133079674 0.731498865809214 1 0.723674267124395 2229 4592 3618 4105 2909 2633 2133 2848 4321 4303 2781 3055 M2263 MIKHAYLOVA_OXIDATIVE_STRESS_RESPONSE_VIA_VHL_UP http://www.broadinstitute.org/gsea/msigdb/cards/MIKHAYLOVA_OXIDATIVE_STRESS_RESPONSE_VIA_VHL_UP.html Proteins significantly induced by oxidative stress (hydrogen peroxide [PubChem=784] in 786-O cells (renal clear cell carcinoma, RCC) expressing VHL [GeneID=7428]. 18285459 6/9 Arthur Liberzon 0.000787234127592265 0.00123832800332237 2475 2895.72727272727 2909 7.87513148624305e-05 964 2.5249832258054 2.5249832258054 1 2.68316466120931 2471 3865 4636 2627 4454 3137 2909 964 1428 3062 2300 3056 M1887 WUNDER_INFLAMMATORY_RESPONSE_AND_CHOLESTEROL_UP http://www.broadinstitute.org/gsea/msigdb/cards/WUNDER_INFLAMMATORY_RESPONSE_AND_CHOLESTEROL_UP.html Genes up-regulated in gastric mucosal tissue of mice on 2% cholesterol [PubChem=5997] diet and infected with H. pylori vs those infected with H. pylori while on 0% cholesterol diet. 16951684 53/197 Jessica Robertson 0.00115001059943762 0.00176744823514749 3340 2754 2910 0.000104601107925955 1378 1.88624672664833 -1.4793691153892 -1 1.89788224872612 3339 2357 1378 1803 2910 3051 3630 4035 2667 1784 3340 3057 M2415 WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_36HR http://www.broadinstitute.org/gsea/msigdb/cards/WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_36HR.html Genes with promoters bound by both PPARG and RXRA [GeneID=5468, 6256] at 36 h time point of adipocyte differentiation of 3T3-L1 cells (preadipocyte). 19414603 116/236 Arthur Liberzon 2.10498769141095e-06 7.62285341727336e-06 3490 2871 2910 1.91362700499307e-07 1055 1.35514555804862 1.66880496142812 1 2.53510236957505 3490 2910 3213 2662 1055 4028 3721 2040 2621 2655 3186 3058 M15015 FARMER_BREAST_CANCER_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_1.html Cluster 1: interferon, T and B lymphocyte genes clustered together across breast cancer samples. 15897907 10/84 Leona Saunders 0.00117651019823787 0.0018058063507837 3570 3088.36363636364 2912 0.000107012712792313 2161 1.19298879364309 -0.924257594056433 -1 1.19628175927851 3569 2901 2161 3191 2912 2767 2537 4265 3168 2706 3795 3059 M7090 TOMLINS_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TOMLINS_METASTASIS_DN.html Top genes down-regulated in hormone refractory metastatic prostate cancer compared to localized prostate cancer. 17173048 14/35 Leona Saunders 0.0839184282471183 0.0965721401684667 2915 2929.36363636364 2912 0.00793650793650794 1302 1.28093858322247 -1.29083019452367 -1 0.475310032485667 2912 3577 2786 4358 3687 2580 1302 2240 3585 1892 3304 3060 M1918 WEST_ADRENOCORTICAL_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_TUMOR_UP.html Up-regulated genes in pediatric adrenocortical tumors (ACT) compared to the normal tissue. 17234769 222/516 Jessica Robertson 0.000214427493261774 0.000370367575902938 1700 3017.54545454545 2912 1.94953087025116e-05 1698 1.44500254092668 1.71480987195692 1 1.81240410189384 1698 4250 2967 3222 2583 3500 2745 2734 2912 3693 2889 3061 M713 REACTOME_NEGATIVE_REGULATION_OF_THE_PI3K_AKT_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEGATIVE_REGULATION_OF_THE_PI3K_AKT_NETWORK.html Genes involved in Negative regulation of the PI3K/AKT network 2/8 Reactome 0.00940172188704457 0.0129084291716059 2330 2992 2913 0.00104902683689531 1512 0.758479313772085 0.758479313772085 1 0.523750021562744 2328 3172 3965 NA 3932 2447 1638 1512 3927 4345 2654 3062 M1688 YANG_MUC2_TARGETS_DUODENUM_3MO_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_MUC2_TARGETS_DUODENUM_3MO_DN.html Genes down-regulated in duodenum of 3 month old MUC2 [GeneID=4583] knockout mice. 18794118 9/66 Jessica Robertson 0.0242430637101475 0.0316884230253142 2550 2969.36363636364 2913 0.00245116739824341 1591 1.35532978848193 -1.59301303246831 -1 0.742667904723289 2546 2955 4425 3903 3402 1986 2913 2790 2736 3416 1591 3063 M14046 DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_UP.html Common up-regulated transcripts in fibroblasts expressing either XP/CS or TDD mutant forms of ERCC3 [GeneID=2071], after UVC irradiation. 15608684 83/179 Arthur Liberzon 5.54604947690652e-06 1.57031950747939e-05 4610 2849.18181818182 2914 5.04187587106103e-07 1448 1.42847569323865 1.73983547524965 1 2.5083965017379 4607 2298 2517 1448 1477 3059 3453 1892 2914 3092 4584 3064 M14951 ZUCCHI_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZUCCHI_METASTASIS_UP.html The 50 most up-regulated genes in primary invasive breast dutcal carcinoma (IDC) or lymph node metastases, compared to normal mammary epithelium. 15608061 34/78 Kate Stafford 0.0481154824998866 0.0610200679281377 1250 2572.09090909091 2915 0.00447283573212238 1249 1.47017031626233 1.38177056841902 1 0.652670803175012 1249 3272 2915 2347 3847 1699 1612 3106 3398 3134 1714 3065 M1534 VIETOR_IFRD1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/VIETOR_IFRD1_TARGETS.html Genes down-regulated in c-JunER cells (mammary gland epithelum) by overexpression of IFRD1 [GeneID=3475] off an adenovirus vector. 12198164 20/44 John Newman 0.01177521168942 0.0159799136914632 2920 2849.18181818182 2917 0.00107624666519989 1343 1.89801770451472 -2.14270172813414 -1 1.24631762707173 2917 3241 2041 3145 4458 3131 3896 1749 2885 2535 1343 3066 M2071 REACTOME_PURINE_RIBONUCLEOSIDE_MONOPHOSPHATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_RIBONUCLEOSIDE_MONOPHOSPHATE_BIOSYNTHESIS.html Genes involved in Purine ribonucleoside monophosphate biosynthesis 5/12 Reactome 0.212154029347527 0.236646936806121 2920 3396.36363636364 2918 0.0235632156157192 2261 1.06795919689037 -1.06795919689037 -1 0.244330814875793 2918 4119 4003 4232 4483 2261 2715 2391 4526 2888 2824 3067 M2275 ZHU_SKIL_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_SKIL_TARGETS_DN.html Genes down-regulated in A549 cells (lung adenocarcinoma) upon SKIL [GeneID=6498] knockdown by RNAi. 17074815 5/11 Arthur Liberzon 3.81929977376982e-05 7.9331732003038e-05 2695 3080.09090909091 2918 3.81936541708609e-06 445 2.8025757523086 2.8025757523086 1 4.20067466008673 2693 4293 4638 2693 4373 3433 4315 445 2177 2918 1903 3068 M5436 KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY.html B cell receptor signaling pathway 38/110 KEGG 8.733187849346e-05 0.000164418313628105 4235 3117.81818181818 2919 7.93957685811989e-06 1334 1.31554412625328 1.37270173409952 1 1.81962340598915 4234 2276 2457 1334 2364 4626 2919 3884 3076 2592 4534 3069 M13608 ZHAN_V1_LATE_DIFFERENTIATION_GENES_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_V1_LATE_DIFFERENTIATION_GENES_UP.html The v1LDG up-regulated set: most variable late differentiation genes (LDG) with similar expression patterns in tonsil plasma cells (TPC) and multiple myeloma (MM) samples. 12393520 25/48 Arthur Liberzon 0.000196250021388559 0.000341741954747971 4385 3023 2919 1.78425027246403e-05 1600 1.29124847948859 1.33930834762535 1 1.63604571046238 4381 1600 2195 2919 2557 3216 2440 4508 3257 2486 3694 3070 M11509 HASLINGER_B_CLL_WITH_11Q23_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_11Q23_DELETION.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with deletions in the 11q23 region. 15459216 19/49 Kevin Vogelsang 0.010686100158707 0.0145778938409609 2920 2946.81818181818 2920 0.000976214698772908 2244 1.17899064823917 -1.29556099281108 -1 0.791360698328259 2920 2998 2888 3914 3255 2409 2456 2244 3167 3902 2262 3071 M19002 STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_DN.html Genes down-regulated by estradiol [PubChem=5757] and down-regulated by ESRRA [GeneID=2101] in MCF-7 cells (breast cancer). 18974123 22/58 Leona Saunders 0.0186512317818727 0.0246335039824846 900 2474.72727272727 2920 0.00171011421656425 751 1.14643309447612 1.14643309447612 1 0.674034237816082 898 2920 2720 3256 3816 952 751 3044 4084 3245 1536 3072 M2381 KUWANO_RNA_STABILIZED_BY_NO http://www.broadinstitute.org/gsea/msigdb/cards/KUWANO_RNA_STABILIZED_BY_NO.html Transcripts stabilized by NO [PubChem=145068] identified as up-regulated by NO [PubChem=145068] in the presence of actinomycin D [PubChemiD=2019] in IMR-90 and NIH 3T3 cells (fibroblast). 19289500 5/9 Arthur Liberzon 0.185430695435617 0.207430947436453 1565 3092.81818181818 2920 0.0203006857669933 1561 1.00940591388217 1.00940591388217 1 0.252049704649351 1561 3300 4660 3778 3711 2331 2250 2512 4286 2920 2712 3073 M15659 RASHI_RESPONSE_TO_IONIZING_RADIATION_5 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_5.html Cluster 5: early responding genes activated in ATM [GeneID=472] deficient but not in the wild type tissues. 16314843 103/258 Arthur Liberzon 5.10997464166252e-06 1.4781074796809e-05 3195 2909.72727272727 2924 4.64544228247243e-07 1437 1.30001961227412 1.2572362525695 1 2.29531723871516 3192 3264 2741 2533 1437 3799 2210 3352 2302 2924 4253 3074 M8880 MCBRYAN_PUBERTAL_BREAST_5_6WK_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_5_6WK_DN.html Genes down-regulated during pubertal mammary gland development between week 5 and 6. 17486082 95/226 Arthur Liberzon 0.0132042721397341 0.0178366155222813 2145 2868.36363636364 2925 0.00120765416377838 2144 1.49260538677971 -1.38366942294248 -1 0.954061722928456 2144 3206 2588 3112 3292 2775 2475 3523 2441 3071 2925 3075 M3559 ZHANG_INTERFERON_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_INTERFERON_RESPONSE.html Interferon-inducible genes up-regulated in A549 cells (lung cancer) infected with a respiratory syncytial virus (RSV) that had its NS1 [GeneID=1494468] gene knocked down by RNAi. 15619625 17/61 Jessica Robertson 8.2864518022229e-07 4.21381153484506e-06 2925 2863.18181818182 2925 7.53314083943073e-08 636 1.10278914430267 1.1499186399393 1 2.16678814778191 2925 2165 2494 2788 636 3997 3280 4017 3090 2806 3297 3076 M17386 REACTOME_COSTIMULATION_BY_THE_CD28_FAMILY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COSTIMULATION_BY_THE_CD28_FAMILY.html Genes involved in Costimulation by the CD28 family 31/72 Reactome 6.02105553740297e-05 0.000118300487414131 3620 3010 2926 5.4738366641635e-06 1897 1.32649445217694 1.17931522573764 1 1.90408827473628 3618 2050 2945 1897 2262 4505 2296 2792 2926 3360 4459 3077 M5077 MARTINEZ_RESPONSE_TO_TRABECTEDIN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RESPONSE_TO_TRABECTEDIN.html Genes down-regulated by trabectedin [PubChem=3199] and its synthetic analog phthalascidin Pt 650 in HCT116 cells (colon cancer). 11755394 31/76 John Newman 0.000630161708192724 0.00100371779897726 2540 2904.54545454545 2927 5.73038438478869e-05 1417 1.0105803651208 -0.945461097072662 -1 1.10758736088214 2537 3056 3210 4076 2814 2095 1417 2927 3299 3697 2822 3078 M14523 IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM.html Genes in the expression cluster 'ST-HSC Shared': up-regulated in short term hematopoietic stem cells (ST-HSC) from adult bone marrow and fetal liver. 12228721 18/52 John Newman 0.000981577062635941 0.00152306957467285 2930 2943.09090909091 2927 8.92741170907222e-05 2141 1.94951402427405 1.81731875992293 1 2.00759296819155 3987 3550 2930 2927 2884 2459 2410 3449 2141 2938 2699 3079 M17700 BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_UP.html Genes up-regulated in A172 cells (glioma, does not express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 48 h. 15980968 7/24 John Newman 0.0193951909750696 0.0255584546988684 2360 3137.72727272727 2929 0.00195665780554641 1595 0.617946635740603 -0.617946635740603 -1 0.359699826061587 2358 2797 4416 4216 3367 1595 2068 2929 3908 4588 2273 3080 M3062 CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2 http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2.html The 'group 2 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 and ERBB2 [GeneID=2099;2064]. 18794137 235/685 Jessica Robertson 2.30901998747438e-06 8.12927698069492e-06 4020 3005.90909090909 2930 2.09911128265486e-07 1096 1.34170974608066 -1.14892998001111 -1 2.49626781346137 4016 2463 2627 2842 1096 4428 3253 3177 2081 2930 4152 3081 M17148 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_GRANULOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_GRANULOCYTE_DN.html Genes down-regulated in granulocytes by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 6/30 Arthur Liberzon 0.0476802806919413 0.0605172793397716 1945 2849.18181818182 2932 0.00487353171476934 1012 1.16192560962764 1.16192560962764 1 0.51735406103245 1944 2932 4136 4501 3499 1553 1012 2618 4264 3049 1833 3082 M11171 DACOSTA_UV_RESPONSE_VIA_ERCC3_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_UP.html Genes up-regulated in fibroblasts expressing mutant forms of ERCC3 [GeneID=2071] after UV irradiation. 15608684 235/511 Arthur Liberzon 5.29017005541044e-07 3.23203870660408e-06 3765 2840.27272727273 2932 4.80924666136109e-08 467 1.53910908867243 1.78344153319293 1 3.08888972216827 3765 2103 2932 2491 467 3122 3994 2862 2285 3359 3863 3083 M6821 NIKOLSKY_BREAST_CANCER_20P13_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_20P13_AMPLICON.html Genes within amplicon 20p13 identified in a copy number alterations study of 191 breast tumor samples. 19010930 3/12 Jessica Robertson 0.0121655731344473 0.0164905628313625 2000 2839.63636363636 2932 0.00122326913781024 671 0.644127979066728 0.644127979066728 1 0.419744868522627 1996 2439 4357 2932 3804 1385 671 3567 3856 4562 1667 3084 M14495 VETTER_TARGETS_OF_PRKCA_AND_ETS1_UP http://www.broadinstitute.org/gsea/msigdb/cards/VETTER_TARGETS_OF_PRKCA_AND_ETS1_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer) after knockdown of PRKCA and ETS1 [GeneID=5578;2113] by RNAi. 15531915 8/21 Leona Saunders 0.00635731215748438 0.00890593864573148 2935 2906.18181818182 2933 0.000637557266073646 1409 1.55180547622939 -0.53387997405423 -1 1.16299605603214 2933 2755 4174 3246 3636 3238 2660 1409 2159 3306 2452 3085 M7076 NAM_FXYD5_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAM_FXYD5_TARGETS_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer) after knockdown of FXYD5 [GeneID=53827] by RNAi. 16849564 12/29 Arthur Liberzon 0.000657854858208136 0.00104498571714011 2520 3060.81818181818 2934 5.98228777823548e-05 914 2.69210678198418 2.69210678198418 1 2.93330640763991 2516 4287 2683 4427 4405 2934 2490 914 3460 3616 1937 3086 M2895 MARKEY_RB1_CHRONIC_LOF_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARKEY_RB1_CHRONIC_LOF_UP.html Genes up-regulated in MEF cells (embryonic fibroblasts) isolated from RB1 [GeneID=5925] knockout mice: chronic loss of function (LOF) of RB1. 17452985 83/168 Arthur Liberzon 0.00051903607048358 0.000835808600098302 2115 2866.63636363636 2934 4.71962331620282e-05 1212 1.79497506908427 1.85876908264738 1 2.01944119971879 2113 3796 1212 2561 2776 3588 3156 3841 2934 2282 3274 3087 M15209 LANDIS_ERBB2_BREAST_PRENEOPLASTIC_UP http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_PRENEOPLASTIC_UP.html Up-regulated genes from top 82 genes out of the 324-gene signature identified in the pre-neoplastic tissue adjacent to the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 17/27 Leona Saunders 0.0839184282471183 0.0965721401684667 2935 3022.54545454545 2934 0.00793650793650794 2396 1.20896291209934 -1.368894512269 -1 0.448602461055524 2934 2843 2396 3249 3676 2524 3049 2584 3373 3834 2786 3088 M459 SESTO_RESPONSE_TO_UV_C0 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C0.html Cluster 0: genes changed in primary keratinocytes by UVB irradiation. 11867738 72/177 John Newman 0.0839184282471183 0.0965721401684667 2625 2995.81818181818 2934 0.00793650793650794 2152 1.29314852984057 -1.51035070317162 -1 0.479840702590892 2624 2977 2731 3075 4321 2152 2583 2444 3512 3601 2934 3089 M5520 TCGA_GLIOBLASTOMA_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/TCGA_GLIOBLASTOMA_COPY_NUMBER_DN.html Genes down-regulated and displaying decreased copy number in glioblastoma samples. 18772890 18/43 Jessica Robertson 3.77012061082749e-05 7.84493125325827e-05 4130 2984.36363636364 2937 3.42744110963839e-06 1926 1.01261243963444 -1.12681726375446 -1 1.51956448575989 4129 1926 2808 3286 2119 3472 2763 3338 3616 2937 2434 3090 M16409 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_OLD http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_OLD.html Human environmental stress response genes not changed in primary fibroblasts from old donors in response to UV radiation. 15897889 15/34 Jessica Robertson 0.117085116684515 0.133624173595625 2230 2966.81818181818 2938 0.0112567521513829 2001 1.33906021390034 1.59553750717413 1 0.42784642959846 2230 3026 2665 3350 4300 2247 2252 2938 3851 3775 2001 3091 M918 REACTOME_N_GLYCAN_TRIMMING_IN_THE_ER_AND_CALNEXIN_CALRETICULIN_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_N_GLYCAN_TRIMMING_IN_THE_ER_AND_CALNEXIN_CALRETICULIN_CYCLE.html Genes involved in N-glycan trimming in the ER and Calnexin/Calreticulin cycle 6/16 Reactome 0.0290648580742002 0.0375822088674675 1990 2641.36363636364 2939 0.00294521512467051 1659 1.1231894092528 -1.1231894092528 -1 0.585049358116083 1989 3168 4053 3104 3588 1659 1727 1764 2939 3045 2019 3092 M1346 SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP.html Genes up-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 6 h. 18794802 122/305 Jessica Robertson 0.000300058048256179 0.000504873254624221 4460 3082.45454545455 2939 2.72817255451018e-05 2042 1.32459680602214 -0.90398503370366 -1 1.59623885593658 4460 2939 2603 3263 2658 2233 3840 2042 2711 3131 4027 3093 M11516 ADDYA_ERYTHROID_DIFFERENTIATION_BY_HEMIN http://www.broadinstitute.org/gsea/msigdb/cards/ADDYA_ERYTHROID_DIFFERENTIATION_BY_HEMIN.html Selected genes changed in K562 (immortalized erythroleukemia) cells induced by hemin [PubChem=26945] treatment to express erythroid properties. 15252187 56/129 Kevin Vogelsang 2.03669701690136e-05 4.59949986563844e-05 2665 3077.36363636364 2940 1.8515598839124e-06 1768 1.50168048109142 1.61731740503098 1 2.38075763582826 2665 4316 1768 2940 1930 3960 3613 4476 3087 2304 2792 3094 M5775 BROWNE_HCMV_INFECTION_12HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_12HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 12 h time point that were not down-regulated at the previous time point, 10 h. 11711622 94/225 John Newman 6.12647005510975e-07 3.48829145543673e-06 2390 2849.90909090909 2940 5.56951978289523e-08 528 1.18215712113107 1.21594094601989 1 2.35819233698679 2386 2940 2611 2892 528 3793 3324 3327 3342 3462 2744 3095 M12618 KESHELAVA_MULTIPLE_DRUG_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/KESHELAVA_MULTIPLE_DRUG_RESISTANCE.html Genes up-regulated in multiple drug resistant neuroblastoma cell lines. 17623797 67/144 Jessica Robertson 0.000343913719703463 0.000572497225765693 2970 3001.18181818182 2941 3.1269772144051e-05 2314 1.34168267797952 -1.10955657392463 -1 1.59005603400264 2970 2912 2955 2749 2691 2314 3949 3867 2449 3216 2941 3096 M10573 SWEET_KRAS_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/SWEET_KRAS_ONCOGENIC_SIGNATURE.html Genes that contributed maximally to the GSEA score of the up-regulated gene set from the KrasLA mouse model in two human lung cancer expression data sets comparing mutant vs normal KRAS [GeneID=3845]. 15608639 64/149 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3195 3019.45454545455 2942 0.00793650793650794 1907 1.94424676398226 -1.95767750593539 -1 0.72143973633425 3191 4094 2141 2942 4063 1907 2204 4074 2642 2767 3189 3097 M542 REACTOME_IL_7_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_7_SIGNALING.html Genes involved in Interleukin-7 signaling 9/13 Reactome 0.00122664981573779 0.00187661803347936 3085 2829 2944 0.000122732744362807 1748 1.37957022426115 1.48364269823385 1 1.37495452199423 3081 1748 3926 2132 2944 3642 2349 4205 2069 1805 3218 3098 M314 NING_CHRONIC_OBSTRUCTIVE_PULMONARY_DISEASE_UP http://www.broadinstitute.org/gsea/msigdb/cards/NING_CHRONIC_OBSTRUCTIVE_PULMONARY_DISEASE_UP.html Up-regulated genes in lung tissue of smokers with chronic obstructive pulmonary disease (COPD) vs smokers without disease (GOLD-2 vs GOLD-0). 15469929 146/280 Kate Stafford 0.000356657752700852 0.000591819486245111 2350 2778.27272727273 2944 3.24286896517698e-05 984 1.72483808479179 1.95056482722304 1 2.03505263032144 2349 3916 2144 3033 2701 3575 3166 984 2473 2944 3276 3099 M11383 BROWNE_HCMV_INFECTION_16HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_16HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 16 h time point that were not up-regulated at the previous time point, 14 h. 11711622 162/382 John Newman 3.4576056281044e-05 7.26888289515353e-05 2115 2867.18181818182 2944 3.14332724579628e-06 2094 1.36201115408325 1.58951883711526 1 2.06037497544192 2115 2971 2976 3126 2094 3527 2932 3081 2915 2858 2944 3100 M163 PID_LIS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LIS1_PATHWAY.html Lissencephaly gene (LIS1) in neuronal migration and development 18832364 25/57 Pathway Interaction Database 2.46190835962784e-07 2.14593063349835e-06 3240 2844.81818181818 2945 2.23809875920687e-08 206 1.16270709404909 -1.14747461120757 -1 2.40906690022132 4190 3236 2940 3062 206 2274 2945 4110 3240 2482 2608 3101 M17856 MULLIGHAN_MLL_SIGNATURE_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_MLL_SIGNATURE_1_UP.html The 'MLL signature 1': genes up-regulated in pediatric AML (acute myeloid leukemia) with rearranged MLL [GeneID=4297] compared to all AML cases with the intact gene. 17597811 249/602 Arthur Liberzon 5.72359977125742e-06 1.61279546170248e-05 2680 2813.81818181818 2945 5.20328605639668e-07 1484 1.40098879599521 1.51687206505146 1 2.45419376530913 2677 3261 2551 3209 1484 3373 1671 4129 2945 2494 3158 3102 M11665 PRAMOONJAGO_SOX4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PRAMOONJAGO_SOX4_TARGETS_DN.html Genes down-regulated in ACC3 cells (adenoid cystic carcinoma) after knockdown of SOX4 [GeneID=6659] by RNAi. 16636670 25/70 Leona Saunders 0.0314769747338898 0.0405891864620274 2350 2901.36363636364 2947 0.002903324656215 1533 1.19574127594923 -0.979169200786018 -1 0.608229753652358 2346 4595 2947 3800 3602 1544 1533 1757 3780 3782 2229 3103 M4447 SHARMA_PILOCYTIC_ASTROCYTOMA_LOCATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHARMA_PILOCYTIC_ASTROCYTOMA_LOCATION_UP.html Genes up-regulated in pilocytic astrocytoma (PA) from supratentorial regions compared to the infratentorial PA tumors. 17283119 14/32 Jessica Robertson 0.00135987553092265 0.00206161930831912 3250 2753.63636363636 2947 0.000123701530222276 1568 1.14181736686578 -1.4119093196282 -1 1.12095503904722 3246 3062 2740 3580 2947 1568 2027 1710 3775 3156 2479 3104 M843 STEIN_ESRRA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESRRA_TARGETS.html Genes regulated by ESRRA [GeneID=2101] in MCF-7 cells (breast cancer). 18974123 411/981 Arthur Liberzon 5.34492643765921e-06 1.52721495651653e-05 3230 2531.09090909091 2947 4.85903583933308e-07 914 1.48253776821677 -1.43965149810811 -1 2.60987974581324 3227 3043 3211 2947 1461 914 2696 3018 2458 3232 1635 3105 M15132 BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_24HR_UP.html Genes up-regulated in T98G cells (glioma, express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 24 h. 15980968 6/14 Arthur Liberzon 0.0205824735574672 0.0270469632894816 2285 3260.63636363636 2947 0.00207756335077166 2283 0.403290350015397 -0.526988584159162 -1 0.23112680193388 2283 2564 4615 3397 3382 2367 2757 2836 4058 4661 2947 3106 M11865 BRUNEAU_SEPTATION_VENTRICULAR http://www.broadinstitute.org/gsea/msigdb/cards/BRUNEAU_SEPTATION_VENTRICULAR.html Genes for which mutations result in developmental defects in ventricular septation and atrioventricular cushion formation, a major class of congenital heart disease. 18288184 5/18 Jessica Robertson 0.013945095238832 0.0187670064012541 2950 3217.45454545455 2948 0.00140333855703679 2258 0.676971934891053 -0.676971934891053 -1 0.427250822135675 2948 2258 4545 2849 3316 2400 2971 2487 4219 4628 2771 3107 M1072 REACTOME_INFLAMMASOMES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INFLAMMASOMES.html Genes involved in Inflammasomes 10/20 Reactome 0.0109875289694225 0.0149673141717192 2990 2843.54545454545 2949 0.00100389010131544 1641 1.24985747525843 -0.907810255460406 -1 0.833697254545531 2987 2290 2704 3198 3260 2145 1641 3637 3770 2698 2949 3108 M7999 RIZ_ERYTHROID_DIFFERENTIATION_HEMGN http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_HEMGN.html Selected gradually up-regulated genes whose expression profile follows that of HEMGN [GeneID=55363] in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). 17213805 16/47 Leona Saunders 0.000124373894230653 0.000224851878227177 4500 2992.09090909091 2950 1.13073569172491e-05 1656 1.78361091760193 -2.24699578221438 -1 2.3784088990172 4498 2282 1656 3093 2466 4144 4487 1907 2950 2125 3305 3109 M12026 LUND_SILENCED_BY_METHYLATION http://www.broadinstitute.org/gsea/msigdb/cards/LUND_SILENCED_BY_METHYLATION.html Genes up-regulated in FE-8 cells (fibroblasts) upon treatment with azacitidine [PubChem=9444]. 16568090 16/29 Arthur Liberzon 0.000168621200122478 0.000297275750103059 3630 3026.54545454545 2950 1.5330375059089e-05 2126 1.94671519626356 -1.83725853112926 -1 2.50961724905372 3630 2950 2148 3342 2528 4245 3885 2378 2161 2126 3899 3110 M4976 DIRMEIER_LMP1_RESPONSE_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/DIRMEIER_LMP1_RESPONSE_LATE_UP.html Cluster 3: genes up-regulated in B2264-19/3 cells (primary B lymphocytes) within 60-180 min after activation of LMP1 (an oncogene encoded by Epstein-Barr virus, EBV). 15674340 34/89 Arthur Liberzon 0.00136638523077859 0.00206945093452763 2365 2778.63636363636 2952 0.000124294055426615 1911 1.20134524235542 1.32274570329821 1 1.1786721830791 2361 2989 3103 2851 2952 3029 2525 1911 3060 3133 2651 3111 M2391 WANG_THOC1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_THOC1_TARGETS_DN.html Genes down-regulated in testis tissue expressing hypomorphic allele of THOC1 [GeneID=9984]. 19307311 11/47 Arthur Liberzon 0.000461660995127141 0.000750900181591733 3630 2755.27272727273 2952 4.19779910243662e-05 1050 1.92855913999153 -2.0383629148172 -1 2.20252736791948 3626 1976 1050 2364 2750 2952 4116 3069 3714 1070 3621 3112 M8818 BIDUS_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BIDUS_METASTASIS_DN.html Genes down-regulated in endometroid endometrial tumors from patients with lymph node metastases compared to those without the metastases. 16397028 113/275 Arthur Liberzon 7.49833246189258e-07 3.97929625327618e-06 3950 2963.90909090909 2953 6.81666819779559e-08 597 1.2695141916798 1.2082950547207 1 2.50591393095227 3948 1334 2261 2300 597 4297 4033 4208 2953 2131 4541 3113 M1011 REACTOME_MEIOTIC_RECOMBINATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOTIC_RECOMBINATION.html Genes involved in Meiotic Recombination 54/98 Reactome 0.106650172334853 0.121952832494173 650 2956.18181818182 2954 0.0102000800301556 646 0.893560825426521 -0.893560825426521 -1 0.298468412660827 646 3417 3233 2954 3900 2116 2558 2931 4212 3982 2569 3114 M7141 RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP.html Up-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: well vs moderately differentiated tumors. 18679425 70/165 Jessica Robertson 9.17187651238228e-06 2.34860182169527e-05 2035 2850.72727272727 2954 8.33810431861602e-07 1657 1.20770855474893 1.23665552866478 1 2.04355558960205 2034 3307 3134 3588 1657 2954 3007 4600 2906 2147 2024 3115 M16922 YAGI_AML_WITH_T_9_11_TRANSLOCATION http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_WITH_T_9_11_TRANSLOCATION.html Genes specifically expressed in samples from patients with pediatric acute myeloid leukemia (AML) bearing t(9;11) translocation. 12738660 92/231 Arthur Liberzon 8.70055681653773e-05 0.000163869812067105 2065 2593.45454545455 2955 7.90990993189571e-06 442 1.59128721122695 2.0768442719227 1 2.20186756008362 2064 4431 2242 3363 3373 3243 3141 577 2697 2955 442 3116 M2879 BLUM_RESPONSE_TO_SALIRASIB_DN http://www.broadinstitute.org/gsea/msigdb/cards/BLUM_RESPONSE_TO_SALIRASIB_DN.html Selected genes down-regulated in response to the Ras inhibitor salirasib [PubChem=5469318] in a panel of cancer cell lines with constantly active HRAS [GeneID=3265]. 17409441 262/576 Jessica Robertson 0.0839184282471183 0.0965721401684667 785 2989.09090909091 2956 0.00793650793650794 783 1.43430012670326 1.62063952117628 1 0.532216961080232 783 4357 2615 2956 3663 2997 2705 2491 3432 4063 2818 3117 M6364 HEIDENBLAD_AMPLIFIED_IN_SOFT_TISSUE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLIFIED_IN_SOFT_TISSUE_CANCER.html Genes from selected recurrently amplified regions in soft tissue tumors with supernumerary ring chromosomes. 16732325 10/18 Arthur Liberzon 0.0289805312994954 0.0374835135714699 2710 3101.36363636364 2958 0.0026699530216601 2561 1.02902949417928 -0.760276317748223 -1 0.536432687952061 2958 3191 2919 3471 3417 3529 2731 2561 3921 2707 2710 3118 M1786 YAMASHITA_SILENCED_BY_METHYLATION http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_SILENCED_BY_METHYLATION.html Genes silenced by DNA methylation in prostate cancer cell lines. 18381416 6/12 Jessica Robertson 0.00830679031352631 0.0114858717642916 1905 2807.90909090909 2959 0.000833800590773382 1463 2.99762185843672 2.99762185843672 1 2.12550005361241 1901 3006 4459 2649 3646 2959 3325 1463 1784 3059 2636 3119 M17411 KEGG_JAK_STAT_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_JAK_STAT_SIGNALING_PATHWAY.html Jak-STAT signaling pathway 59/186 KEGG 4.79243005871021e-07 3.03067844198597e-06 2960 2621.45454545455 2960 4.35675554789329e-08 432 1.30047282999162 1.18072061220224 1 2.62324252194316 2960 1341 2111 3291 432 3081 2268 4247 3069 2145 3891 3120 M10272 REACTOME_IONOTROPIC_ACTIVITY_OF_KAINATE_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IONOTROPIC_ACTIVITY_OF_KAINATE_RECEPTORS.html Genes involved in Ionotropic activity of Kainate Receptors 6/15 Reactome 0.00128424260242296 0.00195960951968544 2590 3032.18181818182 2960 0.000128498538221463 1826 0.751976009954791 -0.751976009954791 -1 0.744294319415564 2588 3005 4038 3707 2960 2372 2132 1826 4205 4407 2114 3121 M97 BAELDE_DIABETIC_NEPHROPATHY_UP http://www.broadinstitute.org/gsea/msigdb/cards/BAELDE_DIABETIC_NEPHROPATHY_UP.html Genes up-regulated in glomeruli of kidneys from patients with diabetic nephropathy (type 2 diabetes mellitus). 15042541 60/162 John Newman 0.000127799951128006 0.00023015779054029 2680 2776.09090909091 2960 1.16188523403945e-05 608 1.73609321943986 -1.73254076914411 -1 2.30861716455418 2676 2468 608 2248 3048 4360 3533 2960 3438 1405 3793 3122 M9271 REACTOME_PURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_METABOLISM.html Genes involved in Purine metabolism 17/39 Reactome 0.00942786949033108 0.0129405379120362 2965 2902.72727272727 2961 0.000860774155127179 2102 1.18045070099358 1.33583662685846 1 0.814666877987782 2961 3157 2102 4053 3242 2421 2318 3119 3048 2803 2706 3123 M7202 FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP.html Genes up-regulated in B-CLL (B-cell chronic lymphocytic leukemia) patients with mutated immunoglobulin variable heavy chain (VH) genes. 15817677 55/138 Kevin Vogelsang 0.0839184282471183 0.0965721401684667 1735 2967.18181818182 2961 0.00793650793650794 1731 1.37656593587496 1.14403736461216 1 0.510793888513525 1731 3830 2750 2814 4006 2283 2230 2961 3505 3515 3014 3124 M3010 HECKER_IFNB1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/HECKER_IFNB1_TARGETS.html Genes transcriptionally modulated in the blood of multiple sclerosis patients in response to subcutaneous treatment with recombinant IFNB1 [GeneID = 3456]. 23636981 55/145 Michael Hecker 1.37245744848486e-06 5.83638198535578e-06 4510 2725.54545454545 2961 1.24768936789578e-07 841 1.67962615564998 -1.53158111213947 -1 3.21331775142167 4510 1485 994 2961 841 3175 3625 4445 2498 1388 4059 3125 M928 REACTOME_INCRETIN_SYNTHESIS_SECRETION_AND_INACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INCRETIN_SYNTHESIS_SECRETION_AND_INACTIVATION.html Genes involved in Incretin Synthesis, Secretion, and Inactivation 12/29 Reactome 0.00284141846850517 0.00415311507904405 3250 2729.81818181818 2963 0.0002586449966302 1546 1.65839300501905 2.23685891404513 1 1.44371103668468 2225 3249 2479 3248 3054 2603 1580 3244 3837 2963 1546 3126 M4502 GAL_LEUKEMIC_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAL_LEUKEMIC_STEM_CELL_DN.html Genes down-regulated in leukemic stem cells (LSC), defined as CD34+CD38- [GeneID=947;952] cells from AML (acute myeloid leukemia patients) compared to the CD34+CD38+ cells. 17039238 136/464 Leona Saunders 1.3151076029711e-06 5.70082722250008e-06 3160 2648.09090909091 2965 1.19555308101069e-07 498 1.62355188731074 2.01619497258195 1 3.11209790300844 3158 2938 498 2418 821 4351 4007 2965 3056 1137 3780 3127 M1456 PARK_HSC_AND_MULTIPOTENT_PROGENITORS http://www.broadinstitute.org/gsea/msigdb/cards/PARK_HSC_AND_MULTIPOTENT_PROGENITORS.html Genes commonly expressed in long term hematopoietic stem cells (HSC) and multipotent progenitors (MPP). 11781229 47/120 Kevin Vogelsang 0.00839574228736535 0.0115985991623214 2595 3021.63636363636 2965 0.000766177704029511 1447 1.42167908455937 1.71478984331774 1 1.00585457251563 2595 3701 2943 4095 3494 2965 3204 1447 2131 3894 2769 3128 M874 REACTOME_SIGNALING_BY_ILS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ILS.html Genes involved in Signaling by Interleukins 61/135 Reactome 9.29115221712799e-06 2.37121088960367e-05 4175 3031.45454545455 2967 8.44653768747997e-07 1663 1.15008208221992 -1.04014816672603 -1 1.94429708361535 4171 1770 3170 1846 1663 2773 4599 4066 2967 2929 3392 3129 M14808 SESTO_RESPONSE_TO_UV_C7 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C7.html Cluster 7: genes changed in primary keratinocytes by UVB irradiation. 11867738 48/113 John Newman 6.96610506119172e-06 1.88036683852214e-05 2760 2967.27272727273 2967 6.33284283531266e-07 1555 1.34269445837378 -1.39881719657607 -1 2.31935844249849 2758 3507 2292 3068 1555 2930 2967 2923 3569 3513 3558 3130 M12008 GHO_ATF5_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GHO_ATF5_TARGETS_UP.html Genes up-regulated in HEP3B cells (liver cancer) overexpressing ATF5 [GeneID=22809] off a plasmid vector. 18701499 11/29 Jessica Robertson 0.0146749857028933 0.0196814490565993 3955 3160.36363636364 2967 0.00134307258624501 1839 1.7975970534214 0.918968440038964 1 1.12092381362501 3955 2790 2317 2967 3304 3839 4635 2949 1839 3570 2599 3131 M34 PID_TCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCR_PATHWAY.html TCR signaling in naïve CD4+ T cells 18832364 35/94 Pathway Interaction Database 9.48931618846376e-06 2.41143902706839e-05 4600 3004.54545454545 2968 8.62668829020073e-07 1674 1.38506660575079 1.37293236968024 1 2.33785651841023 4597 2450 2516 1752 1674 3756 4512 3513 2968 1975 3337 3132 M8292 ZIRN_TRETINOIN_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZIRN_TRETINOIN_RESPONSE_DN.html Genes down-regulated in MS427 cells (Wilms tumor with normal WT1 [GeneID=7490]) after treatment with 10 microM tretinoin (ATRA) [PubChem=444795] for 24 h. 15897880 3/7 Leona Saunders 0.0798127676250777 0.0965721401684667 1795 2946.54545454545 2968 0.00828331433789972 1271 0.610329348811277 0.610329348811277 1 0.226471171377868 1795 2968 4176 4067 3897 1495 1271 2046 4202 4489 2006 3133 M2525 BOUDOUKHA_BOUND_BY_IGF2BP2 http://www.broadinstitute.org/gsea/msigdb/cards/BOUDOUKHA_BOUND_BY_IGF2BP2.html Transcripts bound to IGF2BP2 [GeneID=10644] complexes and differentially regulated in myoblasts with IGF2BP2 [GeneID=10644] knockdown by RNAi. 20956565 94/205 Arthur Liberzon 3.18539600467591e-06 1.025189950406e-05 4065 3149.81818181818 2968 2.89581874258483e-07 1248 1.48505032398174 1.55863092715215 1 2.70826375190118 4063 2142 2968 1973 1248 3810 4350 4291 2866 2519 4418 3134 M19076 GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP.html Genes up-regulated in metastatic breast cancer tumors having type 2 amplification in the 20q13 region; involves MYBL2, STK6 and ZNF217 [GeneID=4605;6790;7764] 16899599 94/223 Leona Saunders 3.95935115379767e-05 8.18056415639148e-05 2970 2938.18181818182 2969 3.59947492021504e-06 2064 1.31698577709717 -1.1100103300196 -1 1.96756008648129 2969 3534 3399 2154 2134 2362 3877 3780 2408 3639 2064 3135 M2546 DUNNE_TARGETS_OF_AML1_MTG8_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/DUNNE_TARGETS_OF_AML1_MTG8_FUSION_UP.html Genes up-regulated in Kasumi-1 cells (acute myeloid leukaemia (AML) with the t(8;21) translocation) after knockdown of the AML1 MTG8 fusion [GeneID=861;862] by RNAi. 16652140 31/93 Leona Saunders 3.06357248332291e-06 9.96245708317221e-06 3715 2768.45454545455 2969 2.78506977223349e-07 1233 1.73545816759247 -2.15263924453342 -1 3.1728187867079 3711 3088 1240 2969 1233 2926 3776 2590 3394 2516 3010 3136 M14146 BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G1, defined by unsupervised clustering 17187432 101/241 Yujin Hoshida 5.84764598488769e-07 3.4235028683673e-06 4080 2728.18181818182 2969 5.31604321745889e-08 502 1.35661773366244 1.19049391424784 1 2.7102475926907 4080 3048 2969 1895 502 4583 2293 2459 1779 3066 3336 3137 M95 PID_CIRCADIAN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CIRCADIAN_PATHWAY.html Circadian rhythm pathway 18832364 11/21 Pathway Interaction Database 0.0245748838747578 0.0320774110966894 2385 2800.81818181818 2970 0.0022594333085823 1469 1.02257639090834 -1.47591627039601 -1 0.558351473412676 2384 3858 2970 3541 3419 1469 1879 2054 4154 3553 1528 3138 M17859 KIM_WT1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_DN.html Genes down-regulated in UB27 cells (osteosarcoma) at any time point after inducing the expression of a mutant form of WT1 [GeneID=7490]. 17430890 319/683 Arthur Liberzon 0.000248957372372221 0.000424841313523754 1360 2841.27272727273 2970 2.26350499509595e-05 1356 1.4509286897584 1.74889999380854 1 1.78823125061751 1356 4301 3136 3617 2615 2970 2255 1940 3007 3971 2086 3139 M3061 BIOCARTA_FEEDER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FEEDER_PATHWAY.html Feeder Pathways for Glycolysis 6/15 BioCarta 0.0013463202673673 0.00204501029915175 3160 2870.18181818182 2971 0.00013471366237535 1436 1.42700412658538 -0.58371703941372 -1 1.40276350233825 3156 2094 3835 2695 2971 3792 4422 1436 1553 3034 2584 3140 M17019 REACTOME_NEF_MEDIATED_DOWNREGULATION_OF_MHC_CLASS_I_COMPLEX_CELL_SURFACE_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEF_MEDIATED_DOWNREGULATION_OF_MHC_CLASS_I_COMPLEX_CELL_SURFACE_EXPRESSION.html Genes involved in Nef mediated downregulation of MHC class I complex cell surface expression 19/45 Reactome 0.161385165508919 0.18131164842359 2530 3048.72727272727 2971 0.0158730158730159 2162 1.33016797846594 -1.10707533651477 -1 0.360562373503196 2528 3398 2800 2583 3792 2162 2699 3840 3761 3002 2971 3141 M1745 MARSON_FOXP3_CORE_DIRECT_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_FOXP3_CORE_DIRECT_TARGETS.html Direct FOXP3 [GeneID=50943] targets that exhibit consistent transcriptional behavior in hybridoma and in ex vivo T lymphocytes. 17237765 11/32 Jessica Robertson 0.0149299960086597 0.0199891317990227 4315 2873.09090909091 2971 0.00136657177952571 192 0.900247897442866 -0.931940057372411 -1 0.559148823437157 4311 192 2718 2519 3308 2321 2990 4454 2971 2109 3711 3142 M2360 TERAO_AOX4_TARGETS_HG_UP http://www.broadinstitute.org/gsea/msigdb/cards/TERAO_AOX4_TARGETS_HG_UP.html Genes up-regulated in Harderian gland tissue upon knockout of AOX4 [GeneID=71872]. 18981221 17/44 Arthur Liberzon 0.000105944840809373 0.000194156247177443 3480 2719 2971 9.6318130101946e-06 1211 0.882302391897528 -0.761756032543217 -1 1.19709044396829 3476 1211 3365 2971 2430 1228 2168 3993 3155 3391 2521 3143 M18161 KORKOLA_YOLK_SAC_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_YOLK_SAC_TUMOR_UP.html Genes from the 12p region that were up-regulated in yolk sac tumor cells compared to normal testis. 16424014 16/42 Arthur Liberzon 0.00537444437853662 0.00758573685476584 2600 2906.90909090909 2972 0.000489783531460693 1941 1.42823063751085 1.7097351702099 1 1.10676116562988 2597 3290 2793 3315 3149 2972 3018 1941 2595 3346 2960 3144 M3346 RODRIGUES_NTN1_AND_DCC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_NTN1_AND_DCC_TARGETS.html Genes down-regulated in HCT8/S11 cells (colon cancer) which lack DCC [GeneID=9423] and stably express NTN1 [GeneID=1630]. 17334389 24/49 Leona Saunders 1.93008253931709e-06 7.19711745980863e-06 2975 3024.54545454545 2972 1.75462202963669e-07 1010 1.97111110642828 2.03599163044698 1 3.70538626678517 2972 2865 2006 2829 1010 4080 3824 4162 3465 2877 3180 3145 M19162 WANG_RESPONSE_TO_FORSKOLIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_FORSKOLIN_DN.html Genes down-regulated in LNCaP cells (prostate cancer) treated with forskolin [PubChem=47936], an activator of PKA pathway. 16751804 7/14 Arthur Liberzon 0.0974923294499934 0.111699035648574 2975 3118.81818181818 2973 0.0102053770682845 1183 0.613980153696526 0.61298531061539 1 0.213642662331229 2973 2526 4124 3978 3920 2121 1183 2150 4064 4472 2796 3146 M3146 MARSON_FOXP3_TARGETS_STIMULATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_FOXP3_TARGETS_STIMULATED_UP.html Genes with promoters bound by FOXP3 [GeneID=50943], dependent on it, and up-regulated in hybridoma cells stimulated by PMA [PubChem=4792] and ionomycin [PubChem=3733]. 17237765 12/41 Arthur Liberzon 0.0801124119272993 0.0965721401684667 4370 3072.45454545455 2973 0.00756251404100054 1874 1.65723797818764 -1.77502603166141 -1 0.614941144128353 4367 2821 2894 3197 3747 4021 3668 2015 1874 2973 2220 3147 M12175 BENNETT_SYSTEMIC_LUPUS_ERYTHEMATOSUS http://www.broadinstitute.org/gsea/msigdb/cards/BENNETT_SYSTEMIC_LUPUS_ERYTHEMATOSUS.html Genes significantly up-regulated in the blood mononuclear cells from patients with systemic lupus erythematosus compared to those from healthy persons. 12642603 21/109 Kevin Vogelsang 5.58190291821787e-07 3.33207606048012e-06 4370 3023 2974 5.07445848588613e-08 487 1.16589625281194 -1.06095889941065 -1 2.33423460613516 4370 1875 2334 2447 487 3791 4529 4108 2974 2084 4254 3148 M17866 KYNG_DNA_DAMAGE_BY_UV http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_UV.html UV only responding genes in primary fibroblasts from young donors. 15897889 40/99 Jessica Robertson 4.53285130089277e-05 9.17139084455247e-05 4170 3350.90909090909 2974 4.12085881623977e-06 2183 1.26404405954352 -1.2498502155439 -1 1.86552454516978 4170 3116 2974 2787 2183 2896 4673 4343 2596 2762 4360 3149 M17331 ALONSO_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ALONSO_METASTASIS_DN.html Down-regulated genes in melanoma tumors that developed metastatic disease compared to primary melanoma that did not. 17409456 5/41 Jessica Robertson 0.0103600974434789 0.0141620235181277 2570 3195.81818181818 2975 0.00104087159821004 1509 2.54802914711823 2.54802914711823 1 1.72199195746466 2570 4209 4507 4539 3903 2134 2975 1509 3727 2915 2166 3150 M20 PID_P38_MKK3_6PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_MKK3_6PATHWAY.html p38 MAPK signaling pathway 18832364 20/36 Pathway Interaction Database 0.00101358935609906 0.00157118085434343 3950 2946.09090909091 2976 9.2186967353335e-05 2009 1.34136983154105 -1.39610037638538 -1 1.37470895286165 3950 3548 2986 2976 2888 2903 3667 2343 3085 2009 2052 3151 M899 REACTOME_IL1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL1_SIGNALING.html Genes involved in Interleukin-1 signaling 25/45 Reactome 8.49824765833294e-05 0.000160317184085943 2360 2667.27272727273 2976 7.72597813616695e-06 1603 1.26036464323881 -1.21060914895318 -1 1.74835460584666 2360 2992 3308 3767 2360 1603 2976 2305 3008 2985 1676 3152 M8458 GRATIAS_RETINOBLASTOMA_16Q24 http://www.broadinstitute.org/gsea/msigdb/cards/GRATIAS_RETINOBLASTOMA_16Q24.html Genes from 16q24 region up-regulated in retinoblastoma tumors with 16q24 LOH (loss of heterozygocity) compared to those without the LOH. 17210724 11/22 Jessica Robertson 0.0839184282471183 0.0965721401684667 2500 3126 2977 0.00793650793650794 2105 1.04757682261704 1.17073471901085 1 0.388717913326806 2500 3377 2916 3633 4208 3537 2977 2105 3523 2838 2772 3153 M17990 BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_DN.html Genes from cluster 2: down-regulated in group C of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 29/69 Jessica Robertson 0.0019860068228714 0.00294973945229014 2580 2616.90909090909 2977 0.000180709265513498 1257 1.47444657060598 -1.37588983587096 -1 1.36365951246548 2579 1443 1257 3040 3010 2427 3577 3209 3728 1539 2977 3154 M2577 NUTT_GBM_VS_AO_GLIOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NUTT_GBM_VS_AO_GLIOMA_DN.html Top 50 marker genes for anaplastic oligodendroglioma (AO), a class of high grade glioma. 12670911 37/82 Arthur Liberzon 0.00304253196760164 0.00442635976410471 2980 2779.36363636364 2979 0.000276977078192369 1044 1.1427265258921 -1.06555041728945 -1 0.983239685959438 2979 2887 3455 3254 3287 1259 2262 3978 3214 2954 1044 3155 M2437 HUANG_GATA2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_GATA2_TARGETS_UP.html Genes up-regulated in G1ME cells (megakaryocyte/erythroid progenitor lacking GATA1 [GeneID=2623]) upon knockdown of GATA2 [GeneID=2624] by RNAi. 19620289 118/247 Arthur Liberzon 2.01793924226936e-05 4.56594074808025e-05 4035 3042.18181818182 2979 1.83450704723279e-06 1925 1.47946628754031 -1.58996407016437 -1 2.34725922941879 4033 2684 2263 2979 1925 3528 4385 2699 2989 2317 3662 3156 M1882 MARSHALL_VIRAL_INFECTION_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARSHALL_VIRAL_INFECTION_RESPONSE_DN.html Genes down-regulated in the influenza-specific CD8+ [GeneID=925] T lymphocytes from bronchoalveolar lavage (BAL) compared to those from spleen. 15831586 18/60 Arthur Liberzon 0.000496761961374687 0.000802473552433145 1990 2820.63636363636 2981 4.51703787400325e-05 862 1.73689970787007 2.13166270457232 1 1.96532563675448 1986 3653 2330 3913 2981 2589 3923 862 3583 3459 1748 3157 M519 REACTOME_GROWTH_HORMONE_RECEPTOR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GROWTH_HORMONE_RECEPTOR_SIGNALING.html Genes involved in Growth hormone receptor signaling 9/54 Reactome 0.0014421960645631 0.00217443074599185 3865 2785.36363636364 2982 0.000144313288863272 809 1.56928454191064 -1.97032227765007 -1 1.52734008813574 3862 1070 3919 1880 2982 3797 4329 2147 809 3398 2446 3158 M1411 LAU_APOPTOSIS_CDKN2A_UP http://www.broadinstitute.org/gsea/msigdb/cards/LAU_APOPTOSIS_CDKN2A_UP.html Genes up-regulated by UV-irradiation in cervical cancer cells after knockdown of CDKN2A [GeneID=1029]. 17369842 42/74 Leona Saunders 0.000104167431218708 0.000191498070886962 3195 2856.27272727273 2982 9.47021488653822e-06 1614 1.70789558638607 2.04904661087126 1 2.32097652437098 3195 3268 2082 2982 2424 4332 3888 1654 1614 2856 3124 3159 M6455 MORI_PRE_BI_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_PRE_BI_LYMPHOCYTE_DN.html Down-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Pre-BI stage. 18922927 52/138 Jessica Robertson 0.0146411271689411 0.0196472857713798 2835 3003.18181818182 2982 0.00133995293897933 2064 1.63302629373791 -1.12105642617332 -1 1.0187531482971 2833 2982 2253 2717 3303 2064 2685 4362 3359 3094 3383 3160 M517 REACTOME_BMAL1_CLOCK_NPAS2_ACTIVATES_CIRCADIAN_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BMAL1_CLOCK_NPAS2_ACTIVATES_CIRCADIAN_EXPRESSION.html Genes involved in BMAL1:CLOCK/NPAS2 Activates Circadian Expression 17/44 Reactome 0.0225886379304745 0.0295754002073774 3385 2945.90909090909 2983 0.00207490525850922 1765 1.19394216394993 -1.3596669983796 -1 0.667313218477668 1814 4036 2983 3923 3381 1765 2443 2190 4003 3384 2483 3161 M15743 ST_GA12_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GA12_PATHWAY.html G alpha 12 Pathway 25/52 Signaling Transduction KE 3.17260943166438e-05 6.75765808944512e-05 3675 3039.27272727273 2984 2.88423198603301e-06 1988 1.24974305725615 -0.951698271002724 -1 1.90501000620399 3672 2774 1988 2384 2066 4421 3016 3237 2727 2984 4163 3162 M2683 WINTER_HYPOXIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/WINTER_HYPOXIA_DN.html Genes down-regulated in head and neck tumor samples which clustered around known hypoxia genes. 17409455 34/115 Arthur Liberzon 3.34730384017005e-05 7.06870923615901e-05 3995 3075.27272727273 2984 3.04304979140116e-06 1575 1.20520124422001 -1.40509076896734 -1 1.82850422838188 3991 1773 1575 2416 2085 4238 2984 4475 3858 2307 4126 3163 M161 PID_IFNG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IFNG_PATHWAY.html IFN-gamma pathway 18832364 25/57 Pathway Interaction Database 8.59948478394937e-05 0.000162096483095683 2475 2938.09090909091 2986 7.81801903989491e-06 2231 0.842090781405543 0.768839780023066 1 1.16665733572255 2472 3186 3516 2986 2362 2231 2273 2694 3587 4001 3011 3164 M4241 BENPORATH_ES_2 http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_ES_2.html Set 'Set 'ES exp2': genes overexpressed in human embryonic stem cells according to a meta-analysis of 8 profiling studies. 18443585 26/66 Jessica Robertson 0.00193932275317499 0.0028886415834005 2325 2813.63636363636 2986 0.00017645767263443 1870 1.70873155649936 1.7295733856228 1 1.58601827534879 2321 4149 1870 3726 3005 3189 2013 3021 2123 2547 2986 3165 M1065 MIDORIKAWA_AMPLIFIED_IN_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/MIDORIKAWA_AMPLIFIED_IN_LIVER_CANCER.html Candidate genes in genomic amplification regions in hepatocellular carcinoma (HCC) samples. 16785998 36/76 Arthur Liberzon 6.20673725701187e-05 0.000121591851113535 2985 3132.45454545455 2987 5.64264761013074e-06 2268 1.27459953839074 1.46825990182851 1 1.82404425310063 2985 2987 2678 3712 2268 3774 2570 2904 3987 3276 3316 3166 M1225 OXFORD_RALA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_TARGETS_UP.html Genes up-regulated in the UMUC-3 cells (bladder cancer) after knockdown of RALA [GeneID=5898] by RNAi. 17496927 10/14 Arthur Liberzon 0.00881494854733485 0.0121312331550106 2950 2932.81818181818 2988 0.000804587967501338 1965 1.26586395487436 1.04337558653596 1 0.886591028618031 2950 3164 2709 3412 3229 3009 2437 3423 2975 1965 2988 3167 M11787 GRADE_COLON_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_CANCER_DN.html Down-regulated genes in colon carcinoma tumors compared to the matched normal mucosa samples. 17210682 25/64 Jessica Robertson 0.0839184282471183 0.0965721401684667 2990 3010 2988 0.00793650793650794 1990 2.12969590334953 2.42090851426805 1 0.790253212596753 2578 3967 1990 3139 4013 3802 2986 2287 2197 2988 3163 3168 M2417 WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D http://www.broadinstitute.org/gsea/msigdb/cards/WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D.html Genes with promoters bound by both PPARG and RXRA [GeneID=5468, 6256] at 8 day time point of adipocyte differentiation of 3T3-L1 cells (preadipocyte). 19414603 633/1344 Arthur Liberzon 3.60061749793396e-07 2.61589047989435e-06 4165 2992.90909090909 2988 3.60061808133418e-08 354 1.24233868869451 -1.0077258247447 -1 2.5350042459004 4165 2215 4663 2988 354 814 3798 4598 2858 3895 2574 3169 M1710 HILLION_HMGA1B_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/HILLION_HMGA1B_TARGETS.html Genes changed in Rat1a cells (fibroblasts) by overexpression of HMGA1 isoform b [GeneID=3159] off a plasmid vector. 19074878 67/192 Leona Saunders 2.59940909382867e-06 8.78849551220857e-06 3135 3268.45454545455 2990 2.36310196833136e-07 1161 1.61688197800896 1.59014990647911 1 2.98821593322312 3133 4058 2980 2813 1161 4542 4638 2951 2990 2927 3760 3170 M13941 DIRMEIER_LMP1_RESPONSE_EARLY http://www.broadinstitute.org/gsea/msigdb/cards/DIRMEIER_LMP1_RESPONSE_EARLY.html Clusters 1 and 2: genes up-regulated in B2264-19/3 cells (primary B lymphocytes) within 30-60 min after activation of LMP1 (an oncogene encoded by Epstein-Barr virus, EBV). 15674340 50/103 Arthur Liberzon 3.12269219575604e-05 6.67544981418562e-05 2830 3020.27272727273 2993 2.83885138209362e-06 1638 1.72423562719549 1.83178977761178 1 2.63163938486437 2828 3537 1928 3732 2059 4337 3742 2882 1638 2993 3547 3171 M1381 PETRETTO_LEFT_VENTRICLE_MASS_QTL_CIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_LEFT_VENTRICLE_MASS_QTL_CIS_UP.html Up-regulated cis-regulated expression quantitative loci (cis-eQTL) in the heart that were identified as candidate genes for the regulation of left ventricle mass (LVM). 18443592 5/8 Jessica Robertson 0.0765897756730953 0.0944224385172651 2790 3134.36363636364 2995 0.00793650793650794 1801 1.56416128821162 1.56416128821162 1 0.585993473660465 2787 3588 4344 3776 3764 2827 1801 2325 3365 2906 2995 3172 M5489 BIOCARTA_IL6_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL6_PATHWAY.html IL 6 signaling pathway 17/36 BioCarta 0.00058195172711898 0.000931361268196565 3000 2957.45454545455 2997 5.29187021879091e-05 1937 1.03350732693895 -0.918940388272759 -1 1.144990315785 2997 3342 3336 2808 2796 1937 2600 3330 3391 3381 2614 3173 M31 PID_BETA_CATENIN_DEG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BETA_CATENIN_DEG_PATHWAY.html Degradation of beta catenin 18832364 10/26 Pathway Interaction Database 0.0770555021395714 0.0949716157354107 1620 2776.63636363636 2997 0.00726314752731348 1545 1.01968807800583 1.01968807800583 1 0.381074644669525 1619 3346 2997 3411 3550 1712 1545 2801 4028 3479 2055 3174 M12086 SCHURINGA_STAT5A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHURINGA_STAT5A_TARGETS_UP.html Genes up-regulated in hematopoietic stem cells (HSC) overexpressing a constitutively active form of STAT5 [GeneID=6776] off retroviral vector. 15353555 9/32 Kevin Vogelsang 1.88234510528922e-05 4.29438615549429e-05 4270 2979.90909090909 2999 1.88236104998324e-06 1245 2.02319180076092 -2.00484353646387 -1 3.22960444857842 4270 1319 4383 2603 1939 3732 2999 3715 2644 1245 3930 3175 M8601 BIOCARTA_RAC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAC1_PATHWAY.html Rac 1 cell motility signaling pathway 17/38 BioCarta 0.00261757595352763 0.00384271958591181 3935 2835.27272727273 3001 0.000238245051094817 876 1.19514171888849 1.17375375240167 1 1.05516593294725 3932 876 2256 2226 3045 2310 3643 4367 3001 2210 3322 3176 M18513 ZHAN_MULTIPLE_MYELOMA_CD2_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD2_UP.html Top 50 up-regulated genes in cluster CD-2 of multiple myeloma samples with the characteristic expression spike of CCND3 [GeneID=896]. 16728703 21/60 Kevin Vogelsang 0.00205052644066884 0.00303978706136482 3605 2767.45454545455 3002 0.000186585467889567 1616 1.23667613785622 -1.12962066600725 -1 1.13785129244783 3601 2054 2266 3142 3014 2328 3002 2625 3179 1616 3615 3177 M736 REACTOME_NFKB_IS_ACTIVATED_AND_SIGNALS_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NFKB_IS_ACTIVATED_AND_SIGNALS_SURVIVAL.html Genes involved in NF-kB is activated and signals survival 7/19 Reactome 1.74388415784753e-06 6.74979256763237e-06 4080 2598.54545454545 3004 1.74388552635842e-07 236 1.82300314089916 2.15737569047238 1 3.44553616319195 4079 987 3983 829 1008 3869 4643 4450 236 1496 3004 3178 M941 REACTOME_FACTORS_INVOLVED_IN_MEGAKARYOCYTE_DEVELOPMENT_AND_PLATELET_PRODUCTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FACTORS_INVOLVED_IN_MEGAKARYOCYTE_DEVELOPMENT_AND_PLATELET_PRODUCTION.html Genes involved in Factors involved in megakaryocyte development and platelet production 73/159 Reactome 0.0839184282471183 0.0965721401684667 2130 3228.36363636364 3006 0.00793650793650794 1803 1.20142337629666 1.36080251556539 1 0.445804811685148 2129 4636 3006 4333 3796 2565 1803 2982 3369 4074 2819 3179 M1090 REACTOME_SIGNALING_BY_FGFR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR.html Genes involved in Signaling by FGFR 53/136 Reactome 5.38506073184753e-06 1.53493884363975e-05 2480 2855.45454545455 3007 4.89552173927397e-07 1464 1.22499844948893 1.26267088709359 1 2.15552298715072 2479 3209 3180 1764 1464 3007 2174 4203 3273 3656 3001 3180 M539 REACTOME_TRANS_GOLGI_NETWORK_VESICLE_BUDDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANS_GOLGI_NETWORK_VESICLE_BUDDING.html Genes involved in trans-Golgi Network Vesicle Budding 45/96 Reactome 9.11749745692722e-05 0.000169946670975183 3010 2881.72727272727 3009 8.288977578956e-06 1299 1.18824690822231 -0.972016198278435 -1 1.63731135588527 3009 3833 3378 2938 2384 1299 3383 2980 3225 3642 1628 3181 M15801 SCHLOSSER_SERUM_RESPONSE_AUGMENTED_BY_MYC http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_SERUM_RESPONSE_AUGMENTED_BY_MYC.html Cluster 2: genes up-regulated in B493-6 cells (B lymphocytes) by serum alone or in combination with MYC [GeneID=4609] but not by MYC alone. 15516975 72/146 Leona Saunders 3.6881695030592e-06 1.14906236026807e-05 4020 2829.27272727273 3009 3.35288698733738e-07 1258 1.34018941759281 -0.80512251782352 -1 2.41981506078068 4020 2446 3009 3848 1306 2728 3186 2024 1258 3600 3697 3182 M2585 SMIRNOV_RESPONSE_TO_IR_2HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_RESPONSE_TO_IR_2HR_UP.html Genes up-regulated in B lymphocytes at 2 h after exprosure to 10 Gy dose of ionizing radiation. 21844125 43/87 Itai Pashtan 0.00118550566389203 0.00181723243081389 1700 2924.27272727273 3011 0.000107831361381242 1700 1.55884162386852 1.61533088457077 1 1.56158359058332 1700 4067 2797 3604 2914 3011 3088 1925 3350 3593 2118 3183 M660 REACTOME_HYALURONAN_UPTAKE_AND_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HYALURONAN_UPTAKE_AND_DEGRADATION.html Genes involved in Hyaluronan uptake and degradation 6/13 Reactome 0.000730333292280745 0.00115152819906715 3615 2819.72727272727 3012 7.30573427384352e-05 1322 1.72240989679249 -1.22073854704435 -1 1.85018336727534 3615 1322 3951 3137 2849 3012 2014 1658 3381 2048 4030 3184 M919 REACTOME_PLATELET_SENSITIZATION_BY_LDL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_SENSITIZATION_BY_LDL.html Genes involved in Platelet sensitization by LDL 10/23 Reactome 0.397739832678321 0.431237588137579 2575 2987.45454545455 3012 0.0450505643387498 1744 0.904194950856613 0.904194950856613 1 0.120728901268246 2574 1978 2743 3065 3893 3163 1744 2915 4290 3485 3012 3185 M6031 BIOCARTA_SKP2E2F_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SKP2E2F_PATHWAY.html E2F1 Destruction Pathway 7/15 BioCarta 0.377321214000284 0.409952981406291 2635 3140.45454545455 3013 0.0462678847067417 2267 1.8818988242565 -1.8818988242565 -1 0.26639424184588 2631 3492 3828 3013 4383 2361 2267 2821 4027 3189 2533 3186 M559 REACTOME_SIGNALING_BY_CONSTITUTIVELY_ACTIVE_EGFR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_CONSTITUTIVELY_ACTIVE_EGFR.html Genes involved in Signaling by constitutively active EGFR 13/35 Reactome 0.00866751246344989 0.0119423591307634 3440 2937.18181818182 3015 0.000791077280670132 1454 1.61653929178644 -1.61653929178644 -1 1.13622527100986 3440 3455 2981 2580 3384 2153 3813 1454 3015 3673 2361 3187 M17115 SCHEIDEREIT_IKK_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SCHEIDEREIT_IKK_TARGETS.html Genes encoding substrates of IkappaB kinase (IKK) complex. 17072322 14/32 Arthur Liberzon 0.00156457603256969 0.00234686404885454 1750 2510.18181818182 3015 0.000142335438422118 964 1.30072849386606 -1.30072849386606 -1 1.25020454194016 1746 3578 3015 3468 4594 964 1139 1094 3269 3724 1021 3188 M1344 FUJIWARA_PARK2_IN_LIVER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/FUJIWARA_PARK2_IN_LIVER_CANCER_DN.html Genes down-regulated in tumorous liver tissues from PARK2 [GeneID=5071] knockout mice compared to the normal, non-tumorous tissue from wild type mice. 18574468 8/16 Jessica Robertson 0.0765897756730953 0.0944224385172651 3030 3163.18181818182 3015 0.00793650793650794 2403 1.79269535419926 -1.79269535419926 -1 0.671610904930348 3026 3462 4324 3015 4627 2507 3971 2436 2544 2403 2480 3189 M2085 VARELA_ZMPSTE24_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VARELA_ZMPSTE24_TARGETS_UP.html Top genes up-regulated in liver tissue from mice with knockout of ZMPSTE24 [GeneID=10269]. 16079796 30/57 John Newman 1.34497439962813e-05 3.22216259542813e-05 2885 2971.36363636364 3016 1.22271147475127e-06 1791 1.09872031833908 1.02016457823189 1 1.80398074413268 2882 2862 2948 3016 1791 3371 3160 3187 3181 2417 3870 3190 M9221 BROWNE_INTERFERON_RESPONSIVE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_INTERFERON_RESPONSIVE_GENES.html Genes up-regulated in primary fibroblast culture after treatment with interferon alpha for 6 h. 11711622 70/192 John Newman 0.000254531926433511 0.000433722402642703 3900 3159.72727272727 3017 2.31419436012821e-05 1961 1.45090180449595 -1.34225923021292 -1 1.7834329192656 3899 3017 1961 2990 2617 2956 3848 3673 3379 2768 3649 3191 M10145 BIOCARTA_PTEN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PTEN_PATHWAY.html PTEN dependent cell cycle arrest and apoptosis 14/25 BioCarta 0.0021840172299086 0.0032315455444748 3195 2987.18181818182 3019 0.000198744399875906 2386 0.925099468043816 1.02115464565532 1 0.84218959575765 2443 3453 3192 2386 3019 3194 2631 2393 3636 3719 2793 3192 M1107 GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN.html Genes down-regulated in ME-A cells (breast cancer, sensitive to apoptotic stimuli) exposed to doxorubicin [PubChem=31703] in the presence of medium concentrate (MC) from ME-C cells (breast cancer, resistant to apoptotic stimuli). 17160024 525/1118 Arthur Liberzon 0.000296763993156931 0.000499510083309403 2895 3250.09090909091 3019 2.96803631597634e-05 1454 1.23087593256119 -0.974363167126981 -1 1.48538491660064 2895 4352 4166 3962 2681 1454 2917 3966 3019 4171 2168 3193 M1888 WUNDER_INFLAMMATORY_RESPONSE_AND_CHOLESTEROL_DN http://www.broadinstitute.org/gsea/msigdb/cards/WUNDER_INFLAMMATORY_RESPONSE_AND_CHOLESTEROL_DN.html Genes down-regulated in gastric mucosal tissue of mice on 2% cholesterol [PubChem=5997] diet and infected with H. pylori vs those infected with H. pylori while on 0% cholesterol diet. 16951684 18/52 Jessica Robertson 0.00321374056685556 0.00465520503749154 3020 2505.27272727273 3019 0.000292585890377685 874 3.59244295755684 4.24475279074346 1 3.06230943234498 3019 3288 1250 1899 3698 3569 3145 1234 874 2327 3255 3194 M17006 RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_DN.html Down-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: moderately vs poorly differentiated tumors. 18679425 15/38 Jessica Robertson 0.0276363008190393 0.0358338975202042 1275 2601 3020 0.00254451797535519 1271 1.03362306418346 -1.03362306418346 -1 0.546212217400922 1271 3061 3020 3258 3408 1384 1946 2253 3869 3262 1879 3195 M11033 MENSE_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MENSE_HYPOXIA_UP.html Hypoxia response genes up-regulated in both astrocytes and HeLa cell line. 16507782 66/142 Kevin Vogelsang 3.96428257778107e-06 1.21257363965288e-05 3020 2929.18181818182 3020 3.60389974656791e-07 1335 1.43903141675463 -1.29736949747901 -1 2.58599204516707 3020 2578 2146 3155 1335 4197 3521 4504 2648 1440 3677 3196 M279 PID_RB_1PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RB_1PATHWAY.html Regulation of retinoblastoma protein 18832364 39/92 Pathway Interaction Database 0.00052551378403227 0.000845658513727753 3670 2892.63636363636 3021 4.77853959503279e-05 2087 1.6246549067957 -1.70532564548712 -1 1.82480042735297 3667 3021 2087 3114 2780 2416 3374 2412 3031 3088 2829 3197 M11725 REACTOME_CD28_CO_STIMULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CD28_CO_STIMULATION.html Genes involved in CD28 co-stimulation 18/41 Reactome 6.6208109881233e-05 0.000129056240808427 3230 2908.81818181818 3021 6.01910022467867e-06 1492 1.13242150640219 1.11595091223302 1 1.60986693201067 3226 2204 3021 1492 2283 3936 2592 3320 2643 3453 3827 3198 M16347 WANG_PROSTATE_CANCER_ANDROGEN_INDEPENDENT http://www.broadinstitute.org/gsea/msigdb/cards/WANG_PROSTATE_CANCER_ANDROGEN_INDEPENDENT.html Genes changed in prostate cancer: androgen independent vs androgen dependent samples. 19047173 43/131 Jessica Robertson 7.44122754546503e-06 1.97897799534899e-05 2810 3049.81818181818 3021 6.7647751951044e-07 1587 1.60655111831807 1.93600538114109 1 2.76210636325831 3080 3960 2441 3021 1587 4099 3174 2808 2980 3590 2808 3199 M143 PID_IL2_PI3K_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL2_PI3K_PATHWAY.html IL2 signaling events mediated by PI3K 18832364 26/58 Pathway Interaction Database 0.0118684625511553 0.016101799512077 3115 2828.63636363636 3022 0.00108481616344124 1524 1.36460319381398 -1.35891213010454 -1 0.894409370324236 3115 3279 2917 2901 3305 1752 4222 1524 3251 3022 1827 3200 M499 REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM.html Genes involved in Bile acid and bile salt metabolism 15/53 Reactome 0.00230146932306873 0.00339889229369684 3405 3087.45454545455 3022 0.00020944367943342 1477 1.52533237248818 1.7384852182659 1 1.37640256940392 3405 2716 1578 2882 3022 4358 3793 2655 3842 1477 4234 3201 M4902 LUI_THYROID_CANCER_PAX8_PPARG_DN http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_PAX8_PPARG_DN.html Top down-regulated genes distinguishing between follicular thyroid carcinoma (FTC) samples by the presence or absence of the PAX8-PPARG [GeneID=7849;5468] fusion protein. 15608688 41/83 Leona Saunders 0.0141104345460268 0.0189731696650449 1695 2611.36363636364 3022 0.00129106887385538 928 1.67293768330269 -1.67293768330269 -1 1.05292364511018 1694 4447 3548 3374 3859 928 1107 1598 3022 3759 1389 3202 M4988 JAERVINEN_AMPLIFIED_IN_LARYNGEAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/JAERVINEN_AMPLIFIED_IN_LARYNGEAL_CANCER.html Genes whose expression was increased due to copy number gain in laryngeal cancer tumors (both in primary cultures and cell lines). 16715129 24/50 Arthur Liberzon 0.00262632104397404 0.00385435026998508 985 2341.63636363636 3023 0.000239041959045279 982 1.51629372303732 -1.39183650418825 -1 1.337976963357 1496 3023 3069 3239 4246 982 982 1192 3050 3369 1110 3203 M12482 CADWELL_ATG16L1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CADWELL_ATG16L1_TARGETS_DN.html Genes down-regulated in Paneth cell (part of intestiinal epithelium) of mice with hypomorphic (reduced function) form of ATG16L1 [GeneID=55054]. 18849966 50/111 Jessica Robertson 3.13933918786324e-05 6.70507904937427e-05 2715 2860.36363636364 3023 2.85398544205513e-06 393 1.70946351208738 2.22349293961358 1 2.60789140696169 2713 4319 2057 4073 3563 3256 2516 393 2262 3289 3023 3204 M18973 NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON.html Genes within amplicon 20q12-q13 identified in a copy number alterations study of 191 breast tumor samples. 19010930 66/193 Jessica Robertson 2.44097810880936e-05 5.39293890517711e-05 3025 3195.63636363636 3026 2.21909562977166e-06 1978 1.69801089919929 1.77471109717657 1 2.64912158126944 3024 4221 2656 3993 1978 4395 3026 2448 2100 3635 3676 3205 M1384 SHIN_B_CELL_LYMPHOMA_CLUSTER_2 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_2.html Cluster 2 of genes distinguishing among different B lymphocyte neoplasms. 19010892 15/41 Jessica Robertson 0.000935665554899255 0.00145472089922293 3380 3170.09090909091 3027 8.50967029933647e-05 1955 0.880332803148238 -0.877926262695646 -1 0.912975654109949 3379 3027 3008 3642 2879 1955 3697 2964 4162 3771 2387 3206 M1000 REACTOME_TRAF6_MEDIATED_INDUCTION_OF_TAK1_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF6_MEDIATED_INDUCTION_OF_TAK1_COMPLEX.html Genes involved in TRAF6 mediated induction of TAK1 complex 11/31 Reactome 0.0406027727244482 0.0518008693130314 2375 2927.72727272727 3030 0.00376109837370076 1719 1.1470752808183 -1.1470752808183 -1 0.539061480124209 2373 4288 3226 3853 3630 1719 3030 1827 3638 2824 1797 3207 M11536 XU_HGF_SIGNALING_NOT_VIA_AKT1_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_SIGNALING_NOT_VIA_AKT1_48HR_DN.html Genes down-regulated in DU-145 cells (prostate cancer) in the absence and presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 25/57 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2620 3026.45454545455 3030 0.00793650793650794 1707 2.6048981804692 -1.47019612545581 -1 0.966583610936877 2619 3123 1875 3030 3560 2786 3929 4595 1707 2986 3081 3208 M9177 BIOCARTA_DC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DC_PATHWAY.html Dendritic cells in regulating TH1 and TH2 Development 21/83 BioCarta 0.00197810563147385 0.0029417337318586 2945 2936.09090909091 3033 0.000179989678668101 1130 1.32790106340909 -1.92281047599495 -1 1.22869804687965 2943 3844 2597 4150 3033 2176 3658 1130 3193 3159 2414 3209 M7775 EHLERS_ANEUPLOIDY_UP http://www.broadinstitute.org/gsea/msigdb/cards/EHLERS_ANEUPLOIDY_UP.html Up-regulated genes in the expression signature of aneuploidy in uveal melanoma tumors: low vs high aneuploidy. 18172260 24/54 Jessica Robertson 0.00248701557083219 0.00366022454928381 2330 3100.54545454545 3035 0.000226348318556941 2155 1.08172267435394 1.08172267435394 1 0.963385756331579 2327 3481 3510 4239 3035 2741 2428 2155 3423 3752 3015 3210 M22 PID_GMCSF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_GMCSF_PATHWAY.html GMCSF-mediated signaling events 18832364 25/57 Pathway Interaction Database 0.000563934431405387 0.00090407004637894 2495 2891.18181818182 3036 5.12799126160882e-05 1590 0.733015277950934 -0.743342711555278 -1 0.815545305400673 2494 3672 3536 3036 2791 1604 3170 1590 4088 4000 1822 3211 M10322 REACTOME_GLUCAGON_TYPE_LIGAND_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCAGON_TYPE_LIGAND_RECEPTORS.html Genes involved in Glucagon-type ligand receptors 9/36 Reactome 6.59043501470405e-06 1.79551037668042e-05 4505 2604.09090909091 3037 6.59045456001078e-07 602 1.85118045564805 -1.50688624816781 -1 3.21128273471503 4504 661 4009 778 1577 4552 3850 3037 1223 602 3852 3212 M18988 LIU_NASOPHARYNGEAL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/LIU_NASOPHARYNGEAL_CARCINOMA.html Low abundance transcripts specific to nasopharyngeal carcinoma (NPC). 18332864 51/167 Jessica Robertson 0.0398885711022971 0.0509174187375004 2375 2813.45454545455 3037 0.00369370048776907 1059 2.04701854043131 -1.76962066704685 -1 0.967574533864094 2372 3416 3037 2492 3735 1059 3206 3552 2768 3602 1709 3213 M7484 DAZARD_RESPONSE_TO_UV_SCC_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_RESPONSE_TO_UV_SCC_DN.html Genes down-regulated in SCC12B2 cells (squamous cell carcinoma) by UV-B irradiation. 12771951 93/230 John Newman 1.32162640480113e-05 3.17323784090975e-05 2885 2713.72727272727 3037 1.20148576763344e-06 1361 1.55863477873839 2.004007708207 1 2.56289659702188 2883 3141 2375 3066 1784 3754 3037 1361 1997 3231 3222 3214 M1033 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_10 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_10.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 10. 12554760 49/111 Arthur Liberzon 0.00249937201758313 0.00367650875253862 1155 2711.09090909091 3037 0.000227474184006265 1151 1.01600091041359 -1.1185123550056 -1 0.904137772434032 1151 3210 3346 4166 3037 1494 1942 1804 3613 4034 2025 3215 M4052 REACTOME_TELOMERE_MAINTENANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TELOMERE_MAINTENANCE.html Genes involved in Telomere Maintenance 45/93 Reactome 0.0791321743540021 0.0965721401684667 580 2914.54545454545 3038 0.00746641992517597 579 0.916628472072855 -0.916628472072855 -1 0.340127710953631 579 3085 3271 3038 3949 2128 2355 2814 4238 3985 2618 3216 M1120 JOHANSSON_GLIOMAGENESIS_BY_PDGFB_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOHANSSON_GLIOMAGENESIS_BY_PDGFB_UP.html Genes up-regulated in brain tumors induced by retroviral delivery of PDGFB [GeneID=5155]. 15750623 40/90 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2735 3141.81818181818 3038 0.00793650793650794 1571 1.70018765164175 -1.02765791031452 -1 0.630878216388706 2734 3993 1571 2760 3578 4183 4588 2615 3038 2333 3167 3217 M1569 BRACHAT_RESPONSE_TO_METHOTREXATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BRACHAT_RESPONSE_TO_METHOTREXATE_UP.html Genes up-regulated in FL5.12 cells (pro-B lymphocyte) in response to methotrexate [PubChem=4112]. 12447701 27/54 John Newman 0.415320710913563 0.448741722697937 2690 3210.18181818182 3038 0.0476190476190476 2460 1.06919848802425 -1.11025098169705 -1 0.136006997749468 2687 4392 2689 3219 4267 2502 2460 3038 4044 3123 2891 3218 M12367 LEE_NAIVE_T_LYMPHOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/LEE_NAIVE_T_LYMPHOCYTE.html Genes enriched in the naive circulating T lymphocytes compared to the earlier differentiation stages. 15210650 9/30 Arthur Liberzon 0.0709593044893321 0.0883879055919751 3040 3078 3039 0.00733325306116875 1101 1.32328603898577 -0.943003637294236 -1 0.509626135019461 3039 2561 4542 3282 4068 2057 1101 2989 4093 2583 3543 3219 M1462 BIOCARTA_CTL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CTL_PATHWAY.html CTL mediated immune response against target cells 20/57 BioCarta 0.161385165508919 0.18131164842359 3005 3226.18181818182 3041 0.0158730158730159 2529 1.53357042758215 1.50808466997845 1 0.415697718348707 3005 3244 2593 2584 3808 4215 3041 2857 3758 2529 3854 3220 M17776 REACTOME_DOWNSTREAM_SIGNALING_OF_ACTIVATED_FGFR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNSTREAM_SIGNALING_OF_ACTIVATED_FGFR.html Genes involved in Downstream signaling of activated FGFR 48/117 Reactome 3.79143005654168e-06 1.17426577957398e-05 2620 2858 3041 3.44676053692903e-07 1317 1.2611799322399 1.33524684614605 1 2.27281349125771 2620 2942 3041 1641 1317 3067 2435 4551 3210 3510 3104 3221 M1506 WEBER_METHYLATED_HCP_IN_SPERM_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_HCP_IN_SPERM_UP.html Methylated germline-specific genes with high-CpG-density promoters (HCP) in sperm. 17334365 8/41 Jessica Robertson 0.000125684987199092 0.000226959479774545 4580 3050.36363636364 3041 1.25692096287188e-05 530 2.21661808941731 -2.85148992621849 -1 2.95253225056491 4577 3254 4479 3041 2821 4417 4354 638 530 2406 3037 3222 M2056 RUAN_RESPONSE_TO_TROGLITAZONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TROGLITAZONE_DN.html Adipocyte abundant genes down-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to troglitazone [PubChem=5591]. 12732648 13/31 Arthur Liberzon 0.0798774012549053 0.0965721401684667 2815 3086.63636363636 3041 0.00753946712212538 1685 1.73790573384216 -1.12389008615254 -1 0.644874034126233 2813 4162 1808 4415 4621 1685 3190 3977 3041 2366 1875 3223 M4364 PASTURAL_RIZ1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PASTURAL_RIZ1_TARGETS_DN.html Genes down-regulated in K562 (chronic myelogenous leukemia, CML) cells engineered to stably express RIZ1 [GeneID=7799]. 16953217 4/6 Aravind Subramanian 0.1786779533526 0.200211594789642 1505 2938.81818181818 3042 0.0194915334969897 1413 1.04968721703423 1.04968721703423 1 0.26801078200376 1505 3042 4155 3460 3870 2040 1413 3159 4383 2669 2631 3224 M9043 BIOCARTA_GH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GH_PATHWAY.html Growth Hormone Signaling Pathway 20/53 BioCarta 0.00135178923559661 0.00205198715840807 3420 3076.45454545455 3044 0.000122965505203463 1885 1.08346334177218 -1.17127575340603 -1 1.06447267902557 3420 2996 3284 2191 2945 3110 4292 1885 3044 3920 2754 3225 M10500 XU_HGF_TARGETS_REPRESSED_BY_AKT1_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_TARGETS_REPRESSED_BY_AKT1_UP.html Genes up-regulated in DU-145 cells (prostate cancer) in the presence but not in the absence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 6/12 Arthur Liberzon 9.65720907560304e-05 0.000178939034117342 3885 2953.81818181818 3045 9.65762877886536e-06 1548 1.92967925438769 -2.52825765873476 -1 2.64315268550413 3883 2324 4245 2440 2431 3270 3830 3418 1548 2058 3045 3226 M17044 WANG_HCP_PROSTATE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/WANG_HCP_PROSTATE_CANCER.html Genes with the high-CpG-density promoters (HCP) that were up-regulated in 1542-CP3TX cells (prostate cancer) compared to 1542-NPTX (normal prostate). 17486081 86/220 Arthur Liberzon 0.000147406055188515 0.000262740500043128 3440 2933.81818181818 3045 1.3401448429681e-05 2102 1.39929024018816 -1.50438879709888 -1 1.83133356638868 3436 3763 3045 2353 2500 2102 3073 2570 3231 3604 2595 3227 M3990 GENTILE_UV_RESPONSE_CLUSTER_D1 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D1.html Cluster d1: genes down-regulated in WS1 cells (fibroblast) at 6 h after irradiation with high dose UV-C. 12907719 13/39 John Newman 1.49308107788242e-05 3.52650097326464e-05 4125 2907.09090909091 3046 1.35735564647281e-06 974 1.11094888887528 -1.174080445404 -1 1.80814174252463 4121 974 2819 2567 1829 2823 3487 3172 4055 3085 3046 3228 M7623 HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_DN.html Genes down-regulated in multiple myeloma (MM) cell lines treated with both decitabine [PubChem=451668] TSA [PubChem=5562]. 18172295 192/450 Jessica Robertson 6.28531442283395e-06 1.73456910396937e-05 4225 3041.27272727273 3047 5.71393852709508e-07 1518 1.27277698362347 -1.19150701212517 -1 2.2148905302243 4221 4128 2719 3124 1518 1802 4236 3047 3229 2652 2778 3229 M19048 RUIZ_TNC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUIZ_TNC_TARGETS_DN.html Genes down-regulated in T98G cells (glioblastoma) by TNC [GeneID=3371]. 15492259 93/241 Arthur Liberzon 0.00991378397597182 0.0135955492278033 1300 2756 3047 0.00090534018227484 933 1.72056654159337 1.96026267823765 1 1.17393145452573 1297 3412 933 2187 3696 3674 3391 3517 2718 2444 3047 3230 M2499 BIOCARTA_CARM_ER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CARM_ER_PATHWAY.html CARM1 and Regulation of the Estrogen Receptor 23/48 BioCarta 0.00279291891107357 0.00408860294198399 3150 2929.54545454545 3049 0.000254224623651458 1332 1.38599642646397 -1.10884559034054 -1 1.21002120274547 3148 3739 2886 3843 3049 1496 2737 3381 2909 3705 1332 3231 M27 BENPORATH_MYC_TARGETS_WITH_EBOX http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_MYC_TARGETS_WITH_EBOX.html Set 'Myc targets1': targets of c-Myc [GeneID=4609] identified by ChIP on chip in cultured cell lines, focusing on E-box-containing genes; high affinity bound subset 18443585 173/414 Jessica Robertson 2.42149513888707e-06 8.39284483788818e-06 3165 2764.81818181818 3049 2.201361640165e-07 1120 1.57138889329551 -1.25296803684375 -1 2.91562934145284 3164 3825 2714 3808 1120 1822 2412 3109 2172 3218 3049 3232 M1383 SHIN_B_CELL_LYMPHOMA_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_1.html Cluster 1 of genes distinguishing among different B lymphocyte neoplasms. 19010892 4/18 Jessica Robertson 0.107971073654112 0.123433142508702 3050 3363.36363636364 3049 0.0113606467279733 1777 0.717816803743411 -0.569674173275134 -1 0.238391302888111 2994 2260 4348 3049 3617 2639 1777 4337 4373 4555 3048 3233 M5989 IVANOV_MUTATED_IN_COLON_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/IVANOV_MUTATED_IN_COLON_CANCER.html Genes mutated in colon cancer cell lines, identified using the GINI method described in the paper. 17086209 6/17 Leona Saunders 0.0037504671159694 0.00539100886669712 3795 2617.90909090909 3052 0.000375681189349912 878 0.997014514278924 -0.997014514278924 -1 0.826660065592243 1551 3793 4196 3826 3857 878 1072 1668 3793 3052 1111 3234 M13760 HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_UP.html Genes up-regulated during differentiation from small pre-BII to immature B lymphocyte. 11779835 41/90 Arthur Liberzon 5.56181922874845e-05 0.000110201627509155 3885 2865 3052 5.05632712914335e-06 1205 1.96156311802376 -1.39855221763762 -1 2.83776676137947 3881 2914 1580 3303 2238 3052 3915 3591 1205 2384 3452 3235 M18979 HAMAI_APOPTOSIS_VIA_TRAIL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAMAI_APOPTOSIS_VIA_TRAIL_UP.html Genes up-regulated in T1 cells (primary melanoma, sensitive to TRAIL [GeneID=8743]) compared to G1 cells (metastatic melanoma, resistant to TRAIL). 16983347 356/869 Leona Saunders 0.000390907177764322 0.000644769811687298 2495 3139.90909090909 3055 3.55433321291915e-05 2135 1.59590141087116 1.92155774019095 1 1.86121708554531 2492 4216 2345 3488 2720 4431 3472 2135 2491 3694 3055 3236 M7248 RASHI_RESPONSE_TO_IONIZING_RADIATION_3 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_3.html Cluster 3: genes activated by ionizing radiation regardless of ATM [GeneID=472] status. 16314843 31/83 Arthur Liberzon 1.54820732833087e-05 3.63108085113036e-05 4435 2762.90909090909 3056 1.40747111240636e-06 487 1.73069522257391 -1.20114193013749 -1 2.80879020458989 4433 1492 1947 3056 1849 3620 4585 3201 487 2039 3683 3237 M647 REACTOME_ACTIVATED_POINT_MUTANTS_OF_FGFR2 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_POINT_MUTANTS_OF_FGFR2.html Genes involved in Activated point mutants of FGFR2 3/20 Reactome 0.0517106020891405 0.0652816073486965 3060 2999 3057 0.00529548435191011 1946 1.83561607901882 -1.83561607901882 -1 0.795236128894823 3057 3329 3945 3820 3509 2833 2623 1946 3157 2446 2324 3238 M14473 WEBER_METHYLATED_IN_COLON_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_IN_COLON_CANCER.html Genes identified as hypermethylated in SW48 cells (colon cancer). 16007088 6/24 John Newman 0.000914522061434298 0.00142421082747794 4565 3454.27272727273 3057 9.14898637334721e-05 1666 1.09945718958121 -0.635193695836396 -1 1.14392467498129 4562 1666 4398 2876 2887 4272 4408 2528 2723 3057 4620 3239 M3661 REACTOME_FGFR_LIGAND_BINDING_AND_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FGFR_LIGAND_BINDING_AND_ACTIVATION.html Genes involved in FGFR ligand binding and activation 3/24 Reactome 0.0517106020891405 0.0652816073486965 3060 3015.90909090909 3058 0.00529548435191011 1966 1.83561607901882 -1.83561607901882 -1 0.795236128894823 3058 3330 4098 3821 3510 2834 2624 1966 3158 2451 2325 3240 M11362 REACTOME_THE_ROLE_OF_NEF_IN_HIV1_REPLICATION_AND_DISEASE_PATHOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THE_ROLE_OF_NEF_IN_HIV1_REPLICATION_AND_DISEASE_PATHOGENESIS.html Genes involved in The role of Nef in HIV-1 replication and disease pathogenesis 34/79 Reactome 0.00294533685537924 0.00429696404243684 2310 3232.09090909091 3059 0.000268117040725247 1932 1.34734310232566 1.43564451178526 1 1.1656442833505 4242 2309 2705 1932 3059 4406 3615 3846 2666 2306 4467 3241 M1562 YIH_RESPONSE_TO_ARSENITE_C2 http://www.broadinstitute.org/gsea/msigdb/cards/YIH_RESPONSE_TO_ARSENITE_C2.html Genes in cluster 2: moderately up-regulated in HFW cells (fibroblast) upon treatment with sodium arsenite [PubChem=26435] at all time points. 12016162 19/36 John Newman 0.0205798130795108 0.0270469632894816 4215 3004.54545454545 3060 0.00188862597077457 1133 1.43962433479567 -0.759403706407193 -1 0.825052645908549 4215 3060 2290 2136 3362 2922 2654 3162 1133 3531 4585 3242 M2094 MARTENS_BOUND_BY_PML_RARA_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/MARTENS_BOUND_BY_PML_RARA_FUSION.html Genes with promoters occupied by PML-RARA fusion [GeneID=5371,5914] protein in acute promyelocytic leukemia(APL) cells NB4 and two APL primary blasts, based on Chip-seq data. 20159609 289/739 Arthur Liberzon 1.44928741748458e-06 6.01097981436963e-06 3835 3060.27272727273 3061 1.31753488384381e-07 872 1.48373697283606 -1.2212123677475 -1 2.83161637418147 3832 2262 1841 3061 872 3949 3469 4674 2440 2769 4494 3243 M1819 MATZUK_MEIOTIC_AND_DNA_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_MEIOTIC_AND_DNA_REPAIR.html Meitic and DNA repair genes important for female fertility, based on mouse models with female fertility defects. 18989307 27/156 Jessica Robertson 0.0609628309772908 0.076423709459493 2335 2997.18181818182 3062 0.00570188374262112 1301 1.03316772768641 -0.694656249125478 -1 0.42174947749001 2333 3278 3062 4359 3518 1730 1301 2335 4098 4033 2922 3244 M2269 MIKHAYLOVA_OXIDATIVE_STRESS_RESPONSE_VIA_VHL_DN http://www.broadinstitute.org/gsea/msigdb/cards/MIKHAYLOVA_OXIDATIVE_STRESS_RESPONSE_VIA_VHL_DN.html Proteins significantly repressed by oxidative stress (hydrogen peroxide [PubChem=784] in 786-O cells (renal clear cell carcinoma, RCC) expressing VHL [GeneID=7428]. 18285459 6/14 Arthur Liberzon 0.0524861508251867 0.0662224293933293 3835 3203.72727272727 3063 0.00537686519311649 2346 1.0757566082667 -0.752912714440807 -1 0.463601886673874 3833 2377 4637 2648 3514 4069 2841 2346 2519 3063 3394 3245 M764 REACTOME_INSULIN_SYNTHESIS_AND_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INSULIN_SYNTHESIS_AND_PROCESSING.html Genes involved in Insulin Synthesis and Processing 10/35 Reactome 0.00259800688490232 0.00381757926078779 2910 3174.18181818182 3065 0.000236461816806259 2657 2.22349699570092 2.22349699570092 1 1.9653964076625 2909 3065 2657 3298 3042 3233 2862 4178 3180 3484 3008 3246 M14301 REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA.html Genes involved in G beta:gamma signalling through PI3Kgamma 13/30 Reactome 0.00302622260689731 0.0044053678583165 3365 2939.45454545455 3065 0.000275490307176371 1613 1.45958351264026 1.40490735435573 1 1.25697537642677 3361 1613 2060 1972 3065 3326 3867 4122 2704 1749 4495 3247 M8344 NAKAJIMA_EOSINOPHIL http://www.broadinstitute.org/gsea/msigdb/cards/NAKAJIMA_EOSINOPHIL.html Top 30 increased eosinophil specific transcripts. 11493461 15/52 Kevin Vogelsang 0.00347809644054273 0.00501796795578301 3210 2885.27272727273 3066 0.000316691577148838 1107 2.03494850843495 1.19612360721521 1 1.71041234449073 3210 2751 1107 4121 3084 3032 1959 3788 3066 1990 3630 3248 M1055 REACTOME_RNA_POL_III_CHAIN_ELONGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_III_CHAIN_ELONGATION.html Genes involved in RNA Polymerase III Chain Elongation 8/20 Reactome 0.00313447860803288 0.00455164758513854 3305 2359 3067 0.000313890863518486 594 0.91343148314624 -0.91343148314624 -1 0.781899337946701 1341 3067 4090 3305 3923 672 594 1252 3188 3304 1213 3249 M1061 REACTOME_MEIOTIC_SYNAPSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOTIC_SYNAPSIS.html Genes involved in Meiotic Synapsis 50/198 Reactome 0.125248949109094 0.142663241498594 1440 3037.72727272727 3067 0.0120913905150056 1437 0.963039609896497 -0.945985781753593 -1 0.297696357806803 1437 3477 3067 2727 3629 2242 3230 2695 4265 3937 2709 3250 M7048 GENTILE_UV_HIGH_DOSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_HIGH_DOSE_UP.html Selected genes up-regulated in WS1 (fibroblast) in response to irradiation with high dose UV-C. 12907719 33/73 John Newman 0.0467251428846681 0.0593532175542301 2425 2855 3067 0.00434073388185489 1457 2.1520065352739 -1.06086382475934 -1 0.964828497316941 2425 3312 1457 2465 3477 2674 3639 3717 2071 3101 3067 3251 M2567 NATSUME_RESPONSE_TO_INTERFERON_BETA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NATSUME_RESPONSE_TO_INTERFERON_BETA_DN.html Genes down-regulated in T98 cells (glioma) 48 h after treatment with interferon beta. 16140920 41/112 John Newman 0.00108300392577822 0.00167324642142985 3070 2900 3068 9.85034026113688e-05 1005 1.95596998255957 -0.971931243322226 -1 1.98504219751098 3068 2944 2702 2850 3205 4535 3565 1005 1742 3172 3112 3252 M5039 NAGY_PCAF_COMPONENTS_HUMAN http://www.broadinstitute.org/gsea/msigdb/cards/NAGY_PCAF_COMPONENTS_HUMAN.html Composition of the 2 MDa human PCAF complex. 17694077 5/12 Arthur Liberzon 0.00187718790315177 0.00279786975641513 1830 2717.72727272727 3069 0.000187877551645827 378 0.826105627352758 -0.826105627352758 -1 0.770965579965235 1829 3069 4207 3909 3301 1105 378 1815 4333 4501 1448 3253 M8365 RHODES_UNDIFFERENTIATED_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/RHODES_UNDIFFERENTIATED_CANCER.html Genes commonly up-regulated in undifferentiated cancer relative to well-differentiated cancer, based on the meta-analysis of the OncoMine gene expression database. 15184677 73/172 John Newman 0.0139133856148234 0.0187297112872917 1595 2834.72727272727 3070 0.00127292405613563 974 1.79502912790007 2.12193004864336 1 1.1334464117165 1591 3076 974 2117 4059 4076 4086 2472 3070 2316 3345 3254 M64 PID_S1P_S1P4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P4_PATHWAY.html S1P4 pathway 18832364 7/18 Pathway Interaction Database 0.000279071487805496 0.000471593578022558 3875 2936.45454545455 3073 2.79106540403924e-05 1044 1.58135030671643 -2.59614464836358 -1 1.92276409028 3875 1808 3895 2178 2668 4020 3786 2760 1044 3194 3073 3255 M12001 SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5 http://www.broadinstitute.org/gsea/msigdb/cards/SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5.html Cluster 5 of method A: up-regulation of these genes in patients with non-small cell lung cancer (NSCLC) predicts good survival outcome. 18641660 50/191 Arthur Liberzon 3.25684542630515e-06 1.04388356139986e-05 4090 2961.90909090909 3073 2.96077295245266e-07 1258 1.31808607808302 1.20739187008559 1 2.39999259099465 4087 1863 3073 3906 1258 2791 4447 1848 2340 3579 3389 3256 M14132 SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP http://www.broadinstitute.org/gsea/msigdb/cards/SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP.html Genes up-regulated in head and neck squamous cell carcinoma (HNSCC) samples positive for HPV compared to the HPV-negative tumors. 16467079 42/105 Leona Saunders 0.047485297096679 0.0602861290151823 1270 2693.36363636364 3074 0.00441293752123768 1102 1.59899499636718 -1.59899499636718 -1 0.712933116608974 1269 4024 3074 4187 3586 1184 1102 2109 3433 3951 1708 3257 M11428 GAURNIER_PSMD4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/GAURNIER_PSMD4_TARGETS.html Inflammatory cytokines, chemokines and their cognate receptors up-regulated in THP-1 cells (monocyte) after treatment with PSMD4 [GeneID=5710]. 18632645 40/115 Jessica Robertson 0.00321053914323396 0.004652005697339 4545 2993.63636363636 3074 0.00029229399938322 1103 1.8159136212389 1.60985404986696 1 1.54813909074699 4544 2859 1201 1801 3074 3790 4111 4004 2515 1103 3928 3258 M1338 FUJIWARA_PARK2_HEPATOCYTE_PROLIFERATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/FUJIWARA_PARK2_HEPATOCYTE_PROLIFERATION_UP.html Genes commonly up-regulated in both non-tumorous and tumorous liver tissues of PARK2 [GeneID=5071] knockout mice. 18574468 13/31 Jessica Robertson 0.183238749220086 0.205174857549659 3285 3086.90909090909 3075 0.0182325079840783 2311 1.43659811320581 -1.43659811320581 -1 0.361214028414578 3282 3939 2865 2943 3824 2366 3075 2311 3871 3084 2396 3259 M1355 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX1_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX1_DN.html Early prostate development genes (down-regulated at 6 h dihydrotestosterone [PubChem=10635]) which are also down-regulated in normal epithelium vs high grade prostatic intraepithelial neoplasia (PIN). 18794802 3/12 Jessica Robertson 0.00294647403570133 0.00429728519492575 3945 2679.81818181818 3075 0.000295038811089314 972 1.95541234812064 -1.70230920101192 -1 1.69168785953187 3941 1898 4325 1519 3075 3091 3169 3232 972 1398 2858 3260 M583 REACTOME_RIP_MEDIATED_NFKB_ACTIVATION_VIA_DAI http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RIP_MEDIATED_NFKB_ACTIVATION_VIA_DAI.html Genes involved in RIP-mediated NFkB activation via DAI 13/35 Reactome 6.83999951481559e-05 0.00013277646116995 3235 2992.72727272727 3076 6.21837471441877e-06 2020 1.01361863610468 -1.00881722428521 -1 1.4364022390467 3235 2020 3088 2791 2292 2678 3778 4146 3335 3076 2481 3261 M19341 KRIGE_AMINO_ACID_DEPRIVATION http://www.broadinstitute.org/gsea/msigdb/cards/KRIGE_AMINO_ACID_DEPRIVATION.html The 'amino acid deprivation response' (AADR): genes up-regulated in HL-60 cells (acute promyelocytic leukemia, APL) after amino acid deprivation or treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703]. 18701491 22/39 Jessica Robertson 6.38485354706054e-06 1.75274889991363e-05 2560 2920.72727272727 3076 5.80442916117919e-07 1526 0.910716901805291 0.871017580555411 1 1.58332506613921 2559 3153 3115 4167 1526 3076 2553 2149 3666 3244 2920 3262 M590 REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT.html Genes involved in Mitochondrial Protein Import 41/74 Reactome 0.102266453025784 0.117054371978218 1080 2858.18181818182 3078 0.00975951587146433 1076 0.850013546056928 -0.850013546056928 -1 0.289454520807491 1076 3924 3675 3078 4143 1637 1741 2113 3960 4136 1957 3263 M15542 BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_UP http://www.broadinstitute.org/gsea/msigdb/cards/BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_UP.html Genes up-regulated in pre B lymphocyte after induction of physiological DNA double-strand breaks (DSB) by RAG2 [GeneID=5897]; the changes are independent of ATM [GeneID=472] signaling. 18849970 31/103 Jessica Robertson 0.011253677066251 0.0153120588654042 4185 3224.27272727273 3078 0.00102833261336288 2341 1.23214211641617 -1.20181771381909 -1 0.817426370606011 4185 3734 3078 4065 3265 2526 4369 2661 2341 2518 2725 3264 M16111 MOOTHA_GLYCOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_GLYCOLYSIS.html Genes involved in glycolysis; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 19/42 Vamsi Mootha 0.0839184282471183 0.0965721401684667 4330 3325.54545454545 3078 0.00793650793650794 2500 1.37933790819186 -1.20114724707883 -1 0.511822467302729 4329 2548 2500 2840 3637 3078 4143 4378 2661 3009 3458 3265 M12039 KEGG_ONE_CARBON_POOL_BY_FOLATE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ONE_CARBON_POOL_BY_FOLATE.html One carbon pool by folate 9/19 KEGG 0.0765897756730953 0.0944224385172651 2050 3069.18181818182 3079 0.00793650793650794 2047 1.804618007398 1.804618007398 1 0.676077577924533 2047 3380 3800 3097 3986 3441 3079 2859 2609 2559 2904 3266 M13763 RADAEVA_RESPONSE_TO_IFNA1_UP http://www.broadinstitute.org/gsea/msigdb/cards/RADAEVA_RESPONSE_TO_IFNA1_UP.html Genes up-regulated in primary hepatocytes and Hep3B (hepatocyte) cells in response to IFNA [GeneID=3439]. 11910354 54/136 Yujin Hoshida 3.49813516183729e-05 7.32451356942338e-05 4665 3091 3079 3.18017344143068e-06 1972 1.45593025433445 1.78543994007653 1 2.20068846963826 4662 3079 1972 2155 2101 3170 4155 3379 2568 2177 4583 3267 M9054 TOMLINS_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TOMLINS_METASTASIS_UP.html Top genes up-regulated in hormone refractory metastatic prostate cancer compared to localized prostate cancer. 17173048 13/28 Leona Saunders 0.00330539934200978 0.00477911179162538 3490 2865.81818181818 3080 0.000300943274961017 1795 1.07139500178335 1.017051842553 1 0.908822429773779 3486 1795 2791 2341 3080 3639 2165 2028 3488 3082 3629 3268 M7151 KEGG_SELENOAMINO_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SELENOAMINO_ACID_METABOLISM.html Selenoamino acid metabolism 12/28 KEGG 0.000424791628187823 0.000695761471404453 3820 2958.45454545455 3082 3.86248792865578e-05 1391 0.767030857351347 -0.713075230256069 -1 0.885280493234272 3820 1391 3312 2780 2737 2628 3935 1508 3743 3607 3082 3269 M671 REACTOME_REVERSIBLE_HYDRATION_OF_CARBON_DIOXIDE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REVERSIBLE_HYDRATION_OF_CARBON_DIOXIDE.html Genes involved in Reversible Hydration of Carbon Dioxide 7/12 Reactome 9.08368962392628e-06 2.32983960469176e-05 3395 2885 3083 9.08372675517762e-07 385 1.63398548794879 -1.99298963381198 -1 2.76693644220735 3392 385 3953 1810 1692 4517 4597 3494 2555 2257 3083 3270 M17450 LIU_SOX4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_SOX4_TARGETS_UP.html Genes up-regulated in LNCaP cells (prostate cancer) by overexpression of SOX4 [GeneID=6659] and down-regulated by its RNAi knockdown. 16618720 84/194 Arthur Liberzon 3.36621435479248e-05 7.09904611456235e-05 2690 3141.90909090909 3083 3.06024169295937e-06 2088 1.15003440802643 1.15275722741907 1 1.74402451025075 2686 2736 3083 3844 2088 3406 2929 3860 3253 2844 3832 3271 M8445 KIM_MYC_AMPLIFICATION_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYC_AMPLIFICATION_TARGETS_UP.html Genes positively correlated with amplifications of MYC [GeneID=4609] in SCLC (small cell lung cancer) cell lines. 16116477 139/298 Arthur Liberzon 0.000103982655950261 0.000191233408862999 2180 2980.09090909091 3083 9.45341554540623e-06 2088 1.40685401909584 1.56059971366153 1 1.91217935104394 2177 3627 3235 3113 2423 3988 3083 2088 2948 3443 2656 3272 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 0.0571402282135722 0.0718237954422745 530 2813 3084 0.00533460308564425 530 0.924522875029702 -0.924522875029702 -1 0.386510279407052 530 3508 3436 3084 3761 1630 2029 2428 4239 4040 2258 3273 M1825 REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_ACETYLCHOLINE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_ACETYLCHOLINE.html Genes involved in Regulation of Insulin Secretion by Acetylcholine 5/13 Reactome 0.0104884378461015 0.0143207516744848 2955 3033.90909090909 3085 0.00105382724994664 1514 2.49872111272945 -2.49872111272945 -1 1.68424786134852 2955 3692 4010 3395 3994 3191 3085 1514 2270 2890 2377 3274 M802 RIZ_ERYTHROID_DIFFERENTIATION_HBZ http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_HBZ.html Selected gradually up-regulated genes whose expression profile follows that of HBZ [GeneID=3050] in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). 17213805 20/65 Leona Saunders 0.00348949227901407 0.00503285959355492 2745 2877 3085 0.000317730854466722 1774 1.49545101450261 -1.87013326578616 -1 1.25625112147812 2741 3284 2669 3976 3085 2138 3165 1774 3367 3109 2339 3275 M16702 REACTOME_ACTIVATED_AMPK_STIMULATES_FATTY_ACID_OXIDATION_IN_MUSCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_AMPK_STIMULATES_FATTY_ACID_OXIDATION_IN_MUSCLE.html Genes involved in Activated AMPK stimulates fatty-acid oxidation in muscle 11/44 Reactome 0.0123972085216941 0.0167996874299186 4495 3089.90909090909 3086 0.00113342037408334 1762 0.791891323393678 -0.835971695069598 -1 0.51369990913887 4491 2174 2405 2705 3281 2887 3086 1762 3991 3556 3651 3276 M7298 BIOCARTA_ASBCELL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ASBCELL_PATHWAY.html Antigen Dependent B Cell Activation 4/14 BioCarta 0.0892438312498226 0.102474048820551 2735 3134.72727272727 3087 0.00930445019666037 1404 0.742030104777191 0.742030104777191 1 0.268353077074311 2731 1404 3814 3571 4430 3087 2227 2090 4117 4264 2747 3277 M5451 HOSHIDA_LIVER_CANCER_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_SURVIVAL_DN.html Survival signature genes defined in adjacent liver tissue: genes correlated with good survival of hepatocellular carcinoma (HCC) patients. 18923165 68/179 Yujin Hoshida 0.0387725046903573 0.0495737945372481 3090 2997.27272727273 3088 0.00358847057102106 1547 1.03770425880079 -1.1395057100267 -1 0.494902256406863 3088 3077 3315 3918 3456 1547 2703 2639 3600 3847 1780 3278 M13096 SA_PROGRAMMED_CELL_DEATH http://www.broadinstitute.org/gsea/msigdb/cards/SA_PROGRAMMED_CELL_DEATH.html Programmed cell death, or apoptosis, eliminates damaged or unneeded cells. 7/19 SigmaAldrich 0.0765897756730953 0.0944224385172651 3320 3057.63636363636 3089 0.00793650793650794 2251 0.914863035059438 -1.01110419383123 -1 0.342741998994448 3320 2251 3892 3456 3737 2936 2408 2312 3040 3193 3089 3279 M17321 REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES.html Genes involved in Synthesis and interconversion of nucleotide di- and triphosphates 14/22 Reactome 0.223527448079584 0.248682246367742 1780 3066.63636363636 3089 0.0227369818842087 1777 0.833747842721598 -0.891519747755174 -1 0.184181601930057 1777 3246 3089 3992 3728 2359 2482 2947 3957 3721 2435 3280 M1659 CARDOSO_RESPONSE_TO_GAMMA_RADIATION_AND_3AB http://www.broadinstitute.org/gsea/msigdb/cards/CARDOSO_RESPONSE_TO_GAMMA_RADIATION_AND_3AB.html Down-regulated synergystically by gamma-irradiation and 3-aminobenzamine [PubChem=1645], an inhibitor of PARP1 [GeneID=142]. 12379459 12/42 John Newman 0.00122809067520556 0.00187820917232809 3685 3056.72727272727 3089 0.00011170697817746 1562 0.978314890727741 0.875741524148527 1 0.974910066908258 3684 1562 3231 3143 2924 4188 2043 2774 3089 2971 4015 3281 M1345 RHODES_CANCER_META_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/RHODES_CANCER_META_SIGNATURE.html Genes commonly up-regulated in cancer relative to normal tissue, according to the meta-analysis of the OncoMine gene expression database. 15184677 58/130 John Newman 2.50049857110827e-05 5.49335973005783e-05 3635 2958.81818181818 3090 2.27320635634883e-06 1911 1.6322931259471 2.14535375692386 1 2.54181250629233 3631 3392 1911 2466 1987 3113 3303 2580 2943 3090 4131 3282 M846 REACTOME_FRS2_MEDIATED_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FRS2_MEDIATED_CASCADE.html Genes involved in FRS2-mediated cascade 11/43 Reactome 0.0150978670132157 0.0201908118789751 2240 2852.27272727273 3093 0.00138204410712933 1143 1.25629400695494 -1.25629400695494 -1 0.778288899201736 2237 4404 3093 3665 3312 1143 1644 3067 3814 3559 1437 3283 M19752 REACTOME_COMPLEMENT_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COMPLEMENT_CASCADE.html Genes involved in Complement cascade 13/39 Reactome 0.00385161477310823 0.00553300638466743 3000 3031.36363636364 3096 0.000350761318189978 1747 1.30078668376319 1.41779207712256 1 1.07315971814589 2996 1971 1747 3450 3096 3654 3845 2364 3885 3080 3257 3284 M14344 DASU_IL6_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/DASU_IL6_SIGNALING_UP.html Genes up-regulated in normal fibroblasts in response to IL6 [GeneID=3569]. 15095275 76/166 Arthur Liberzon 0.00388488540024605 0.00557909070963928 3565 2964.09090909091 3097 0.000353796596368605 1063 1.83033245826001 2.14829746304279 1 1.50762930606973 3562 3501 1063 2116 3097 4244 4113 2514 2735 1670 3990 3285 M4629 KEGG_NITROGEN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NITROGEN_METABOLISM.html Nitrogen metabolism 11/23 KEGG 3.26989643309987e-06 1.04592045634853e-05 3870 2933.09090909091 3098 2.97263753928291e-07 1261 1.63398548794879 -1.99298963381198 -1 2.97468173600958 3870 1508 1458 2683 1261 4403 4249 3200 3098 2811 3723 3286 M13618 REACTOME_CD28_DEPENDENT_VAV1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CD28_DEPENDENT_VAV1_PATHWAY.html Genes involved in CD28 dependent Vav1 pathway 7/22 Reactome 0.000246976710661583 0.000422076172924938 4255 3103.18181818182 3099 2.4700416382889e-05 1525 1.48253767346705 1.3769107830647 1 1.82872528600807 4254 1949 4019 1674 2632 3099 4644 4340 1525 2260 3739 3287 M4399 MOHANKUMAR_TLX1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOHANKUMAR_TLX1_TARGETS_UP.html Up-regulated in MCF7 cells (breast cancer) by TLX1 (HOX11) [GeneID=3195]. 17213808 308/650 Arthur Liberzon 1.06252531146076e-07 1.26050471126711e-06 4305 2890.09090909091 3102 9.65932147979207e-09 64 1.36245028571372 -1.29756638873098 -1 2.93800037045349 4303 2529 2897 1061 64 3704 3698 3682 2676 3102 4075 3288 M2203 PHESSE_TARGETS_OF_APC_AND_MBD2_DN http://www.broadinstitute.org/gsea/msigdb/cards/PHESSE_TARGETS_OF_APC_AND_MBD2_DN.html Genes down-regulated in small intestine upon loss of both APC and MBD2 [GeneID=324, 8932]. 18644872 9/22 Arthur Liberzon 0.0043564954994159 0.00621825705460339 2055 2726.81818181818 3103 0.000436505971237871 1061 1.45583049837835 1.45583049837835 1 1.17408839388693 2051 3620 4629 3103 4413 1524 1061 1532 3493 3425 1144 3289 M7547 JIANG_HYPOXIA_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_HYPOXIA_CANCER.html Genes up-regulated in 786-0 cells (renal carcinoma, RCC) by hypoxia and in the absensce of VHL [GeneID=7428]. 12692265 64/138 John Newman 0.00260443276599377 0.00382582192521843 3105 3124 3105 0.000237047372668923 2436 1.47434091563145 -1.16405134375191 -1 1.3026965809429 3105 3883 2957 3261 3043 2454 2586 3691 2436 3577 3371 3290 M1343 FUJIWARA_PARK2_IN_LIVER_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/FUJIWARA_PARK2_IN_LIVER_CANCER_UP.html Genes up-regulated in tumorous liver tissues from PARK2 [GeneID=5071] knockout mice compared to the normal, non-tumorous tissue from wild type mice. 18574468 3/9 Jessica Robertson 0.0027630274055646 0.00404610825702367 1900 2719.81818181818 3106 0.00027664688735765 1042 1.96128939350297 -1.96128939350297 -1 1.71552409813729 1896 3106 4323 4054 3177 1279 1464 3392 3721 2464 1042 3291 M8077 SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_DN.html Down-regulated genes whose expression correlated with histologic grade of invasive breast cancer tumors: comparison of grade 1 vs grade 3. 16478745 25/78 Arthur Liberzon 0.000673589650241079 0.00106853117841222 2235 3070.36363636364 3108 6.12541796747957e-05 2103 0.808534669705635 0.852095672454347 1 0.878115522553422 2234 3122 3391 3402 2827 2865 2103 2756 3962 4004 3108 3292 M13055 DAVIES_MULTIPLE_MYELOMA_VS_MGUS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVIES_MULTIPLE_MYELOMA_VS_MGUS_UP.html Genes up-regulated in multiple myeloma (MM) compared to monoclonal gammopathy of uncertain significance (MGUS). 12947006 16/40 Arthur Liberzon 0.0128662573948009 0.0174151594893233 2430 2866.81818181818 3109 0.00117655681994321 1788 1.10452192401085 1.14886527661434 1 0.710194558365061 2429 1788 2401 2272 3284 2243 3989 3121 3547 3352 3109 3293 M926 REACTOME_PROSTACYCLIN_SIGNALLING_THROUGH_PROSTACYCLIN_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROSTACYCLIN_SIGNALLING_THROUGH_PROSTACYCLIN_RECEPTOR.html Genes involved in Prostacyclin signalling through prostacyclin receptor 6/22 Reactome 1.80512353015781e-05 4.13547875365233e-05 4535 2867.81818181818 3110 1.80513819344476e-06 789 1.6348595623573 -1.54159775006705 -1 2.61949852073654 4532 789 4056 1650 1919 4630 4458 3110 2160 867 3375 3294 M14539 BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP.html Genes up-regulated in medullary breast cancer (MBC) relative to ductal breast cancer (DBD). 16651414 134/307 Arthur Liberzon 5.18294798000026e-06 1.49460272210961e-05 3555 2911.81818181818 3111 4.71178199133841e-07 1444 1.22880920060923 -1.02691573428316 -1 2.16742313881334 3551 1678 3407 3919 1444 1810 2143 4325 3111 3855 2787 3295 M1487 MORI_PLASMA_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_PLASMA_CELL_UP.html Up-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: plasma cell. 18922927 26/65 Jessica Robertson 0.028373171906134 0.0367182224667616 2525 3075.72727272727 3111 0.00261325856600093 2379 0.762904129664695 -0.762904129664695 -1 0.40019985998394 2524 2840 3678 3208 3414 2517 3111 3012 3136 4014 2379 3296 M1407 WELCH_GATA1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WELCH_GATA1_TARGETS.html Genes up-regulated after GATA1 [GeneID=2623] activation in G1E-ER4 cells (erythroid precursors engineered to express GATA1 upon addition of estradiol [PubChem=5757]). 15297311 10/30 Jean-Pierre Bourquin 0.000259099010814653 0.000441023597776049 2140 2652.63636363636 3111 2.35572300479579e-05 751 1.04339128293099 -1.13064474390017 -1 1.27976031219591 2136 3519 3111 3775 4221 1154 2092 751 3395 3492 1533 3297 M13045 SAMOLS_TARGETS_OF_KHSV_MIRNAS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SAMOLS_TARGETS_OF_KHSV_MIRNAS_UP.html Genes up-regulated in 293 cells (embryonic kidney) upon expression of KHSV (Kaposi sarcoma-associated herpesvirus) microRNAs. 17500590 9/44 Arthur Liberzon 0.000313734415925693 0.000524869501259478 3115 3047 3112 3.13778717906363e-05 2023 1.15965022082505 -0.789261135824363 -1 1.39031532945818 3112 2674 4119 2568 2693 2479 3544 2023 3753 3407 3145 3298 M8493 BASSO_CD40_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/BASSO_CD40_SIGNALING_UP.html Gene up-regulated by CD40 [GeneID=958] signaling in Ramos cells (EBV negative Burkitt lymphoma). 15331443 83/201 Kevin Vogelsang 0.00106829700610186 0.00165161325324754 4620 3143.18181818182 3112 9.71651011726076e-05 1425 1.5187186679748 -1.65126465536129 -1 1.54442923086705 4619 3112 1425 2156 2896 4008 3916 3185 2893 2527 3838 3299 M23 PID_WNT_NONCANONICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_WNT_NONCANONICAL_PATHWAY.html Noncanonical Wnt signaling pathway 18832364 25/51 Pathway Interaction Database 1.18507183371472e-05 2.90138276530155e-05 3975 2957.45454545455 3113 1.07734383397967e-06 1370 1.37685255339026 1.33540188449715 1 2.28356443302535 3971 1370 2027 2053 1751 3846 4548 3657 3113 1995 4201 3300 M5784 SHAFFER_IRF4_TARGETS_IN_MYELOMA_VS_MATURE_B_LYMPHOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/SHAFFER_IRF4_TARGETS_IN_MYELOMA_VS_MATURE_B_LYMPHOCYTE.html IRF4 [GeneID=3662] target genes up-regulated in primary myeloma vs. mature B lymphocytes. 18568025 64/146 Jessica Robertson 8.10909576134521e-06 2.12396737148495e-05 3070 3130.45454545455 3114 7.37193241022019e-07 1616 1.29382762696536 1.32491812051078 1 2.20992589872612 2834 3503 3114 3071 1616 3717 3211 3879 3068 3070 3352 3301 M904 RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_UP.html Up-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: well vs poorly differentiated tumors. 18679425 155/403 Jessica Robertson 2.14563618636237e-06 7.71638616215968e-06 2385 2905.18181818182 3116 1.95058025361907e-07 1062 1.31929070682749 1.4822084066717 1 2.46547375574381 2385 3826 3165 3116 1062 3851 3238 3008 3233 2631 2442 3302 M389 NAKAJIMA_MAST_CELL http://www.broadinstitute.org/gsea/msigdb/cards/NAKAJIMA_MAST_CELL.html Top 50 most-increased mast cell specific genes. 11493461 39/75 Kevin Vogelsang 4.27549777070454e-07 2.82882663468366e-06 2705 2773.63636363636 3117 3.88681691055314e-08 391 1.51587916373904 -1.15020103039197 -1 3.07433437625706 2703 3117 1664 3850 391 4405 3121 1608 3412 3089 3150 3303 M2662 SINGH_NFE2L2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SINGH_NFE2L2_TARGETS.html Selected electrophile and drug detoxication genes down-regulated in A549 and H460 cells (lung cancer) upon knockdown of NFE2L2 [GeneID=4780] by RNAi. 18829555 16/38 Jessica Robertson 4.17512861938444e-05 8.55472352883056e-05 3570 2900.36363636364 3117 3.79564350589555e-06 970 1.13990955248181 1.10171728765766 1 1.69491762928877 3570 970 2288 2051 2149 4141 4054 3117 3750 1575 4239 3304 M1833 MATZUK_SPERMATOZOA http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_SPERMATOZOA.html Spermatozoa genes, based on mouse models with male reproductive defects. 18989307 64/220 Jessica Robertson 4.94408952198663e-05 9.92630826907856e-05 2615 3129.18181818182 3117 4.49472784969981e-06 2047 1.29397927079098 1.63077343017483 1 1.89345586010409 2614 4262 3117 3164 2208 3451 3773 3601 3115 3069 2047 3305 M2411 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_5 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_5.html Genes regulated in MCF7 cells (breast cancer) by expression of the truncated (611-CTF) form of ERBB2 [GeneID=2064] at 15 h time point. 19364815 5/13 Arthur Liberzon 0.00126069004067346 0.00192555199823854 2910 2954.36363636364 3117 0.000126140581496064 1060 1.43912705769956 -1.43912705769956 -1 1.42843130469594 2910 3524 4662 3148 4256 3117 3385 1060 1459 2921 2056 3306 M170 KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN.html Genes down-regulated in MEWO cells (melanoma) after 96 h of methionine [PubChem=876] deprivation. 16908595 49/107 Arthur Liberzon 2.46345406671331e-05 5.42979574629284e-05 4320 3306.09090909091 3118 2.23952877428927e-06 1983 1.44081049628538 1.70222855622208 1 2.2462970939351 4316 2885 2206 3118 1983 4001 4589 2855 2560 3273 4581 3307 M1405 KIM_GERMINAL_CENTER_T_HELPER_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_GERMINAL_CENTER_T_HELPER_UP.html Genes up-regulated in germinal center T helper cells compared to other CD4+ [GeneID=920] T lymphocyte types. 15213097 40/100 Kate Stafford 0.00440984054270841 0.0062905670572699 3430 3105.81818181818 3119 0.000401700439492535 2109 1.53445970108261 2.05193853943851 1 1.23468446518547 3427 3084 2109 3582 3119 4112 2812 2206 2365 3127 4221 3308 M7591 REACTOME_G1_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G1_PHASE.html Genes involved in G1 Phase 20/48 Reactome 0.0839184282471183 0.0965721401684667 3120 3213.90909090909 3120 0.00793650793650794 1989 2.04413728923626 -1.45207462392387 -1 0.758505501707266 3120 4105 2723 3849 4141 1989 2784 3547 2677 3107 3311 3309 M6984 GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_UP.html Genes up-regulated in common hematopoietic progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 35/87 Arthur Liberzon 0.00940059713101337 0.0129084291716059 3515 3268.45454545455 3120 0.000858273438426021 2489 1.5490258463556 1.94047056521431 1 1.06964330749596 3512 3086 3011 2673 3240 4229 3100 2489 3120 3549 3944 3310 M13183 ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP.html Genes down-regulated in P493-6 cells (B lymphocyte, Burkitt's lymphoma model) by MYC [GeneID=4609] and up-regulated by RNAi knockdown of TFRC [GeneID=7037]. 16508012 62/186 Leona Saunders 0.000226360512102227 0.000388828944175599 3290 3199.27272727273 3120 2.05803459953892e-05 2470 1.64510320058012 -1.36433844679699 -1 2.05067823344267 3290 3504 2470 3120 2601 2742 3767 4560 2927 2982 3229 3311 M7910 CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_HD_MTX_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_HD_MTX_DN.html Genes specifically down-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490] and high dose methotrexate (HDMTX) [PubChem=4112]. 12704389 12/33 Arthur Liberzon 0.466738071388703 0.50186659075894 2490 3433.63636363636 3120 0.0555555555555556 2489 1.48040191801531 1.48040191801531 1 0.162019643705591 2489 4406 2699 4311 3924 3044 2547 4186 4068 2976 3120 3312 M6768 REACTOME_E2F_MEDIATED_REGULATION_OF_DNA_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_E2F_MEDIATED_REGULATION_OF_DNA_REPLICATION.html Genes involved in E2F mediated regulation of DNA replication 18/40 Reactome 0.751985672431077 0.78691488633587 2050 3344.27272727273 3122 0.119047619047619 2048 1.14717066743448 -1.14717066743448 -1 0.0436397409800564 2048 3681 2863 3122 4659 2831 3019 3393 4237 3875 3059 3313 M4175 FERRANDO_LYL1_NEIGHBORS http://www.broadinstitute.org/gsea/msigdb/cards/FERRANDO_LYL1_NEIGHBORS.html Nearest neighbors of LYL1 [GeneID=4066], based on the close agreement of their expression profiles with that of LYL1 in pediatric T cell acute lymphoblastic leukemia (T-ALL). 12086890 9/18 Jean Junior 0.0253948707331229 0.033055656737615 2285 3044 3124 0.00256898306469999 837 1.03783614426611 -0.811385032410593 -1 0.561734395494597 2282 3103 4380 3836 4204 1446 837 3124 4335 3413 2524 3314 M15926 BIOCARTA_TFF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TFF_PATHWAY.html Trefoil Factors Initiate Mucosal Healing 19/40 BioCarta 0.0046354788599327 0.00659837604424199 2510 3193.90909090909 3125 0.000422297717188803 1846 0.705931322165748 0.740430015643974 1 0.562665552257198 2506 4191 3541 3220 3125 2961 2497 1846 3913 4291 3042 3315 M2337 BILANGES_SERUM_RESPONSE_TRANSLATION http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_SERUM_RESPONSE_TRANSLATION.html Genes translationally repressed upon serum deprivation in MEF cells (embryonic fibroblast). 17562867 27/69 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3305 3136 3125 0.00793650793650794 2249 2.09556302130299 1.70161545978714 1 0.777587733120849 3303 2618 2646 3060 3626 3874 3621 2784 2249 3125 3590 3316 M3815 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_27 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_27.html Amplification hot spot 27: colocalized fragile sites and cancer genes in the 5p15.3-p15.1; 5p12-q35 region. 16751803 7/22 Arthur Liberzon 9.3404336318807e-05 0.000173481062223515 4200 3228.72727272727 3126 9.34082625175869e-06 1950 1.26362982201203 1.61048871848263 1 1.73705408881687 4197 1950 4220 3003 2422 3857 3223 3126 2995 2267 4256 3317 M88 PID_CD8_TCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CD8_TCR_PATHWAY.html TCR signaling in naïve CD8+ T cells 18832364 43/109 Pathway Interaction Database 0.0138514730315398 0.0186536201258467 4245 3062.18181818182 3127 0.00126722365252628 1491 1.54484326796318 1.55943498765111 1 0.976468328701605 4245 3211 2418 1491 3295 2804 4156 3735 3053 2149 3127 3318 M1997 KYNG_WERNER_SYNDROM_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_WERNER_SYNDROM_DN.html Genes distinctly down-regulated in primary fibroblast cultures from Werner syndrom patients compared to those from normal young donors. 14527998 26/63 Arthur Liberzon 0.236288942859285 0.261761226061137 1340 3001 3127 0.0242081444546047 1339 0.946522223330914 -0.951964581444124 -1 0.201392686331357 1339 3674 2836 3127 4232 2019 1673 3490 4343 4018 2260 3319 M19509 MORI_PLASMA_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_PLASMA_CELL_DN.html Down-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: plasma cell. 18922927 28/60 Jessica Robertson 0.016627804130267 0.0221106385228238 1765 2735.36363636364 3128 0.00152316588300921 1361 1.48659657734747 1.63155865330141 1 0.89952863344668 1762 3837 2365 3361 3329 2164 1361 3128 3873 3182 1727 3320 M1962 MIKKELSEN_MEF_ICP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_ICP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the bivalent tri-methylation marks at H3K4 (H3K4me3) and H3K27 (H3K27me3) in MEF cells (embryonic fibroblasts). 18509334 19/63 Jessica Robertson 0.000134867650584404 0.000241887535520028 4160 3300.18181818182 3128 1.2261447195459e-05 1495 1.69952606817144 -2.21355649430699 -1 2.24658017052746 4158 3128 1495 3770 2486 3907 4683 2838 2952 3008 3877 3321 M176 PID_FOXM1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FOXM1_PATHWAY.html FOXM1 transcription factor network 18832364 16/51 Pathway Interaction Database 0.0839184282471183 0.0965721401684667 3525 3022.72727272727 3129 0.00793650793650794 1479 1.53457234888705 -1.40867651085194 -1 0.569424360395081 3521 3129 2296 1479 3589 3678 4433 2879 2438 2120 3688 3322 M16309 RAY_TARGETS_OF_P210_BCR_ABL_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAY_TARGETS_OF_P210_BCR_ABL_FUSION_UP.html Genes up-regulated in HL-60 cells (acute myeloid leukemia, AML) by expression of p210 BCR-ABL [GeneID=613;25] fusion protein. 15155749 24/54 Arthur Liberzon 0.140676812063902 0.159615385310277 2030 3207 3129 0.0136881974244363 2030 0.961096842915632 -0.990877248829527 -1 0.2799651575226 2030 3092 3141 3129 3649 2797 3930 2670 3976 3991 2872 3323 M16679 SHAFFER_IRF4_MULTIPLE_MYELOMA_PROGRAM http://www.broadinstitute.org/gsea/msigdb/cards/SHAFFER_IRF4_MULTIPLE_MYELOMA_PROGRAM.html Direct targets of IRF4 [GeneID=3662] that constitute a multiple myeloma program. 18568025 27/62 Jessica Robertson 0.00472453086827043 0.00671290225855526 2405 3058.90909090909 3129 0.000430427952176264 2153 1.09610515102595 1.14606219301742 1 0.870661051492536 2402 3151 2991 3847 3129 2878 2269 3785 3866 2153 3177 3324 M1096 KOINUMA_COLON_CANCER_MSI_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOINUMA_COLON_CANCER_MSI_UP.html Genes up-regulated in colorectal carcinoma samples positive for MSI (microsatellite instability) compared to the MSI negative ones. 16247484 11/21 Arthur Liberzon 0.00579457946912768 0.00816152671846478 2665 2981.45454545455 3130 0.000528172575283234 1513 1.41721310890744 1.48503378493292 1 1.08176381152127 2662 3130 2350 3146 3161 3079 2301 4420 3769 1513 3265 3325 M6862 NADERI_BREAST_CANCER_PROGNOSIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NADERI_BREAST_CANCER_PROGNOSIS_UP.html Up-regulated genes in the breast cancer prognostic signature of 70 genes that significantly correlated with survival. 16936776 37/147 Arthur Liberzon 2.13719535771801e-05 4.79411079285141e-05 3130 2999.90909090909 3130 1.94292374530612e-06 1778 1.24744784981771 -1.33231578206488 -1 1.96949193744964 3130 2772 1778 3407 1944 3181 4178 2769 3510 2950 3380 3326 M2042 BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_48HR_UP.html Genes up-regulated in T98G cells (glioma, express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 48 h. 15980968 10/39 John Newman 0.000272262113426887 0.000461250999102817 4655 3340.18181818182 3131 2.47541648364924e-05 2493 1.47360111176407 1.72744202821851 1 1.79693924006504 4652 3131 2505 2846 2633 3746 4267 2826 2493 3494 4149 3327 M5940 BIOCARTA_NDKDYNAMIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NDKDYNAMIN_PATHWAY.html Endocytotic role of NDK, Phosphins and Dynamin 9/24 BioCarta 5.42713006604468e-05 0.000107786869684088 3940 3148.27272727273 3132 5.42726261243396e-06 1563 0.896608220064846 -0.94259007757761 -1 1.30026446053719 3936 1563 3831 2700 2259 2976 3591 4185 3132 3395 3063 3328 M16005 IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR.html Genes in the expression cluster 'Intermediate Progenitors Shared': up-regulated in hematopoietic intemediate progenitor cells from adult bone marrow and fetal liver. 12228721 98/189 John Newman 0.00799301292119907 0.0110683388146391 1475 2727.90909090909 3133 0.000729291055717674 1405 1.16604662755767 -1.13260971445536 -1 0.833653756688207 1471 3731 3560 4558 3214 1405 1655 1735 3133 4007 1538 3329 M1560 RASHI_RESPONSE_TO_IONIZING_RADIATION_6 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_6.html Cluster 6: late responding genes activated in ATM [GeneID=472] deficient but not in the wild type tissues. 16314843 44/120 Arthur Liberzon 6.648287632311e-08 8.87574810399126e-07 4570 2875.54545454545 3134 6.04389803019898e-09 23 1.64671365687974 -1.44588700585455 -1 3.64268441953882 4568 2070 1268 3134 23 3557 4075 3675 2672 2622 3967 3330 M1518 KUMAMOTO_RESPONSE_TO_NUTLIN_3A_UP http://www.broadinstitute.org/gsea/msigdb/cards/KUMAMOTO_RESPONSE_TO_NUTLIN_3A_UP.html Genes up-regulated in response to nutlin-3a [PubChem=216345], an inhibitor of MDM2 [GeneID=4193], in skin fibroblast cultures after knockdown of TP53 [GeneID=7157] by RNAi. 18451145 5/13 Jessica Robertson 0.0180304606192167 0.0238539634279077 2465 3073.27272727273 3135 0.0018178447220847 985 0.644163411255851 0.644163411255851 1 0.38201797633891 2465 3135 4472 3783 3360 2444 985 1904 4314 4603 2341 3331 M2556 HOLLEMAN_DAUNORUBICIN_B_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_DAUNORUBICIN_B_ALL_UP.html Genes distinguishing daunorubicin [PubChem=30323] resistant and sensitive B-lineage ALL; here - genes up-regulated in the drug resistant samples. 15295046 7/26 Arthur Liberzon 5.22500243998679e-05 0.00010418877205863 4105 2891.27272727273 3135 5.22512529697959e-06 521 2.49286457979499 -2.46528229613337 -1 3.62859688887569 4103 521 4681 1617 2249 4504 3135 4124 946 1503 4421 3332 M2750 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_13 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_13.html Amplification hot spot 13: colocolized fragile sites and cancer genes in the Xq12-q28 region. 16751803 4/9 Arthur Liberzon 7.43896269734852e-05 0.00014257251206452 3350 3013.45454545455 3137 7.43921173082848e-06 547 1.99068171075647 1.99068171075647 1 2.7985064607859 3348 3137 4238 2553 4058 4501 3392 547 2003 2673 2698 3333 M1205 SCHRAMM_INHBA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHRAMM_INHBA_TARGETS_UP.html Genes up-regulated in Kelly cells (neuroblastoma) by overexpressing INHBA [GeneID=3624] off a plasmid vector. 15580313 5/8 Arthur Liberzon 0.00451036890492517 0.00643201116508805 4355 3055.09090909091 3137 0.000451954968374986 791 1.414092213786 -1.414092213786 -1 1.1328406301114 4352 791 4258 2264 3137 4120 2442 3398 1855 2901 4088 3334 M15510 NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP http://www.broadinstitute.org/gsea/msigdb/cards/NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP.html Genes up-regulated in K562 cells (bone marrow) after treatment with dasatinib [PubChem=3062316] or imatinib [PubChem=5291]. 17213809 20/39 Arthur Liberzon 0.323387101738417 0.354146286222533 3140 3278.09090909091 3139 0.0348909493119875 1718 1.11896031432175 -0.916817728000914 -1 0.184388788857642 3139 3058 3144 3864 4564 1838 1718 4588 3998 3108 3040 3335 M11673 KEGG_BIOSYNTHESIS_OF_UNSATURATED_FATTY_ACIDS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BIOSYNTHESIS_OF_UNSATURATED_FATTY_ACIDS.html Biosynthesis of unsaturated fatty acids 14/33 KEGG 0.00770896479781553 0.0106939636005221 2455 2849.63636363636 3140 0.000703282804742836 1084 0.963130185641391 -0.876669317343131 -1 0.693841552731732 2452 2869 3172 4050 3210 1785 1084 3964 3464 3140 2156 3336 M3903 LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_QTL http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_QTL.html Genes changed in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of reciprocal congenic strains D.B. Chr3 (DB), B.D. Chr3 (BD) and the parental strains B6 and D2. 17220891 16/33 Arthur Liberzon 0.00506665735724279 0.00718159600001202 3335 3051.27272727273 3142 0.000461669432989444 1818 1.34411507796785 -1.47061132604965 -1 1.05326031536984 3334 3423 2628 3109 3142 3062 3958 1818 3244 3803 2043 3337 M14309 REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING.html Genes involved in G-protein beta:gamma signalling 14/34 Reactome 0.0051183440962201 0.00724828057869065 3360 3085.36363636364 3143 0.000466390086996473 1887 1.45958351264026 1.40490735435573 1 1.14160083863966 3357 2285 2103 2343 3143 3403 3954 4107 2859 1887 4498 3338 M2427 NAKAMURA_CANCER_MICROENVIRONMENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_CANCER_MICROENVIRONMENT_DN.html Genes down-regulated in pancreatic cancer cells grown in orthotopic xenograft tumors compared to those grown in vitro. 17210693 25/56 Arthur Liberzon 0.0144831962656862 0.0194520658357711 4535 3284.81818181818 3144 0.00132540283689734 1997 1.6527139672836 2.1479189319796 1 1.03365510793061 3096 2993 2201 3144 3299 4531 4532 4016 2640 1997 3684 3339 M8577 WANG_CLIM2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_CLIM2_TARGETS_DN.html Genes down-regulated in MCF7 cells (breast cancer) engineered to conditionally express a dominant negative form of CLIM2 [GeneID=8861] by a Tet Off system. 17452977 132/317 Arthur Liberzon 0.00519007459067745 0.0073432033610853 3225 3143.90909090909 3144 0.000472941746998187 1983 1.23603500343205 -1.1622674935119 -1 0.964201326981382 3223 3917 3576 3805 3144 1983 2358 3133 2795 3973 2676 3340 M942 REACTOME_REGULATION_OF_IFNG_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_IFNG_SIGNALING.html Genes involved in Regulation of IFNG signaling 7/20 Reactome 0.214139132665174 0.238577264781028 3150 3252.72727272727 3146 0.0238095238095238 2218 0.674508140203351 0.674508140203351 1 0.153446063076935 3146 2249 4059 2562 3838 2463 2218 4000 3888 4421 2936 3341 M7641 ZIRN_TRETINOIN_RESPONSE_WT1_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZIRN_TRETINOIN_RESPONSE_WT1_DN.html Genes down-regulated in MZ128 cells (Wilms tumor with mutated WT1 [GeneID=7490]) after treatment with 10 microM tretinoin (ATRA) [PubChem=444795] for 24 h. 15897880 14/46 Leona Saunders 1.89407483359582e-05 4.31694293299126e-05 4595 3263.09090909091 3147 1.72190103699916e-06 1907 1.23774190427737 0.732991650823237 1 1.97476786153065 4595 3063 2274 2981 1907 4675 3941 2508 3314 3147 3489 3342 M1978 ONO_AML1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONO_AML1_TARGETS_DN.html Genes down-regulated in CD4+ [GeneID=920] T lymphocytes by expression of AML1 [GeneID=861] off a viral vector. 17377532 22/54 Jessica Robertson 0.0839184282471183 0.0965721401684667 3765 3183 3148 0.00793650793650794 1721 1.4710763216789 -1.69809760207312 -1 0.545863278494354 3763 3803 2281 4138 4147 2768 3122 3148 2928 1721 3194 3343 M11736 SA_MMP_CYTOKINE_CONNECTION http://www.broadinstitute.org/gsea/msigdb/cards/SA_MMP_CYTOKINE_CONNECTION.html Cytokines can induce activation of matrix metalloproteinases, which degrade extracellular matrix. 6/15 SigmaAldrich 0.0153402181688491 0.0204856831972719 3520 2978.27272727273 3150 0.00154471536019103 1268 2.83367012658679 -2.83367012658679 -1 1.74896996227184 3520 3223 3891 3568 3333 2631 3150 2442 1268 3038 2697 3344 M7030 ELVIDGE_HYPOXIA_BY_DMOG_DN http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HYPOXIA_BY_DMOG_DN.html Genes down-regulated in MCF7 cells (breast cancer) treated with hypoxia mimetic DMOG [PubChem=3080614]. 16565084 44/89 Arthur Liberzon 9.16759934355633e-06 2.34860182169527e-05 4325 3226.81818181818 3151 8.33421595090577e-07 1656 1.24958778058754 1.2471115085048 1 2.11441914835505 4323 2500 3035 3307 1656 4558 2432 3151 3281 2994 4258 3345 M14529 KUUSELO_PANCREATIC_CANCER_19Q13_AMPLIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/KUUSELO_PANCREATIC_CANCER_19Q13_AMPLIFICATION.html List of genes in the 19q13 amplicon region based on a copy number alterations study of a panel of 16 pancreatic cancer cell lines and 31 primary tumors. 17332321 25/72 Jessica Robertson 5.74704092347911e-05 0.000113487710777173 2845 3198 3151 5.22471914401963e-06 2248 1.03417241810771 1.13299830883395 1 1.49129939232935 2841 3237 3487 4370 2248 3102 2833 2627 3499 3783 3151 3346 M2920 KEGG_LINOLEIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LINOLEIC_ACID_METABOLISM.html Linoleic acid metabolism 4/62 KEGG 5.08504100186482e-05 0.00010174424481101 3790 2758.45454545455 3152 5.08515736500129e-06 1012 2.55483564357547 -3.19379569295086 -1 3.72843065471387 3786 2492 3794 3334 2239 3152 3248 2110 1012 1619 3557 3347 M2059 FERRANDO_HOX11_NEIGHBORS http://www.broadinstitute.org/gsea/msigdb/cards/FERRANDO_HOX11_NEIGHBORS.html Nearest neighbors of HOX11 [GeneID=3195], based on the close agreement of their expression profiles with that of HOX11 in pediatric T cell acute lymphoblastic leukemia (T-ALL). 12086890 15/28 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2585 3145.18181818182 3152 0.00793650793650794 1951 1.14585354766301 1.34290962664479 1 0.425184855741215 2583 2717 1951 2525 4388 3757 3152 3536 3618 2617 3753 3348 M18837 BIOCARTA_EGFR_SMRTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EGFR_SMRTE_PATHWAY.html Map Kinase Inactivation of SMRT Corepressor 5/18 BioCarta 0.00501867595831072 0.00711573843892406 3330 2914.09090909091 3153 0.000503004631436696 1747 1.3402516331317 -1.3402516331317 -1 1.05219296509113 3329 1757 3847 2223 3153 2098 3893 3204 3922 2882 1747 3349 M12922 REACTOME_REGULATION_OF_RHEB_GTPASE_ACTIVITY_BY_AMPK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_RHEB_GTPASE_ACTIVITY_BY_AMPK.html Genes involved in Regulation of Rheb GTPase activity by AMPK 6/32 Reactome 0.165286950059414 0.185606194099788 2470 3411.27272727273 3153 0.0179045017175756 2151 0.747810951717757 0.747810951717757 1 0.199926561954882 2467 2933 4041 3839 4424 3016 3028 3153 4062 4410 2151 3350 M7250 MA_PITUITARY_FETAL_VS_ADULT_UP http://www.broadinstitute.org/gsea/msigdb/cards/MA_PITUITARY_FETAL_VS_ADULT_UP.html Up-regulated in human fetal pituitary tissue, compared to adult pituitary tissue 15894316 14/42 John Newman 0.0839184282471183 0.0965721401684667 3110 3172.36363636364 3153 0.00793650793650794 2009 1.85712281748028 2.46721725861577 1 0.689111187142996 3107 3579 2312 2009 3662 4309 4674 3553 2044 3153 2494 3351 M6761 GOLUB_ALL_VS_AML_DN http://www.broadinstitute.org/gsea/msigdb/cards/GOLUB_ALL_VS_AML_DN.html Down-regulated genes highly correlated with acute lymphoblastic leukemia (ALL) vs acute myeloid leukemia (AML). 10521349 14/35 Jean Junior 0.00104865593842932 0.00162285393906201 3270 2989.36363636364 3155 9.53778296788002e-05 1418 1.17749667504648 -1.30358968977072 -1 1.20071419108416 3269 2168 1942 3631 2893 2248 1418 4269 4164 3726 3155 3352 M5755 KAPOSI_LIVER_CANCER_MET_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAPOSI_LIVER_CANCER_MET_UP.html Selected up-regulated MET [GeneID=4233] target genes from a classifier of hepatocellular carcinoma (HCC) cases; associated with poor survival. 16710476 15/40 Yujin Hoshida 2.36350603888361e-05 5.244029023773e-05 3435 2716.18181818182 3155 2.14866493718682e-06 506 0.935967244554475 -0.878522140456154 -1 1.46439302599399 3433 506 2549 1139 1970 3607 3155 3554 2722 3267 3976 3353 M17936 NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON.html Genes within amplicon 8q23-q24 identified in a copy number alterations study of 191 breast tumor samples. 19010930 99/226 Jessica Robertson 0.000100712052017318 0.000185728719304664 2940 3139.72727272727 3156 9.1560602481662e-06 1963 1.44361546901794 1.44700821691437 1 1.96883854533535 2939 3473 2992 4422 2418 3520 1963 3156 2593 3228 3833 3354 M1382 PETRETTO_LEFT_VENTRICLE_MASS_QTL_CIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_LEFT_VENTRICLE_MASS_QTL_CIS_DN.html Down-regulated cis-regulated expression quantitative loci (cis-eQTL) in the heart that were identified as candidate genes for the regulation of left ventricle mass (LVM). 18443592 4/12 Jessica Robertson 0.00508401190626803 0.00720401566155791 2150 3057.72727272727 3157 0.000509568072563387 1397 0.570977226915871 -0.570977226915871 -1 0.447140218477143 2149 3408 4345 4139 3157 1397 1825 2967 4279 4554 1415 3355 M15228 KRISHNAN_FURIN_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KRISHNAN_FURIN_TARGETS_UP.html Genes up-regulated in naive T lymphocytes lacking FURIN [GeneID=5045]: Cre-Lox knockout of FURIN in CD4+ [GeneID=920] cells. 18690214 14/25 Jessica Robertson 0.763407909678834 0.798154722167562 2640 3495.90909090909 3157 0.122815540000183 2303 1.08486253219124 1.08486253219124 1 0.0388270066687556 2639 4602 2878 3935 4078 2816 2303 4393 4540 3157 3114 3356 M1990 WORSCHECH_TUMOR_EVASION_AND_TOLEROGENICITY_DN http://www.broadinstitute.org/gsea/msigdb/cards/WORSCHECH_TUMOR_EVASION_AND_TOLEROGENICITY_DN.html Selected genes with immunologic function which were reciprocally changed in evasion and tolerogenic tumor models. 18381452 10/27 Arthur Liberzon 0.0243410684333321 0.0317810662241834 1760 2954.72727272727 3157 0.0022376934414583 1375 0.81658425232173 0.81658425232173 1 0.447077917842176 1757 3324 3143 3157 3387 1436 1375 4607 4125 4647 1544 3357 M1221 YAN_ESCAPE_FROM_ANOIKIS http://www.broadinstitute.org/gsea/msigdb/cards/YAN_ESCAPE_FROM_ANOIKIS.html Genes up-regulated in IEC-18 cells (intestinal epithelial cells) which avoided anoikis (a form of apoptosis) after detachment. 16007176 29/64 Arthur Liberzon 0.0048189980625705 0.00684297724885011 3865 2994.27272727273 3158 0.000439053303561782 1712 1.43250762801413 -1.22600382851456 -1 1.13350887620401 3863 2312 1712 2151 3134 3158 3656 3329 3766 1933 3923 3358 M2200 LEE_DIFFERENTIATING_T_LYMPHOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/LEE_DIFFERENTIATING_T_LYMPHOCYTE.html Genes enriched at every T lymphocyte differentiation stage compared to the early passage fetal thymic stromal cultures (TSC). 15210650 115/361 Arthur Liberzon 5.11401572941131e-05 0.000102256771658131 3845 3158.63636363636 3158 4.6492132829691e-06 2211 1.28801061326996 -1.20733451222002 -1 1.87864664953573 3845 2464 2602 3158 2211 2889 4096 3727 3400 3509 2844 3359 M2158 REACTOME_BASE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BASE_EXCISION_REPAIR.html Genes involved in Base Excision Repair 15/21 Reactome 0.617512710311101 0.65586232106025 2420 3370.36363636364 3160 0.0836611671094036 2418 0.682644927281669 -0.682644927281669 -1 0.0457098194716589 2418 3160 3409 4308 3971 2543 2582 3089 4465 4312 2817 3360 M2554 HOLLEMAN_ASPARAGINASE_RESISTANCE_B_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_ASPARAGINASE_RESISTANCE_B_ALL_DN.html Genes distinguishing asparaginase resistant and sensitive B-lineage ALL; here - genes down-regulated in the drug resistant samples. 15295046 16/36 Arthur Liberzon 0.155628657432466 0.175686795646479 2720 3224.09090909091 3160 0.0152608011586907 2541 1.0842390058893 1.11844089943202 1 0.299323809857192 2719 2597 2606 2806 3669 2541 4293 3755 3966 3353 3160 3361 M1848 MATTHEWS_SKIN_CARCINOGENESIS_VIA_JUN http://www.broadinstitute.org/gsea/msigdb/cards/MATTHEWS_SKIN_CARCINOGENESIS_VIA_JUN.html Genes up-regulated by skin tumor promoters but completely blocked by expression of TAM67, a dominan-negative form of JUN [GeneID=3725]. 17363560 13/23 Jessica Robertson 9.05210912148354e-05 0.000168862194837866 3470 2945.63636363636 3161 8.22952872779494e-06 1278 1.88747558049261 1.77667807735141 1 2.60271195538184 3469 3161 1428 3183 2381 4017 4227 3283 2911 1278 3064 3362 M4619 LIU_PROSTATE_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_PROSTATE_CANCER_UP.html Genes up-regulated in prostate cancer samples. 16618720 71/169 Arthur Liberzon 1.17673926664853e-05 2.88550507771585e-05 3915 3001.18181818182 3162 1.06976869168738e-06 1748 1.41898301316399 -1.23807169511829 -1 2.35467556865561 3912 3143 1924 3162 1748 3276 3499 4554 2670 1944 3181 3363 M2189 WAGSCHAL_EHMT2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WAGSCHAL_EHMT2_TARGETS_UP.html Genes up-regulated in placenta of mice with EHMT2 [GeneID=10919] knocked out. 18039842 6/18 Arthur Liberzon 0.00501511909338324 0.00711284747929597 4470 3218.27272727273 3163 0.000502647331253955 1362 1.14728292211426 -0.924979647737219 -1 0.900772795252859 4469 2256 4626 3454 3332 2808 2517 1362 3163 3061 4353 3364 M13115 REACTOME_G_PROTEIN_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_PROTEIN_ACTIVATION.html Genes involved in G-protein activation 9/30 Reactome 1.71308665851119e-05 3.95834520798e-05 3230 2562.27272727273 3164 1.71309986465102e-06 378 1.42038213863344 1.35977433291663 1 2.28571705681207 3230 378 3997 1511 1906 3166 3164 3326 2193 885 4429 3365 M1008 REACTOME_TRANSCRIPTIONAL_REGULATION_OF_WHITE_ADIPOCYTE_DIFFERENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSCRIPTIONAL_REGULATION_OF_WHITE_ADIPOCYTE_DIFFERENTIATION.html Genes involved in Transcriptional Regulation of White Adipocyte Differentiation 41/93 Reactome 0.000200294712716087 0.000348396816550699 3900 3209.09090909091 3164 1.82102682256829e-05 2561 1.26952970335988 -1.32190028550205 -1 1.6046406483584 3897 4066 3149 3862 2561 2655 3354 2830 3164 3170 2592 3366 M2284 LINSLEY_MIR16_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LINSLEY_MIR16_TARGETS.html Transcripts down-regulated by overexpression of MIR16 family of microRNA molecules in DLD-1 and HCT116 (colon cancer) cells hypomorphic for DICER1 [GeneID=23405]. 17242205 163/325 Arthur Liberzon 0.00610292052318326 0.0085751980724548 2435 3155 3165 0.000556356036571959 1653 1.08865075968369 1.26675514073362 1 0.822426324780347 2433 4488 3636 4334 3165 2649 1653 2534 3463 3992 2358 3367 M2404 BIOCARTA_PPARA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PPARA_PATHWAY.html Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa(alpha) 34/86 BioCarta 0.0152361861014528 0.0203641665919589 3645 2909.45454545455 3171 0.00139479449658578 1638 1.26094891459352 -1.27840763303851 -1 0.779461373038458 3642 3509 2197 1638 3314 2705 3171 1829 3577 3524 2898 3368 M1729 GAVIN_FOXP3_TARGETS_CLUSTER_T4 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_T4.html Cluster T4 of genes with similar expression profiles in thymic T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 65/126 Jessica Robertson 0.000614660800823896 0.000981028784966205 3495 3198 3172 5.58938726263411e-05 1533 1.34641120080325 -1.0743970702449 -1 1.48054204199191 3495 1533 2765 3772 2805 4266 4393 2197 3172 3117 3663 3369 M2017 MIKKELSEN_NPC_WITH_LCP_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_WITH_LCP_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing histone H3 trimethylation mark at K27 in neural progenitor cells (NPC). 17603471 5/11 Arthur Liberzon 4.73296770016792e-08 6.76179470822771e-07 3900 2415.90909090909 3172 4.73296780097235e-09 14 1.96153439429289 -2.23396063226059 -1 4.4238050427117 3896 209 4598 523 14 3890 3172 4255 1068 730 4220 3370 M1583 VISALA_AGING_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/VISALA_AGING_LYMPHOCYTE_DN.html Genes down-regulated in peripheral lymphocytes from old individuals compared to those from young donors. 12618007 12/31 John Newman 0.00601724872494136 0.00846497373913996 3430 2977.18181818182 3174 0.000548524534301668 1377 1.7172023538035 1.64867019815493 1 1.30079524520306 3426 3375 2811 4289 3324 3843 2261 1377 1900 2969 3174 3371 M5536 TCGA_GLIOBLASTOMA_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/TCGA_GLIOBLASTOMA_COPY_NUMBER_UP.html Genes up-regulated and displaying increased copy number in glioblastoma samples. 18772890 43/106 Jessica Robertson 0.00653260140683622 0.00914057037695865 4240 3101.90909090909 3175 0.000595643645765571 2261 1.33226625421448 -1.40560193599491 -1 0.992963285106038 4238 2632 2552 2269 3175 3743 3865 3388 2261 2543 3455 3372 M16355 BIOCARTA_NKCELLS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NKCELLS_PATHWAY.html Ras-Independent pathway in NK cell-mediated cytotoxicity 25/65 BioCarta 0.0839184282471183 0.0965721401684667 2330 3067.54545454545 3176 0.00793650793650794 1966 1.66117238573859 -1.322079615826 -1 0.616401060639898 2329 3673 2812 2064 4580 1966 3176 3684 3410 3433 2616 3373 M19806 REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION.html Genes involved in Post-translational protein modification 92/203 Reactome 5.25288832170144e-06 1.50919893779846e-05 4395 3195 3176 4.77536442176493e-07 1448 1.13410412282945 -0.795319614000783 -1 1.9986288285475 4392 2388 3481 2960 1448 3187 4566 2685 2624 3176 4238 3374 M2037 KAMMINGA_SENESCENCE http://www.broadinstitute.org/gsea/msigdb/cards/KAMMINGA_SENESCENCE.html Genes down-regulated on serial passage of MEF cells (embryonic fibroblast). 16293602 22/47 Arthur Liberzon 2.01755838677703e-07 1.91770357006839e-06 3530 2914.72727272727 3176 1.83414415618335e-08 164 1.07866723585379 -1.04937532776995 -1 2.25419524726215 3528 2588 3176 2921 164 3195 4301 3989 2720 3250 2230 3375 M141 PID_PI3KCI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PI3KCI_PATHWAY.html Class I PI3K signaling events 18832364 28/68 Pathway Interaction Database 0.000568019886777912 0.000910308204323288 3695 3226.63636363636 3178 5.16515088503116e-05 1729 1.27885969850058 -1.48461190975459 -1 1.42145022530873 3693 1729 2456 1851 2792 4416 3162 4022 3588 3178 4606 3376 M9575 WAKASUGI_HAVE_ZNF143_BINDING_SITES http://www.broadinstitute.org/gsea/msigdb/cards/WAKASUGI_HAVE_ZNF143_BINDING_SITES.html DNA repair genes whose promoters contain putative ZNF143 [GeneID=7702] binding sites. 17297437 42/67 Leona Saunders 0.0839184282471183 0.0965721401684667 2205 3407.54545454545 3178 0.00793650793650794 2203 1.16427666646694 -0.721675657503639 -1 0.432021009593539 2203 3962 3026 4527 3709 2706 3052 4419 2636 4065 3178 3377 M503 REACTOME_METABOLISM_OF_STEROID_HORMONES_AND_VITAMINS_A_AND_D http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_STEROID_HORMONES_AND_VITAMINS_A_AND_D.html Genes involved in Metabolism of steroid hormones and vitamins A and D 13/53 Reactome 0.0199717272318386 0.0262898223194109 1940 2940.54545454545 3181 0.00183230636151744 770 0.964263578934406 0.964263578934406 1 0.556968282222296 1936 3938 3181 4156 3988 1843 770 3040 4123 3672 1699 3378 M12645 ST_GA13_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GA13_PATHWAY.html G alpha 13 Pathway 28/53 Signaling Transduction KE 0.067344683238617 0.084041860361161 2645 3062.36363636364 3182 0.0063181001358492 2039 0.89655663162297 -0.81070560141036 -1 0.352459437648274 2645 3182 3190 3262 3527 2039 2738 3029 3603 3862 2609 3379 M1538 YANAGIHARA_ESX1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/YANAGIHARA_ESX1_TARGETS.html Genes down-regulated in U2-OS Tet-On cells (osteosarcoma) after induction of ESX1 [GeneID=80712] expression. 15897875 18/70 Arthur Liberzon 0.000131820352847172 0.000236761277670313 3650 3123.90909090909 3182 1.19843865424376e-05 1210 1.3455026838918 1.0998858573669 1 1.78317680557707 3649 1210 2904 1842 2482 4468 3182 4460 2853 3456 3857 3380 M905 CHOW_RASSF1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHOW_RASSF1_TARGETS_DN.html Genes down-regulated in C666-1 cells (nasopharyngeal carcinoma) by stable expression of RASSF1 [GeneID=11186]. 16116475 18/39 Lauren Kazmierski 0.00676062734424694 0.00944271229065311 2330 3101.18181818182 3183 0.000616499332599281 2279 0.772598594803335 -0.772598594803335 -1 0.571843829266685 2330 2921 3588 3796 3183 2279 3222 2554 3895 3876 2469 3381 M4322 AUNG_GASTRIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/AUNG_GASTRIC_CANCER.html Selected genes specifically expressed in gastric cancer. 16331256 29/111 Arthur Liberzon 0.0125019385843161 0.0169318162445391 3675 3281.45454545455 3183 0.00114305034081328 2005 1.27554163408739 1.48422760798684 1 0.825857546142955 3673 3183 3030 2664 3283 4427 2848 2005 3057 3272 4654 3382 M12307 NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON.html Genes within amplicon 16q24 identified in a copy number alterations study of 191 breast tumor samples. 19010930 28/71 Jessica Robertson 0.000665288368776156 0.00105607767482557 4050 3300.63636363636 3183 6.04990581569019e-05 2785 1.08718454741694 -0.827953390370593 -1 1.18276871631195 4050 2811 3068 3577 2824 2840 2785 4290 3291 3183 3588 3383 M1821 MATZUK_EMBRYONIC_GERM_CELL http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_EMBRYONIC_GERM_CELL.html Genes important for embryonic germ cell, based on mouse models with female fertility defects. 18989307 12/31 Jessica Robertson 0.0115838522844984 0.0157384551479152 4365 2888.72727272727 3183 0.00105866356298252 517 1.72560704684532 -1.80139924385381 -1 1.13727635826087 4364 3294 2559 2137 3271 4156 3183 2283 517 2248 3764 3384 M199 PID_P38_MK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_MK2_PATHWAY.html p38 signaling mediated by MAPKAP kinases 18832364 17/24 Pathway Interaction Database 0.00119553409835847 0.00183020999180261 2920 3155.90909090909 3184 0.000108744025062816 1602 1.13567272604073 -1.5563445462134 -1 1.13638744664322 3184 3094 2918 3403 2919 2232 1602 4296 3511 3828 3728 3385 M10885 DAZARD_UV_RESPONSE_CLUSTER_G4 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G4.html Cluster G4: genes increasingly up-regulated in NHEK cells (normal keratinocyte) after 12 h time point after UV-B irradiation. 12771951 33/83 John Newman 0.0317068292480387 0.0408743333855046 3755 3211.63636363636 3184 0.00292483931805941 1941 1.19945100755916 -1.17969597884662 -1 0.608783778963057 3753 2617 2016 1941 3430 4445 2714 3184 3576 3100 4552 3386 M777 REACTOME_METABOLISM_OF_NUCLEOTIDES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_NUCLEOTIDES.html Genes involved in Metabolism of nucleotides 46/85 Reactome 7.24937741591253e-05 0.000139624260464308 4595 3537.72727272727 3185 6.59056027850504e-06 2133 1.16969074238186 -0.828626996101117 -1 1.64823484669673 4594 3081 2133 3147 2307 4107 4338 4403 3185 3114 4506 3387 M1594 BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP.html Genes specifically up-regulated in FL5.12 cells (pro-B lymphocyte) by camptothecin [PubChem=2538]. 12447701 28/56 John Newman 0.232850105696956 0.258012673278774 3310 3243.45454545455 3185 0.0238095238095238 2539 1.03211899951605 -1.11025098169705 -1 0.221968523175901 3310 2812 2973 2539 4106 3018 3647 2976 3902 3185 3210 3388 M14553 LIANG_SILENCED_BY_METHYLATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_SILENCED_BY_METHYLATION_UP.html Genes up-regulated in LD419 cells (fibroblast) after treatment with decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 11861364 38/98 John Newman 0.00802997149166535 0.0111129493236692 3185 3122.45454545455 3186 0.000732675584880499 914 1.92557166304491 -1.48894461593538 -1 1.37543929027808 3182 2616 914 2059 3481 3333 4406 4569 3186 2595 4006 3389 M18009 KEGG_CIRCADIAN_RHYTHM_MAMMAL http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CIRCADIAN_RHYTHM_MAMMAL.html Circadian rhythm - mammal 7/14 KEGG 0.0153988555343739 0.0205581302091384 3200 2686.54545454545 3188 0.00155066140953274 1359 1.47591627039601 -1.47591627039601 -1 0.910123380978417 1443 3198 3808 3199 3579 1359 2357 1611 3872 3188 1938 3390 M14863 BIOCARTA_P53_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P53_PATHWAY.html p53 Signaling Pathway 15/22 BioCarta 0.0839184282471183 0.0965721401684667 4440 3010.36363636364 3188 0.00793650793650794 577 1.99933683208868 -1.23851142675277 -1 0.741881670477893 4438 3188 1874 2274 3944 4115 3309 2369 577 2604 4422 3391 M841 REACTOME_ADP_SIGNALLING_THROUGH_P2RY12 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADP_SIGNALLING_THROUGH_P2RY12.html Genes involved in ADP signalling through P2Y purinoceptor 12 7/23 Reactome 8.50971655389948e-06 2.20678095028074e-05 3625 2639.09090909091 3188 8.50974914094923e-07 785 1.4211988428997 1.34093290478812 1 2.41885327355808 3625 785 4033 1463 1667 3188 3347 3404 2125 1003 4390 3392 M2258 IVANOVSKA_MIR106B_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVSKA_MIR106B_TARGETS.html A consensus set of genes that were significantly down-regulated by MIR106B [GeneID=406900]. 18212054 66/153 Arthur Liberzon 0.00303001777697779 0.00440952276488134 2395 3065.18181818182 3188 0.00027583627516278 1356 1.0900944726725 1.31368999390355 1 0.938612824296912 2395 3413 3255 3995 3066 2915 1356 3188 3584 3795 2755 3393 M4856 MORI_LARGE_PRE_BII_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_LARGE_PRE_BII_LYMPHOCYTE_DN.html Down-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Large Pre-BII stage. 18922927 40/100 Jessica Robertson 1.77077623854157e-05 4.06757718323814e-05 3490 2727.27272727273 3191 1.6098095378635e-06 600 1.54221814136033 -1.49383982244577 -1 2.47511442296522 3489 600 1748 2006 1892 3335 3951 4226 3191 1956 3606 3394 M9905 FLECHNER_PBL_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_PBL_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN.html Genes downregulated in peripheral blood lymphocytes (PBL) from patients with well functioning kidneys more than 1-year post transplant compared to those from normal living kidney donors. 15307835 27/52 Jean Junior 0.0839184282471183 0.0965721401684667 1525 3136.54545454545 3191 0.00793650793650794 1525 1.19194615588325 1.3299011770223 1 0.442288157554652 1525 4329 3191 4441 4332 2136 1977 2874 3594 3826 2277 3395 M2821 BIOCARTA_NTHI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NTHI_PATHWAY.html NFkB activation by Nontypeable Hemophilus influenzae 21/42 BioCarta 0.00718105486006062 0.00999418564723614 4300 3454 3192 0.000654963848352545 2258 1.63142517635192 -2.12388117018639 -1 1.19280994391537 4297 3396 3098 2637 3192 4628 4253 2876 2258 3161 4198 3396 M9160 ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_DN.html Genes down-regulated in BxPC3 cells (pancreatic cancer) after treatment with TNF [GeneID=7124] or IKI-1, an inhibitor of IkappaB kinase (IKK). 19010928 78/182 Jessica Robertson 7.62611659167204e-06 2.02012336622811e-05 4660 3211.63636363636 3193 6.93285729736157e-07 1597 1.28054252365376 -1.19855651167972 -1 2.19742415819344 4660 2737 2553 3193 1597 3902 3657 3707 2973 2557 3792 3397 M16257 BIOCARTA_MITOCHONDRIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MITOCHONDRIA_PATHWAY.html Role of Mitochondria in Apoptotic Signaling 16/28 BioCarta 0.0344431310165327 0.0442556928827728 2420 3124.63636363636 3195 0.00318131773946071 1554 0.914863035059438 -1.01110419383123 -1 0.452797364426929 2420 4197 3195 4442 4057 2063 1554 1780 4281 3797 2585 3398 M8754 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_7 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_7.html Amplification hot spot 7: colocalized fragile sites and cancer genes in the 3q26.3-q29 region. 16751803 9/13 Arthur Liberzon 0.0361352254407025 0.0463155542710974 2335 2919.09090909091 3195 0.00367366248641882 1034 0.622122574290093 -0.622122574290093 -1 0.303417027946704 2335 3195 4219 3657 3800 1056 1034 2382 4251 4509 1672 3399 M13265 KEGG_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI_ANCHOR_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI_ANCHOR_BIOSYNTHESIS.html Glycosylphosphatidylinositol(GPI)-anchor biosynthesis 13/25 KEGG 0.00316783705218166 0.00459439319917154 2775 3286.36363636364 3196 0.000288400701777583 2519 0.659123695800721 -0.616207050567385 -1 0.563233265614182 2772 2519 3525 4068 3072 2586 3714 3196 3657 4242 2799 3400 M16561 JAZAERI_BREAST_CANCER_BRCA1_VS_BRCA2_DN http://www.broadinstitute.org/gsea/msigdb/cards/JAZAERI_BREAST_CANCER_BRCA1_VS_BRCA2_DN.html Down-regulated genes distinguishing between breast cancer tumors with mutated BRCA1 [GeneID=672] from those with mutated BRCA2 [GeneID=675]. 12096084 27/68 John Newman 0.00732663420282816 0.010190741429045 3240 3200 3196 0.000668286216200315 1731 1.42112594311636 1.52765917284578 1 1.034656724836 3237 2947 1824 4352 3196 4246 3119 2468 3938 1731 4142 3401 M10867 OHASHI_AURKB_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/OHASHI_AURKB_TARGETS.html Candidate substrate proteins of AURKB [GeneID=9212]. 16785988 9/17 Arthur Liberzon 0.08313451029537 0.0965721401684667 3020 3226.36363636364 3197 0.00864189257502763 2061 1.88527264279166 2.44076770020626 1 0.699556570402622 3016 3197 4242 3099 3996 3424 2603 2061 3738 2576 3538 3402 M14766 REACTOME_INTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTRINSIC_PATHWAY.html Genes involved in Intrinsic Pathway 7/23 Reactome 0.039731080813213 0.0507302029130016 2540 3207.36363636364 3198 0.00404598382215848 1853 1.45455665270868 1.45455665270868 1 0.688383167389627 2538 3813 4071 4231 4014 2456 2040 1853 4288 3198 2779 3403 M827 REACTOME_REPAIR_SYNTHESIS_FOR_GAP_FILLING_BY_DNA_POL_IN_TC_NER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REPAIR_SYNTHESIS_FOR_GAP_FILLING_BY_DNA_POL_IN_TC_NER.html Genes involved in Repair synthesis for gap-filling by DNA polymerase in TC-NER 8/15 Reactome 0.566397342434164 0.602939106462174 2945 3326.18181818182 3199 0.0801665610786312 2052 0.71112730430769 -0.71112730430769 -1 0.05711486069225 2279 3199 4024 3597 4342 2356 2052 2945 4450 4399 2945 3404 M10064 REACTOME_HORMONE_SENSITIVE_LIPASE_HSL_MEDIATED_TRIACYLGLYCEROL_HYDROLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HORMONE_SENSITIVE_LIPASE_HSL_MEDIATED_TRIACYLGLYCEROL_HYDROLYSIS.html Genes involved in Hormone-sensitive lipase (HSL)-mediated triacylglycerol hydrolysis 7/13 Reactome 0.184942556486407 0.206934293145966 2245 3122.54545454545 3199 0.0202419921141253 2241 1.06940241992427 1.06940241992427 1 0.267437849053269 2241 3222 4075 3469 3710 2568 2369 2461 4245 3199 2789 3405 M4290 LUI_THYROID_CANCER_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_CLUSTER_3.html Cluster 3: genes with similar expression profiles across follicular thyrorid carcinoma (FTC) samples; genes in this cluster correlated well with the presence of PAX8-PPARG [GeneID=7849;5468] fusion protein. 15608688 26/55 Leona Saunders 0.0535742046529959 0.0675225182904623 1900 2822.72727272727 3199 0.00499319330352441 1121 1.86589933094489 -1.86589933094489 -1 0.798358467396296 1897 4666 3434 3740 4211 1263 1121 1968 3199 3811 1740 3406 M3896 KEGG_INOSITOL_PHOSPHATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_INOSITOL_PHOSPHATE_METABOLISM.html Inositol phosphate metabolism 30/55 KEGG 0.0173471787523966 0.0230149715837288 1590 2799 3200 0.00158959017742037 1274 0.940714069796183 -0.983735620150824 -1 0.56323290286114 1586 3995 3200 4163 3411 1274 2362 1619 3948 3646 1585 3407 M1455 WANG_TARGETS_OF_MLL_CBP_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_TARGETS_OF_MLL_CBP_FUSION_DN.html Top 50 genes down-regulated in granulocyte/macrophage progenitors (GMP) upon expression of MLL-CBP fusion [GeneID=4297;1387]. 15635450 28/65 Kevin Vogelsang 0.0074659158968676 0.0103660094496953 2525 3141.90909090909 3202 0.000681033931487742 2112 0.971601174174184 1.13699879344328 1 0.704748175238947 2522 3277 3268 3787 3202 3159 2330 2112 4023 4043 2838 3408 M16067 REACTOME_PREFOLDIN_MEDIATED_TRANSFER_OF_SUBSTRATE_TO_CCT_TRIC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PREFOLDIN_MEDIATED_TRANSFER_OF_SUBSTRATE_TO_CCT_TRIC.html Genes involved in Prefoldin mediated transfer of substrate to CCT/TriC 19/39 Reactome 0.00139641443992163 0.00211015738970422 2945 2744.09090909091 3203 0.000127027416350288 583 2.00148765555603 2.98049251039108 1 1.95752435697615 2942 3650 1740 2493 3203 3666 3936 1062 583 3528 3382 3409 M5076 CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_HD_MTX_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_HD_MTX_UP.html Genes specifically up-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490] and high dose methotrexate (HDMTX) [PubChem=4112]. 12704389 3/9 Arthur Liberzon 0.156940203514977 0.177124709458377 1820 3093.54545454545 3203 0.0169268426327895 1354 0.625223561625019 0.625223561625019 1 0.171795260311674 1820 3203 4555 3462 3863 2308 1354 2480 4083 4630 2271 3410 M10628 BIOCARTA_ATM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ATM_PATHWAY.html ATM Signaling Pathway 20/32 BioCarta 0.0670984251233227 0.0837791686991447 4530 3119.27272727273 3205 0.00629425103789245 1297 2.21089344487157 3.06400283704495 1 0.870257753883943 4528 3576 2414 2430 3582 3035 3205 1963 1297 3918 4364 3411 M1001 BIOCARTA_RHO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RHO_PATHWAY.html Rho cell motility signaling pathway 24/53 BioCarta 0.0839184282471183 0.0965721401684667 4180 3180.54545454545 3205 0.00793650793650794 2237 1.10193497907499 -1.42828183037783 -1 0.408888261498035 4178 2237 2964 2934 3719 3559 2782 2354 3205 3744 3310 3412 M6302 LIANG_SILENCED_BY_METHYLATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_SILENCED_BY_METHYLATION_DN.html Genes down-regulated in LD419 cells (fibroblast) after treatment with decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 11861364 7/16 John Newman 0.147859119791321 0.167157499479404 3790 3320.27272727273 3206 0.0158730158730159 1987 2.41949877070937 2.41949877070937 1 0.68706103173381 1987 3790 4415 4357 4611 2616 2495 2396 3787 3206 2863 3413 M2444 PLASARI_TGFB1_TARGETS_1HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_TARGETS_1HR_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) upon stimulation with TGFB1 [GeneID=7040] for 1 h. 19752192 5/7 Arthur Liberzon 0.030710969692661 0.0396232389812251 2850 3191.63636363636 3206 0.0031143836819716 1883 1.01462494150029 -1.00423547851022 -1 0.519981979417036 2846 2961 4669 3634 3438 3315 2610 2557 3989 1883 3206 3414 M15774 DANG_BOUND_BY_MYC http://www.broadinstitute.org/gsea/msigdb/cards/DANG_BOUND_BY_MYC.html Genes whose promoters are bound by MYC [GeneID=4609], according to MYC Target Gene Database. 14519204 758/1799 Chi Dang 0.00699911405370105 0.00976126442132235 2595 3237.90909090909 3208 0.000702125668905865 1572 1.31438301268699 -1.08468169741932 -1 0.96592621308133 2592 4246 4594 3755 3208 1572 2356 3624 3071 4228 2371 3415 M2144 DEMAGALHAES_AGING_UP http://www.broadinstitute.org/gsea/msigdb/cards/DEMAGALHAES_AGING_UP.html Genes consistently overexpressed with age, based on meta-analysis of microarray data. 19189975 51/116 Joao Pedro de Magalhaes 0.00419908972168786 0.00600455734996317 4120 3002.63636363636 3208 0.000382465991852335 1128 1.66157005538914 -1.89407720030987 -1 1.34923605893638 4116 2469 1128 1930 3109 3603 4035 4399 3208 1212 3820 3416 M16977 CHIBA_RESPONSE_TO_TSA http://www.broadinstitute.org/gsea/msigdb/cards/CHIBA_RESPONSE_TO_TSA.html Genes up-regulated in more than one of several human hepatoma cell lines by TSA [PubChem=5562]. 15336447 49/90 John Newman 9.9522880635954e-07 4.7250680715307e-06 4435 3124.90909090909 3209 9.04753869616527e-08 714 1.05013152638096 -0.849622035384455 -1 2.04423506217393 4431 1486 3209 1806 714 3197 3940 4329 3137 3763 4362 3417 M1123 HUMMERICH_BENIGN_SKIN_TUMOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_BENIGN_SKIN_TUMOR_DN.html Genes down-regulated in benign skin tumors (papilloma) induced by treatment with DMBA and TPA [PubChem=6001;4792] chemicals in the two stage skin carcinogenesis model. 16247483 16/41 Leona Saunders 0.0699462134347064 0.0871955190622597 2600 2925.36363636364 3212 0.00657039805354211 1436 2.68841769679555 3.55306749089301 1 1.04116448921068 2598 3807 1436 3791 3534 3212 2265 2441 2153 3348 3594 3418 M17083 MORI_MATURE_B_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_MATURE_B_LYMPHOCYTE_UP.html Up-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the mature B 18922927 65/156 Jessica Robertson 0.00798977894328205 0.0110671309867631 3690 3382 3213 0.000728994905437647 2255 1.62484131799822 1.64137067012528 1 1.16169273206231 3689 2765 2255 2894 3213 4355 4525 2715 3289 3116 4386 3419 M2342 FEVR_CTNNB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FEVR_CTNNB1_TARGETS_UP.html Genes up-regulated in intestinal crypt cells upon deletion of CTNNB1 [GeneID=1499]. 17785439 503/1201 Arthur Liberzon 4.94635337922156e-07 3.09688721232308e-06 4665 2519.45454545455 3213 4.94635448021043e-08 9 1.66918272687243 -1.63348440422645 -1 3.36125751701644 4664 9 4650 639 476 3213 4396 3606 2058 122 3881 3420 M654 REACTOME_OXYGEN_DEPENDENT_PROLINE_HYDROXYLATION_OF_HYPOXIA_INDUCIBLE_FACTOR_ALPHA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OXYGEN_DEPENDENT_PROLINE_HYDROXYLATION_OF_HYPOXIA_INDUCIBLE_FACTOR_ALPHA.html Genes involved in Oxygen-dependent Proline Hydroxylation of Hypoxia-inducible Factor Alpha 14/27 Reactome 0.0839184282471183 0.0965721401684667 2270 3294 3214 0.00793650793650794 2268 1.26008771057045 1.49218108988936 1 0.467573026883009 2268 3780 3105 3987 3899 2897 2980 3053 3331 3720 3214 3421 M7084 LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_UP.html Genes up-regulated in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of congenic B.D. chr3 (BD, large HSC size) vs parental B6 strain (tiny HSC size). 17220891 37/89 Leona Saunders 0.228640678686467 0.254250170936114 4185 3436 3214 0.0233237838086019 2388 1.14116721169405 -1.12292853139002 -1 0.248081720693623 4558 3214 2568 2803 4285 4184 4183 2388 4060 2951 2602 3422 M4357 XU_CREBBP_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_CREBBP_TARGETS_DN.html Genes down-regulated in pro-B lymphocytes after knockout of CREBBP [GeneID=1387]. 16424387 47/87 Kevin Vogelsang 0.000427234500921895 0.000699518124150944 4600 3221 3214 3.88470446689175e-05 2023 1.75143362421319 1.66422020947256 1 2.01994697086774 4600 3595 2647 3214 2738 3483 4499 2869 2023 2070 3693 3423 M376 PUJANA_BREAST_CANCER_WITH_BRCA1_MUTATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BREAST_CANCER_WITH_BRCA1_MUTATED_DN.html The XPRSS-Int network genes down-regulated in breast tumors from patients with germline mutations in BRCA1 [GeneID=672] compared to those with the wild type allele. 17922014 7/11 Arthur Liberzon 0.00612119273614306 0.00859571745926472 2385 3065.54545454545 3215 0.000613811944401964 1402 1.63996100199275 1.63996100199275 1 1.23829402345206 2382 3812 4585 3649 4195 2770 2008 1402 3428 3215 2275 3424 M2804 HAHTOLA_CTCL_CUTANEOUS http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_CTCL_CUTANEOUS.html Genes showing similar expression profiles in all subtypes of cutaneous T cell lymphoma (CTCL). 16914566 20/65 Arthur Liberzon 0.0839184282471183 0.0965721401684667 1455 2891.36363636364 3215 0.00793650793650794 1454 0.961086834262244 -1.01583521880387 -1 0.356624603102214 1454 3317 2780 3427 3631 1666 3215 2264 3708 3927 2416 3425 M1611 WENG_POR_TARGETS_GLOBAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/WENG_POR_TARGETS_GLOBAL_UP.html Genes up-regulated in liver from transgenic mice with reduced expression of POR [GeneID=5447] in all tissues. 16006652 11/49 John Newman 0.00741783962368385 0.0103114792277017 4635 3434.72727272727 3216 0.000676633581219311 2339 1.32519239680899 -1.5478069449589 -1 0.962334138940233 4633 2849 2686 3911 3199 4601 2339 3311 3216 2835 4202 3426 M606 REACTOME_AMINE_COMPOUND_SLC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINE_COMPOUND_SLC_TRANSPORTERS.html Genes involved in Amine compound SLC transporters 9/33 Reactome 1.72575744800073e-06 6.71252655339338e-06 3985 2575 3217 1.72575878820964e-07 778 1.69778360978126 -1.72995658666188 -1 3.21035925405623 3984 778 4034 1495 998 4391 3301 3217 1307 886 3934 3427 M18326 WILLIAMS_ESR2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WILLIAMS_ESR2_TARGETS_UP.html Genes uniquely up-regulated in T47D cells (breast cancer) by induction of ESR2 [GeneID=2100] expression in the Tet-Off system. 17700529 27/70 Jessica Robertson 2.14260094113735e-05 4.80393684697111e-05 4210 3130.90909090909 3218 1.94783800765126e-06 1275 1.61595222145784 1.36905840739819 1 2.55076768303608 4208 3218 2316 2301 1945 4457 4172 3599 1275 2637 4312 3428 M1412 PARK_HSC_VS_MULTIPOTENT_PROGENITORS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PARK_HSC_VS_MULTIPOTENT_PROGENITORS_UP.html Genes up-regulated in long term hematopoietic stem cells (LT-HSC) compared to multipotent progenitor (MPP) cells. 11781229 14/30 Kate Stafford 0.00839954791515557 0.0116004366432122 2470 3161.63636363636 3220 0.00076652633272041 1932 1.45773094277158 1.51447296431601 1 1.03132502612882 2470 3900 2857 3574 3220 3284 3342 4605 1932 2508 3086 3429 M11814 GRANDVAUX_IRF3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRANDVAUX_IRF3_TARGETS_DN.html Genes down-regulated in Jurkat cells (T lymphocyte) by expression of a constitutively active form of IRF3 [GeneID=3661]. 11991981 7/33 Yujin Hoshida 0.424552558315705 0.458188228527728 4385 3362.36363636364 3220 0.0537616046478251 1841 1.23768515062313 1.23768515062313 1 0.153346138755175 2504 3621 4381 4502 4384 3088 1841 3220 4249 2272 2924 3430 M10595 BUDHU_LIVER_CANCER_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BUDHU_LIVER_CANCER_METASTASIS_UP.html Genes up-regulated in tumor-adjacent liver tissue, which is asociated with intrahepatic metastasis of hepatocellular carcinoma 16904609 2/9 Yujin Hoshida 0.0181072845361931 0.0239488386499014 3595 3034.9 3221 0.00202829884410002 1672 1.00601323991843 -1.00601323991843 -1 0.595977333241371 3594 2033 4566 NA 3390 3064 2760 1672 3718 2174 3378 3431 M1497 LEE_AGING_NEOCORTEX_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_NEOCORTEX_DN.html Downregulated in the neocortex of aged adult mice (30-month) vs young adult (5-month) 10888876 47/137 John Newman 0.00853402117481097 0.0117722764866542 3575 3180 3223 0.000778846036839911 1945 1.98414992009499 -1.16045017165109 -1 1.39912777418384 3571 3539 1983 3170 3223 4372 3972 2294 1945 3138 3773 3432 M30 PID_HDAC_CLASSII_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HDAC_CLASSII_PATHWAY.html Signaling events mediated by HDAC Class II 18832364 31/63 Pathway Interaction Database 5.79129572846483e-06 1.6269791237162e-05 3370 3032.90909090909 3225 5.26482815779027e-07 1487 1.16676261437968 1.24539686800811 1 2.04226432321395 3369 3273 2447 2721 1487 3225 2170 3056 3494 3931 4189 3433 M12084 WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP.html Genes up-regulated in non-neoplastic rectal mucosa samples from patients having cancer associated with ulcerative collitis, compared to those who did not have the cancer. 17255260 13/34 Arthur Liberzon 1.48694646642128e-06 6.07483098661735e-06 3965 2881 3226 1.35177042856971e-07 886 1.29907244408368 -1.17271469200473 -1 2.47701698967996 3962 1800 1827 2247 886 4538 3601 4029 3226 1751 3824 3434 M12809 BOYAULT_LIVER_CANCER_SUBCLASS_G23_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G23_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G23, defined by unsupervised clustering. 17187432 5/12 Yujin Hoshida 0.0765897756730953 0.0944224385172651 3740 3103.27272727273 3226 0.00793650793650794 629 1.78132989699306 -2.82502317599512 -1 0.667352978450121 3740 2565 4564 3226 4271 3385 1605 2631 629 2917 4603 3435 M881 REACTOME_TRANSPORT_OF_VITAMINS_NUCLEOSIDES_AND_RELATED_MOLECULES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_VITAMINS_NUCLEOSIDES_AND_RELATED_MOLECULES.html Genes involved in Transport of vitamins, nucleosides, and related molecules 15/37 Reactome 0.00867637759956812 0.0119510597976415 3780 3214 3227 0.000791889608726184 2016 1.00649140152489 -0.992342840739947 -1 0.707321414040443 3778 2016 2481 2920 3227 3969 3299 2662 4015 2607 4380 3436 M6663 HOLLMANN_APOPTOSIS_VIA_CD40_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLMANN_APOPTOSIS_VIA_CD40_DN.html Genes down-regulated in DLBCL (diffuse large B-cell lymphoma) cell lines sensitive to stimulation of CD40 [GeneID=958] relative to the resistant ones. 16585179 216/543 Arthur Liberzon 0.000342311871833155 0.000570033202349028 4555 3393 3227 3.1124104172819e-05 2690 1.28922423222104 -1.04118104057413 -1 1.52876919340834 4552 3227 3261 2763 2690 3211 4453 2858 2739 3469 4100 3437 M11891 MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP.html The postradiation tumor escape signature: genes up-regulated in tumors from irradiated stroma vs those from non-irradiated stroma. 18794119 265/559 Jessica Robertson 0.000124822763666735 0.00022557634806877 2775 3371.63636363636 3227 1.13481678523503e-05 2468 1.60154654472534 1.62434553733867 1 2.13481191910765 2773 4170 3227 4257 2468 3990 2878 3608 2743 3222 3752 3438 M9183 STEGMEIER_PRE-MITOTIC_CELL_CYCLE_REGULATORS http://www.broadinstitute.org/gsea/msigdb/cards/STEGMEIER_PRE-MITOTIC_CELL_CYCLE_REGULATORS.html Pre-mitotic cell cycle regulators (CDC) identified in an shRNA screen of the ubiquitin pathway components. 17443180 3/12 Jessica Robertson 0.0016065837995794 0.00240756369837834 3650 3409.72727272727 3228 0.000160774648296497 2139 0.922076636981213 0.922076636981213 1 0.882522821333592 3648 2139 4359 2822 2998 4252 3228 2566 3747 4563 3185 3439 M18160 STEIN_ESRRA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESRRA_TARGETS_DN.html Genes down-regulated by ESRRA [GeneID=2101] only. 18974123 99/207 Leona Saunders 9.43251305967084e-05 0.000174983199515509 4235 3213.27272727273 3229 8.57537954864107e-06 2090 1.6848155787715 -1.75936269910718 -1 2.31373297698896 4232 3563 2417 3027 2396 2567 4678 3826 2090 3229 3321 3440 M214 PID_ERBB1_INTERNALIZATION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB1_INTERNALIZATION_PATHWAY.html Internalization of ErbB1 18832364 27/64 Pathway Interaction Database 0.00484277668942193 0.00687465966877648 3970 3159 3233 0.000441224534438472 1547 1.52697324870535 -1.10572826233286 -1 1.2071375447941 3967 3276 2574 1889 3135 3595 4290 3233 1547 3120 4123 3441 M568 REACTOME_PI3K_EVENTS_IN_ERBB4_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_EVENTS_IN_ERBB4_SIGNALING.html Genes involved in PI3K events in ERBB4 signaling 22/44 Reactome 0.00906644420675279 0.0124663607842851 3270 2967 3233 0.000827638639451614 667 2.21573069103286 -1.93320626396721 -1 1.54227755662497 3266 3544 2563 1636 3233 4458 2783 3692 667 3660 3135 3442 M13438 STEARMAN_TUMOR_FIELD_EFFECT_UP http://www.broadinstitute.org/gsea/msigdb/cards/STEARMAN_TUMOR_FIELD_EFFECT_UP.html Up-regulated genes in the 'Field Effect' signature of normal lung tissue adjacent to the tumor. 18172294 21/69 Jessica Robertson 1.81498018628507e-06 6.93153802194935e-06 4560 3052.36363636364 3233 1.64998334875374e-07 974 1.39345648574935 -1.5707229550831 -1 2.62780135983697 4556 2658 2050 3233 974 4035 3654 4187 3459 2086 2684 3443 M60 PID_NFAT_TFPATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFAT_TFPATHWAY.html Calcineurin-regulated NFAT-dependent transcription in lymphocytes 18832364 27/61 Pathway Interaction Database 0.00240023016057871 0.00353694293473958 3720 3424.36363636364 3234 0.000218441168310277 2332 1.22893852420937 -1.29973718319839 -1 1.10118077399751 3719 2742 2332 3107 3030 4265 3234 3992 3458 3119 4670 3444 M8043 ROSS_AML_WITH_AML1_ETO_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_AML_WITH_AML1_ETO_FUSION.html Top 100 probe sets for pediatric acute myeloid leukemia (AML) subtype t(8;21) ; has AML1 ETO fusion [GeneID=861;862]. 15226186 56/177 Kate Stafford 0.00207989463040051 0.00308137408727689 3235 3096.63636363636 3234 0.000189260325741318 2037 1.68526187914648 1.88475537792585 1 1.54695457403103 3234 2415 2037 3461 3017 3785 2915 3250 2929 3277 3743 3445 M2182 WANG_CLASSIC_ADIPOGENIC_TARGETS_OF_PPARG http://www.broadinstitute.org/gsea/msigdb/cards/WANG_CLASSIC_ADIPOGENIC_TARGETS_OF_PPARG.html Classic adipogenic genes (group 1) that are induced by PPARG [GeneID=5468] during adipogenesis in 3T3-L1 preadipocytes. 17954559 10/34 Arthur Liberzon 0.0550627658852708 0.0693426823268957 3195 3067.27272727273 3234 0.00513556517299525 1152 1.53186543920796 -1.09768587346164 -1 0.648967674288786 3194 2248 1152 2773 3831 3234 3739 4090 4115 1973 3391 3446 M8626 SIG_BCR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/SIG_BCR_SIGNALING_PATHWAY.html Members of the BCR signaling pathway 27/63 Signaling Gateway 0.00856293155642737 0.0118052066117736 4025 3276.36363636364 3235 0.000781494846177864 2014 1.0894383858122 -1.14660263040966 -1 0.767736829818624 4021 2232 3033 2014 3224 3235 4407 3408 3142 3537 3787 3447 M5071 IIZUKA_LIVER_CANCER_PROGRESSION_G1_G2_UP http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_G1_G2_UP.html Genes up-regulated during transition from G1 (well differentiated tumor, infected with HCV) to G2 (moderately differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 12/22 Yujin Hoshida 7.00826809724033e-06 1.88957101862302e-05 4475 3165.45454545455 3235 6.37117311155763e-07 1557 0.968755756066799 -0.805974842782489 -1 1.67266912953344 4474 1657 2691 3235 1557 4034 3592 2726 3341 2966 4547 3448 M7602 ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_DN.html Genes down-regulated in CD-1 compared to CD-2 cluster of multiple myeloma samples. 16728703 27/81 Kevin Vogelsang 0.0491454106598425 0.0622364303728468 2435 2886.18181818182 3235 0.00457080656171039 963 1.07392341453613 -1.1036529067878 -1 0.473395123282986 2431 3235 3296 3593 4105 1913 963 2621 3637 3539 2415 3449 M11193 AMIT_SERUM_RESPONSE_20_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_20_MCF10A.html Genes whose expression peaked at 20 min after stimulation of MCF10A cells with serum. 17322878 16/33 Leona Saunders 0.00922549035091065 0.0126776093209288 3655 3208 3236 0.000842218656199915 2768 0.897918358479292 0.687313783469538 1 0.622608258707167 3653 3402 3377 3020 3236 3111 3217 2892 3263 3349 2768 3450 M1652 MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_6 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_6.html Cluster 6: genes down-regulated in SW260 cells (colon cancer) by sodium butyrate and sulindac [PubChem=5222465;5352]. 10969808 41/95 John Newman 0.00363359566504514 0.00523103818322627 3240 3322.72727272727 3236 0.00033087372275388 2487 1.06182791724758 0.975234393989042 1 0.885476687468056 3236 2986 3224 2487 3090 4064 3187 3255 3582 3520 3919 3451 M14722 GAUTSCHI_SRC_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/GAUTSCHI_SRC_SIGNALING.html Genes down-regulated in A549 cells (lung cancer) after treatment with AZD0530 [PubChem=10302451], a SRC [GeneID=6714] kinase inhibitor. 18381431 4/8 Jessica Robertson 0.147859119791321 0.167157499479404 2665 3384.72727272727 3236 0.0158730158730159 2153 1.22144774129034 1.22144774129034 1 0.346852477606831 2663 4243 4460 4419 4500 2253 2153 3236 3799 2681 2825 3452 M5955 COLLER_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/COLLER_MYC_TARGETS_UP.html Genes up-regulated in 293T (transformed fetal renal cell) upon expression of MYC [GeneID=4609]. 10737792 14/35 Yujin Hoshida 0.153624155264903 0.17350754195501 2695 3251.81818181818 3237 0.0150485092678142 2256 0.548663710806455 -0.548663710806455 -1 0.152555692505324 2694 2639 3413 4298 3666 2465 2717 2256 3812 4573 3237 3453 M290 PID_IL12_STAT4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL12_STAT4_PATHWAY.html IL12 signaling mediated by STAT4 18832364 16/40 Pathway Interaction Database 0.00140920389181824 0.0021274257207024 3370 3033.72727272727 3238 0.000128191578524133 1883 1.47692054987568 1.44562920499843 1 1.44256868639041 3370 3289 2458 1883 2959 4228 3560 3238 2096 2722 3568 3454 M1211 YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_UP http://www.broadinstitute.org/gsea/msigdb/cards/YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_UP.html Genes up-regulated in HUVEC cells (endothelium) by ETS1 [GeneID=2113] which were down-regulated by SP100 [GeneID=6672]. 15592518 15/37 Arthur Liberzon 6.76984893420318e-05 0.000131632830314009 4645 3226.54545454545 3238 6.15459751385876e-06 2124 1.02380673702877 -0.835895976979968 -1 1.45224575878773 4645 2124 2362 3238 2289 3185 3266 4220 3806 2610 3747 3455 M1449 NADLER_OBESITY_DN http://www.broadinstitute.org/gsea/msigdb/cards/NADLER_OBESITY_DN.html Genes down-regulated in adipose tissue from obese mouse strains compared to the lean ones. 11027337 34/80 Kevin Vogelsang 8.78904818400359e-05 0.000165051860175776 4030 3090.09090909091 3239 7.99036302549386e-06 1605 1.68590714094396 -1.86543623193902 -1 2.33086977525023 4029 2988 1605 3398 2367 3593 3514 3239 2916 2757 3585 3456 M2563 HOLLEMAN_DAUNORUBICIN_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_DAUNORUBICIN_ALL_UP.html Genes distinguishing daunorubicin [PubChem=30323] resistant and sensitive ALL (B- and T-lineage ALL); here - genes up-regulated in the drug resistant samples. 15295046 6/11 Arthur Liberzon 0.000186379999203488 0.000326252026995722 3715 3073.54545454545 3239 1.86395632925781e-05 1076 2.85291178673172 -3.2023537495492 -1 3.63572171446046 3714 1076 4682 3689 2567 2636 4212 4102 1824 2068 3239 3457 M2078 WHITFIELD_CELL_CYCLE_M_G1 http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_M_G1.html Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the M/G1 phase of cell cycle. 12058064 112/254 Jessica Robertson 0.000173768108669718 0.000305774448826998 2810 3327.18181818182 3241 1.57983486681151e-05 2534 1.34540575614756 1.53569862495463 1 1.7284160440434 2807 3632 2965 3076 2534 4295 3509 3241 3092 3848 3600 3458 M2455 PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_DN.html Genes down-regulated after 10 h of TGFB1 [GeneID=7040] stimulation in MEF cells (embryonic fibroblast) with NFIC [GeneID=4782] knockout vs wild type MEFs. 19752192 16/51 Arthur Liberzon 0.000424327669451535 0.000695244566101362 3805 3010 3241 3.85826849338359e-05 1440 1.98653303576255 -2.01233722483455 -1 2.29302211761262 3801 3287 1440 4214 2736 3337 3241 2757 3032 1580 3685 3459 M15967 SMIRNOV_CIRCULATING_ENDOTHELIOCYTES_IN_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_CIRCULATING_ENDOTHELIOCYTES_IN_CANCER_DN.html Genes down-regulated in circulating endothelial cells (CEC) from cancer patients compared to those from healthy donors. 16540638 2/8 Arthur Liberzon 0.0510649803311735 0.0645509840388128 3130 3278.2 3242 0.00580695796690481 1928 0.453279198533254 0.453279198533254 1 0.197182080600784 3129 3355 4126 NA 4579 2433 1928 1935 4507 4473 2317 3460 M8244 BROCKE_APOPTOSIS_REVERSED_BY_IL6 http://www.broadinstitute.org/gsea/msigdb/cards/BROCKE_APOPTOSIS_REVERSED_BY_IL6.html Genes changed in INA-6 cells (multiple myeloma, MM) by re-addition of IL6 [GeneID=3569] after its initial withdrawal for 12h. 12969979 103/330 Kate Stafford 3.23834613366689e-05 6.87268568041805e-05 3290 3064.90909090909 3242 2.94399436573766e-06 2073 1.34820048737867 1.28284658142369 1 2.05147838661909 2370 4174 2394 3550 2073 3242 2628 4068 3286 2641 3288 3461 M19682 TRACEY_RESISTANCE_TO_IFNA2_DN http://www.broadinstitute.org/gsea/msigdb/cards/TRACEY_RESISTANCE_TO_IFNA2_DN.html Genes down-regulated in huT78R cells (cutaneous T-cell lymphoma, CTCL) resistant to IFNA2 [GeneID=3440] compared to the IFN2A sensitive parental cell line. 12414529 23/45 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3320 3182.18181818182 3242 0.00793650793650794 2299 1.48419818514662 1.46319122897638 1 0.550732327999443 3319 3774 2395 2381 4144 3119 3242 3805 3425 2299 3101 3462 M17651 FRASOR_TAMOXIFEN_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_TAMOXIFEN_RESPONSE_UP.html Genes preferentially up-regulated in MCF-7 cells (breast cancer) by tamoxifen [PubChem=5376] but not by estradiol or fulvestrant (ICI 182780) [PubChem=5757;3478439]. 16849584 28/76 Arthur Liberzon 0.00174470773192421 0.002606216267707 4460 3491.36363636364 3244 0.000158735718977705 2461 1.34221496945655 -1.35616970185926 -1 1.26774550945469 4459 3965 3244 3204 2996 4444 3196 3531 2461 3179 3726 3463 M4288 SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_UP http://www.broadinstitute.org/gsea/msigdb/cards/SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_UP.html Genes up-regulated in MCF10A cells (breast cancer) grown at low (mesenchymal phenotype) compared to those grown at high (epithelial, basal-like phenotype) confluency. 18281472 131/277 Jessica Robertson 0.000126695397153959 0.000228431947311832 3720 3125.27272727273 3246 1.15184267254814e-05 1325 1.37325862369554 -1.10267557770167 -1 1.827768829835 3716 2733 1325 2236 2471 3510 3948 4513 3246 2598 4082 3464 M3590 ASTIER_INTEGRIN_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/ASTIER_INTEGRIN_SIGNALING.html Integrin signaling signature in precursor B leukemia (PBL) cells: fibronectin (FN1) [GeneID=2335] vs control treatment with poly-L-lysine. 12393420 36/81 Kevin Vogelsang 0.0839184282471183 0.0965721401684667 3145 3357.63636363636 3247 0.00793650793650794 2277 1.23238091657492 -1.01110416683112 -1 0.457292036540175 3142 2277 2911 4071 3619 2690 3731 4229 3247 3841 3176 3465 M1148 MOTAMED_RESPONSE_TO_ANDROGEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOTAMED_RESPONSE_TO_ANDROGEN_UP.html Genes up-regulated in ovarian epithelial cells in response to dihydrotestosterone (DHT) [PubChem=10635]. 16832351 2/6 Arthur Liberzon 0.273427275113172 0.301619635400265 3275 3364.4 3249 0.0348683327566863 2438 1.14286299871611 -0.0976836375143062 -1 0.217454225862256 3272 3226 4186 NA 3858 2519 2438 2524 4160 4493 2968 3466 M13448 MOOTHA_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_GLUCONEOGENESIS.html Genes involved in gluconeogenesis; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 22/51 Vamsi Mootha 0.0839184282471183 0.0965721401684667 4155 3365.45454545455 3249 0.00793650793650794 2823 1.30704575903693 -1.37976568162984 -1 0.484997462307766 4155 2994 2823 3057 3754 3274 4158 3377 3018 3249 3161 3467 M1296 BIOCARTA_IL7_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL7_PATHWAY.html IL-7 Signal Transduction 14/27 BioCarta 0.0101043685867614 0.0138407106686828 4275 3209.72727272727 3250 0.000922825227910039 1929 1.1275703688865 -0.973810498556016 -1 0.766134976626829 4272 1929 2264 2227 3250 3458 4159 4387 2918 2500 3943 3468 M541 REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_MULTIPLE_NUCLEOTIDE_PATCH_REPLACEMENT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_MULTIPLE_NUCLEOTIDE_PATCH_REPLACEMENT_PATHWAY.html Genes involved in Resolution of AP sites via the multiple-nucleotide patch replacement pathway 13/19 Reactome 0.457432401499662 0.492991774017345 2225 3274.63636363636 3250 0.0540690371255223 2221 0.682644927281669 -0.682644927281669 -1 0.0766441883340978 2221 3250 3318 4153 4029 2239 2509 2870 4491 4324 2617 3469 M816 BONOME_OVARIAN_CANCER_POOR_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/BONOME_OVARIAN_CANCER_POOR_SURVIVAL_UP.html Top highly correlated genes positively associated with poor survival of patients with suboptimally debulked ovarian tumors. 18593951 24/45 Jessica Robertson 0.0208655221160158 0.0274035416579737 2185 3264.45454545455 3250 0.00191509870733606 2184 1.50479497908277 1.79246793467269 1 0.859273375482419 2184 3969 2760 4372 3363 3085 3250 2925 3678 3372 2951 3470 M26 PID_NFKAPPAB_ATYPICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFKAPPAB_ATYPICAL_PATHWAY.html Atypical NF-kappaB pathway 18832364 13/30 Pathway Interaction Database 0.000671792893137833 0.00106604182094273 4095 3305.36363636364 3251 6.10907381662835e-05 2425 0.949683549955481 -0.522456316846259 -1 1.03176302173737 4095 2640 2921 2425 2825 2992 3251 4455 3328 3671 3756 3471 M2432 VERNOCHET_ADIPOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/VERNOCHET_ADIPOGENESIS.html Genes up-regulated during adipogenic differentiation of 3T3-L1 cells (preadipocyte) and down-regulated by troglitazone [PubChem=5591]. 19564408 13/26 Arthur Liberzon 0.010153926834103 0.0139004677606213 3025 2824 3251 0.000927372414404221 937 2.52039421215873 2.39157459131703 1 1.71077442134036 3022 3427 937 3335 3251 3670 3304 3190 1795 1284 3849 3472 M14971 BIOCARTA_DEATH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DEATH_PATHWAY.html Induction of apoptosis through DR3 and DR4/5 Death Receptors 22/48 BioCarta 0.0149847769724079 0.0200452940030555 3520 3089.81818181818 3252 0.00137162056556567 1820 1.26548590707859 -0.99185787386523 -1 0.785436481539855 3516 3647 2837 3252 3310 2130 1820 3543 3004 3237 3692 3473 M939 HADDAD_B_LYMPHOCYTE_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/HADDAD_B_LYMPHOCYTE_PROGENITOR.html Genes up-regulated in hematopoietic progenitor cells (HPC) of B lymphocyte lineage CD34+CD45RA+CD10+ [GeneID=947;5788;4311]. 15331438 235/684 Kevin Vogelsang 0.000392214399035656 0.000646698337044716 3355 2925.54545454545 3252 3.56622127446001e-05 1050 1.48636638978597 -1.08383023131581 -1 1.73276737315979 3351 3822 1303 2495 2721 3728 4306 1050 3252 2253 3900 3474 M538 REACTOME_VITAMIN_B5_PANTOTHENATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_VITAMIN_B5_PANTOTHENATE_METABOLISM.html Genes involved in Vitamin B5 (pantothenate) metabolism 7/12 Reactome 0.00967628122499937 0.0132776145886814 2670 2994.18181818182 3254 0.000971867494680928 1287 0.807087529682997 -0.807087529682997 -1 0.553702366071264 2670 3863 3922 3653 3254 1325 1287 2279 4186 4321 2176 3475 M15123 MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN.html Genes down-regulated in at least 8 of 11 sarcoma cell lines by trabectedin [PubChem=3199]. 15897246 213/435 John Newman 3.27368992208371e-06 1.04641957536727e-05 2330 3188.54545454545 3254 2.97608617588933e-07 1262 1.32765249748223 1.70351869616312 1 2.41689988339963 2326 4016 3254 3667 1262 4418 3588 3249 3075 3641 2578 3476 M15671 WALLACE_PROSTATE_CANCER_RACE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WALLACE_PROSTATE_CANCER_RACE_DN.html Genes down-regulated in prostate cancer samples from African-American patients compared to those from the European-American patients. 18245496 63/165 Jessica Robertson 9.41642399229072e-05 0.000174753912189601 4230 3334.09090909091 3254 8.56075187048931e-06 2075 1.60174912102677 -1.23243724080805 -1 2.19999240709066 4230 2269 3065 2617 2395 3254 4188 4123 2075 3893 4566 3477 M2117 THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_UP http://www.broadinstitute.org/gsea/msigdb/cards/THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_UP.html Genes up-regulated in polymorphonuclear neutrophilic granulocytes (PMNs) attracted to skin wounds. 15187151 49/117 Kevin Vogelsang 0.000493722161609971 0.000798062107383347 3255 3294.45454545455 3255 4.48939088317763e-05 2223 1.82020491647734 -1.47066665230572 -1 2.06117944690142 3255 3476 2223 2754 2768 4648 4266 4194 2322 2554 3779 3478 M14118 ZHANG_RESPONSE_TO_CANTHARIDIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_RESPONSE_TO_CANTHARIDIN_UP.html Genes up-regulated in HL-60 cells (promyeloid leukemia) by cantharidin [PubChem=6708701]. 14639605 7/31 John Newman 0.000129450608771118 0.00023277266028452 2805 2921.54545454545 3256 1.29458150246467e-05 642 1.95952492470059 1.95952492470059 1 2.60221737602548 2804 3256 4404 3578 3656 3788 4380 642 1141 2273 2215 3479 M16664 SIMBULAN_UV_RESPONSE_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/SIMBULAN_UV_RESPONSE_NORMAL_UP.html Genes up-regulated in HFK cells (primary keratinocytes) in response to UVB irradiation. 16007217 7/12 Leona Saunders 0.0141202530871759 0.0189809254063415 3805 3240.27272727273 3257 0.0014210785454527 2268 1.80591541726462 -1.93332905988956 -1 1.13650081195269 3805 3789 4275 3725 3319 2476 2804 3257 2760 2268 3165 3480 M2237 JOHNSTONE_PARVB_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_1_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer) upon overexpression of PARVB [GeneID=29780] under all three culture conditions. 17998334 46/108 Arthur Liberzon 0.00733734603605195 0.0102026123219405 3260 3397.54545454545 3257 0.000669266555804496 2366 1.29639519595423 1.43442115411658 1 0.94360639079599 3257 3702 3048 2899 3197 4388 3833 2366 3573 3115 3995 3481 M593 REACTOME_TRAFFICKING_AND_PROCESSING_OF_ENDOSOMAL_TLR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAFFICKING_AND_PROCESSING_OF_ENDOSOMAL_TLR.html Genes involved in Trafficking and processing of endosomal TLR 24/64 Reactome 0.000334978700192119 0.000559013600106934 4685 3363.72727272727 3258 3.0457246904043e-05 1792 1.44607316830894 -1.84298568608038 -1 1.71924269744993 4685 3239 1792 3718 2685 4284 3969 3258 2890 2873 3608 3482 M17261 KAYO_AGING_MUSCLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAYO_AGING_MUSCLE_DN.html Downregulated in the vastus lateralis muscle of aged vs young adult rhesus monkeys 11309484 101/237 John Newman 1.60397361855685e-05 3.73755364324088e-05 4500 3063.72727272727 3258 1.45816846628156e-06 1515 1.92156873773793 2.16425204872615 1 3.10974779245834 4500 3562 2055 2231 1862 3258 4323 3979 1515 1848 4568 3483 M914 REACTOME_IL_3_5_AND_GM_CSF_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_3_5_AND_GM_CSF_SIGNALING.html Genes involved in Interleukin-3, 5 and GM-CSF signaling 26/66 Reactome 8.83931458009453e-05 0.000165750412654354 4385 3305.81818181818 3259 8.03606341115019e-06 1936 0.996742776155212 -0.942322430865868 -1 1.37738960972851 4382 2115 3146 1936 2371 4319 3056 3602 3259 3503 4675 3484 M18387 KORKOLA_SEMINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_SEMINOMA_UP.html Genes from the 12p region that were up-regulated in seminoma tumors compared to normal testis. 16424014 33/79 Arthur Liberzon 0.012924878510029 0.0174844055132783 3580 3282.18181818182 3259 0.00118194926643211 1984 1.55158629578762 -1.27197429638039 -1 0.996674244335699 3579 2584 2600 3259 3286 4668 4073 1984 2845 3098 4128 3485 M8382 MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5.html Cluster 5: genes up-regulated in SW260 cells (colon cancer) by curcumin and sulindac [PubChem=969516;5352]. 10969808 19/40 John Newman 0.000200953204936593 0.00034941251144077 4025 3324 3259 1.82701420750364e-05 1816 0.999605658627827 -1.40940509467184 -1 1.26300425753032 4024 4075 3259 4423 2562 2955 3097 1816 3643 3903 2807 3486 M10651 SCHWAB_TARGETS_OF_BMYB_POLYMORPHIC_VARIANTS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHWAB_TARGETS_OF_BMYB_POLYMORPHIC_VARIANTS_DN.html Genes down-regulated in 293 cells (embryonic kidney) expressing polymorphic variants S427G (SNP ID=rs2070235) or I624M (SNP ID=rs11556379) of BMYB [GeneID=4605]. 18026132 15/28 Jessica Robertson 2.06342506240687e-06 7.53053726046618e-06 4060 3238.72727272727 3260 1.8758427252164e-07 1044 1.44836007179145 -1.23164758982054 -1 2.71228238559369 4058 2925 2271 3192 1044 3381 4314 4593 3785 3260 2803 3487 M3218 MOSERLE_IFNA_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/MOSERLE_IFNA_RESPONSE.html Top 50 genes up-regulated in ovarian cancer progenitor cells (also known as side population, SP, cells) in response to interferon alpha (IFNA). 18632618 27/74 Jessica Robertson 1.6230474455884e-07 1.67524236344213e-06 3260 2829.27272727273 3260 1.47549778666232e-08 114 1.20463208013131 -1.09142096275127 -1 2.54328494899485 3260 1598 2097 2708 114 4402 3689 3720 3486 2152 3896 3488 M1989 WORSCHECH_TUMOR_EVASION_AND_TOLEROGENICITY_UP http://www.broadinstitute.org/gsea/msigdb/cards/WORSCHECH_TUMOR_EVASION_AND_TOLEROGENICITY_UP.html Selected genes with immunologic function which were reciprocally changed in evasion and tolerogenic tumor models. 18381452 11/40 Arthur Liberzon 0.00369549423021166 0.00531361950376552 3350 2945.36363636364 3263 0.000336519677138342 1069 1.72773418842637 1.32832722314114 1 1.43649141557002 3347 1658 1279 3384 3092 4024 3263 4678 2265 1069 4340 3489 M19553 BIOCARTA_AHSP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AHSP_PATHWAY.html Hemoglobin's Chaperone 6/21 BioCarta 0.0101206036774262 0.0138588979638864 2185 3145 3264 0.00101669932773622 1645 0.975254497334946 -0.975254497334946 -1 0.662439668704663 2181 3558 3840 4350 3264 1645 1995 2820 4550 4272 2120 3490 M591 REACTOME_SIGNALING_BY_HIPPO http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_HIPPO.html Genes involved in Signaling by Hippo 9/26 Reactome 0.00315681129042748 0.00458265728220048 1785 2751.45454545455 3264 0.000316130473271826 998 1.82615590790061 -1.82615590790061 -1 1.56122511691125 1785 4206 3933 3264 4444 998 1192 1805 4163 3400 1076 3491 M18441 THUM_SYSTOLIC_HEART_FAILURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/THUM_SYSTOLIC_HEART_FAILURE_DN.html Genes down-regulated in samples with systolic heart failure compared to normal hearts. 17606841 130/337 Arthur Liberzon 3.94556296777976e-05 8.15927099162222e-05 3935 3213.27272727273 3264 3.58693975524612e-06 2132 1.22129556531363 -1.23746140046634 -1 1.82510541823837 3933 3047 3363 3596 2132 2828 4102 2680 3264 3546 2855 3492 M11620 WIELAND_UP_BY_HBV_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/WIELAND_UP_BY_HBV_INFECTION.html Genes induced in the liver during hepatitis B (HBV) viral clearance in chimpanzees. 15100412 71/193 Kate Stafford 0.000104822574140875 0.000192475933551778 3285 3004.90909090909 3264 9.5297789923542e-06 1057 1.43475847414739 -1.10284840233817 -1 1.94863167326478 3283 2268 1057 1978 2426 4545 4275 3264 3558 2206 4194 3493 M1625 BRACHAT_RESPONSE_TO_CAMPTOTHECIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/BRACHAT_RESPONSE_TO_CAMPTOTHECIN_DN.html Genes specifically down-regulated in FL5.12 cells (pro-B lymphocyte) by camptothecin [PubChem=2538]. 12447701 41/92 John Newman 0.0114778495286775 0.015603482126888 4145 3380.90909090909 3267 0.0010489248076804 2091 1.32930725766666 -1.4198543377524 -1 0.877909063961946 4143 3418 3032 2540 3267 4495 3421 2091 3081 3174 4528 3494 M7857 KEGG_NON_HOMOLOGOUS_END_JOINING http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NON_HOMOLOGOUS_END_JOINING.html Non-homologous end-joining 7/13 KEGG 0.0104790797557425 0.0143121444871493 2850 3044.63636363636 3269 0.00105288252235353 1291 0.307451902146675 -0.36213788566891 -1 0.207265437679541 2849 3036 3806 4072 3269 1515 1291 3312 4040 4256 2045 3495 M8699 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_CIS.html Transcripts in hematopoietic stem cells (HSC) which are cis-regulated (i.e., modulated by a QTL (quantitative trait locus) in close proximity to the gene). 15711547 88/211 Jean Junior 0.00109786226808091 0.00169452654421183 3705 3444.45454545455 3269 9.98555014083481e-05 2901 1.19313368771202 -1.23944380494928 -1 1.20847397404708 3703 2911 2982 3024 2901 3232 3842 4654 3455 3916 3269 3496 M2247 BRUINS_UVC_RESPONSE_LATE http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_LATE.html Late response genes: differentially expressed only 12 h after UV-C irradiation of MEF cells (embryonic fibroblast). 18195040 774/1740 Arthur Liberzon 1.96845549061905e-06 7.30858431250307e-06 2930 2994.81818181818 3269 1.96845723428888e-07 1066 1.44420398017504 1.81960980109587 1 2.7113582346773 2930 2214 4634 3269 1066 4130 3484 2115 2239 3545 3317 3497 M108 PID_NETRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NETRIN_PATHWAY.html Netrin-mediated signaling events 18832364 29/58 Pathway Interaction Database 1.9316612927769e-06 7.19711745980863e-06 4415 3225.63636363636 3270 1.75605726257402e-07 1011 1.26351561144935 -1.33789528407463 -1 2.37521536862794 4412 2476 3027 2185 1011 4533 4057 4173 2462 3270 3876 3498 M2935 LAMB_CCND1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LAMB_CCND1_TARGETS.html The cyclin D1 signature: genes whose expression correlated with the levels of CCND1 [GeneID=595]. 12914697 17/36 Jean Junior 0.0633998407311637 0.079330214597125 2020 2870.90909090909 3270 0.00593674494212644 1205 0.992794735784826 0.992794735784826 1 0.39938613102335 2020 4192 3379 3270 4249 1319 1205 1971 4339 3836 1800 3499 M168 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_MAGENTA_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_MAGENTA_DN.html Genes from the magenta module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 5/15 Arthur Liberzon 0.00875506997138895 0.0120559088703875 3300 3288.36363636364 3271 0.000878975551615007 2079 0.322704278202959 -0.373520066051821 -1 0.22633602785417 3297 2604 4127 3396 3247 2079 3271 2668 4324 4474 2685 3500 M1410 SCHLOSSER_SERUM_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_SERUM_RESPONSE_DN.html Cluster 4: genes down-regulated in B493-6 cells (B lymphocytes) upon serum stimulation but not affected by MYC [GeneID=4609]. 15516975 456/1138 Leona Saunders 0.0349594544402504 0.0448821927416475 1685 3128 3271 0.00322978774154815 1682 1.40603905700238 1.63920517577471 1 0.692759776203218 1682 4419 3366 3381 3442 3271 3038 2002 3139 4111 2557 3501 M2260 CAFFAREL_RESPONSE_TO_THC_8HR_5_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_8HR_5_DN.html Genes down-regulated in EVSA-T cells (breast cancer) treated with 5 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 8 h. 18454173 17/27 Jessica Robertson 0.799620194332754 0.832671162365174 1825 3464.27272727273 3272 0.135963324229222 1824 0.821483999950457 0.890144476880937 1 0.0238797658796795 1824 4460 3272 3428 4376 2560 2911 3208 4426 4546 3096 3502 M767 REACTOME_HOMOLOGOUS_RECOMBINATION_REPAIR_OF_REPLICATION_INDEPENDENT_DOUBLE_STRAND_BREAKS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HOMOLOGOUS_RECOMBINATION_REPAIR_OF_REPLICATION_INDEPENDENT_DOUBLE_STRAND_BREAKS.html Genes involved in Homologous recombination repair of replication-independent double-strand breaks 16/26 Reactome 0.561662163780429 0.598442223618711 1395 3147.09090909091 3273 0.0722367230342491 1395 0.564322762328095 -0.564322762328095 -1 0.0459947617480947 1395 3656 3376 3273 4130 2204 2033 2950 4487 4371 2743 3503 M1151 RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_SMAD4_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_SMAD4_DN.html Apoptotic genes dependent on SMAD4 [GeneID=4089] and down-regulated in AML12 cells (hepatocytes) after stimulation with TGFB1 [GeneID=7040]. 16909112 11/15 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4125 3116.36363636364 3273 0.00793650793650794 2103 1.8338202977745 -0.795900951932639 -1 0.680464463884525 4124 2929 2496 2103 3890 3636 2657 3284 2324 3564 3273 3504 M17723 CHAUHAN_RESPONSE_TO_METHOXYESTRADIOL_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHAUHAN_RESPONSE_TO_METHOXYESTRADIOL_DN.html Genes down-regulated by 2-methoxyestradiol (2ME2) [PubChem=1573] in the MM.1S cell line (multiple myeloma) sensitive to dexamethasone [PubChem=5743]. 12480690 91/223 Arthur Liberzon 9.84108589871925e-05 0.000181842778081224 3480 3223.27272727273 3273 8.94684194527018e-06 2317 1.31258887491907 -1.10722794495223 -1 1.79454711162804 3478 3230 3551 2394 2410 2317 3273 4500 3351 3950 3002 3505 M3923 YU_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/YU_MYC_TARGETS_DN.html Genes down-regulated in B cell lymphoma tumors expressing an activated form of MYC [GeneID=4609]. 16382050 36/100 Kevin Vogelsang 3.24633286904595e-05 6.88340082549742e-05 4380 3002.72727272727 3274 2.95125524828481e-06 1116 1.21400893265495 -1.22198457971846 -1 1.84698665744147 4379 1116 2154 2471 2075 3637 4184 3917 3274 1689 4134 3506 M14990 REACTOME_FANCONI_ANEMIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FANCONI_ANEMIA_PATHWAY.html Genes involved in Fanconi Anemia pathway 12/27 Reactome 0.833630313197638 0.865586449732801 1970 3516.36363636364 3275 0.15045074466075 1967 0.527065563706588 -0.527065563706588 -1 0.0120775539518031 1967 4005 3034 4435 4169 2940 2883 3275 4442 4390 3140 3507 M1858 MALONEY_RESPONSE_TO_17AAG_DN http://www.broadinstitute.org/gsea/msigdb/cards/MALONEY_RESPONSE_TO_17AAG_DN.html Down-regulated genes in A2780 cells (ovarian cancer) treated with 17AAG [PubChem=6440175], a chemical with anticancer properties. 17409432 83/188 Jessica Robertson 0.0839184282471183 0.0965721401684667 1810 2914.63636363636 3277 0.00793650793650794 1305 1.29946939243199 -1.15425328777607 -1 0.482186146357182 1806 3920 3586 3277 4341 1305 1398 2543 3434 4023 2428 3508 M2545 ROESSLER_LIVER_CANCER_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROESSLER_LIVER_CANCER_METASTASIS_DN.html Genes down-regulated in liver samples containing tumor thrombi in the major branches of the portal vein at surgery (PT) compared to those from metastasis-free HCC patients (PN) at the time of surgery and at follow-up. 21159642 24/68 Yujin Hoshida 0.00240822769911081 0.00354761238542384 3310 3158.45454545455 3281 0.000219169810006887 2255 1.20730635944301 -1.16058373694976 -1 1.08122016908456 3307 3799 2578 4147 3031 2315 3281 2255 3996 3376 2658 3509 M17693 GARY_CD5_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARY_CD5_TARGETS_UP.html Genes up-regulated in Daudi cells (B lymphocytes) stably expressing CD5 [GeneID=921] off a plasmid vector. 17878328 330/741 Arthur Liberzon 3.87107178960638e-06 1.1910599084764e-05 4605 3372 3282 3.51916236461477e-07 1325 1.32034360685138 -1.1386434252342 -1 2.37645785810024 4603 2907 3107 3487 1325 2621 4472 4610 2651 4027 3282 3510 M13135 ENGELMANN_CANCER_PROGENITORS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ENGELMANN_CANCER_PROGENITORS_UP.html Up-regulated genes in the cancer progenitor (stem) cells corresponding to side population (SP) MCF7 cells (breast cancer) positive for MUC1 [GeneID=4582]. 18381450 28/66 Jessica Robertson 5.2335262321317e-06 1.50640687492439e-05 4495 3084.81818181818 3282 4.75776243825528e-07 1445 1.31344430619602 -1.43281206313585 -1 2.31506567718083 4494 1447 1936 2830 1445 3354 4352 4083 3282 2752 3958 3511 M630 REACTOME_GLUTAMATE_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUTAMATE_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Glutamate Neurotransmitter Release Cycle 8/28 Reactome 9.02517211192168e-05 0.000168493850663207 3305 2950 3283 9.02553867466678e-06 420 3.80140438161947 3.80140438161947 1 5.24321904649046 3305 2903 3970 3283 2412 4471 3687 1877 420 3301 2821 3512 M1003 REACTOME_IKK_COMPLEX_RECRUITMENT_MEDIATED_BY_RIP1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IKK_COMPLEX_RECRUITMENT_MEDIATED_BY_RIP1.html Genes involved in IKK complex recruitment mediated by RIP1 8/22 Reactome 0.000933857889713226 0.00145239232366285 3330 3186.18181818182 3283 9.34250562728132e-05 2399 1.01361863610468 -1.00881722428521 -1 1.05146151529791 3328 3460 4069 2884 2889 2830 3431 3698 3283 2399 2777 3513 M1009 REACTOME_ENDOSOMAL_SORTING_COMPLEX_REQUIRED_FOR_TRANSPORT_ESCRT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENDOSOMAL_SORTING_COMPLEX_REQUIRED_FOR_TRANSPORT_ESCRT.html Genes involved in Endosomal Sorting Complex Required For Transport (ESCRT) 18/32 Reactome 0.0027065814804463 0.0039659289610292 1595 2530.18181818182 3283 0.000246356094320095 411 0.840239914271994 -0.697259309238419 -1 0.737620861503067 1594 3484 3283 3921 4115 611 411 1460 4171 3454 1328 3514 M2161 FIGUEROA_AML_METHYLATION_CLUSTER_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_1_DN.html Cluster 1 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 43/122 Arthur Liberzon 0.0721698086427697 0.0898240964940289 3310 3278.81818181818 3283 0.00678655266368577 2629 1.23451968513973 1.49022259608332 1 0.472281531194977 3306 3213 2629 2810 3541 3077 3868 3210 3556 3283 3574 3515 M1020 REACTOME_PKB_MEDIATED_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PKB_MEDIATED_EVENTS.html Genes involved in PKB-mediated events 18/56 Reactome 0.218981211820638 0.243798041955693 2725 3295.36363636364 3285 0.0222181918576025 1454 0.839033144568995 0.751367072402533 1 0.187991162018253 2724 3970 3285 3212 3961 2721 1454 4153 4030 3874 2865 3516 M1362 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX5_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX5_UP.html Early prostate development genes (up-regulated at 12 hr dihydrotestosterone [PubChem=10635]) which are also up-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 6/20 Jessica Robertson 0.0765897756730953 0.0944224385172651 4080 3050.27272727273 3285 0.00793650793650794 1198 1.97016772515803 -1.62249209984053 -1 0.738098710401275 4077 1707 4329 3285 3564 2552 2838 4096 1198 2060 3847 3517 M789 BROWNE_HCMV_INFECTION_4HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_4HR_DN.html Genes down-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 4 h time point that were not down-regulated at the previous time point, 2 h. 11711622 183/570 Arthur Liberzon 1.70666419773074e-05 3.94545063175444e-05 4570 3390.81818181818 3286 1.55152494312017e-06 1878 1.32485659774265 1.41777631448365 1 2.13268102970748 4567 3108 3113 3942 1878 2399 4304 4261 3148 3286 3293 3518 M7089 OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_DN http://www.broadinstitute.org/gsea/msigdb/cards/OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_DN.html Genes down-regulated in hematopoietic stem cells (HSC, CD34+ [GeneID=947]) cultured in a three-dimentional collagen gel compared to the cells grown in suspension. 16166251 193/496 Leona Saunders 2.00781124354304e-06 7.38508907946837e-06 3095 3272.36363636364 3287 1.82528461450655e-07 1032 1.48206770805651 1.65505113638569 1 2.77999386507893 3091 4358 2295 4197 1032 4683 3461 3287 3131 2746 3715 3519 M1931 MEISSNER_ES_ICP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_ES_ICP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone trimethylation marks at K4 (H3K4me3) and K27 (H3K27me3)ES cells (embryonic stem). 18600261 9/23 Jessica Robertson 2.13313392334422e-06 7.68321719046198e-06 3785 2860.45454545455 3288 2.13313597096414e-07 380 0.862300135941635 -1.10194797270677 -1 1.61204524524511 3783 380 4553 2335 1103 3288 2234 2422 3630 3420 4317 3520 M1005 REACTOME_FORMATION_OF_INCISION_COMPLEX_IN_GG_NER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_INCISION_COMPLEX_IN_GG_NER.html Genes involved in Formation of incision complex in GG-NER 15/21 Reactome 0.00636703660191531 0.00891689585073973 3130 3195.18181818182 3289 0.000580503499927554 1714 0.571368141212304 -0.511279682844146 -1 0.428098648906672 3126 3372 3598 4242 3172 1726 1714 3289 3912 4426 2570 3521 M247 PID_INSULIN_GLUCOSE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INSULIN_GLUCOSE_PATHWAY.html Insulin-mediated glucose transport 18832364 18/41 Pathway Interaction Database 0.0130877994798326 0.0176894803468404 1845 2860.54545454545 3290 0.00119693759009548 692 1.20472047036717 0.816790856957204 1 0.771632061093098 1842 4157 3341 3489 3290 1674 692 2732 3997 3872 2380 3522 M162 PID_RXR_VDR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RXR_VDR_PATHWAY.html RXR and RAR heterodimerization with other nuclear receptor 18832364 12/36 Pathway Interaction Database 0.00701069695754375 0.00977160200566628 3510 3121 3291 0.000639376180888988 2011 1.55290114849627 -1.82252757949869 -1 1.14094974184282 3509 3376 2065 3771 3188 3291 3564 2011 3384 2960 3212 3523 M598 REACTOME_RORA_ACTIVATES_CIRCADIAN_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RORA_ACTIVATES_CIRCADIAN_EXPRESSION.html Genes involved in RORA Activates Circadian Expression 10/34 Reactome 0.181825958944418 0.203641597421975 3380 3237 3291 0.0180782465686248 2488 1.0529551107269 -1.2434177263632 -1 0.2660057667638 3380 3132 2879 3643 3697 2488 2684 2939 3993 3481 3291 3524 M1292 GROSS_HYPOXIA_VIA_HIF1A_ONLY http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_HIF1A_ONLY.html Genes uniquely up-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of HIF1A [GeneID=3091] by RNAi. 17704799 5/9 Jessica Robertson 0.055920400792551 0.070384904140181 3040 3441.81818181818 3292 0.00573795421581128 2625 0.805004007256427 0.923527930514353 1 0.339129789813512 3037 3068 4302 3393 3519 4562 2625 2909 4250 2903 3292 3525 M12113 WEI_MYCN_TARGETS_WITH_E_BOX http://www.broadinstitute.org/gsea/msigdb/cards/WEI_MYCN_TARGETS_WITH_E_BOX.html Genes whose promoters contain E-box motifs and whose expression changed in MYCN-3 cells (neuroblastoma) upon induction of MYCN [GeneID=4613]. 18504438 488/1100 Jessica Robertson 0.0323956937329914 0.0417508858176011 2825 3522.36363636364 3292 0.00298934569027181 2566 1.31161946876746 -1.22087035001286 -1 0.661297135722479 2822 4548 3719 4460 3433 2566 3216 3292 3261 4162 3267 3526 M15531 MOOTHA_FFA_OXYDATION http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_FFA_OXYDATION.html Genes involved in free fatty acid oxidation; based on literature and sequence annotation resources and coverted to Affymetrix HG-U133A probe sets. 12808457 14/29 Vamsi Mootha 0.0223618708105733 0.0292866759693534 3590 3204.90909090909 3293 0.0020538596171994 1676 0.589581838368677 -0.522913653406882 -1 0.330444824904605 3588 2516 3293 4141 3972 2060 2761 1676 4190 4654 2403 3527 M111 BIOCARTA_BARRESTIN_SRC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BARRESTIN_SRC_PATHWAY.html Roles of fl-arrestin-dependent Recruitment of Src Kinases in GPCR Signaling 8/35 BioCarta 0.000148455813781021 0.000264310008882168 3870 3164.36363636364 3294 1.48465732321486e-05 1706 1.14359783367349 1.3769107830647 1 1.49561261738671 3729 1706 3868 2055 2521 4656 4125 2006 2981 3294 3867 3528 M258 PID_BARD1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BARD1_PATHWAY.html BARD1 signaling events 18832364 17/36 Pathway Interaction Database 0.0839184282471183 0.0965721401684667 3295 3097.81818181818 3294 0.00793650793650794 838 2.22143601580275 -0.55276944236951 -1 0.824294654213354 3294 3400 2426 3422 3806 3183 2905 2991 838 3829 3982 3529 M6267 ZAIDI_OSTEOBLAST_TRANSCRIPTION_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/ZAIDI_OSTEOBLAST_TRANSCRIPTION_FACTORS.html An assortment of osteoblast transcriptional regulators. 17618270 8/16 Jessica Robertson 0.00155344515192585 0.00233166046826538 3340 3249.63636363636 3294 0.000155453215785554 2298 1.04623262294924 -0.606601045730527 -1 1.00667345035041 3336 3298 4524 2797 2993 4023 2298 3046 3729 2408 3294 3530 M2487 FORTSCHEGGER_PHF8_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FORTSCHEGGER_PHF8_TARGETS_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) upon knockdown of PHF8 [GeneID=23133] by RNAi. 20421419 161/415 Arthur Liberzon 9.46788940808796e-06 2.40860639339306e-05 3085 3331.18181818182 3294 8.6072092311006e-07 1672 1.26354546000439 1.373387036338 1 2.13297650525606 3085 3699 2876 4004 1672 4631 3464 3260 3294 3016 3642 3531 M11338 GENTILE_RESPONSE_CLUSTER_D3 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_RESPONSE_CLUSTER_D3.html Cluster d3: genes progressively down-regulated in WS1 cells (fibroblast) through 12 h irradiation with high dose UV-C. 12907719 40/80 John Newman 0.0184074117776218 0.0243320540451159 3085 3344.54545454545 3295 0.00168756866330177 2057 1.36589888410249 1.46978121658187 1 0.805736844871217 3083 4225 3289 4085 3349 3906 3295 2057 2938 3128 3435 3532 M139 PID_MYC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MYC_PATHWAY.html C-MYC pathway 18832364 14/39 Pathway Interaction Database 0.223469045287033 0.248676311141068 3055 3476.72727272727 3297 0.022730299807806 2381 0.826105627352758 -0.826105627352758 -1 0.182496505039975 3051 3901 3297 4479 4145 2499 2863 2381 4492 4301 2835 3533 M19193 REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS.html Genes involved in Glycogen breakdown (glycogenolysis) 8/17 Reactome 0.0146014206078877 0.0195996152874711 2250 3091.63636363636 3297 0.00146982579936493 1594 2.27029121375704 2.27029121375704 1 1.41718235476697 2246 3689 3908 3984 4007 2370 3153 1594 3725 3297 2035 3534 M635 REACTOME_SIGNALING_BY_FGFR_IN_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR_IN_DISEASE.html Genes involved in Signaling by FGFR in disease 61/165 Reactome 1.04548169156689e-06 4.87475343948504e-06 2880 2950.27272727273 3297 9.50438353090852e-08 738 1.13021254133515 1.20749431014811 1 2.19452892567563 2880 3207 3328 1450 738 3452 2551 4252 3297 3853 3445 3535 M10880 STEARMAN_LUNG_CANCER_EARLY_VS_LATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/STEARMAN_LUNG_CANCER_EARLY_VS_LATE_DN.html Down-regulated genes classifying non-tumor lung tissues by age after incution of lung cancer by urethane injection [PubChem=5641]: early (24-26 weeks) vs late (46 weeks). 18172294 38/107 Jessica Robertson 3.54895069008071e-05 7.42427809540992e-05 3655 2940.63636363636 3298 3.22637085600502e-06 1278 1.53353432569521 -1.40405526114824 -1 2.314696215323 3651 1278 1629 2436 2106 4059 4572 3477 3298 1834 4007 3536 M2278 ISHIDA_TARGETS_OF_SYT_SSX_FUSIONS http://www.broadinstitute.org/gsea/msigdb/cards/ISHIDA_TARGETS_OF_SYT_SSX_FUSIONS.html Genes down-regulated in synovial sarcoma samples with SYT-SSX fusions resulting from translocation of SS18 [GeneID=SS18] to one of the SSX genes. 17101797 6/8 Arthur Liberzon 0.0765897756730953 0.0944224385172651 4510 3553.09090909091 3298 0.00793650793650794 2564 2.21720595069278 -2.21720595069278 -1 0.830648493753489 4507 3007 4639 3102 3686 3298 4200 3145 2564 3064 3872 3537 M612 REACTOME_CIRCADIAN_REPRESSION_OF_EXPRESSION_BY_REV_ERBA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CIRCADIAN_REPRESSION_OF_EXPRESSION_BY_REV_ERBA.html Genes involved in Circadian Repression of Expression by REV-ERBA 8/30 Reactome 0.147859119791321 0.167157499479404 2975 3241.72727272727 3299 0.0158730158730159 2073 1.0529551107269 -1.2434177263632 -1 0.299005906119105 2971 3434 3938 4064 3729 2318 2073 3001 3771 3299 3061 3538 M520 REACTOME_TRIF_MEDIATED_TLR3_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRIF_MEDIATED_TLR3_SIGNALING.html Genes involved in TRIF mediated TLR3 signaling 51/102 Reactome 4.65745907634663e-06 1.37126688371108e-05 3400 2888.90909090909 3300 4.23406266940162e-07 1399 1.15489390649799 -1.16223129416223 -1 2.05283817509065 4404 1633 3300 1412 1399 4007 3399 4013 2485 2330 3396 3539 M1500 BURTON_ADIPOGENESIS_10 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_10.html Strongly down-regulated at 8-48 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 21/42 John Newman 0.0839184282471183 0.0965721401684667 2485 3396.72727272727 3300 0.00793650793650794 2462 1.32852719967355 1.33748105950581 1 0.492968448910218 2483 4106 2462 4430 4005 3287 3127 3300 3578 3165 3421 3540 M2159 FIGUEROA_AML_METHYLATION_CLUSTER_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_1_UP.html Cluster 1 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 60/191 Arthur Liberzon 5.26272766559429e-06 1.51109937751071e-05 3185 3121.81818181818 3301 4.78430932260441e-07 1451 1.13954192937737 1.26824564898221 1 2.00798421101228 3183 3415 3301 3851 1451 3647 2569 2745 3321 3653 3204 3541 M14970 SHAFFER_IRF4_TARGETS_IN_ACTIVATED_DENDRITIC_CELL http://www.broadinstitute.org/gsea/msigdb/cards/SHAFFER_IRF4_TARGETS_IN_ACTIVATED_DENDRITIC_CELL.html IRF4 [GeneID=3662] target genes up-regulated in plasmacytoid dendritic cells compared to monocytes. 18568025 43/97 Jessica Robertson 3.47690331545209e-05 7.29764615851793e-05 3820 3243 3304 3.160871150924e-06 1635 1.4284522266346 -1.18876101669305 -1 2.15998781347659 3819 1635 2598 4070 2097 3304 3964 4217 3453 3282 3234 3542 M611 REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION.html Genes involved in NOTCH1 Intracellular Domain Regulates Transcription 22/56 Reactome 0.0839184282471183 0.0965721401684667 2405 3272 3306 0.00793650793650794 2404 1.00168323732853 1.0321636197768 1 0.371688461733623 2404 3546 3306 3999 3915 2806 2540 3073 3560 3956 2887 3543 M1803 GEORGANTAS_HSC_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/GEORGANTAS_HSC_MARKERS.html Genes up-regulated in HSC (hematopoietic stem cells) compared to HPC (hematopoietic progenitor cells). 15231652 74/161 John Newman 0.0149558590037721 0.0200180392149889 3310 3263.63636363636 3308 0.0013689553627508 1868 1.58417381227481 -1.34124481082508 -1 0.983575479163676 3293 3308 1868 2494 3309 3001 3831 4582 3471 3230 3513 3544 M1269 KREPPEL_CD99_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KREPPEL_CD99_TARGETS_DN.html Genes down-regulated in ESFT cells (Ewing's sarcoma family of tumors) after knockdown of CD99 [GeneID=4267] by RNAi. 16314831 8/14 Arthur Liberzon 0.0205229774288202 0.0269839147675229 1420 2894 3310 0.00207150149286847 1190 1.32440460824123 1.32440460824123 1 0.75951057270265 1419 4166 4285 4081 3380 1677 1190 2171 3798 3310 2357 3545 M2126 CHICAS_RB1_TARGETS_LOW_SERUM http://www.broadinstitute.org/gsea/msigdb/cards/CHICAS_RB1_TARGETS_LOW_SERUM.html Genes up-regulated in IMR90 cells (fibroblast) grown under low serum conditions and after knockdown of RB1 [GeneID=5925] by RNAi. 20385362 50/154 Arthur Liberzon 0.00325108565827426 0.00470639091587061 1890 3105.72727272727 3310 0.000295990905994441 1747 1.30271950659176 -0.881352345625124 -1 1.1082169171902 1888 3884 3310 4324 3076 1747 1889 4256 3442 3580 2767 3546 M15936 NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON.html Genes within amplicon 17q21-q25 identified in a copy number alterations study of 191 breast tumor samples. 19010930 197/497 Jessica Robertson 2.52355740645962e-07 2.17979909250208e-06 3775 2952.18181818182 3311 2.29414335993615e-08 211 1.74271825906085 2.07838305652838 1 3.60648683572258 3775 3533 1490 3311 211 4089 3146 3982 2187 2135 4615 3547 M8293 NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON.html Genes within amplicon 8p12-p11 identified in a copy number alterations study of 191 breast tumor samples. 19010930 27/85 Jessica Robertson 0.0672589655328024 0.0839572489309302 2010 2942.45454545455 3314 0.0063097980748484 1216 1.34088504933107 -1.64149350217348 -1 0.527350762043334 2007 3838 3314 4581 4056 1216 1494 2249 3767 4032 1813 3548 M3268 CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP.html Top 200 marker genes up-regulated in the 'proliferation' subclass of hepatocellular carcinoma (HCC); characterized by increased proliferation, high levels of serum AFP [GeneID=174], and chromosomal instability. 18701503 108/260 Yujin Hoshida 7.91111001941446e-05 0.000150758282029183 3315 3210.18181818182 3314 7.19217683092511e-06 1693 1.31410245705799 -1.13029351791343 -1 1.83572325059434 3314 3263 1693 2802 2331 4316 3589 3795 3448 2346 4415 3549 M6616 BENPORATH_NANOG_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_NANOG_TARGETS.html Set 'Nanog targets': genes upregulated and identified by ChIP on chip as Nanog [GeneID=79923] transcription factor targets in human embryonic stem cells. 18443585 667/1499 Jessica Robertson 3.843897817922e-06 1.18503323518306e-05 3315 3021.54545454545 3315 3.84390446693588e-07 1359 1.42822846968962 1.73875879497152 1 2.57178761447576 3315 3697 4336 2904 1359 3583 3444 2035 2339 2311 3914 3550 M17330 MARCHINI_TRABECTEDIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARCHINI_TRABECTEDIN_RESISTANCE_UP.html Genes up-regulated in chondrosarcoma and ovarian carcinoma cell lines which developed resistance to trabectedin [PubChem=3199]. 15661559 13/37 John Newman 0.0303360669796655 0.0391685055120711 2815 3390.54545454545 3315 0.00279660295624783 2619 1.24438886441229 1.55849450094739 1 0.640013166032075 2814 4079 3077 4470 3423 3048 2619 3728 3315 3682 3041 3551 M1943 IRITANI_MAD1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IRITANI_MAD1_TARGETS_UP.html Genes up-regulated by overexpression of MAD1 [GeneID=4084] in primary thymocytes from RAG2 [GeneID=5897] knockout mice. 12234922 8/22 Jessica Robertson 0.0138424131975283 0.0186502438883316 4060 3156.81818181818 3315 0.00139294023758321 666 2.58373837981968 -2.58373837981968 -1 1.63320994890081 4057 2877 4558 2799 4019 4088 4280 1581 666 3315 2485 3552 M1675 GERHOLD_ADIPOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GERHOLD_ADIPOGENESIS_UP.html Selected genes up-regulated during differentiation of 3T3-L1 cells (fibroblast) into adipocytes in response to adipogenic hormones. 12021175 37/71 John Newman 0.000748458818719186 0.0011789169830313 3540 3246.63636363636 3316 6.806487019608e-05 1943 1.47692070008089 1.788042593363 1 1.58097187425857 3540 3118 2287 3316 2845 4061 4563 1943 3368 2953 3719 3553 M1416 HAHTOLA_CTCL_PATHOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_CTCL_PATHOGENESIS.html Differentially expressed genes relevant to pathogenesis of cutaneous T cell lymphoma (CTCL). 16914566 8/46 Arthur Liberzon 0.00132764046215151 0.00202056615967586 2910 3115.09090909091 3316 0.000132843431287195 1074 4.27398224906942 4.27398224906942 1 4.20953856064234 2908 3944 4593 3290 4188 4000 3406 1074 1236 3316 2311 3554 M1677 WENG_POR_TARGETS_LIVER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WENG_POR_TARGETS_LIVER_DN.html Genes down-regulated in liver from mice with liver specific knockout of POR [GeneID=5447]. 16006652 11/35 John Newman 0.00329138176366272 0.00476148344573075 2130 2935 3317 0.000299665116476082 1067 0.952420618150245 -0.952420618150245 -1 0.808459844420263 2127 3685 2832 3317 3851 1276 1805 4449 4307 3569 1067 3555 M12975 BIOCARTA_VEGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VEGF_PATHWAY.html VEGF, Hypoxia, and Angiogenesis 18/64 BioCarta 0.00280683164265996 0.00410640433265831 4205 3405.09090909091 3318 0.000255492645391164 2454 1.42402961538998 1.29568983112568 1 1.24224334302624 4203 3318 2645 2454 3051 3944 3463 3931 3258 2934 4255 3556 M495 REACTOME_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS.html Genes involved in Apoptotic cleavage of cellular proteins 26/60 Reactome 0.00392572713299876 0.00563429015167908 4445 3184.72727272727 3319 0.000357522712265261 1061 2.44687592686258 2.23427787329936 1 2.01164666970261 4444 3512 1719 2451 3100 4362 3645 3319 1061 3025 4394 3557 M12977 KORKOLA_EMBRYONAL_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_EMBRYONAL_CARCINOMA_DN.html Genes from the 12p region that were down-regulated in embryonic carcinoma tumors compared to normal tissue. 16424014 26/70 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3190 3494.63636363636 3319 0.00793650793650794 2870 1.08200473834377 -1.34376455398417 -1 0.401492869143327 3187 4030 2870 3275 4437 3319 3542 3033 3687 3809 3252 3558 M632 KORKOLA_SEMINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_SEMINOMA_DN.html Genes from the 12p region that were down-regulated in seminoma tumors compared to normal testis. 16424014 26/69 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3190 3495.63636363636 3320 0.00793650793650794 2871 1.08200473834377 -1.34376455398417 -1 0.401492869143327 3188 4031 2871 3276 4438 3320 3543 3034 3688 3810 3253 3559 M576 REACTOME_GLYCOSPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOSPHINGOLIPID_METABOLISM.html Genes involved in Glycosphingolipid metabolism 19/36 Reactome 0.0166905589481289 0.0221877898527467 3330 3081.27272727273 3321 0.00152895866327112 1679 1.47928265811214 -1.07890321269499 -1 0.894285059374531 3321 3806 2631 3627 3330 2792 3330 2363 1679 3003 4012 3560 M12123 REACTOME_EFFECTS_OF_PIP2_HYDROLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EFFECTS_OF_PIP2_HYDROLYSIS.html Genes involved in Effects of PIP2 hydrolysis 11/25 Reactome 0.124053809668907 0.141405047946606 3525 3145.27272727273 3321 0.0119687628010337 2041 1.40914757509669 -1.385363878688 -1 0.437579579724881 3523 2320 2444 3048 3627 3321 2041 3903 4095 2101 4175 3561 M4078 ABE_VEGFA_TARGETS_30MIN http://www.broadinstitute.org/gsea/msigdb/cards/ABE_VEGFA_TARGETS_30MIN.html Genes up-regulated in HUVEC cells (endothelium) at 30 min after VEGFA [GeneID=7422] stimulation. 12197474 14/42 John Newman 4.60248282711234e-05 9.296221779245e-05 3520 2940.36363636364 3321 4.1841628323691e-06 1576 1.67000836500631 -0.950117072536083 -1 2.46107816817618 3518 3321 2010 3702 2188 2054 1576 3830 3479 3729 2937 3562 M633 REACTOME_SMAD2_SMAD3_SMAD4_HETEROTRIMER_REGULATES_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SMAD2_SMAD3_SMAD4_HETEROTRIMER_REGULATES_TRANSCRIPTION.html Genes involved in SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription 11/41 Reactome 0.134258984246117 0.152666246099807 2855 3148.27272727273 3322 0.0130208019841006 1525 0.797539268330461 -0.947373714465565 -1 0.237956858796244 2855 3322 3331 3860 4054 1525 2515 2198 4211 4333 2427 3563 M120 PID_ARF6_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF6_DOWNSTREAM_PATHWAY.html Arf6 downstream pathway 18832364 11/29 Pathway Interaction Database 0.049253683561376 0.0623454244107531 3325 3290.27272727273 3323 0.00458111151045688 2022 1.48177507069614 -1.69379145427173 -1 0.652768221927568 4684 2022 2900 2273 3488 3375 3323 3954 3323 2817 4034 3564 M16381 SCHLOSSER_SERUM_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_SERUM_RESPONSE_UP.html Cluster 1: genes up-regulated in B493-6 cells (B lymphocytes) upon serum stimulation but not by affected by MYC [GeneID=4609]. 15516975 101/270 Leona Saunders 0.0032576171072279 0.0047143896740179 3640 3226.27272727273 3323 0.00029658643621899 2429 1.26537924084818 -1.0370791996715 -1 1.07611063476655 3640 2650 3349 3323 3077 2429 3357 3726 3026 3784 3128 3565 M733 REACTOME_REGULATION_OF_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_APOPTOSIS.html Genes involved in Regulation of Apoptosis 37/77 Reactome 0.0839184282471183 0.0965721401684667 2800 3223.36363636364 3324 0.00793650793650794 2141 1.50209015235639 -0.956695177390897 -1 0.557371390683043 2796 4143 3555 3324 4165 2141 2176 3273 2626 3857 3401 3566 M1142 SCIBETTA_KDM5B_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCIBETTA_KDM5B_TARGETS_UP.html Genes up-regulated in HB2 cells (mammary epithelium) upon expression of KDM5B [GeneID=10765] off an adenoviral vector. 17709396 15/25 Leona Saunders 0.0192228507463702 0.0253598757312755 1530 2911.18181818182 3324 0.00176299066127049 1253 0.731498108674637 -0.731498108674637 -1 0.426702618332362 1528 3935 3324 4244 4194 1253 1768 2119 4413 3770 1475 3567 M4276 NIKOLSKY_BREAST_CANCER_6P24_P22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_6P24_P22_AMPLICON.html Genes within amplicon 6p24-p22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 14/26 Jessica Robertson 0.00390186085219116 0.00560175243669356 4540 3161 3324 0.000355345301778758 1727 1.52733526384855 -1.91330029549486 -1 1.25707023981834 4540 3485 2579 3628 3099 3388 3570 2281 1727 3150 3324 3568 M9210 LINDSTEDT_DENDRITIC_CELL_MATURATION_C http://www.broadinstitute.org/gsea/msigdb/cards/LINDSTEDT_DENDRITIC_CELL_MATURATION_C.html Maturation of monocyte-derived dendritic cells (DC) in response to inflammatory stimuli: genes up-regulated only at 48 hr after the stimulation (cluster C). 12356685 46/118 Arthur Liberzon 0.00704523730875013 0.00981682486732178 4310 3386.18181818182 3324 0.000642536410181523 1786 1.32785607086911 -1.49086100840889 -1 0.974631008395188 4309 2536 1786 3115 3189 3324 4196 4257 3575 3689 3272 3569 M13686 GENTILE_UV_RESPONSE_CLUSTER_D9 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D9.html Cluster d9: genes progressively down-regulated in WS1 cells (fibroblast) through 24 h after irradiation with high dose UV-C. 12907719 23/42 John Newman 2.76742186428157e-05 6.00098975290303e-05 4340 3348.18181818182 3325 2.51586970620082e-06 2019 1.09555568117681 -1.21257727899765 -1 1.69063169581119 3818 2427 2564 2926 2019 4339 4300 3262 3513 3325 4337 3570 M744 REACTOME_PROCESSIVE_SYNTHESIS_ON_THE_LAGGING_STRAND http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROCESSIVE_SYNTHESIS_ON_THE_LAGGING_STRAND.html Genes involved in Processive synthesis on the lagging strand 9/16 Reactome 0.840007967522519 0.871243323552573 2460 3524.18181818182 3326 0.167450938557551 2458 0.71112730430769 -0.71112730430769 -1 0.0155599129344157 2458 3326 3987 3924 4338 2695 2615 3315 4481 4359 3268 3571 M2298 VANDESLUIS_COMMD1_TARGETS_GROUP_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_COMMD1_TARGETS_GROUP_2_UP.html Genes up-regulated in 9.5 days post coitus (dpc) embryos with COMMD1 [GeneID=150684] knockout compared to normal 8.5 dpc and 9.5 dpc embryos. 17371845 9/26 Arthur Liberzon 0.184157148878928 0.206153941626052 2535 3276 3326 0.0201476213528878 2193 0.782125704116827 -0.704835828306164 -1 0.196064325053417 3018 2522 4643 2532 3873 2535 3326 3946 4022 3426 2193 3572 M15652 REACTOME_DOUBLE_STRAND_BREAK_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOUBLE_STRAND_BREAK_REPAIR.html Genes involved in Double-Strand Break Repair 18/32 Reactome 0.541604537679378 0.579178197983926 1430 3147.09090909091 3327 0.0684553745121382 1427 0.564322762328095 -0.564322762328095 -1 0.0489259356705273 1427 3680 3460 3327 4044 2167 2022 2914 4457 4402 2718 3573 M8156 BENPORATH_CYCLING_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_CYCLING_GENES.html Genes showing cell-cycle stage-specific expression [PMID=12058064]. 18443585 449/1017 Jessica Robertson 2.66383180395585e-05 5.79782435361686e-05 1920 3228.90909090909 3327 2.42169459913412e-06 1918 1.39317603566476 1.57175408767523 1 2.157528497167 1918 4215 2960 3621 2010 3820 3025 3146 3327 4049 3427 3574 M9464 WONG_ENDOMETRIAL_CANCER_LATE http://www.broadinstitute.org/gsea/msigdb/cards/WONG_ENDOMETRIAL_CANCER_LATE.html Genes down-regulated in late stage (stage 3) endometrial cancers compared to the earlier stages (stage 1 and 2). 17043662 6/28 Arthur Liberzon 0.147859119791321 0.167157499479404 3125 3378.27272727273 3328 0.0158730158730159 2055 2.33787947856278 -1.5881758638962 -1 0.663883737371376 3123 3328 4192 2743 3834 3922 4652 2722 3754 2055 2836 3575 M7919 BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_UP.html Genes up-regulated in NIH3T3 cells (fibroblasts) transfrormed by expression of constitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector; their expression did NOT reverted completely after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins. 17213802 16/31 Leona Saunders 0.000119875624923066 0.000217558938183379 4420 3119.18181818182 3329 1.08983779377071e-05 1873 1.96163957044251 -2.35695883553337 -1 2.62607409044131 4419 3424 1873 1888 2457 3951 4613 3763 2471 2123 3329 3576 M1058 REACTOME_ADAPTIVE_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADAPTIVE_IMMUNE_SYSTEM.html Genes involved in Adaptive Immune System 293/690 Reactome 2.50388840854297e-06 8.57525404595596e-06 3065 3267.72727272727 3330 2.27626478027343e-07 1139 1.29584585766003 -1.13169181411054 -1 2.39995074603891 3062 3819 3408 3330 1139 4118 2926 3259 3102 4096 3686 3577 M13095 SU_THYMUS http://www.broadinstitute.org/gsea/msigdb/cards/SU_THYMUS.html Genes up-regulated specifically in human thymus. 11904358 5/22 John Newman 0.00133007450553155 0.00202230017291397 4340 3408.27272727273 3331 0.000133087127097875 2095 0.892885342596282 -0.701938434818721 -1 0.879300705513987 4338 2095 4406 2413 2970 3735 4286 3331 3037 2908 3972 3578 M12751 MIZUKAMI_HYPOXIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/MIZUKAMI_HYPOXIA_DN.html Genes down-regulated in DLD-1 cells (colon cancer) in response to hypoxia; might not be direct targets of HIF1A [GeneID=3091]. 16127434 3/13 Jessica Robertson 0.481063017846562 0.516321873941592 3290 3578 3331 0.0634920634920635 2471 1.04235288485935 1.04235288485935 1 0.109379557128731 3287 3331 4536 3195 4126 3662 4263 3171 4097 2471 3219 3579 M1995 KYNG_NORMAL_AGING_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_NORMAL_AGING_DN.html Genes distinctly down-regulated in primary fibroblast cultures from normal old donors compared to those from normal young donors. 14527998 24/60 Arthur Liberzon 0.298735036746822 0.327992591892129 2190 3219.81818181818 3331 0.0317460317460317 2188 1.42882944066351 -1.07049318497338 -1 0.252852344109861 2188 3712 2482 2461 4315 2684 2281 4243 3968 3753 3331 3580 M3430 BIOCARTA_CALCINEURIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CALCINEURIN_PATHWAY.html Effects of calcineurin in Keratinocyte Differentiation 8/22 BioCarta 3.23142251939389e-05 6.86342401183961e-05 4310 2738.90909090909 3334 3.23146950976732e-06 512 2.31502017286036 -2.54743288054652 -1 3.52312733661823 4307 1944 3829 1133 2107 4392 3661 3334 512 1126 3783 3581 M16884 BIOCARTA_ACH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ACH_PATHWAY.html Role of nicotinic acetylcholine receptors in the regulation of apoptosis 12/21 BioCarta 0.0220649077316265 0.028913914326175 4380 3322.72727272727 3335 0.00202630598938107 2490 1.02730485929368 -1.29805047483814 -1 0.577865872749386 4377 3293 2909 2490 3375 3582 3659 3335 3128 3611 2791 3582 M2844 REACTOME_FORMATION_OF_FIBRIN_CLOT_CLOTTING_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_FIBRIN_CLOT_CLOTTING_CASCADE.html Genes involved in Formation of Fibrin Clot (Clotting Cascade) 13/39 Reactome 0.257576606080425 0.28446947350763 3335 3299.18181818182 3335 0.026712694558839 1484 1.26746956715488 -1.38236163270123 -1 0.252942064093867 3335 3219 1484 4282 3758 3536 2589 3248 4184 2350 4306 3583 M10558 LU_IL4_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/LU_IL4_SIGNALING.html Genes up-regulated in peripheral B lymphocytes after incubation with IL4 [GeneID=3565] for 4 h. 15591113 62/180 Kate Stafford 1.98023182216613e-06 7.32838542988004e-06 3880 3206.90909090909 3335 1.80021236780517e-07 1020 1.3163315340142 1.31473082846459 1 2.47072427046646 3879 3335 2397 3012 1020 3289 4575 3428 3413 2633 4295 3584 M2355 YUAN_ZNF143_PARTNERS http://www.broadinstitute.org/gsea/msigdb/cards/YUAN_ZNF143_PARTNERS.html Proteins associated with ZNF143 [GeneID=7702] in HeLa cells, based on MudPIT analysis. 17938208 11/39 Arthur Liberzon 0.314130946953313 0.344251079846404 1835 3198.90909090909 3335 0.0336980920390339 1635 0.606119283272796 -0.606119283272796 -1 0.102606595406751 1835 3296 3335 3925 4121 1990 1635 3507 4376 4673 2495 3585 M1319 HESS_TARGETS_OF_HOXA9_AND_MEIS1_UP http://www.broadinstitute.org/gsea/msigdb/cards/HESS_TARGETS_OF_HOXA9_AND_MEIS1_UP.html Genes up-regulated in hematopoietic precursor cells conditionally expressing HOXA9 and MEIS1 [GeneID=3205;4211]. 16507773 37/85 Kevin Vogelsang 0.00437450806472095 0.00624206601439779 3070 3301.45454545455 3336 0.000398475516715814 2222 1.30445213857693 -1.04470456222274 -1 1.0512144330389 3069 3360 2222 4059 3117 3003 3711 3598 3534 3336 3307 3586 M2785 EHLERS_ANEUPLOIDY_DN http://www.broadinstitute.org/gsea/msigdb/cards/EHLERS_ANEUPLOIDY_DN.html Down-regulated genes in the expression signature of aneuploidy in uveal melanoma tumors: low vs high aneuploidy. 18172260 7/18 Jessica Robertson 0.000458746856640465 0.000746678628071282 4590 3537.36363636364 3336 4.58841586069595e-05 1848 0.900945936517301 -0.815709883590449 -1 1.0297393042497 4587 1848 4481 3227 2770 3129 4664 3336 3393 3209 4267 3587 M87 PID_LKB1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LKB1_PATHWAY.html LKB1 signaling events 18832364 38/103 Pathway Interaction Database 0.0839184282471183 0.0965721401684667 3340 3150 3337 0.00793650793650794 1887 1.7752027451039 2.08952329377362 1 0.658713607649622 3337 4099 2432 3034 3615 3508 1887 2542 2297 3654 4245 3588 M1021 REACTOME_SIGNALING_BY_INSULIN_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_INSULIN_RECEPTOR.html Genes involved in Signaling by Insulin receptor 51/149 Reactome 0.0175708662440143 0.0233051455475378 3120 3196.90909090909 3337 0.00161025363297919 1877 0.975548286811092 -1.07506102409769 -1 0.582148827486232 3119 4062 3535 3741 3337 1877 3283 2160 3656 4050 2346 3589 M14340 FUJII_YBX1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FUJII_YBX1_TARGETS_DN.html Genes down-regulated in MCF-7 cells (breast cancer) after knockdown of YBX1 [GeneID=4904] by RNAi. 18316615 134/317 Jessica Robertson 0.0839184282471183 0.0965721401684667 1425 3167.36363636364 3337 0.00793650793650794 1424 1.72878150960984 1.993325345118 1 0.641488364126541 1424 4052 1616 3083 4212 3849 3285 3445 3114 3337 3424 3590 M2471 TIAN_BHLHA15_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TIAN_BHLHA15_TARGETS.html Genes up-regulated in both AGS and HGC-27 cells (gastric cancer) by BHLHA15 [GeneID=168620] transfection. 20038531 8/22 Arthur Liberzon 0.000344554097446368 0.000573156017264352 3890 3294 3338 3.44607531993825e-05 2062 1.79185017238745 1.90315886651649 1 2.12323175346675 3889 2062 4672 2197 2711 4681 3488 4354 2430 2412 3338 3591 M17879 REACTOME_COMMON_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COMMON_PATHWAY.html Genes involved in Common Pathway 6/15 Reactome 0.177920516940032 0.19945826372751 3080 3338.90909090909 3339 0.0194011469316816 2050 1.38236163270123 -1.38236163270123 -1 0.353777942042094 3077 3437 3988 3339 3958 2714 3093 4614 4277 2050 2181 3592 M15973 SHEPARD_BMYB_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SHEPARD_BMYB_TARGETS.html Human orthologs of BMYB [GeneID=4605] target genes in zebra fish, identified as commonly changed in the BMYB loss of function mutant crb ('crush and burn') and after knockdown of BMYB by morpholino. 16150706 49/158 Jennifer Shepard 0.0114366974950653 0.015552050046975 3260 3234.54545454545 3340 0.00104514431665006 950 1.87630983941785 2.02223012491991 1 1.24014720357852 3256 3179 950 3019 4440 4366 3671 3473 3340 1884 4002 3593 M2308 WANG_TNF_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WANG_TNF_TARGETS.html Representative genes up-regulated in MEF cells (embryonic fibroblast) in response to TNF [GeneID=7124]. 17438126 11/31 Arthur Liberzon 0.0179971666758365 0.0238166402267636 4500 3160 3340 0.00164964559761976 1394 1.55033876091462 -1.13800723350582 -1 0.919806239631333 4499 2061 1394 2696 3344 3694 2973 3340 3983 2114 4662 3594 M12530 NEBEN_AML_WITH_FLT3_OR_NRAS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NEBEN_AML_WITH_FLT3_OR_NRAS_DN.html Genes down-regulated in acute myeloid leukemia (AML) samples with constitutively activated FLT3 [GeneID=2322] or with activating point mutations within NRAS [GeneID=4893]. 15674343 10/29 Arthur Liberzon 1.17061658383381e-05 2.87500488042204e-05 4130 3218.27272727273 3341 1.06420255701171e-06 1744 1.74384171251849 -1.69379145427173 -1 2.89475876559263 4127 2930 2338 1802 1744 3855 4546 3341 3506 2708 4504 3595 M19744 GRAHAM_CML_QUIESCENT_VS_CML_DIVIDING_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_CML_DIVIDING_UP.html Genes up-regulated in quiescent (G0) vs dividing (M) CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients. 17717066 24/59 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2325 3142.72727272727 3343 0.00793650793650794 1952 1.49150035506305 1.78046244463307 1 0.553441899464287 2325 3776 1952 2427 4071 3580 3191 3343 3562 2876 3467 3596 M1977 ONO_AML1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONO_AML1_TARGETS_UP.html Genes up-regulated in CD4+ [GeneID=920] T lymphocytes by expression of AML1 [GeneID=861] off a viral vector. 17377532 7/29 Jessica Robertson 0.00396835569617588 0.00568850253664123 3345 3360.90909090909 3343 0.000397546008921758 2070 0.834141006697104 0.834141006697104 1 0.684503167309147 3343 3523 4576 3786 3116 3909 2070 2701 4127 3213 2606 3597 M662 REACTOME_SYNTHESIS_OF_PIPS_AT_THE_PLASMA_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PIPS_AT_THE_PLASMA_MEMBRANE.html Genes involved in Synthesis of PIPs at the plasma membrane 16/36 Reactome 0.0795443295599947 0.0965721401684667 3855 3418 3344 0.00750681276471732 2742 0.864915111871027 -0.847597580439112 -1 0.32093875112969 2781 3851 3153 3852 3553 2879 4513 3107 3823 3344 2742 3598 M11121 REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PLC_BETA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PLC_BETA.html Genes involved in G beta:gamma signalling through PLC beta 7/23 Reactome 1.77007497523062e-05 4.06757718323814e-05 4635 3094.54545454545 3345 1.77008907463306e-06 1002 1.6348595623573 -1.54159775006705 -1 2.62379515190399 4634 1662 4014 2362 1915 4667 4510 3345 2404 1002 3525 3599 M14139 FUNG_IL2_SIGNALING_1 http://www.broadinstitute.org/gsea/msigdb/cards/FUNG_IL2_SIGNALING_1.html Genes up-regulated by IL2 [GeneID=3558] in both primary thymocytes and T1 cells (primary thymocytes immortalized by Tax, an HTLV-1 encoded gene). 15735688 4/14 Arthur Liberzon 0.063873937265572 0.0798594637210433 3345 3250.09090909091 3345 0.00657877737929311 1597 2.31589561865601 -2.31589561865601 -1 0.929204820684845 3890 2880 4262 3345 3805 3681 4295 1978 1597 2674 3344 3600 M9729 WIKMAN_ASBESTOS_LUNG_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WIKMAN_ASBESTOS_LUNG_CANCER_DN.html Genes negatively correlated with the asbestos exposure of lung cancer patients. 17297452 16/41 Arthur Liberzon 0.0154668068721657 0.0206429669618253 3480 3179.45454545455 3347 0.00141605696653594 916 1.52534417591262 1.79512806252444 1 0.939605897478674 3479 3715 3022 3358 3317 4490 3829 3100 916 3347 2401 3601 M2399 MADAN_DPPA4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MADAN_DPPA4_TARGETS.html Genes differentially expressed in ES cells with DPPA4 [GeneID=55211] knockout. 19332562 17/76 Arthur Liberzon 0.0799486246105734 0.0965721401684667 4115 3372.36363636364 3347 0.0075464512563166 1445 1.82485758526548 2.05415029827382 1 0.677138725050733 4111 3341 1445 3347 4152 4260 4307 2013 3287 2807 4026 3602 M1028 REACTOME_RAF_MAP_KINASE_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RAF_MAP_KINASE_CASCADE.html Genes involved in RAF/MAP kinase cascade 6/14 Reactome 0.0270326694385948 0.035099775281035 2180 2914.63636363636 3348 0.00273672565491728 1162 0.676971934891053 -0.676971934891053 -1 0.359966476803779 2178 3348 4080 2350 3777 1162 1233 3516 4412 4436 1569 3603 M16093 GENTILE_UV_RESPONSE_CLUSTER_D7 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D7.html Cluster d7: genes progressively down-regulated in WS1 cells (fibroblast) through 18 h after irradiation with high dose UV-C. 12907719 31/70 John Newman 0.0184681455520017 0.0244054512286182 2565 3188.36363636364 3350 0.00169318411905576 2126 1.06942430757601 1.06313998286716 1 0.630336662410205 2562 3892 3370 3928 3350 2777 2126 2613 4029 3698 2727 3604 M614 REACTOME_PRE_NOTCH_PROCESSING_IN_GOLGI http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PRE_NOTCH_PROCESSING_IN_GOLGI.html Genes involved in Pre-NOTCH Processing in Golgi 8/24 Reactome 0.0168227087515176 0.0223507834447438 3400 3174 3351 0.00169514339613747 1657 1.06393180702737 -1.05286553061093 -1 0.641952804641377 3396 1986 3939 3287 3351 3162 3779 3957 4063 1657 2337 3605 M1271 CALVET_IRINOTECAN_SENSITIVE_VS_REVERTED_DN http://www.broadinstitute.org/gsea/msigdb/cards/CALVET_IRINOTECAN_SENSITIVE_VS_REVERTED_DN.html Genes down-regulated in neuroblastoma xenografts: resistant vs those that reverted to be sensitive to the topoisomerase inhibitor irinotecan [PubChem=3750]. 16501609 4/9 Arthur Liberzon 0.278729175070567 0.307251214862545 2985 3468.36363636364 3351 0.032146028350188 2162 0.716975314005731 0.798302073146655 1 0.134314448540815 2982 3351 4289 3785 4224 2764 2162 2483 4384 4537 3191 3606 M15031 STREICHER_LSM1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/STREICHER_LSM1_TARGETS_UP.html Genes up-regulated in MCF10A cells (breast cancer) by expression of LSM1 [GeneID=27257] off a letiviral vector. 17001308 29/62 Arthur Liberzon 1.35584926128919e-05 3.24324126513585e-05 3520 2874.63636363636 3352 1.23259783399464e-06 1220 1.32192186361467 1.35814830676404 1 2.16908538438505 2759 3571 1826 3520 1796 3476 3352 2994 3518 1220 3589 3607 M1590 LEE_AGING_NEOCORTEX_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_NEOCORTEX_UP.html Upregulated in the neocortex of aged adult mice (30-month) vs young adult (5-month) 10888876 80/194 John Newman 7.84812747277985e-05 0.000149740738344651 4565 3451.09090909091 3352 7.13491586856485e-06 2328 1.23715139142987 -1.26879507894237 -1 1.72955722271504 4564 3074 3023 2809 2328 3352 4383 3938 3426 3913 3152 3608 M16720 GOERING_BLOOD_HDL_CHOLESTEROL_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/GOERING_BLOOD_HDL_CHOLESTEROL_QTL_CIS.html Top scoring cis-regulated QTL (quantitative trait loci) influencing blood levels of high-density lipoprotein (HDL) cholesterol. 17873875 9/25 Leona Saunders 0.0278454417416079 0.0360751285599045 3355 3182.72727272727 3354 0.00282006378936479 1739 0.657252628551111 -0.657252628551111 -1 0.346621374018007 3354 2876 4297 3721 3425 1739 2256 2731 4142 4540 1929 3609 M3231 SEIDEN_ONCOGENESIS_BY_MET http://www.broadinstitute.org/gsea/msigdb/cards/SEIDEN_ONCOGENESIS_BY_MET.html Genes changed in xenograft tumors formed by DLD-1 or DKO-4 cells (colon cancer) overexpressing MET [GeneID=4233]. 16158056 72/151 Arthur Liberzon 0.0839184282471183 0.0965721401684667 1505 2911.45454545455 3355 0.00793650793650794 1503 1.31646265838031 1.19825325282997 1 0.488491733468275 1503 3536 3019 3661 3850 2382 1715 3355 3361 3378 2266 3610 M15669 GNATENKO_PLATELET_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/GNATENKO_PLATELET_SIGNATURE.html Top 50 most up-regulated genes in human platelet cells. 12433680 73/172 Kate Stafford 0.0159147611464553 0.0212045978766818 3365 3248.81818181818 3355 0.00145736980647918 1728 2.0427334945 2.46435875584519 1 1.24961097724939 3362 3955 1728 2766 3322 4106 3355 2600 2719 3634 4190 3611 M2248 BRUINS_UVC_RESPONSE_EARLY_LATE http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_EARLY_LATE.html Early-late response genes: differentially expressed in the first 3 h and after 12 h following UV-C irradiation of MEF cells (embryonic fibroblast). 18195040 205/493 Arthur Liberzon 2.86530966634097e-06 9.47554064677048e-06 3445 3219.63636363636 3355 2.60483036196883e-07 1203 1.37317575256993 -1.12731911633452 -1 2.52140605789741 3444 3757 3145 3355 1203 4422 2890 4089 2219 3091 3801 3612 M190 PID_TCR_JNK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCR_JNK_PATHWAY.html JNK signaling in the CD4+ TCR pathway 18832364 7/18 Pathway Interaction Database 0.147859119791321 0.167157499479404 3360 3366.81818181818 3356 0.0158730158730159 2637 0.922463146828257 -0.922463146828257 -1 0.261950320611471 3356 3750 3901 3156 3743 3311 2814 3380 3792 3195 2637 3613 M16082 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_25 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_25.html Amplification hot spot 25: colocalized fragile sites and cancer genes in the 2q13-q36 region. 16751803 5/11 Arthur Liberzon 0.121711050670603 0.138802137610719 2535 3241.63636363636 3356 0.0128941133564597 1410 0.80255745429698 0.80255745429698 1 0.251583468419907 2535 3406 4218 3356 3707 3149 1410 2196 4014 4508 3159 3614 M11480 REACTOME_MEMBRANE_TRAFFICKING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEMBRANE_TRAFFICKING.html Genes involved in Membrane Trafficking 89/177 Reactome 0.0839184282471183 0.0965721401684667 4615 3598 3358 0.00793650793650794 2658 1.30561544139507 -1.03090077620161 -1 0.484466723101146 4611 3827 3110 3267 3693 2658 3962 4618 3154 3320 3358 3615 M8897 AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN.html Down-regulated genes whose expression correlates with copy number losses in pancreatic adenocarcinoma cell lines and primary tumor specimens. 15199222 160/354 Arthur Liberzon 2.32319112185065e-06 8.16077481033895e-06 3360 3133.63636363636 3358 2.11199415921339e-07 1100 1.44219074081032 1.73303324356936 1 2.68232861481056 3364 3305 3479 3656 1100 4684 3120 3022 2022 3358 3360 3616 M12812 GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_DN.html Genes down-regulated in common hematopoietic progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 44/122 Arthur Liberzon 1.1292824655994e-05 2.79251590174079e-05 4550 3365 3359 1.02662569305752e-06 1126 1.25092958846618 -0.898421548461437 -1 2.08231082100676 4549 3146 3166 3359 1728 4258 4558 3178 1126 3605 4342 3617 M18825 KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN.html Genes down-regulated in AIDS-related primary effusion lymphoma (PEL) samples compared to other tumor subtypes and normal B lymphocytes. 12531789 32/78 Kate Stafford 0.000242394564953043 0.000414699135220868 3640 3165.72727272727 3360 2.20382978134898e-05 1640 1.37136263610536 1.36589517923789 1 1.69542832461515 3639 1640 2004 3094 2611 4374 3970 4052 3360 2141 3938 3618 M19652 CHEOK_RESPONSE_TO_MERCAPTOPURINE_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_UP.html Genes specifically up-regulated in pediadric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490]. 12704389 9/20 Jean Junior 0.000908503383355767 0.00141596468280021 4505 3087.90909090909 3360 9.0887501748537e-05 64 5.55876916266923 5.55876916266923 1 5.78871740097905 4505 3031 4375 3360 2885 3108 3407 1317 64 3412 4503 3619 M17394 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_LIGHTYELLOW_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_LIGHTYELLOW_DN.html Genes from the lightyellow module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 7/14 Arthur Liberzon 0.0186810315789739 0.0246659098278591 4175 3376.18181818182 3361 0.00188399565464337 2265 1.24797123968212 -1.48229419287279 -1 0.733472160066269 4174 2828 4129 3626 3361 3348 3117 2395 3941 2265 3954 3620 M219 PID_HEDGEHOG_GLI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HEDGEHOG_GLI_PATHWAY.html Hedgehog signaling events mediated by Gli proteins 18832364 25/86 Pathway Interaction Database 0.00824288772063346 0.011400877172045 1380 2565.81818181818 3363 0.000752175898288676 583 0.867281917730567 0.702784459835556 1 0.615979331178098 1380 3363 3411 3371 3385 1080 583 2141 3604 4002 1904 3621 M2515 YU_BAP1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/YU_BAP1_TARGETS.html Genes deregulated in U2OS cells (osteosarcoma) upon knockdown of BAP1 [GeneID=8314] by RNAi. 20805357 19/46 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4605 3436.54545454545 3364 0.00793650793650794 1684 2.14222607834185 1.77476414483719 1 0.794902707883394 4604 3399 1684 2489 4125 3364 3229 4317 2936 3010 4645 3622 M3494 BIOCARTA_PAR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PAR1_PATHWAY.html Thrombin signaling and protease-activated receptors 24/59 BioCarta 0.0839184282471183 0.0965721401684667 4300 3341.81818181818 3365 0.00793650793650794 2294 1.38654140189775 -1.7305579549031 -1 0.514495423590521 4299 2892 2294 2625 3795 3485 4004 3247 3212 3365 3542 3623 M505 REACTOME_CTNNB1_PHOSPHORYLATION_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CTNNB1_PHOSPHORYLATION_CASCADE.html Genes involved in Beta-catenin phosphorylation cascade 6/18 Reactome 0.168400697344679 0.189057419203921 3370 3419 3367 0.0182714712578035 2188 0.320574289266382 -0.360468348884122 -1 0.0847676612444652 3367 3038 3915 3362 3830 2188 4209 2313 4298 4315 2774 3624 M641 REACTOME_REGULATION_OF_HYPOXIA_INDUCIBLE_FACTOR_HIF_BY_OXYGEN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_HYPOXIA_INDUCIBLE_FACTOR_HIF_BY_OXYGEN.html Genes involved in Regulation of Hypoxia-inducible Factor (HIF) by Oxygen 17/35 Reactome 0.0839184282471183 0.0965721401684667 3390 3279.36363636364 3367 0.00793650793650794 2442 1.10712517040565 1.33278583710918 1 0.410814154005001 2442 3679 3092 4142 3814 3039 3109 2614 3389 3386 3367 3625 M16737 VANTVEER_BREAST_CANCER_BRCA1_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_BRCA1_UP.html Up-regulated genes from the optimal set of 100 markers discriminating ER(-) breast cancer tumors by BRCA1 [GeneID=672] mutation status. 11823860 26/54 Arthur Liberzon 0.0217153279469788 0.0284797164174483 3370 3410.63636363636 3369 0.00199388008241657 2642 1.86749702898823 -1.60370577737604 -1 1.05496525843988 4181 3572 2642 4613 3369 3367 2816 2956 2959 3505 3537 3626 M985 REACTOME_NEGATIVE_REGULATORS_OF_RIG_I_MDA5_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEGATIVE_REGULATORS_OF_RIG_I_MDA5_SIGNALING.html Genes involved in Negative regulators of RIG-I/MDA5 signaling 22/48 Reactome 0.140597423680259 0.159563944627197 3595 3372.81818181818 3370 0.0136799141178297 2375 0.896240859360177 -0.861164753523958 -1 0.261118627763416 3595 3933 3232 4471 3648 2699 3370 2375 3791 3242 2745 3627 M952 OLSSON_E2F3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OLSSON_E2F3_TARGETS_DN.html Genes down-regulated in the 5637 cell line (bladder cancer) after knockdown of E2F3 [GeneID=1871] by RNAi. 16909110 51/100 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2715 3263.63636363636 3370 0.00793650793650794 1802 1.37146701616432 -0.987694026853853 -1 0.508901863607561 2711 3178 1802 2352 3733 3370 3902 4028 3541 3357 3926 3628 M3862 REACTOME_AKT_PHOSPHORYLATES_TARGETS_IN_THE_CYTOSOL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AKT_PHOSPHORYLATES_TARGETS_IN_THE_CYTOSOL.html Genes involved in AKT phosphorylates targets in the cytosol 10/14 Reactome 0.191774697961005 0.214425252838289 2685 3307.72727272727 3371 0.0191697345746353 1737 0.758479313772085 0.758479313772085 1 0.185400090565071 2684 4114 3371 4016 3953 2798 1737 2328 4300 4348 2736 3629 M947 REACTOME_INHIBITION_OF_VOLTAGE_GATED_CA2_CHANNELS_VIA_GBETA_GAMMA_SUBUNITS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INHIBITION_OF_VOLTAGE_GATED_CA2_CHANNELS_VIA_GBETA_GAMMA_SUBUNITS.html Genes involved in Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits 6/28 Reactome 0.0765897756730953 0.0944224385172651 3430 3266.45454545455 3371 0.00793650793650794 2307 2.04480390815241 -2.04480390815241 -1 0.766060223448148 3428 3037 4060 3638 3671 3431 3371 2797 3145 3046 2307 3630 M1393 SHIN_B_CELL_LYMPHOMA_CLUSTER_9 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_9.html Cluster 9 of genes distinguishing among different B lymphocyte neoplasms. 19010892 4/25 Jessica Robertson 0.0199726349673715 0.0262898223194109 2850 3123.81818181818 3371 0.00201544467878714 1314 0.499502710967207 -0.524003199205281 -1 0.288517758147777 2847 2679 4350 3780 3371 1457 1314 3565 4410 4557 2032 3631 M677 REACTOME_ABACAVIR_TRANSPORT_AND_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ABACAVIR_TRANSPORT_AND_METABOLISM.html Genes involved in Abacavir transport and metabolism 6/16 Reactome 0.019995967382548 0.0263131432616174 3280 3377.36363636364 3372 0.00201782069809931 2241 1.88207060320283 -0.565499037709678 -1 1.08683788151286 3277 3039 3955 3971 3372 3608 3277 2241 3848 3041 3522 3632 M7933 SESTO_RESPONSE_TO_UV_C1 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C1.html Cluster 1: genes changed in primary keratinocytes by UVB irradiation. 11867738 56/129 John Newman 5.05920244113496e-05 0.000101313771962215 3375 3323.63636363636 3372 4.59938071654177e-06 2210 1.52603363554717 -1.42886747186873 -1 2.22806298275297 3372 4500 3214 3731 2210 3285 3404 2866 2419 3907 3652 3633 M8751 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_14 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_14.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 14. 12554760 118/227 Arthur Liberzon 0.0839184282471183 0.0965721401684667 1710 3005.72727272727 3372 0.00793650793650794 1705 1.56204162551221 1.90953351857564 1 0.579617216622092 1708 3441 3203 2724 3643 3835 3372 2235 1705 3711 3486 3634 M1529 SA_G1_AND_S_PHASES http://www.broadinstitute.org/gsea/msigdb/cards/SA_G1_AND_S_PHASES.html Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition. 14/30 SigmaAldrich 0.0839184282471183 0.0965721401684667 3165 3112.27272727273 3373 0.00793650793650794 938 3.29050979313023 -1.02225042359124 -1 1.22098931265175 3161 3373 1978 3794 3782 4354 3976 2232 938 3143 3504 3635 M550 REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES.html Genes involved in Antiviral mechanism by IFN-stimulated genes 40/100 Reactome 0.0151993179643865 0.0203206858719301 2295 3274.09090909091 3373 0.00139139579634946 1580 1.41017560202296 -1.41017560202296 -1 0.872185024496124 2294 4227 3350 4389 4089 2638 3373 1580 3595 3928 2552 3636 M19312 REACTOME_DNA_STRAND_ELONGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_STRAND_ELONGATION.html Genes involved in DNA strand elongation 16/31 Reactome 0.957528049318057 0.978407422395207 3375 3499.45454545455 3374 0.249618671813993 2101 0.71112730430769 -0.71112730430769 -1 0.00246426039047385 2101 3374 3334 3372 4301 3020 2920 3538 4506 4459 3569 3637 M4967 KORKOLA_CORRELATED_WITH_POU5F1 http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_CORRELATED_WITH_POU5F1.html Genes whose expression pattern in adult male germ cell tumors (GCT) correlates with POU5F1 [GeneID=5460]. 16424014 24/57 Arthur Liberzon 3.83311402289554e-05 7.95129363049512e-05 4645 3129.54545454545 3374 3.48470982710138e-06 1372 1.21832206238833 -0.996791593482333 -1 1.82565554267711 4642 1372 2000 2439 2128 3942 3774 3125 3779 3374 3850 3638 M973 REACTOME_INTERFERON_ALPHA_BETA_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERFERON_ALPHA_BETA_SIGNALING.html Genes involved in Interferon alpha/beta signaling 47/120 Reactome 0.0218495403176424 0.0286477185026503 2900 3399.63636363636 3375 0.0020063279483426 2896 1.20695833754743 1.25689624995124 1 0.680694295457909 2896 3445 3164 2946 3370 3912 2963 3834 3375 3710 3781 3639 M15501 MOREIRA_RESPONSE_TO_TSA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOREIRA_RESPONSE_TO_TSA_UP.html Up-regulated in CD4+ [GeneID=920] T lymphocytes after 4 h treatment with 100 nM TSA [PubChem=5562]. 14606959 26/46 John Newman 0.0614937229950691 0.0770686242190142 2385 3246.18181818182 3375 0.00575299999142117 1931 5.55876916266923 5.55876916266923 1 2.2617302665627 2383 4393 2971 3613 3875 3697 3375 1931 2091 4017 3362 3640 M1228 OXFORD_RALB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALB_TARGETS_DN.html Genes down-regulated in the UMUC-3 cells (bladder cancer) after knockdown of RALB [GeneID=5899] by RNAi. 17496927 6/13 Arthur Liberzon 0.0203514682260712 0.0267659220059977 3445 3418.63636363636 3377 0.00205402885875459 2462 0.831477510426732 0.782284569364124 1 0.477900742466758 3443 2462 4269 3301 3377 4105 3527 3927 2828 3054 3312 3641 M2099 MARTENS_TRETINOIN_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTENS_TRETINOIN_RESPONSE_DN.html Genes down-regulated in NB4 cells (acute promyelocytic leukemia, APL) in response to tretinoin [PubChem=444795]; based on Chip-seq data. 20159609 525/1412 Arthur Liberzon 0.000101840603513211 0.000187514761517842 1785 3107.09090909091 3377 1.01845270993098e-05 1432 1.14095584379393 -0.879938494945517 -1 1.55433042346587 1784 4247 4620 4575 2442 1432 1897 3422 3377 4239 2143 3642 M13314 LUI_TARGETS_OF_PAX8_PPARG_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/LUI_TARGETS_OF_PAX8_PPARG_FUSION.html Genes down-regulated in follicular thyroid carcinoma (FTC) samples that bear PAX8-PPARG [GeneID=7849;5468] fusion protein. 15608688 42/93 Leona Saunders 0.0839184282471183 0.0965721401684667 2875 3367.36363636364 3380 0.00793650793650794 2298 1.9823324292616 -1.80830286270791 -1 0.735571950873412 2873 4654 3380 3499 4618 2298 2354 3286 3399 3787 2893 3643 M10514 NAGY_STAGA_COMPONENTS_HUMAN http://www.broadinstitute.org/gsea/msigdb/cards/NAGY_STAGA_COMPONENTS_HUMAN.html Composition of the 2 MDa human STAGA complex containing KAT2A [GeneID=2648]. 17694077 7/18 Arthur Liberzon 0.0239531721437945 0.0313182379089903 1950 2864.81818181818 3382 0.00242153477880316 1103 0.826105627352758 -0.826105627352758 -1 0.45421470257521 1950 3382 4206 3846 3400 1290 1103 1871 4316 4500 1649 3644 M11234 THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN http://www.broadinstitute.org/gsea/msigdb/cards/THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN.html Genes down-regulated in polymorphonuclear neutrophilic granulocytes (PMNs) attracted to skin wounds. 15187151 190/390 Kevin Vogelsang 5.83680904298173e-07 3.4235028683673e-06 2565 3054.36363636364 3382 5.30619144685746e-08 501 1.15879642072511 1.07551156203922 1 2.31504065692456 2561 4049 3382 3491 501 2910 2060 3350 3414 3974 3906 3645 M2522 JIANG_HYPOXIA_VIA_VHL http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_HYPOXIA_VIA_VHL.html Genes up-regulated in 786-0 cells (renal carcinoma, RCC) by the loss of VHL [GeneID=7428] and in response to hypoxia. 12692265 28/50 Arthur Liberzon 0.0538289053342827 0.0678252891627988 1955 3064 3382 0.00501753943909723 1579 1.33574466910973 1.40008391366445 1 0.570573612089559 1953 4070 3426 3866 3503 2511 1579 3382 4100 3186 2128 3646 M9461 REACTOME_LAGGING_STRAND_SYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LAGGING_STRAND_SYNTHESIS.html Genes involved in Lagging Strand Synthesis 10/20 Reactome 0.908378880147486 0.935736080978483 2495 3571.54545454545 3385 0.195296364772143 2491 0.71112730430769 -0.71112730430769 -1 0.00749827731884492 2491 3585 3343 4168 4367 2814 2860 3385 4497 4427 3350 3647 M5109 KEGG_PYRIMIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PYRIMIDINE_METABOLISM.html Pyrimidine metabolism 57/106 KEGG 0.0839184282471183 0.0965721401684667 2400 3425.27272727273 3386 0.00793650793650794 2400 1.19134988333344 -0.748687794953985 -1 0.442066902351784 2400 3767 3208 4521 3638 2598 2702 4063 3386 4019 3376 3648 M1746 ZHENG_FOXP3_TARGETS_IN_THYMUS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_IN_THYMUS_UP.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are up-regulated only in developing (located in the thymus) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 119/299 Jessica Robertson 7.50366605694839e-06 1.99445145450143e-05 2890 3378.90909090909 3387 6.82153786386761e-07 1589 1.20047051309134 1.47936504876103 1 2.0624570669319 2886 3758 3387 3797 1589 4559 4294 2236 3357 3932 3373 3649 M13713 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 13. 12554760 118/223 Arthur Liberzon 0.0024996493567196 0.00367650875253862 3390 3176.54545454545 3387 0.000227499454082315 2013 0.957732009703228 -0.743700719826779 -1 0.852284360045166 2013 3387 3746 3432 3038 2187 2383 4318 3390 3978 3070 3650 M5113 REACTOME_GLYCOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOLYSIS.html Genes involved in Glycolysis 18/44 Reactome 0.0654713412046507 0.0817693776345931 3025 3484.54545454545 3388 0.00613681824857311 2990 1.19872822003557 -1.19872822003557 -1 0.476467216813343 4243 3024 2994 3722 3523 3322 4228 3023 3388 3873 2990 3651 M2250 LINDGREN_BLADDER_CANCER_CLUSTER_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_1_UP.html Up-regulated genes whose expression profile is specific to Custer I of urothelial cell carcinoma (UCC) tumors. 16532037 71/189 Leona Saunders 3.20354350960401e-06 1.02891054736151e-05 2270 2929.36363636364 3388 2.91231652224824e-07 1252 0.992559860675551 0.940344600171199 1 1.80954556604173 2267 3388 3514 4545 1252 1939 1469 3443 3572 3757 3077 3652 M1558 BURTON_ADIPOGENESIS_12 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_12.html Strongly down-regulated at 2 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 20/54 John Newman 0.143213488812274 0.16241491010995 1265 2991.27272727273 3388 0.0139532387414179 1261 1.11965726082531 1.26658562376859 1 0.323063001653167 1261 4333 3388 4553 3909 1551 1282 2591 3965 3587 2484 3653 M877 REACTOME_INTERACTION_BETWEEN_L1_AND_ANKYRINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERACTION_BETWEEN_L1_AND_ANKYRINS.html Genes involved in Interaction between L1 and Ankyrins 4/27 Reactome 0.0134581697747322 0.0181586477294543 3570 3116 3389 0.00135403763841403 1011 2.28071318215885 -2.28071318215885 -1 1.45133565048451 3566 3527 4044 3389 4527 3625 3362 1572 1011 2666 2987 3654 M12393 LIU_VAV3_PROSTATE_CARCINOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_VAV3_PROSTATE_CARCINOGENESIS_DN.html Selected genes down-regulated in prostate tumors developed by transgenic mice overexpressing VAV3 [GeneID=10451] in prostate epithelium. 18676865 17/44 Jessica Robertson 0.0839184282471183 0.0965721401684667 3135 3390.18181818182 3389 0.00793650793650794 2092 1.95265412064364 1.73779728267897 1 0.724559402675232 3135 4598 2116 3070 4328 4242 4157 2092 3601 3389 2564 3655 M3501 ST_B_CELL_ANTIGEN_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/ST_B_CELL_ANTIGEN_RECEPTOR.html B Cell Antigen Receptor 35/69 Signaling Transduction KE 9.37530977728441e-05 0.000174059832077475 4255 3246.27272727273 3391 8.52337211851381e-06 1765 1.39430523262958 1.43978276253371 1 1.915950384883 4252 2338 2875 1765 2394 3391 4239 3912 2335 3548 4660 3656 M17481 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_7 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_7.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 7. 12554760 60/120 Arthur Liberzon 2.75631141897534e-05 5.97966449505483e-05 4085 2934.36363636364 3391 2.50576904777055e-06 1532 1.34593317683805 1.12626721121346 1 2.07776805606682 4082 3391 3470 3606 2018 1532 3905 2208 2825 3652 1589 3657 M2553 HOLLEMAN_ASPARAGINASE_RESISTANCE_B_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_ASPARAGINASE_RESISTANCE_B_ALL_UP.html Genes distinguishing asparaginase resistant and sensitive B-lineage ALL; here - genes up-regulated in the drug resistant samples. 15295046 17/47 Arthur Liberzon 0.061606057417399 0.0771681328676641 4220 3029.63636363636 3392 0.00576381933490071 726 1.8507775220408 2.18103740838038 1 0.752658015804533 4217 2666 2734 2790 3520 4075 3479 1992 726 3392 3735 3658 M2626 CHOW_RASSF1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHOW_RASSF1_TARGETS_UP.html Genes up-regulated in C666-1 cells (nasopharyngeal carcinoma) by stable expression of RASSF1 [GeneID=11186]. 16116475 20/36 Lauren Kazmierski 0.0345200571041091 0.0443423759840612 2915 3486.54545454545 3394 0.00318853770290834 2551 0.729371688666359 -0.729371688666359 -1 0.360764714944931 2913 3894 3342 4009 3440 2627 3394 3318 4382 4482 2551 3659 M1433 MA_MYELOID_DIFFERENTIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/MA_MYELOID_DIFFERENTIATION_DN.html Genes down-regulated during myeloid differentiation induced by tretinoin (ATRA) [PubChem=444795] and IL3 [GeneID=3652] in the EML cell line (myeloid progenitor). 12130493 23/71 Kevin Vogelsang 9.58647067979927e-05 0.00017776890227756 4670 3423.63636363636 3394 8.71535312224254e-06 2398 1.16439787371964 1.35076667249656 1 1.59613133032793 4666 3800 2724 3025 2398 2945 3435 3394 3590 3324 4359 3660 M2552 HOLLEMAN_VINCRISTINE_RESISTANCE_B_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_VINCRISTINE_RESISTANCE_B_ALL_DN.html Genes distinguishing vincristine [PubChem=5978] resistant and sensitive B-lineage ALL; here - genes down-regulated in the drug resistant samples. 15295046 14/27 Arthur Liberzon 0.000382357139826056 0.000632001960220423 2635 3222.54545454545 3394 3.47657826521478e-05 814 1.50112990491585 1.50112990491585 1 1.75545617552868 2633 4339 3087 4371 4412 3394 2372 814 3789 3733 2504 3661 M871 REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE.html Genes involved in Deposition of New CENPA-containing Nucleosomes at the Centromere 44/81 Reactome 0.0839184282471183 0.0965721401684667 1345 3162.63636363636 3395 0.00793650793650794 1344 1.3117819906992 -0.945985781753593 -1 0.486754906781101 1344 3395 2205 2994 3919 2868 3566 3639 3674 3819 3366 3662 M4785 FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_DN.html Genes down-regulated in monocyte-derived dendritic cells (MDDC) after stimulation with galecin-1 (lectin, LGALS1) [GeneID=3956] compared to that with bacterial lipopolysaccharide (LPS). 16785517 301/774 Arthur Liberzon 3.30635004668456e-06 1.05541936776321e-05 3155 3200.09090909091 3396 3.00577728705771e-07 1264 1.26992342549596 -1.19767057139443 -1 2.31008166449916 3153 2970 2324 3542 1264 4679 3980 3396 3436 2336 4121 3663 M1216 LI_WILMS_TUMOR_ANAPLASTIC_DN http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_ANAPLASTIC_DN.html Selected down-regulated genes distinguishing between Wilms tumors of different histological types: anaplastic vs favorable histology. 15531917 4/19 Leona Saunders 0.481063017846562 0.516321873941592 3310 3534.63636363636 3399 0.0634920634920635 2566 0.9961847818139 0.9961847818139 1 0.104534895766067 3308 2566 4266 3399 3908 3349 2672 3137 4107 4531 3638 3664 M2162 FIGUEROA_AML_METHYLATION_CLUSTER_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_2_UP.html Cluster 2 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 36/98 Arthur Liberzon 0.0259845474995867 0.0337763077900314 2665 3024.63636363636 3399 0.00239060253615681 1438 0.897801448488727 0.966321523168714 1 0.482866092062069 2664 3598 3556 4171 3399 2282 1438 2582 3898 3997 1686 3665 M4517 MUNSHI_MULTIPLE_MYELOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MUNSHI_MULTIPLE_MYELOMA_UP.html Genes up-regulated in multiple myeloma (MM) compared to normal plasma cells from the patient's identical twin. 12969976 68/189 Kevin Vogelsang 0.000130809812638134 0.000235126498666013 3085 3403 3400 1.18925082824585e-05 2480 1.22238983282647 1.42432470365152 1 1.6213614959228 3082 3666 3400 2722 2480 4483 4087 3222 3489 3846 2956 3666 M5291 BIOCARTA_CDC42RAC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CDC42RAC_PATHWAY.html Role of PI3K subunit p85 in regulation of Actin Organization and Cell Migration 16/29 BioCarta 0.0839184282471183 0.0965721401684667 4580 3594.18181818182 3401 0.00793650793650794 2898 1.28600935213325 -1.08690704301949 -1 0.477191611646752 4576 3401 3016 2898 4525 3463 3297 4262 3084 3342 3672 3667 M4123 WEBER_METHYLATED_LCP_IN_FIBROBLAST_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_LCP_IN_FIBROBLAST_UP.html Methylated germline-specific genes with low-CpG-density promoters (LCP) in primary fibroblasts. 17334365 3/12 Arthur Liberzon 0.140548637259516 0.159547217586748 2075 3143 3401 0.0150319790338781 1305 0.349589497481273 0.349589497481273 1 0.101858269683228 2072 2680 4581 3768 3762 1669 1305 3401 4326 4643 2366 3668 M14547 WEBER_METHYLATED_LCP_IN_SPERM_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_LCP_IN_SPERM_UP.html Methylated germline-specific genes with low-CpG-density promoters (LCP) in sperm. 17334365 3/18 Arthur Liberzon 0.140548637259516 0.159547217586748 2075 3144.27272727273 3402 0.0150319790338781 1306 0.349589497481273 0.349589497481273 1 0.101858269683228 2073 2681 4584 3769 3763 1670 1306 3402 4327 4645 2367 3669 M15243 REACTOME_GAP_JUNCTION_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAP_JUNCTION_DEGRADATION.html Genes involved in Gap junction degradation 6/11 Reactome 0.0765897756730953 0.0944224385172651 3310 3351.45454545455 3403 0.00793650793650794 2102 1.26874483873029 -0.525782310085308 -1 0.475319393408333 3309 3403 3910 3698 4244 3986 2102 4397 2469 3039 2309 3670 M19104 REACTOME_REGULATION_OF_AMPK_ACTIVITY_VIA_LKB1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_AMPK_ACTIVITY_VIA_LKB1.html Genes involved in Regulation of AMPK activity via LKB1 9/38 Reactome 0.29343093035143 0.323153311310647 3360 3323.36363636364 3403 0.0341371497836335 2510 0.865884421501299 0.747810951717757 1 0.155274125971587 3359 2722 4037 2887 3914 3765 2510 2516 3988 3403 3456 3671 M1024 REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION.html Genes involved in RNA Polymerase III Transcription Termination 9/22 Reactome 0.00292086914580254 0.00426392299602203 1430 2462.54545454545 3405 0.000292471542733952 522 0.91343148314624 -0.91343148314624 -1 0.791368038190124 1428 3584 4079 3533 3955 692 522 1233 3450 3405 1207 3672 M16530 ZHAN_MULTIPLE_MYELOMA_CD1_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_DN.html Top 50 down-regulated genes in cluster CD-1 of multiple myeloma samples with the characteristic expression spike of CCND1 [GeneID=595]. 16728703 25/101 Kevin Vogelsang 0.00617455840586074 0.00866805892446478 4480 3520 3405 0.000562905129927814 2228 1.69966968789489 -1.17037375691738 -1 1.28111730816096 4478 3772 2228 3405 3168 3090 4291 3845 2790 2990 4663 3673 M529 REACTOME_MEIOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOSIS.html Genes involved in Meiosis 74/238 Reactome 0.359506755822706 0.391142014809659 1320 3232.90909090909 3406 0.0396922938857454 1320 0.915088689254877 -0.893560825426521 -1 0.136359821882927 1320 3882 3406 3680 3821 2312 3014 3058 4258 4076 2735 3674 M19990 TIEN_INTESTINE_PROBIOTICS_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_6HR_DN.html Genes down-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 6h. 16394013 121/273 Arthur Liberzon 4.95567603462645e-07 3.09688721232308e-06 2930 3254.81818181818 3409 4.50516104630225e-08 442 1.15325411630887 1.28203686312588 1 2.32232457485919 2927 3110 3396 2983 442 3714 3409 4499 3437 3764 4122 3675 M14092 OXFORD_RALA_AND_RALB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_AND_RALB_TARGETS_UP.html Genes up-regulated in the UMUC-3 cells (bladder cancer) after knockdown of both RALA and RALB [GeneID=5898;5899] by RNAi. 17496927 3/12 Arthur Liberzon 0.0993147144667027 0.113703579768133 2845 3204.09090909091 3409 0.0104054227940762 1194 0.346060104948595 -0.346060104948595 -1 0.119439140832931 2842 3409 4270 3840 4668 1703 1194 2336 4372 4533 2078 3676 M6451 ODONNELL_TFRC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_TFRC_TARGETS_DN.html Genes down-regulated in P493-6 cells (B lymphocyte, Burkitt's lymphoma model) upon knockdown of TFRC [GeneID=7037] by RNAi. 16508012 68/184 Leona Saunders 0.0839184282471183 0.0965721401684667 3045 3460.63636363636 3414 0.00793650793650794 1260 1.84086282385266 -1.20910468741389 -1 0.683077690900629 3045 3414 1260 3022 4335 4378 4302 3821 3074 3236 4180 3677 M16845 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_12 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_12.html Amplification hot spot 12: colocolized fragile sites and cancer genes in the 17q11.1-q21; 17q25 region. 16751803 6/14 Arthur Liberzon 0.0633814972116413 0.0793284444267498 3415 3530.09090909091 3415 0.00652653178376192 2499 0.753512178383234 -0.753512178383234 -1 0.303129088276993 3415 2756 4232 3314 3531 2557 2499 4663 4200 4517 3147 3678 M6416 BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_24HR_UP.html Genes up-regulated in A172 cells (glioma, does not express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 24 h. 15980968 9/24 John Newman 0.0139606530098468 0.0187825495274597 3630 3176.45454545455 3415 0.00140491413345006 1582 1.90535300463382 1.90535300463382 1 1.20225681589612 3627 2523 4401 3458 3321 4200 2427 1582 2101 3415 3886 3679 M5275 OSMAN_BLADDER_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/OSMAN_BLADDER_CANCER_UP.html Genes up-regulated in blood samples from bladder cancer patients. 16740760 248/594 Leona Saunders 8.76035532265946e-07 4.34402381396637e-06 3940 3048.90909090909 3417 7.9639625554701e-08 667 1.24824958004281 -1.26165229570282 -1 2.44656196592412 3937 3410 3448 4181 667 1654 3749 2768 3417 3778 2529 3680 M3190 WU_HBX_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_1_UP.html Genes up-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] in SK-Hep-1 cells (hepatocellular carcinoma). 11439330 14/24 John Newman 0.0839184282471183 0.0965721401684667 3105 3493.63636363636 3417 0.00793650793650794 2613 1.26645019750927 -1.32263445531011 -1 0.469933915940941 4425 3425 3040 3417 3781 2613 3102 4669 3103 3154 3701 3681 M19861 REACTOME_ENERGY_DEPENDENT_REGULATION_OF_MTOR_BY_LKB1_AMPK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENERGY_DEPENDENT_REGULATION_OF_MTOR_BY_LKB1_AMPK.html Genes involved in Energy dependent regulation of mTOR by LKB1-AMPK 11/41 Reactome 0.35943518917414 0.391142014809659 3200 3405.09090909091 3419 0.0396825396825397 2413 0.865884421501299 0.747810951717757 1 0.129027761773397 3196 3613 2853 3357 4541 3493 2413 3017 3994 3560 3419 3682 M9936 PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_UP http://www.broadinstitute.org/gsea/msigdb/cards/PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_UP.html Genes up-regulated in unstable ateroslerotic plaques compared to the stable ones. 16741146 41/108 Arthur Liberzon 0.00140067359694595 0.00211591117836515 4090 3491.54545454545 3420 0.000127415105384012 2577 1.21019942450808 1.24384662031615 1 1.18309388900624 4088 2945 2831 2577 2956 3919 3910 4044 3420 3171 4546 3683 M2483 REICHERT_MITOSIS_LIN9_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/REICHERT_MITOSIS_LIN9_TARGETS.html Genes with known mitosis function that were down-regulated in MEF cells (embryonic fibroblast) upon knockout of LIN9 [GeneID=286826]. 20404087 12/33 Arthur Liberzon 0.63389956273523 0.671137223447195 2085 3252 3420 0.0873015873015873 1901 1.85795613698642 -1.22073854704435 -1 0.117618107109652 2083 3684 1901 3420 4234 3222 3033 3499 4167 2980 3549 3684 M17946 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS.html Valine, leucine and isoleucine biosynthesis 7/11 KEGG 0.0765897756730953 0.0944224385172651 3425 3357 3421 0.00793650793650794 167 2.02781065923228 -0.548663710806455 -1 0.759693915146655 3421 3982 3789 2610 4037 4635 4650 3059 167 3187 3390 3685 M5967 REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS.html Genes involved in Synthesis of bile acids and bile salts 11/32 Reactome 0.00149415284474601 0.00224770472888597 4010 3413.81818181818 3421 0.000135924416371194 1856 1.70305236673079 2.14334357342294 1 1.64857228601614 4008 2928 1856 3050 2973 4461 3693 3421 3730 2819 4613 3686 M2105 KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_UP.html Genes whose expression was significantly and positively correlated with the number of perineuronal oligodendrocytes in the layer III of BA9 brain region. 18762803 505/1159 Jessica Robertson 1.39369674695068e-06 5.86253407200259e-06 3425 3140.54545454545 3422 1.39369762102723e-07 898 1.3682716901775 1.62062397358765 1 2.61668979003447 3422 2495 4621 2022 898 3980 3859 3179 2037 3845 4188 3687 M2426 LOPEZ_TRANSLATION_VIA_FN1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_TRANSLATION_VIA_FN1_SIGNALING.html Genes translationally up-regulated in HUVEC cells (endothelium) grown on FN1 [GeneID=2335] compared to those grown on laminin 1. 19451229 29/54 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3425 3236.09090909091 3424 0.00793650793650794 2182 1.7782823420105 1.8293695553916 1 0.659856334811112 3424 2364 2182 3583 3603 4182 3677 4085 2977 2341 3179 3688 M8511 SCIAN_INVERSED_TARGETS_OF_TP53_AND_TP73_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCIAN_INVERSED_TARGETS_OF_TP53_AND_TP73_DN.html Genes that were inversely correlated in H1299 cells (lung cancer): down-regulated by P53 [GeneID=7157] and up-regulated by P73 [GeneID=7161]. 17982488 27/63 Jessica Robertson 0.326714745292542 0.357706844962816 1895 3269.63636363636 3425 0.0353234163912667 1893 0.952251701835476 0.952251701835476 1 0.155405347818852 1893 3893 3480 3425 4680 2346 2733 3026 4253 3825 2412 3689 M10970 CHUANG_OXIDATIVE_STRESS_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHUANG_OXIDATIVE_STRESS_RESPONSE_UP.html Genes up-regulated in MCF7 cells (breast cancer) after treatment with the oxydants: hydrogen peroxyde, menadione, and t-butyl hydroperoxyde [PubChem=784;4055;6410]. 12414654 24/43 John Newman 0.150629084932143 0.170247923780034 4300 3353.27272727273 3426 0.0147321588821888 1466 1.05536805962269 -1.16415243615896 -1 0.296621974255323 4298 3801 2634 3426 4304 1466 2748 2990 4122 3750 3347 3690 M13806 ZHAN_V1_LATE_DIFFERENTIATION_GENES_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_V1_LATE_DIFFERENTIATION_GENES_DN.html The v1LDG down-regulated set: most variable late differentiation genes (LDG) with similar expression patterns in tonsil plasma cells (TPC) and multiple myeloma (MM) samples. 12393520 18/42 Arthur Liberzon 0.984820313430663 0.997736449858204 3265 3754.18181818182 3426 0.316623162054089 3128 0.629903086258145 -0.579537496998247 -1 0.000226597942249077 3263 3371 3178 3128 4294 3350 3426 4496 4557 4634 3599 3691 M18213 WANG_BARRETTS_ESOPHAGUS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_BARRETTS_ESOPHAGUS_DN.html Genes down-regulated in Barrett's esophagus compared to the normal tissue. 16449976 11/44 Arthur Liberzon 0.434659409278953 0.468879832385169 4345 3427.45454545455 3430 0.0505267304650112 1963 1.70799248628542 -1.70799248628542 -1 0.205361884120557 4341 3430 1963 3296 3869 3766 3360 3784 4067 2827 2999 3692 M719 REACTOME_SHC1_EVENTS_IN_EGFR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC1_EVENTS_IN_EGFR_SIGNALING.html Genes involved in SHC1 events in EGFR signaling 9/25 Reactome 0.0341758613684105 0.0439243242930256 2930 3092.45454545455 3432 0.003471312260972 1175 0.676971934891053 -0.676971934891053 -1 0.335864524045015 2926 3432 3968 2391 3616 1175 1821 4376 4331 4349 1632 3693 M1491 LY_AGING_PREMATURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LY_AGING_PREMATURE_DN.html Genes down-regulated in fibroblasts from patients with Hutchinson-Gilford progeria (premature aging), compared to those from normal young individuals. 10741968 25/57 Arthur Liberzon 0.0839184282471183 0.0965721401684667 1945 3300 3432 0.00793650793650794 1942 1.93510442842005 2.37809947680246 1 0.718047345874304 1942 4103 2276 3803 4589 3619 3272 2548 3280 3436 3432 3694 M5248 ST_JAK_STAT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_JAK_STAT_PATHWAY.html Jak-STAT Pathway 5/13 Signaling Transduction KE 0.0295088190442141 0.0381247107916149 3805 3213.09090909091 3434 0.00299081492823816 1858 1.36486796963775 1.21136668873462 1 0.707830160559804 3804 2029 3885 2410 3434 4240 3061 4417 2154 1858 4052 3695 M2557 HOLLEMAN_DAUNORUBICIN_B_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_DAUNORUBICIN_B_ALL_DN.html Genes distinguishing daunorubicin [PubChem=30323] resistant and sensitive B-lineage ALL; here - genes down-regulated in the drug resistant samples. 15295046 14/21 Arthur Liberzon 0.204190689385806 0.227872724568204 2230 3399 3437 0.020549171784443 2142 0.712895702516214 0.712895702516214 1 0.167374133088793 2228 4160 3437 4321 4536 2200 2142 2353 4391 4681 2940 3696 M3871 REACTOME_ASSOCIATION_OF_TRIC_CCT_WITH_TARGET_PROTEINS_DURING_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ASSOCIATION_OF_TRIC_CCT_WITH_TARGET_PROTEINS_DURING_BIOSYNTHESIS.html Genes involved in Association of TriC/CCT with target proteins during biosynthesis 16/35 Reactome 0.0340108129727024 0.0437241891879515 4670 3405.81818181818 3439 0.00314075188598624 2199 1.32275722996864 -0.878970716687074 -1 0.657215437994944 4669 3849 2755 2650 3439 3886 4495 2687 2199 2725 4110 3697 M17256 HEDENFALK_BREAST_CANCER_HEREDITARY_VS_SPORADIC http://www.broadinstitute.org/gsea/msigdb/cards/HEDENFALK_BREAST_CANCER_HEREDITARY_VS_SPORADIC.html Genes distinguishing between sporadic breast cancer tumors and hereditary breast cancer tumors that have mutated BRCA1 and BRCA2 [GeneID=672;675]. 11207349 33/83 John Newman 0.0187284607706974 0.0247215682173206 4270 3558.54545454545 3439 0.00171725649025961 2474 0.809934365796735 0.818430107222447 1 0.475734238031993 4266 2474 3456 2984 3352 3268 4353 3439 3886 3099 4567 3698 M10237 RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP.html Genes up-regulated in anaplastic thyroid carcinoma (ATC) compared to normal thyroid tissue. 17406368 487/1173 Arthur Liberzon 0.0032921908587639 0.00476148344573075 2875 3603 3440 0.000299738891383106 2872 1.48640148974011 1.76850089681941 1 1.26172816421664 2872 4481 3090 3440 3079 4541 3844 3362 2961 3849 4114 3699 M2317 KASLER_HDAC7_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/KASLER_HDAC7_TARGETS_1_UP.html Genes up-regulated in DO11.10 cells (hybridoma) by expression of transciptionally activating form of HDAC7 [GeneID=51564] and down-regulated by its transcriptionally repressing form. 17470548 125/263 Arthur Liberzon 1.28030666393389e-06 5.59423905389947e-06 3565 3289.18181818182 3440 1.1639158263806e-07 811 1.26361513335749 1.34489826524972 1 2.42594081328655 3563 3440 3266 4365 811 4262 2207 3175 2842 3714 4536 3700 M1606 IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR.html Genes in the expression cluster 'Early Progenitors Shared': up-regulated in hematopoietic progenitors from adult bone marrow and from fetal liver. 12228721 340/783 John Newman 3.24009716405689e-06 1.03993803498429e-05 3500 3130.45454545455 3443 2.94554721453572e-07 1255 1.1326916003732 -0.97355259031571 -1 2.06310421801238 3498 2034 3673 3874 1255 2078 3443 4266 3206 4089 3019 3701 M18550 BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_UP http://www.broadinstitute.org/gsea/msigdb/cards/BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_UP.html Up-regulated genes in MDA-MB-435 cells (breast cancer) undergoing G2/M arrest after treatment with 2-methoxyestradiol (2ME2)[PubChem=1573]. 17234781 84/205 Jessica Robertson 4.24149886478082e-07 2.82649481163302e-06 4305 3041.09090909091 3443 3.8559088022932e-08 386 1.33416461472775 -1.12467586527489 -1 2.70597617044937 4302 3443 2135 2192 386 3563 3992 3648 3429 2587 3775 3702 M6562 CHAUHAN_RESPONSE_TO_METHOXYESTRADIOL_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHAUHAN_RESPONSE_TO_METHOXYESTRADIOL_UP.html Genes up-regulated by 2-methoxyestradiol (2ME2) [PubChem=1573] in the MM.1S cell line (multiple myeloma) sensitive to dexamethasone [PubChem=5743]. 12480690 37/89 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2570 3384.09090909091 3443 0.00793650793650794 2569 1.69229510596466 -1.74911933735542 -1 0.627949577806428 2569 4448 3286 2989 3650 3487 3031 3748 2937 3637 3443 3703 M13736 PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP.html Up-regulated genes in head and neck cancer compared to cervical carcinoma samples. 17510386 110/306 Arthur Liberzon 0.0156240805150298 0.0208350715120745 1545 2933.81818181818 3443 0.0014305596715484 1282 1.37411988255551 -1.38133050920246 -1 0.844431737062833 1541 4562 3443 4405 4154 1282 1864 1945 3690 3975 1411 3704 M58 PID_AR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AR_PATHWAY.html Coregulation of Androgen receptor activity 18832364 53/113 Pathway Interaction Database 0.00182850142535241 0.00272790757058305 3680 3371.81818181818 3444 0.000166365721024459 2369 1.34268714634287 -1.35791289106882 -1 1.25846446006609 3680 3444 2891 3915 3001 2919 3827 4555 2369 3655 2834 3705 M3844 TONG_INTERACT_WITH_PTTG1 http://www.broadinstitute.org/gsea/msigdb/cards/TONG_INTERACT_WITH_PTTG1.html Proteins that interact with PTTG1 [GeneID=9232], based on protein array. 18663361 40/83 Jessica Robertson 1.43508448452077e-05 3.39808281680866e-05 3850 3162.54545454545 3444 1.30463076892916e-06 1820 1.21594553898755 1.33153209573169 1 1.98619091953582 3846 3233 3451 3594 1820 2293 2398 4111 3034 3444 3564 3706 M1415 BYSTROEM_CORRELATED_WITH_IL5_UP http://www.broadinstitute.org/gsea/msigdb/cards/BYSTROEM_CORRELATED_WITH_IL5_UP.html Genes whose expression in bone marrow samples correlated directly with increased levels of serum IL5 [GeneID=3567]. 14525773 36/96 Kate Stafford 0.0839184282471183 0.0965721401684667 4585 3433.45454545455 3445 0.00793650793650794 2544 1.73974735596583 -1.81628198272007 -1 0.645557393567663 4581 3925 2544 4136 3647 3205 3445 2851 2868 2860 3706 3707 M1588 MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_4 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_4.html Cluster 4: genes down-regulated in SW260 cells (colon cancer) by sodium butyrate and sulindac [PubChem=5222465;5352]. 10969808 14/34 John Newman 0.00234322815302114 0.00345838334647466 4585 3486.54545454545 3445 0.000213247969266942 2018 1.18629145649381 -1.15492049937276 -1 1.06719714400941 4585 2018 2787 2556 3026 4014 4598 4404 3445 2510 4409 3708 M18000 GOERING_BLOOD_HDL_CHOLESTEROL_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/GOERING_BLOOD_HDL_CHOLESTEROL_QTL_TRANS.html Top scoring trans-regulated expression quantitative trait loci (eQTL) influencing blood levels of high-density lipoprotein (HDL) cholesterol. 17873875 9/31 Leona Saunders 0.00594422713634058 0.00836727196181795 3180 3302.09090909091 3447 0.000596018748104069 1653 0.872290982535825 -0.660405110611102 -1 0.66237529897617 3447 2487 4298 3695 3176 3612 3595 1653 3178 3410 3772 3709 M1770 GAZIN_EPIGENETIC_SILENCING_BY_KRAS http://www.broadinstitute.org/gsea/msigdb/cards/GAZIN_EPIGENETIC_SILENCING_BY_KRAS.html Genes required for epigenetic silencing of FAS [GeneID=355] by activated KRAS [GeneID=3845] in NIH 3T3 cells, based on RNAi screen. 17960246 18/36 Jessica Robertson 0.0446346532740628 0.0567592904320918 4010 3476.18181818182 3447 0.00414243721528197 2046 1.25089783172488 1.25089783172488 1 0.569700039443824 4010 3369 2843 4506 3472 2046 3388 3309 3969 3879 3447 3710 M1947 CHEN_LIVER_METABOLISM_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_LIVER_METABOLISM_QTL_CIS.html Cis-regulated expression quantitative loci (cis-eQTL) in the liver that contribute to metabolic quantitative traits (weight, fat mass, and plasma glucose and cholesterol levels). 18344982 62/185 Arthur Liberzon 2.07977704399601e-05 4.67874950944085e-05 3980 3112.72727272727 3447 1.89072427772282e-06 1494 1.2610353581638 -1.56374336535713 -1 1.99582009974671 3978 3636 3137 4367 1940 2820 3887 1651 3447 3883 1494 3711 M1820 MATZUK_CENTRAL_FOR_FEMALE_FERTILITY http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_CENTRAL_FOR_FEMALE_FERTILITY.html Genes central for female fertility pathways, based on mouse models with female fertility defects. 18989307 9/37 Jessica Robertson 0.00137782753965046 0.00208610657538031 3245 3106 3448 0.000137868256979274 1084 1.40476575073062 -0.973615035664227 -1 1.37646591839773 3245 2027 4489 4125 3448 4056 3686 1084 3746 1822 2438 3712 M2239 JOHNSTONE_PARVB_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_2_DN.html Genes down-regulated upon overexpression of PARVB [GeneID=29780] in MDA-MB-231 cells (breast cancer) cultured in 3D collagen I and 3D Matrigel only. 17998334 211/524 Arthur Liberzon 7.62957588759258e-07 4.01259176310425e-06 2350 3062.90909090909 3448 6.93598048502039e-08 604 1.27530877832883 1.51570826759321 1 2.51566506260067 2347 3664 3459 2939 604 3958 3770 3170 2826 3507 3448 3713 M965 REACTOME_INTERFERON_GAMMA_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERFERON_GAMMA_SIGNALING.html Genes involved in Interferon gamma signaling 47/110 Reactome 0.0839184282471183 0.0965721401684667 3200 3399.45454545455 3449 0.00793650793650794 2202 1.44769100433991 1.38655843533435 1 0.537185832025267 3197 3638 3004 2588 3913 4232 3797 2202 3182 3449 4192 3714 M3873 BIOCARTA_CHEMICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CHEMICAL_PATHWAY.html Apoptotic Signaling in Response to DNA Damage 18/34 BioCarta 0.00926945335854966 0.0127342886069082 4205 3226.09090909091 3450 0.000846249191423107 297 1.81236751632393 2.34654306465239 1 1.25539540506523 4204 4000 2635 3424 3237 4326 4055 1472 297 3450 4387 3715 M19681 FLECHNER_PBL_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_PBL_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP.html Genes upregulated in peripheral blood lymphocytes (PBL) from patients with well functioning kidneys more than 1-year post transplant compared to those from normal living kidney donors. 15307835 136/253 Jean Junior 7.96120479058886e-05 0.000151466527197318 2335 3337.45454545455 3450 7.23772081786142e-06 2333 1.43418865472063 1.76976846451849 1 2.00240947880524 3670 3629 3450 2815 2334 4340 3306 3130 2333 3886 3819 3716 M14775 ST_G_ALPHA_S_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_G_ALPHA_S_PATHWAY.html G alpha s Pathway 12/21 Signaling Transduction KE 0.0109611051561603 0.0149400054571748 3900 3566.45454545455 3451 0.00100146371715945 2413 1.14174335312187 -1.4891046573039 -1 0.761912472753074 3900 3064 2413 3451 3259 3932 4665 4536 3305 3612 3094 3717 M1265 STANHILL_HRAS_TRANSFROMATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/STANHILL_HRAS_TRANSFROMATION_UP.html Selected genes up-regulated in Rat1Ras cells (fibroblasts) which were transformed by expression of an oncogenic activated form of HRAS [GeneID=3265] compared to the parental Rat1 cells. 16278678 10/14 Leona Saunders 0.00714764018091987 0.00995359342876389 3455 3470.72727272727 3451 0.000651906229341755 2773 1.414092213786 -1.414092213786 -1 1.03482143231966 3451 4113 2825 2811 3190 3711 2773 3212 4257 3490 4345 3718 M9416 JIANG_CORE_DUPLICON_GENES http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_CORE_DUPLICON_GENES.html Genes mapped to core duplicons - elements shared by a majority of segmental duplication blocks. 17922013 3/15 Leona Saunders 0.00118019429492601 0.00181086786706721 3975 3471.45454545455 3451 0.000118082155018091 1814 0.571923830453745 0.571923830453745 1 0.573248368457679 3974 1814 4294 2962 2937 3447 2751 3451 4458 4539 3559 3719 M11038 GEORGES_CELL_CYCLE_MIR192_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/GEORGES_CELL_CYCLE_MIR192_TARGETS.html Experimentally validated direct targets of MIR192 [GeneID=406967] microRNA; MIR192 caused cell cycle arrest in HCT116 cells (colon cancer). 19074876 44/85 Jessica Robertson 0.0839184282471183 0.0965721401684667 2490 3509.54545454545 3453 0.00793650793650794 2490 1.71644532953111 1.8397131299303 1 0.636910853344265 2490 4652 2759 3213 4262 4146 3952 3015 2841 3822 3453 3720 M2569 KLEIN_TARGETS_OF_BCR_ABL1_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/KLEIN_TARGETS_OF_BCR_ABL1_FUSION.html Genes changed in pre-B lymphoblastic leukemia cells with BCR-ABL1 fusion [GeneID=613, 25] vs normal pre-B lymphocytes. 16205638 18/75 Arthur Liberzon 0.415320710913563 0.448741722697937 3010 3565.54545454545 3455 0.0476190476190476 2206 1.31169062769532 1.07818751200912 1 0.166853120990026 3006 4524 2262 4604 4407 3024 2206 4416 4046 3455 3271 3721 M2623 BIOCARTA_IGF1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IGF1_PATHWAY.html IGF-1 Signaling Pathway 17/41 BioCarta 0.000894850132100384 0.00139543018935854 3495 3484.09090909091 3458 8.13831199862701e-05 2761 0.591754584869037 -0.556639807277097 -1 0.617605837140522 3494 3095 3458 2761 2871 2861 4002 3969 4280 4273 3261 3722 M982 REACTOME_REGULATION_OF_IFNA_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_IFNA_SIGNALING.html Genes involved in Regulation of IFNA signaling 10/31 Reactome 0.0393304186245862 0.0502460037281383 3970 3517.54545454545 3458 0.00364106039143887 1804 0.816670628992366 0.760074247212574 1 0.387740701658826 3966 1804 3294 3005 3458 3777 3427 4012 3446 4424 4080 3723 M1222 DARWICHE_PAPILLOMA_RISK_HIGH_VS_LOW_UP http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_HIGH_VS_LOW_UP.html Genes that classify skin lesions into high risk papilloma. 17525749 4/9 Arthur Liberzon 0.133815214376761 0.152198566643083 3305 3557.36363636364 3458 0.0142630071436787 2675 1.17908539990417 1.17908539990417 1 0.352370694430857 3304 2965 4268 3391 3658 4367 3458 4457 3724 2675 2864 3724 M5032 DER_IFN_ALPHA_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_ALPHA_RESPONSE_DN.html Genes down-regulated in HT1080 cells (fibrosarcoma) by treatment with interferon alpha for 6 h. 9861020 2/5 Yujin Hoshida 7.47979963099166e-05 0.000143296570199619 3725 2931.5 3458 8.31116477536112e-06 778 0.809754920051647 -0.512869173661334 -1 1.13770478173616 3721 1327 4455 NA 2385 3948 3502 3414 778 2169 3616 3725 M4275 GOLUB_ALL_VS_AML_UP http://www.broadinstitute.org/gsea/msigdb/cards/GOLUB_ALL_VS_AML_UP.html Up-regulated genes highly correlated with acute lymphoblastic leukemia (ALL) vs acute myeloid leukemia (AML). 10521349 19/38 Jean Junior 0.362959930822348 0.39471576603238 1935 3215.90909090909 3459 0.0401641270055543 1931 0.824939035590396 0.823886042598722 1 0.121735305774549 1931 3652 2661 3856 4526 2498 2056 3459 4365 3900 2471 3726 M140 PID_RANBP2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RANBP2_PATHWAY.html Sumoylation by RanBP2 regulates transcriptional repression 18832364 9/19 Pathway Interaction Database 0.00369178661033608 0.00530991775814453 2025 2721.18181818182 3460 0.000369793416877933 464 0.776781783799484 0.776781783799484 1 0.645926232627267 2022 3686 3899 4225 3460 1072 464 1398 4254 4302 1151 3727 M2361 TERAO_AOX4_TARGETS_HG_DN http://www.broadinstitute.org/gsea/msigdb/cards/TERAO_AOX4_TARGETS_HG_DN.html Genes down-regulated in Harderian gland tissue upon knockout of AOX4 [GeneID=71872]. 18981221 2/10 Arthur Liberzon 0.309837521104086 0.339784372547098 3045 3545.8 3460 0.0403658270014046 2260 0.33466503938082 -0.33466503938082 -1 0.0573474400272909 3043 3332 4656 NA 3826 2260 2954 3588 4448 4674 2677 3728 M682 FARMER_BREAST_CANCER_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_5.html Cluster 5: selected 17q21_23 amplicon genes clustered together across breast cancer samples. 15897907 13/23 Leona Saunders 8.01210193226773e-05 0.000152187716475908 2265 2803 3461 7.28399430640271e-06 428 0.976168122645385 -0.976168122645385 -1 1.36218663242896 2263 4405 3461 4383 3811 775 737 1517 4367 4686 428 3729 M9433 MOOTHA_HUMAN_MITODB_6_2002 http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_HUMAN_MITODB_6_2002.html Mitochondrial genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 275/545 Vamsi Mootha 0.0422125258016117 0.0538252777976469 3465 3076.81818181818 3462 0.00391317520963252 1347 1.10372980381521 -0.903228271706454 -1 0.511974507057537 1347 4553 3783 4341 3464 1639 1960 2743 3462 4224 2329 3730 M14742 HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_UP.html Genes up-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with high risk of myelodysplastic syndrom (MDS) compared to the low risk patients. 12411319 14/43 Arthur Liberzon 0.0517126176863768 0.0652816073486965 2660 3298.18181818182 3462 0.00481542998562208 1890 1.25101213844065 -1.63913699543007 -1 0.541970655244715 3462 3654 2202 4540 4640 2657 3051 1890 3794 3731 2659 3731 M228 PID_SMAD2_3PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SMAD2_3PATHWAY.html Regulation of cytoplasmic and nuclear SMAD2/3 signaling 18832364 10/22 Pathway Interaction Database 0.460101449393711 0.495708085943659 2945 3421.27272727273 3463 0.0544930141561407 1965 1.02657366782396 -1.3402516331317 -1 0.114363456912072 2941 3456 3101 3463 3876 2723 1965 4611 4353 3480 3665 3732 M10389 FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN.html Genes down-regulated in B-CLL (B-cell chronic lymphocytic leukemia) patients with mutated immunoglobulin variable heavy chain (VH) genes. 15817677 40/76 Kevin Vogelsang 0.000463046501425516 0.000752631254138039 3065 3432.72727272727 3463 4.21039991074313e-05 2751 1.18809531103223 -0.712485404939961 -1 1.35644005588018 3064 3597 3292 3161 2751 4304 3579 3811 3003 3735 3463 3733 M17646 JAIN_NFKB_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/JAIN_NFKB_SIGNALING.html Genes abnormally regulated in response to CD40L and IL4 [GeneID=959;3565] stimulation of B lymphocytes from patients with a hypomorphic mutation of IKBKG [GeneID=8517]. 15578091 50/119 Kevin Vogelsang 0.0839184282471183 0.0965721401684667 3375 3499.90909090909 3464 0.00793650793650794 2371 1.21123342050571 -1.20833834154177 -1 0.449444964702933 3373 3991 3464 4188 3691 2371 2936 3911 3352 3938 3284 3734 M975 REACTOME_ADVANCED_GLYCOSYLATION_ENDPRODUCT_RECEPTOR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADVANCED_GLYCOSYLATION_ENDPRODUCT_RECEPTOR_SIGNALING.html Genes involved in Advanced glycosylation endproduct receptor signaling 6/16 Reactome 5.99565157652551e-05 0.000117900223615604 4035 3310.72727272727 3465 5.99581334793863e-06 2134 1.85426666510063 -1.85426666510063 -1 2.66266531795538 4032 2134 4066 3292 2281 3565 3815 2984 3737 3047 3465 3735 M19938 SU_PANCREAS http://www.broadinstitute.org/gsea/msigdb/cards/SU_PANCREAS.html Genes up-regulated specifically in human pancreas. 11904358 22/94 John Newman 0.0222483475975354 0.0291461439312415 3465 3505.72727272727 3465 0.00204332550259045 2747 1.01757036804787 -1.09373903443078 -1 0.571097924272362 3465 2747 3031 3639 3376 4033 4415 3453 3608 3662 3134 3736 M7300 BLUM_RESPONSE_TO_SALIRASIB_UP http://www.broadinstitute.org/gsea/msigdb/cards/BLUM_RESPONSE_TO_SALIRASIB_UP.html Selected genes up-regulated in response to the Ras inhibitor salirasib [PubChem=5469318] in a panel of cancer cell lines with constantly active HRAS [GeneID=3265]. 17409441 177/391 Jessica Robertson 4.67134417173793e-05 9.42718294089747e-05 3645 3254.81818181818 3465 4.24676669374966e-06 1649 1.31613229852707 -0.969284429779171 -1 1.93665100529377 3645 4425 3465 3673 2190 1649 2698 4233 2680 3936 3209 3737 M15109 BIOCARTA_GLYCOLYSIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GLYCOLYSIS_PATHWAY.html Glycolysis Pathway 13/35 BioCarta 0.0839184282471183 0.0965721401684667 4195 3515.90909090909 3466 0.00793650793650794 2671 1.35534236229785 -1.35534236229785 -1 0.502918587061402 4193 3292 2671 3466 3618 4566 2711 3229 3190 3668 4071 3738 M7987 LEE_LIVER_CANCER_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_SURVIVAL_DN.html Genes highly expressed in hepatocellular carcinoma with poor survival. 15349906 132/330 Yujin Hoshida 0.0839184282471183 0.0965721401684667 2260 3415.54545454545 3466 0.00793650793650794 2256 1.39101906051784 1.6401975615491 1 0.516156920948861 2256 4051 3424 3081 4073 3698 3466 3213 2891 3817 3601 3739 M5635 BUSA_SAM68_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BUSA_SAM68_TARGETS_DN.html Genes down-regulated in LNCaP cells (prostate cancer) after knockdown of SAM68 [GeneID=10657] by RNAi. 17237817 5/7 Arthur Liberzon 0.0765897756730953 0.0944224385172651 2805 3357.72727272727 3467 0.00793650793650794 2380 2.38236779657299 -2.38236779657299 -1 0.892524314878646 2803 3866 4178 3824 4127 2546 2380 4163 3467 2898 2683 3740 M4223 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_DN.html Genes down-regulated by RUNX1-RUNX1T1 [GeneID=861;862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing monocytes. 17898786 2/14 Arthur Liberzon 0.768655955901014 0.802746113071574 4480 3584.4 3468 0.150111337286075 2422 0.924417428820191 0.924417428820191 1 0.0322429599880784 2897 3354 4138 NA 4120 3068 2422 3308 4477 4478 3582 3741 M1520 ZHOU_TNF_SIGNALING_4HR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_TNF_SIGNALING_4HR.html Genes up-regulated in HeLa cells (cervical carcinoma) at 4 h after stimulation with TNF [GeneID=7124]. 12673210 50/93 John Newman 0.0839184282471183 0.0965721401684667 3920 3467.18181818182 3468 0.00793650793650794 2332 1.60184693761381 1.10939025936422 1 0.594387529974694 3917 3145 3193 2538 3640 4336 3696 3468 2332 3288 4586 3742 M19270 PARK_TRETINOIN_RESPONSE_AND_PML_RARA_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/PARK_TRETINOIN_RESPONSE_AND_PML_RARA_FUSION.html Genes up-regulated by tretinoin (ATRA) [PubChem=444795] in U937 cells (acute promyelocytic leukemia, APL) made sensitive to the drug by expression of the PML-RARA fusion [GeneID=5371;5914]. 12893766 20/43 Arthur Liberzon 1.51260888258305e-05 3.56185187124834e-05 2985 3240.90909090909 3471 1.3751084387435e-06 1742 1.23907473471279 1.00958689811123 1 2.01471295137224 2981 3367 1742 3905 1837 3471 4327 3894 3477 2538 4111 3743 M645 REACTOME_SYNTHESIS_OF_PIPS_AT_THE_GOLGI_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PIPS_AT_THE_GOLGI_MEMBRANE.html Genes involved in Synthesis of PIPs at the Golgi membrane 13/19 Reactome 0.00581906861601308 0.00819355635055207 3410 3574.27272727273 3473 0.000530410679285383 2209 0.768244001675976 -0.768244001675976 -1 0.585925705749062 3409 4341 3473 4378 3162 2209 3105 3847 4489 4337 2567 3744 M875 REACTOME_NETRIN1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NETRIN1_SIGNALING.html Genes involved in Netrin-1 signaling 18/54 Reactome 0.0839184282471183 0.0965721401684667 4595 3408.54545454545 3473 0.00793650793650794 2164 1.66199766827804 -1.90243016849591 -1 0.616707293176928 4593 4156 2674 3473 4450 3979 4078 2458 2164 2325 3144 3745 M10986 CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN.html Marker genes down-regulated in the 'unannotated' subclass of hepatocellular carcinoma (HCC) samples. 18701503 142/288 Yujin Hoshida 0.0839184282471183 0.0965721401684667 2685 3463.36363636364 3473 0.00793650793650794 2682 1.2472258647616 -1.11693415147562 -1 0.462800460537977 2682 4255 3625 3331 3759 2885 2799 3871 3473 4048 3369 3746 M17977 BIOCARTA_P27_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P27_PATHWAY.html Regulation of p27 Phosphorylation during Cell Cycle Progression 7/17 BioCarta 0.0765897756730953 0.0944224385172651 2990 3280.54545454545 3474 0.00793650793650794 2491 1.8818988242565 -1.8818988242565 -1 0.705029869992099 2990 3751 3859 3525 4067 2671 2531 3474 3536 3191 2491 3747 M15513 BIOCARTA_D4GDI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_D4GDI_PATHWAY.html D4-GDI Signaling Pathway 10/26 BioCarta 0.0136067934407171 0.0183486141189066 3080 3473.63636363636 3475 0.00124469874285908 2747 1.51084000090833 1.51084000090833 1 0.958929511495239 3079 4203 2884 4364 3294 3875 3653 2747 3097 3475 3539 3748 M13007 GLINSKY_CANCER_DEATH_UP http://www.broadinstitute.org/gsea/msigdb/cards/GLINSKY_CANCER_DEATH_UP.html Genes whose over-expression is associated with the risk of death in multiple cancer types 15931389 2/12 Yujin Hoshida 0.0615945340041833 0.0771681328676641 3650 3377.5 3475 0.00703879491620437 1086 0.236963687467573 -0.390514831292453 -1 0.0963663183734369 3647 3303 4574 NA 3740 2306 1086 2628 4615 4640 3236 3749 M12771 SA_PTEN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/SA_PTEN_PATHWAY.html PTEN is a tumor suppressor that dephosphorylates the lipid messenger phosphatidylinositol triphosphate. 10/22 SigmaAldrich 0.0197086613646024 0.0259569384919975 4130 3474.81818181818 3478 0.00180795160802242 2488 0.920725230479141 1.06262087811406 1 0.533682624827595 4128 3101 2931 2488 3359 3748 4220 2992 3786 3478 3992 3750 M10797 AMIT_EGF_RESPONSE_60_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_60_HELA.html Genes whose expression peaked at 60 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 40/71 Leona Saunders 4.07453781955071e-05 8.37870435421322e-05 3680 3159.54545454545 3478 3.70419389500033e-06 1592 1.76591390190789 1.5817747637945 1 2.63154406423435 3679 3478 2451 2307 2142 4610 4233 4080 2113 1592 4070 3751 M1993 KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_DN.html Genes down-regulated similarly in primary fibroblast cultures from Werner syndrom patients and normal old donors compared to those from normal young donors. 14527998 163/433 Arthur Liberzon 0.00288389384457084 0.0042112578858395 3120 3571.36363636364 3479 0.000262516470948845 2772 1.45169536995031 1.42025470998095 1 1.26056688564151 3118 4556 3275 4022 3058 4003 3055 3479 2772 3882 4065 3752 M17496 LEE_RECENT_THYMIC_EMIGRANT http://www.broadinstitute.org/gsea/msigdb/cards/LEE_RECENT_THYMIC_EMIGRANT.html Candidate genes specific for recent thymic emigrants (RTEs). 15210650 165/387 Arthur Liberzon 0.000225125465435909 0.000386849259637943 4660 3578.72727272727 3480 2.04680459791772e-05 2600 1.2102487880964 1.36617684671022 1 1.50959778753527 4657 3357 2619 3480 2600 3362 4452 3537 3293 3952 4057 3753 M14079 BENPORATH_ES_CORE_NINE_CORRELATED http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_ES_CORE_NINE_CORRELATED.html Breast cancer compendium: 100 transcription regulators showing most correlated expression with the 9 'embryonic stem cell' transcription factors that are preferentially and coordinately overexpressed in the high-grade, ER-negative breast cancer tumors. 18443585 55/141 Jessica Robertson 0.007775200255583 0.010782654157343 3500 3415.81818181818 3481 0.00070934690575918 2693 1.26615469926247 1.12546377020854 1 0.910481120389535 3500 3144 3058 3017 3211 4259 3665 3481 2693 3514 4032 3754 M19152 PUIFFE_INVASION_INHIBITED_BY_ASCITES_DN http://www.broadinstitute.org/gsea/msigdb/cards/PUIFFE_INVASION_INHIBITED_BY_ASCITES_DN.html Genes down-regulated in OV-90 cells (ovarian cancer) exposed to ascites which inhibited invasion. 17971902 91/201 Arthur Liberzon 0.0393524181791547 0.0502604065378901 4485 3608.09090909091 3482 0.00364313467203856 3142 1.2286715421729 -0.836911464661408 -1 0.583295513091236 4481 3142 3482 3729 3459 3281 3558 3789 3162 3362 4244 3755 M2511 ZHANG_ADIPOGENESIS_BY_BMP7 http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_ADIPOGENESIS_BY_BMP7.html Genes up-regulated in C3H10T1/2 cells (mesenchyme multipotent cells) upon their differentiation to brown adipocytes in response to BMP7 [GeneID=655]. 20584981 11/30 Arthur Liberzon 0.933115237506978 0.95680043828396 2825 3708.72727272727 3482 0.217991339686721 2823 0.758479313772085 0.758479313772085 1 0.00531716974876575 2823 4204 3126 4327 4135 3286 2827 3370 4537 4679 3482 3756 M2532 BOSCO_INTERFERON_INDUCED_ANTIVIRAL_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/BOSCO_INTERFERON_INDUCED_ANTIVIRAL_MODULE.html Genes representing interferon-induced antiviral module in sputum during asthma exacerbations. 20336062 44/139 Antony Bosco 4.27509085544034e-07 2.82882663468366e-06 4050 3069.09090909091 3482 3.88644698744192e-08 390 1.22945793799775 -0.90200130955511 -1 2.49344729636026 4047 2359 1996 3188 390 3699 4029 3873 3482 2995 3702 3757 M5827 GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP http://www.broadinstitute.org/gsea/msigdb/cards/GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP.html Genes up-regulated in non-metastatic breast cancer tumors having type 1 amplification in the 20q13 region; involves ZNF217 [GeneID=7764] locus only. 16899599 50/109 Leona Saunders 5.08732466217701e-06 1.47246469221504e-05 3530 3274.27272727273 3483 4.62485129658902e-07 1436 1.07092297992717 1.08546562373205 1 1.89147401327579 3529 2358 3483 2975 1436 4206 2472 4628 3219 3578 4133 3758 M15258 BIOCARTA_AKT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKT_PATHWAY.html AKT Signaling Pathway 16/33 BioCarta 0.557443745451391 0.594352990030767 3585 3375.45454545455 3484 0.0714285714285714 2462 0.757718392555973 -0.757337931947917 -1 0.0625820920350101 3583 2951 3524 2462 4238 2582 2972 3484 4128 4263 2943 3759 M10973 MATTIOLI_MGUS_VS_PCL http://www.broadinstitute.org/gsea/msigdb/cards/MATTIOLI_MGUS_VS_PCL.html Genes changed in MGUS (monoclonal gammopathy of undetermined significance) compared to PCL (plasma cell leukemia) samples. 15735737 79/226 Leona Saunders 0.0483748771670545 0.0613324335510869 2165 3514.45454545455 3484 0.00449750129385279 2165 1.16440850066475 1.3245615014752 1 0.515986374395153 2165 4261 3446 4026 3484 3723 2800 4230 3478 4057 2989 3760 M1619 RAMPON_ENRICHED_LEARNING_ENVIRONMENT_EARLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMPON_ENRICHED_LEARNING_ENVIRONMENT_EARLY_UP.html Genes up-regulated in the brain cortex of mice that were exposed to an enriched learning environment for one day. 11070096 16/36 John Newman 0.0844366365726364 0.0971207852183048 2925 3466.54545454545 3485 0.0079875383064406 2032 0.224371060727781 0.244161969129539 1 0.0830542128929009 2921 4110 3485 3497 4567 2676 2476 2032 4639 4587 3142 3761 M3293 REACTOME_SHC_MEDIATED_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC_MEDIATED_SIGNALLING.html Genes involved in SHC-mediated signalling 8/20 Reactome 0.0330702029310268 0.0425850428510007 2095 2977.81818181818 3486 0.00335729014102207 1036 0.676971934891053 -0.676971934891053 -1 0.339192250642509 2094 3785 4082 2586 3720 1036 1372 3486 4535 4438 1622 3762 M14278 SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_UP.html Cluster 5: genes up-regulated in B493-6 cells (B lymphocytes) by MYC [GeneID=4609] alone or in combination with serum but not by serum alone. 15516975 33/88 Leona Saunders 0.000196888529769178 0.00034272646749568 4520 3486.81818181818 3486 1.79005593158275e-05 1870 0.846190827130398 -0.658797121099857 -1 1.07175955506671 4516 1870 3486 2660 2558 3547 3963 4501 3457 3466 4331 3763 M825 REACTOME_SHC_RELATED_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC_RELATED_EVENTS.html Genes involved in SHC-related events 8/25 Reactome 0.0330702029310268 0.0425850428510007 2095 2983.09090909091 3487 0.00335729014102207 1037 0.676971934891053 -0.676971934891053 -1 0.339192250642509 2095 3786 4104 2587 3721 1037 1373 3487 4536 4465 1623 3764 M11675 KEGG_HOMOLOGOUS_RECOMBINATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HOMOLOGOUS_RECOMBINATION.html Homologous recombination 22/27 KEGG 0.680034735855928 0.717389187802989 4255 3326.90909090909 3488 0.0984094552597569 1722 0.599325436006393 -0.599325436006393 -1 0.0315997193290664 1722 3514 3488 4255 4213 2364 2382 3061 4436 4255 2906 3765 M2555 MATTIOLI_MGUS_VS_MULTIPLE_MYELOMA http://www.broadinstitute.org/gsea/msigdb/cards/MATTIOLI_MGUS_VS_MULTIPLE_MYELOMA.html Genes distinguishing between MGUS (monoclonal gammopathy of undetermined significance) and multiple myeloma (MM) samples. 15735737 10/24 Leona Saunders 0.588532239003183 0.626075385236984 4035 3564.09090909091 3489 0.0775568303948483 2258 0.666496251801078 -0.323586589719987 -1 0.0495462777252777 4034 4290 3304 4520 3925 2414 2258 3094 4404 3489 3473 3766 M13465 KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS.html Terpenoid backbone biosynthesis 8/17 KEGG 0.000930026997441281 0.00144739505480234 3120 3380 3490 9.30416454454873e-05 990 1.27831054982248 -1.27831054982248 -1 1.32673497074821 3116 3255 3803 3986 4646 3490 3906 990 3731 3291 2966 3767 M4707 IIZUKA_LIVER_CANCER_PROGRESSION_G2_G3_DN http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_G2_G3_DN.html Genes down-regulated during transition from G2 (moderately differentiated tumor, infected with HCV) to G3 (poorly differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 7/11 Yujin Hoshida 0.0248883945222914 0.0324504776659593 3530 3634.27272727273 3490 0.0025171613608083 2677 0.842545339956887 -0.63167438187452 -1 0.458503585956232 3527 3490 4374 4463 3405 3160 2677 4515 3971 3205 3190 3768 M1674 JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP.html Genes up-regulated in H460 cells (non-small cell lung carcinoma, NSCLC) after treatment with sodium butyrate [PubChem=5222465]. 15318170 24/58 John Newman 0.0339599647162263 0.043670799851876 2290 2950.72727272727 3492 0.00313598170818349 1020 1.71075314734538 -1.71075314734538 -1 0.850324048733626 2286 4150 3472 3492 3849 1020 1218 3809 3606 3751 1805 3769 M17287 LIU_SOX4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_SOX4_TARGETS_DN.html Genes down-regulated in LNCaP cells (prostate cancer) by overexpression of SOX4 [GeneID=6659] and up-regulated by its RNAi knockdown. 16618720 232/471 Arthur Liberzon 0.00119187745790401 0.00182520842082948 3905 3367.72727272727 3493 0.000108411242051896 2282 1.12334097168648 -1.09059355050724 -1 1.12453592576481 3902 3823 3693 3493 2918 2329 4523 2660 3364 4058 2282 3770 M19472 HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_DN.html Genes down-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with low risk of myelodysplastic syndrome (MDS) compared with healthy controls. 12411319 23/59 Arthur Liberzon 0.0467571157623246 0.0593777356266269 3495 3413 3493 0.0043437697874541 2490 1.06634877601666 -1.23956987612768 -1 0.478015849896799 3493 3841 2850 3540 3478 2490 3258 4295 3664 3972 2662 3771 M1040 REACTOME_G1_S_SPECIFIC_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G1_S_SPECIFIC_TRANSCRIPTION.html Genes involved in G1/S-Specific Transcription 10/22 Reactome 0.968396998631951 0.986445482493741 2655 3529 3494 0.269514387865522 2439 0.779806589023477 -0.779806589023477 -1 0.0016894064538625 2655 3521 2439 3322 4670 3176 3067 3532 4496 4447 3494 3772 M2470 MALIK_REPRESSED_BY_ESTROGEN http://www.broadinstitute.org/gsea/msigdb/cards/MALIK_REPRESSED_BY_ESTROGEN.html Genes consistently and robustly repressed by estradiol [PubChem=5757] in MCF7 cells (breast cancer); this reperession was prevented by fulvestrant [PubChem=3478439]. 19917725 7/15 Arthur Liberzon 1.76421793960515e-06 6.80421832509441e-06 4640 2483.18181818182 3495 1.76421934021593e-07 14 3.795065098468 -2.97632047953996 -1 7.16796012768043 4640 1564 4671 432 1013 3495 3641 3615 14 674 3556 3773 M19540 KEGG_OXIDATIVE_PHOSPHORYLATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OXIDATIVE_PHOSPHORYLATION.html Oxidative phosphorylation 62/155 KEGG 0.082004714009649 0.0965721401684667 3740 2814.36363636364 3496 0.00774828277034347 1046 0.913169934332215 -0.913169934332215 -1 0.338844372537877 1046 4060 3738 3496 3738 1393 1429 2401 3647 4122 1888 3774 M907 REACTOME_CALNEXIN_CALRETICULIN_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CALNEXIN_CALRETICULIN_CYCLE.html Genes involved in Calnexin/calreticulin cycle 4/14 Reactome 0.71656093235478 0.753715943662065 3395 3639.09090909091 3496 0.118451986597328 2771 0.156791492946308 -0.189103657332775 -1 0.00703740850601576 3391 3496 4049 3537 3990 2771 3270 3400 4508 4418 3200 3775 M11068 KORKOLA_CHORIOCARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_CHORIOCARCINOMA_DN.html Genes from the 12p region that were down-regulated in choriocarcinoma cells compared to normal testis. 16424014 25/69 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3335 3537.54545454545 3496 0.00793650793650794 2771 1.08200473834377 -1.34376455398417 -1 0.401492869143327 3331 4074 2771 3080 4426 3496 3814 3113 3686 3781 3341 3776 M15112 WONG_MITOCHONDRIA_GENE_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/WONG_MITOCHONDRIA_GENE_MODULE.html Genes that comprise the mitochondria gene module 18199530 144/284 Jessica Robertson 0.0839184282471183 0.0965721401684667 930 2890.81818181818 3497 0.00793650793650794 927 1.01193820597832 -0.912974851944019 -1 0.375493710138457 927 4257 3758 4037 3620 1606 1505 2204 3497 4180 2208 3777 M1615 WENG_POR_TARGETS_GLOBAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/WENG_POR_TARGETS_GLOBAL_DN.html Genes down-regulated in liver from transgenic mice with reduced expression of POR [GeneID=5447] in all tissues. 16006652 15/39 John Newman 0.0515531921822081 0.0651329896375916 3500 3466.81818181818 3498 0.00480022116316307 2073 0.911972567972008 -0.952420618150245 -1 0.395419946014117 4199 2456 3173 3526 3498 4283 4149 2073 4019 3263 3496 3778 M9788 MOOTHA_PGC http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_PGC.html Genes up-regulated in differentiating C2C12 cells (myoblasts) upon expression of PPARGC1A [GeneID=10891] off an adenoviral vector. 12808457 313/643 Vamsi Mootha 3.95663597924226e-05 8.17856029939534e-05 4380 3498.90909090909 3498 3.59700649089154e-06 2133 1.38443626064771 1.67480213495997 1 2.06838409652148 4378 3498 3529 2953 2133 3449 4462 3256 2742 3944 4144 3779 M2999 MOOTHA_ROS http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_ROS.html Reactive oxidative species (ROS) genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 4/9 Vamsi Mootha 0.197488202348454 0.220655630950133 2700 3428.90909090909 3498 0.0217606182637167 2217 0.661605875704528 -0.661605875704528 -1 0.158712476257639 2698 2934 4517 3980 3722 2217 3239 3498 4069 4619 2225 3780 M2428 WELCSH_BRCA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WELCSH_BRCA1_TARGETS_DN.html Down-regulated by induction of exogenous BRCA1 in EcR-293 cells 12032322 102/216 John Newman 8.36023065680015e-05 0.000158159228331714 4655 3555.36363636364 3499 7.60049851930301e-06 2351 1.31040507448593 -1.05679534512407 -1 1.82058887353469 4651 3499 3253 3119 2351 3551 3884 4584 2879 2848 4490 3781 M833 REACTOME_AUTODEGRADATION_OF_THE_E3_UBIQUITIN_LIGASE_COP1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AUTODEGRADATION_OF_THE_E3_UBIQUITIN_LIGASE_COP1.html Genes involved in Autodegradation of the E3 ubiquitin ligase COP1 32/62 Reactome 0.0839184282471183 0.0965721401684667 2810 3324.18181818182 3500 0.00793650793650794 1047 2.34860109888451 -0.74351706699215 -1 0.871481022701893 2809 4146 3427 3674 4549 2664 3006 3665 1047 4079 3500 3782 M854 LINDGREN_BLADDER_CANCER_CLUSTER_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_3_UP.html Genes whose expression profile is specific to Cluster III of urothelial cell carcinoma (UCC) tumors. 16532037 214/547 Leona Saunders 0.0196153462647748 0.0258413023887362 3240 3531.09090909091 3500 0.0017993138826952 2908 1.31392898184217 -1.31158863134636 -1 0.762527741043834 3238 3824 2908 3888 3358 3178 3500 3885 3571 4038 3454 3783 M92 PID_ANGIOPOIETIN_RECEPTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ANGIOPOIETIN_RECEPTOR_PATHWAY.html Angiopoietin receptor Tie2-mediated signaling 18832364 35/84 Pathway Interaction Database 0.0839184282471183 0.0965721401684667 4075 3420.90909090909 3501 0.00793650793650794 1967 1.29314987552021 -1.36347007493382 -1 0.479841201923994 4075 3181 1967 2426 3856 4301 3501 3469 3544 3223 4087 3784 M8520 SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6 http://www.broadinstitute.org/gsea/msigdb/cards/SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6.html Cluster 6 of method A: up-regulation of these genes in patients with non-small cell lung cancer (NSCLC) predicts poor survival outcome. 18641660 314/733 Arthur Liberzon 0.0528304024233491 0.0666209003648585 1565 3307 3501 0.00492212938021147 1563 1.56406637801826 1.75920172513321 1 0.672551537880652 1563 4303 2550 3507 3501 3750 3381 3206 3159 3713 3744 3785 M11166 IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR.html Genes in the expression cluster 'Late Progenitors Shared': up-regulated in hematopoietic late progenitor cells from adult bone marrow and fetal liver. 12228721 342/849 John Newman 5.2844549348898e-06 1.51640880740316e-05 2935 3472.45454545455 3502 4.80406148029563e-07 1454 1.40447145430291 -1.22855247435808 -1 2.47403391262793 4602 3531 2934 4559 1454 2704 4573 4638 2767 2933 3502 3786 M2341 REACTOME_APOPTOTIC_EXECUTION_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOTIC_EXECUTION_PHASE.html Genes involved in Apoptotic execution phase 31/78 Reactome 0.0179945572805317 0.0238166402267636 4580 3378 3503 0.00164940443116314 1296 2.24140964952264 2.23427787329936 1 1.32981425377395 4579 3994 1950 3159 3343 4350 3805 3503 1296 2956 4223 3787 M4324 LOPEZ_MBD_TARGETS_IMPRINTED_AND_X_LINKED http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MBD_TARGETS_IMPRINTED_AND_X_LINKED.html X chromosome and imprinted genes up-regulated in HeLa cells (cervical cancer) after knockdown of the MBD (methyl-CpG binding domain) proteins by RNAi. 18223687 13/54 Jessica Robertson 0.0839184282471183 0.0965721401684667 3505 3546.54545454545 3503 0.00793650793650794 2357 1.99068171075647 1.99068171075647 1 0.738670067618069 3503 3248 3182 4133 3862 4375 4208 2357 3156 3680 3308 3788 M9052 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM.html Phosphatidylinositol signaling system 37/77 KEGG 0.000474444058843704 0.00076928887880332 4065 3348.81818181818 3505 4.31405824217222e-05 2556 1.12012965807321 -1.06925298849637 -1 1.27495154243816 4062 3835 2978 3587 2757 3686 3505 2556 3345 2948 3578 3789 M18108 NIKOLSKY_MUTATED_AND_AMPLIFIED_IN_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_MUTATED_AND_AMPLIFIED_IN_BREAST_CANCER.html Genes both mutated and amplified in a panel of 191 breast tumor samples. 19010930 49/172 Jessica Robertson 0.000300519009309183 0.000505467364545166 4275 3242.36363636364 3505 2.73236425384332e-05 1823 1.34571533872669 -0.639821128511057 -1 1.62143703922833 4273 3505 2851 3916 2659 2391 3828 2789 1823 3762 3869 3790 M15303 REACTOME_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOSIS.html Genes involved in Apoptosis 95/213 Reactome 0.00531042425262149 0.00749989392639672 4170 3336.90909090909 3506 0.000483935108724369 1100 1.74362047073322 1.99308702332741 1 1.35431247259736 4169 4054 2677 2312 3147 3498 3875 3779 1100 3506 4589 3791 M19133 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_UP.html Genes from the grey module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 11/29 Arthur Liberzon 0.0558299443714259 0.0702899299635953 3785 3492.18181818182 3506 0.00520902078781591 2738 1.19793117947856 -1.29814422188537 -1 0.504917804071 3784 3615 2738 3982 3506 3179 4476 3254 3500 2825 3555 3792 M13396 MORI_SMALL_PRE_BII_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_SMALL_PRE_BII_LYMPHOCYTE_DN.html Down-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Small Pre-BII stage. 18922927 73/154 Jessica Robertson 2.20747978406099e-06 7.8703867605922e-06 2235 3200.36363636364 3507 2.00680181731737e-07 1076 1.22106687494233 1.16610717485224 1 2.27808382196863 2232 3922 3221 3879 1076 3353 2670 3848 3507 3917 3579 3793 M1360 ZEMBUTSU_SENSITIVITY_TO_FLUOROURACIL http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_FLUOROURACIL.html Top genes associated with chemosensitivity to 5-fluorouracil [PubChem=3385] across 85 tumor xenografts. 11809704 16/41 Arthur Liberzon 0.476451581170641 0.512076171872849 3420 3650 3507 0.0571325938380642 2727 0.69909219230313 -0.694491022232102 -1 0.0742757555196329 4140 3025 3418 3416 4079 3368 3507 2727 4220 4659 3591 3794 M5500 KEGG_BASE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASE_EXCISION_REPAIR.html Base excision repair 21/35 KEGG 0.631044200882523 0.669172465565853 4255 3412.27272727273 3508 0.0866567342585054 2153 0.682644927281669 -0.682644927281669 -1 0.0435326184800546 2153 3549 3508 4251 4027 2472 2947 3043 4493 4252 2840 3795 M104 SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP.html Top 50 up-regulated markers distinguishing diffuse large B-cell lymphoma (DLBCL) from follicular lymphoma (FL) samples. 11786909 48/118 Jean Junior 0.0839184282471183 0.0965721401684667 4230 3429.18181818182 3508 0.00793650793650794 2387 1.3757501615651 -1.14889184145264 -1 0.510491184137012 4229 2913 2570 2387 4239 3199 3508 3711 3376 3512 4077 3796 M1207 NIKOLSKY_BREAST_CANCER_1Q32_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_1Q32_AMPLICON.html Genes within amplicon 1q32 identified in a copy number alterations study of 191 breast tumor samples. 19010930 9/15 Jessica Robertson 2.09030892878837e-06 7.5990594571779e-06 3515 2985 3511 2.09031089501711e-07 1094 1.32844438866593 1.18955020019639 1 2.48581115727025 3511 1227 4351 1616 1094 3701 2938 4491 3715 1813 4378 3797 M901 REACTOME_GLOBAL_GENOMIC_NER_GG_NER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLOBAL_GENOMIC_NER_GG_NER.html Genes involved in Global Genomic NER (GG-NER) 22/34 Reactome 0.437108451160052 0.471304694462956 2390 3295.90909090909 3513 0.0509013865418053 1983 0.599319973831381 -0.577895556665327 -1 0.0715689719740551 2388 3513 3609 4253 3895 2005 1983 3139 4291 4417 2762 3798 M19918 ABE_VEGFA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ABE_VEGFA_TARGETS.html Genes most profoundly induced in HUVEC cells (endothelium) by VEGFA [GeneID=7422]. 12197474 8/29 John Newman 0.0765897756730953 0.0944224385172651 4205 3612.72727272727 3514 0.00793650793650794 2671 2.06143862028418 -2.06143862028418 -1 0.7722922104234 4202 2958 4414 4284 4257 3317 3530 2671 3514 3312 3281 3799 M14515 COATES_MACROPHAGE_M1_VS_M2_DN http://www.broadinstitute.org/gsea/msigdb/cards/COATES_MACROPHAGE_M1_VS_M2_DN.html Down-regulated genes distinguishing between M1 (pro-inflammatory) and M2 (anti-inflammatory) macrophage subtypes. 18199539 50/138 Jessica Robertson 0.00145666271583169 0.00219412455364426 3515 3313.63636363636 3514 0.000132511645044789 1947 1.75695007395514 1.67636082933619 1 1.70747491310234 3514 3959 2005 2668 2968 4484 3614 4418 2554 1947 4319 3800 M3988 ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_DN.html Genes down-regulated in 3 out of 4 NSCLC cell lines (non-small cell lung cancer) after treatment with azacitidine [PubChem=9444] and TSA [PubChem=5562]. 17043644 57/121 Leona Saunders 0.000827362412710971 0.0012966622963089 1880 2916.45454545455 3515 7.52430659979211e-05 1084 0.988262066721741 -0.881451697453295 -1 1.04295171114975 1876 4096 3519 4386 2856 1084 1360 3515 3695 3575 2119 3801 M1881 MARSHALL_VIRAL_INFECTION_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARSHALL_VIRAL_INFECTION_RESPONSE_UP.html Genes up-regulated in the influenza-specific CD8+ [GeneID=925] T lymphocytes from bronchoalveolar lavage (BAL) compared to those from spleen. 15831586 6/8 Arthur Liberzon 0.00347339551478823 0.0050127290983362 4395 3520.72727272727 3515 0.00034788365021645 2257 0.926197530214733 -1.06709596285454 -1 0.778639957580772 4391 2257 4529 3515 3095 3783 4432 2632 3309 3060 3725 3802 M10540 KANG_FLUOROURACIL_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_FLUOROURACIL_RESISTANCE_UP.html Genes up-regulated in gastric cancer cell lines resistant to 5-fluorouracil [PubChem=3385]. 14734480 20/37 John Newman 0.00161262009242518 0.0024150647980519 3930 3181.27272727273 3516 0.000146709397468711 1097 2.33177855875689 -1.10470994028781 -1 2.2306020401234 3928 3648 1478 3516 3512 4586 4640 1097 1572 3112 3905 3803 M17042 CAFFAREL_RESPONSE_TO_THC_24HR_5_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_24HR_5_DN.html Genes down-regulated in EVSA-T cells (breast cancer) treated with 5 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 24 h. 18454173 48/97 Jessica Robertson 0.000193236293898023 0.000336994891405335 3435 3475.90909090909 3517 1.75684789848452e-05 2249 1.18257348796189 -0.967309131331424 -1 1.50097762985727 3434 4064 3517 3329 2554 2249 3737 4298 3900 4024 3129 3804 M648 BIOCARTA_G1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_G1_PATHWAY.html Cell Cycle: G1/S Check Point 17/39 BioCarta 0.0839184282471183 0.0965721401684667 4090 3175.90909090909 3518 0.00793650793650794 911 2.34046713649106 -1.26769979443167 -1 0.868462803097363 4086 3846 1918 2630 4313 3518 3812 3129 911 2797 3975 3805 M15589 PENG_GLUTAMINE_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/PENG_GLUTAMINE_DEPRIVATION_UP.html Genes up-regulated in BJAB cells (B-lymphoma) after glutamine [PubChem=738] deprivation. 12101249 41/87 Broad Institute 0.0376181297610604 0.0481372354069714 4060 3525.36363636364 3518 0.00347974547413298 2251 1.26449221177593 -1.24437514930783 -1 0.6089648807623 4060 3640 2251 3274 3452 3267 4411 3777 3668 3518 3461 3806 M11685 SHIPP_DLBCL_CURED_VS_FATAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHIPP_DLBCL_CURED_VS_FATAL_DN.html Top 50 down-regulated markers for the diffused large B-cell lymphoma (DLBCL) that distinguished between cured and fatal/refractory clinical outcomes. 11786909 38/90 Jean Junior 0.180188250513542 0.201855639948949 3005 3224.36363636364 3520 0.0178997292862801 1541 0.919549855001214 -0.80646517554724 -1 0.233589749484363 3002 4141 3520 3931 4020 1541 1603 3349 3967 4026 2368 3807 M4950 ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_UP.html Genes up-regulated in liver tumor compared to the normal adjacent tissue. 18413731 598/1311 Jessica Robertson 0.00337421169720177 0.00487259045087442 3255 3623.18181818182 3520 0.000337934605979809 2425 1.19117817458551 -0.965563050334852 -1 1.00676684328497 3254 4214 4466 3966 3093 2425 3189 4425 3520 4223 3080 3808 M16853 KEGG_DNA_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DNA_REPLICATION.html DNA replication 20/36 KEGG 0.970172113078189 0.987665983463913 2210 3574.18181818182 3521 0.273343241681392 2208 0.71112730430769 -0.71112730430769 -1 0.0014010287584324 2208 3606 3491 3433 4410 3141 3140 3521 4513 4248 3605 3809 M12016 OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_UP http://www.broadinstitute.org/gsea/msigdb/cards/OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_UP.html Genes up-regulated in epithelial ovarian cancer (EOC) biopsies: invasive (TOV) vs low malignant potential (LMP) tumors. 15940270 94/234 Leona Saunders 0.0839184282471183 0.0965721401684667 3525 3517.63636363636 3522 0.00793650793650794 2267 1.133736323861 -1.2557385142369 -1 0.420688591723424 3522 4497 3623 3505 4451 2267 2951 3097 3662 4090 3029 3810 M18107 WILENSKY_RESPONSE_TO_DARAPLADIB http://www.broadinstitute.org/gsea/msigdb/cards/WILENSKY_RESPONSE_TO_DARAPLADIB.html Atherosclerotic process genes whose coronary expression changed after darapladib [PubChem=9939609] treatment. 18806801 13/39 Jessica Robertson 0.0129789765616057 0.0175525206833144 3010 3461.90909090909 3522 0.00118692590308989 2467 1.11957016174212 -0.837447748255218 -1 0.718474079587929 3008 3581 2467 4149 3288 3492 3180 3522 4085 3685 3624 3811 M1992 KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP.html Genes up-regulated similarly in primary fibroblast cultures from Werner syndrom patients and normal old donors compared to those from normal young donors. 14527998 65/142 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3070 3398.81818181818 3522 0.00793650793650794 2319 1.07350273459678 1.24686571362229 1 0.398338082688003 3070 4178 3317 3804 3677 3522 3366 2457 3593 4084 2319 3812 M2547 HOLLEMAN_PREDNISOLONE_RESISTANCE_B_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_PREDNISOLONE_RESISTANCE_B_ALL_UP.html Genes distinguishing prednisolone [PubChem=5755] resistant and sensitive B-lineage ALL; here - genes up-regulated in the drug resistant samples. 15295046 20/35 Arthur Liberzon 0.0176461700027067 0.0233851675997408 2250 3067.18181818182 3523 0.0016172108889122 892 0.599791225856082 -0.599791225856082 -1 0.357593128152701 2248 3713 3523 4616 4487 920 892 2796 4414 4680 1450 3813 M4385 XU_RESPONSE_TO_TRETINOIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_RESPONSE_TO_TRETINOIN_UP.html Genes up-regulated in NB4 cells (acute promyelocytic leukemia, APL) by tretinoin [PubChem=444795] alone. 16140955 15/71 Kevin Vogelsang 0.091367509264618 0.1048354917762 4535 3569.09090909091 3525 0.008672589437179 2431 1.59417720774608 1.59417720774608 1 0.570764020938837 4534 3291 3085 3318 3576 3525 3485 2431 3742 3774 4499 3814 M17772 MACLACHLAN_BRCA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MACLACHLAN_BRCA1_TARGETS_UP.html Genes up-regulated in SW480 cells (colon cancer with mutated p53 [GeneID=7157]) upon expression of BRCA1 [GeneID=672] off an adenovirus vector. 10644742 22/51 John Newman 0.00293398430494449 0.0042817348031672 3525 3066.63636363636 3525 0.000267082224854501 1216 2.30500856044995 -1.40512895015758 -1 1.99546089317814 3525 3802 1927 2636 4017 4540 4023 1216 1811 2191 4045 3815 M19360 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_11 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_11.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 11. 12554760 84/171 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2955 3417.54545454545 3525 0.00793650793650794 2567 1.34166569667833 -1.44081753005097 -1 0.497843670520024 2953 4020 3174 3554 4421 2675 3880 2567 3525 3734 3090 3816 M1880 PIONTEK_PKD1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PIONTEK_PKD1_TARGETS_DN.html Genes down-regulated during later stages of renal maturation (days P14-P16) in kidney specific knockout of PKD1 [GeneID=5310]. 17965720 18/48 Jessica Robertson 0.0839184282471183 0.0965721401684667 4270 3572.72727272727 3526 0.00793650793650794 2021 1.20450479663061 -1.15777816177315 -1 0.446948215454659 4267 3422 2659 2021 4076 4666 3526 2993 3615 3458 4597 3817 M19275 LAU_APOPTOSIS_CDKN2A_DN http://www.broadinstitute.org/gsea/msigdb/cards/LAU_APOPTOSIS_CDKN2A_DN.html Genes down-regulated by UV-irradiation in cervical cancer cells after knockdown of CDKN2A [GeneID=1029]. 17369842 5/8 Leona Saunders 0.0765897756730953 0.0944224385172651 4135 3404.45454545455 3527 0.00793650793650794 2113 0.595259946394576 -0.432040579017068 -1 0.223006696692134 4132 2708 4156 3064 4375 2701 2113 2571 3527 4483 3619 3818 M10292 HONMA_DOCETAXEL_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/HONMA_DOCETAXEL_RESISTANCE.html Genes up-regulated in MCF7-ADR cell line (breast cancer) resistant to docetaxel [PubChem=148124]. 18724378 32/83 Jessica Robertson 0.63389956273523 0.671137223447195 2055 3514.18181818182 3527 0.0873015873015873 2054 1.07101759874051 0.936177333425439 1 0.0678008800763959 2054 4145 3373 3221 4031 2890 2802 4492 4173 3948 3527 3819 M627 REACTOME_TGF_BETA_RECEPTOR_SIGNALING_IN_EMT_EPITHELIAL_TO_MESENCHYMAL_TRANSITION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TGF_BETA_RECEPTOR_SIGNALING_IN_EMT_EPITHELIAL_TO_MESENCHYMAL_TRANSITION.html Genes involved in TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) 13/32 Reactome 0.0839184282471183 0.0965721401684667 3985 3553.18181818182 3530 0.00793650793650794 2852 1.37468797377754 -1.98057969718709 -1 0.510097044620619 3981 3903 3139 4000 3713 3420 2852 3438 3435 3674 3530 3820 M17730 GRAHAM_CML_QUIESCENT_VS_NORMAL_DIVIDING_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_NORMAL_DIVIDING_UP.html Genes up-regulated in quescent CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloblastic leukemia) patients compared to the dividing cells from normal donors. 17717066 63/146 Arthur Liberzon 0.00352294985779666 0.00507955170265696 4415 3368.72727272727 3532 0.000320782180110401 1872 1.38650803094027 1.54597999016557 1 1.16270116965544 4414 2739 1872 2464 3086 3901 4245 4051 3532 2653 4099 3821 M11884 GOLDRATH_ANTIGEN_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/GOLDRATH_ANTIGEN_RESPONSE.html Genes up-regulated at the peak of an antigen response of naive CD8+ [GeneID=925;926] T-cells. 15548615 234/541 Arthur Liberzon 8.30510537931773e-05 0.000157243328515082 3555 3380 3532 7.55038083417705e-06 1615 1.4175143356068 1.51898492713762 1 1.9707062012861 3553 3532 1615 2280 2346 4331 4625 4389 3356 2544 4609 3822 M12347 REACTOME_NEF_MEDIATES_DOWN_MODULATION_OF_CELL_SURFACE_RECEPTORS_BY_RECRUITING_THEM_TO_CLATHRIN_ADAPTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEF_MEDIATES_DOWN_MODULATION_OF_CELL_SURFACE_RECEPTORS_BY_RECRUITING_THEM_TO_CLATHRIN_ADAPTERS.html Genes involved in Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters 27/60 Reactome 0.069749962282139 0.0869740083166854 4520 3568.81818181818 3533 0.00655134314313418 2578 1.35066668425316 1.53336019505694 1 0.523628606947446 4520 3090 2972 2578 3533 3755 4423 3859 3101 3121 4305 3823 M1315 SIG_PIP3_SIGNALING_IN_B_LYMPHOCYTES http://www.broadinstitute.org/gsea/msigdb/cards/SIG_PIP3_SIGNALING_IN_B_LYMPHOCYTES.html Genes related to PIP3 signaling in B lymphocytes 22/60 Signaling Gateway 0.0839184282471183 0.0965721401684667 3825 3585.27272727273 3534 0.00793650793650794 2635 1.06831029596618 -1.43273171787148 -1 0.396411356289216 3822 2635 3007 3069 3674 4604 3416 3534 3483 3659 4535 3824 M1982 ONO_FOXP3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONO_FOXP3_TARGETS_DN.html Genes down-regulated in CD4+ [GeneID=920] T lymphocytes transduced with FOXP3 [GeneID=50943]. 17377532 21/53 Jessica Robertson 0.155218220605267 0.175265682350911 2795 3290.90909090909 3534 0.0152172955309102 2252 1.2425165300669 -0.984603385875274 -1 0.343492541172448 2791 4033 2300 3534 3950 3894 3818 2252 3801 2629 3198 3825 M164 PID_ERBB1_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB1_DOWNSTREAM_PATHWAY.html ErbB1 downstream signaling 18832364 83/159 Pathway Interaction Database 3.10171817890303e-06 1.00578868680434e-05 4225 3026.36363636364 3535 2.81974777448815e-07 939 1.17010888039606 -1.1271852319299 -1 2.13745874982843 4225 1767 3469 939 1237 3555 4008 3948 2886 3535 3721 3826 M1447 BROWN_MYELOID_CELL_DEVELOPMENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWN_MYELOID_CELL_DEVELOPMENT_DN.html Genes defining proliferation and self renewal potential of the bipotential myeloid cell line FDB. 16769770 73/182 Kevin Vogelsang 0.011046954327835 0.0150438907236951 3345 3669.27272727273 3535 0.00100934708952406 2966 1.4553077591907 1.51237523788331 1 0.969560583309316 3342 3535 2966 3861 3261 4620 4169 3856 3170 3432 4150 3827 M953 REACTOME_TRAF3_DEPENDENT_IRF_ACTIVATION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF3_DEPENDENT_IRF_ACTIVATION_PATHWAY.html Genes involved in TRAF3-dependent IRF activation pathway 7/18 Reactome 0.000274532461345255 0.000464761240557755 3915 3407.54545454545 3536 2.74566382875909e-05 2063 0.847155693981799 -0.772333795795308 -1 1.03201934973226 3913 2063 4062 3629 2661 3455 3520 4608 3774 2262 3536 3828 M747 REACTOME_METABOLISM_OF_POLYAMINES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_POLYAMINES.html Genes involved in Metabolism of polyamines 10/17 Reactome 0.00310941187079616 0.00451664724939579 3825 3442.09090909091 3537 0.000283074121173951 2643 1.01202164847783 -0.974313046311087 -1 0.867532878217427 3821 2643 2899 3697 3070 4328 3537 4137 3795 2695 3241 3829 M765 BIOCARTA_INSULIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INSULIN_PATHWAY.html Insulin Signaling Pathway 17/44 BioCarta 0.000632434899152163 0.00100699624105574 3335 3352.90909090909 3538 5.75106162431168e-05 2429 0.591754584869037 -0.556639807277097 -1 0.64825158632071 3332 3551 3538 2429 2815 2521 3631 3604 4188 4275 2998 3830 M911 REACTOME_PASSIVE_TRANSPORT_BY_AQUAPORINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PASSIVE_TRANSPORT_BY_AQUAPORINS.html Genes involved in Passive Transport by Aquaporins 6/10 Reactome 0.0653688596457685 0.0816631501733061 4235 3201 3538 0.00673753333813251 1761 3.56895025600191 -3.54679132496305 -1 1.41931309691503 4231 2323 4051 2067 3538 4264 1761 3544 2894 2052 4486 3831 M15847 MORI_MATURE_B_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_MATURE_B_LYMPHOCYTE_DN.html Down-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the mature B 18922927 51/109 Jessica Robertson 0.161385165508919 0.18131164842359 2845 3413.81818181818 3538 0.0158730158730159 2750 1.05288422343684 -1.00155138508516 -1 0.285400370685556 2844 3538 3372 4094 3880 2750 2904 3906 3813 3603 2848 3832 M2179 FIGUEROA_AML_METHYLATION_CLUSTER_7_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_7_UP.html Cluster 7 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 76/215 Arthur Liberzon 1.78701326466385e-06 6.85265479395647e-06 3615 3114.36363636364 3538 1.62455883292583e-07 967 1.43545419758311 1.93742822799071 1 2.70960942181717 3614 3880 3135 3538 967 4103 3933 1101 2724 3851 3412 3833 M14025 REACTOME_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSCRIPTION.html Genes involved in Transcription 123/275 Reactome 0.0720741107378242 0.0897288211789172 765 2979.36363636364 3540 0.00677724022394119 765 0.839516993602925 -0.857999918635902 -1 0.321309556418275 765 4219 3760 4043 3540 1599 1992 2337 4138 4215 2165 3834 M8341 PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN.html Antigen processing and presentation genes down-regulated in JY cells (B lymphocytes) treated with trichostatin A (TSA) [PubChem=5562]. 18829567 45/89 Jessica Robertson 0.0839184282471183 0.0965721401684667 1780 3096.63636363636 3540 0.00793650793650794 1549 1.42891313445088 -1.17900562224579 -1 0.530218042860658 1776 4379 3540 4329 4107 1549 1700 2913 3598 3852 2320 3835 M2586 SMIRNOV_RESPONSE_TO_IR_2HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_RESPONSE_TO_IR_2HR_DN.html Genes down-regulated in B lymphocytes at 2 h after exprosure to 10 Gy dose of ionizing radiation. 21844125 37/81 Itai Pashtan 0.0565241538920669 0.0711257210360434 4115 3484.18181818182 3542 0.00527553656727665 2285 1.10300900819996 -0.879799527709865 -1 0.462839165864025 4113 4506 3029 4606 3508 2285 2680 3542 3627 3859 2571 3836 M894 REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION.html Genes involved in Asparagine N-linked glycosylation 47/94 Reactome 4.48052807097009e-05 9.09694737459525e-05 4650 3503.72727272727 3543 4.07329029470093e-06 2179 0.949328162315396 1.12485966957146 1 1.40228302311634 4647 2691 3622 3708 2179 3096 4048 3263 3543 3448 4296 3837 M511 REACTOME_SIGNALING_BY_NODAL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NODAL.html Genes involved in Signaling by NODAL 6/22 Reactome 0.0282005574366041 0.0365150075014996 3545 3385.09090909091 3544 0.00285649549310868 2046 0.997183249707668 0.976205625502617 1 0.523975184824374 3544 2627 3917 3459 3428 4516 2276 3555 3985 2046 3883 3838 M7455 REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS.html Genes involved in Intrinsic Pathway for Apoptosis 25/55 Reactome 0.000478766418506169 0.000775224408127127 3750 3290.27272727273 3544 4.35336945395417e-05 914 1.46036377435711 1.92391584307812 1 1.66043025563195 3750 3364 2822 3544 2761 4686 4375 2406 914 3780 3791 3839 M18933 BIOCARTA_TGFB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TGFB_PATHWAY.html TGF beta signaling pathway 13/26 BioCarta 0.00510195797270248 0.00722725969168193 3550 3075.90909090909 3546 0.000464893485184799 92 2.24082145606998 2.91175711638133 1 1.75367259261064 3546 4466 2610 3728 3755 4587 3013 1342 92 3670 3026 3840 M231 PID_KIT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_KIT_PATHWAY.html Signaling events mediated by Stem cell factor receptor (c-Kit) 18832364 35/85 Pathway Interaction Database 0.00901857418478127 0.0124041792280261 4060 3594.27272727273 3546 0.000823250733781014 2422 0.758252417211379 -0.681003611639186 -1 0.528389725632733 4056 2422 3546 2585 3231 3390 4470 4386 3953 4103 3395 3841 M18912 XU_HGF_TARGETS_INDUCED_BY_AKT1_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_TARGETS_INDUCED_BY_AKT1_48HR_DN.html Genes down-regulated in DU-145 cells (prostate cancer) in the absence but not in the presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 20/54 Arthur Liberzon 0.00190495391999455 0.00283835105535596 3870 3486.81818181818 3546 0.000173327763577592 3004 1.42636872431882 -0.929803701123544 -1 1.32791027088472 3869 3575 3084 3546 3004 3413 3173 4075 3804 3585 3227 3842 M10245 LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP.html Genes up-regulated in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of congenic D.B. Chr 3 (DB, small HSC population) vs parental D2 strain (huge HSC population). 17220891 20/53 Leona Saunders 0.002227844391503 0.00329223551516337 4370 3418.36363636364 3546 0.000202736694211258 1963 1.51079429308305 -1.95357965881207 -1 1.37093049065645 4368 3125 3207 4290 3021 4015 3716 2427 1963 3924 3546 3843 M1724 KEGG_RNA_POLYMERASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RNA_POLYMERASE.html RNA polymerase 14/29 KEGG 0.0816218357841298 0.0965721401684667 1475 2878.18181818182 3547 0.00771066725024819 1303 0.91343148314624 -0.91343148314624 -1 0.338941423854302 1474 3781 3547 4310 4219 1303 1581 2020 3821 3717 1887 3844 M13515 KEGG_MISMATCH_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MISMATCH_REPAIR.html Mismatch repair 14/23 KEGG 0.8883142137625 0.917487415845509 3550 3772.45454545455 3548 0.180678493112558 3126 0.71112730430769 -0.71112730430769 -1 0.00972157826597404 3548 3517 3478 4434 4518 3245 3126 3272 4483 4254 3622 3845 M2228 PILON_KLF1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PILON_KLF1_TARGETS_DN.html Genes down-regulated in erythroid progenitor cells from fetal livers of E13.5 embryos with KLF1 [GeneID=10661] knockout compared to those from the wild type embryos. 18852285 1271/2834 Arthur Liberzon 0.0765897756730953 0.0944224385172651 3550 3640.27272727273 3550 0.00793650793650794 1855 1.14609491542271 -1.05834621568916 -1 0.429370132698941 3550 4544 4631 4500 3718 1855 3430 3093 3529 4668 2525 3846 M12139 GALE_APL_WITH_FLT3_MUTATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/GALE_APL_WITH_FLT3_MUTATED_DN.html Genes down-regulated in acute promyelocytic leukemia (APL) patients with mutated FLT3 [GeneID=2322]. 16105978 24/50 Kevin Vogelsang 0.0839184282471183 0.0965721401684667 3880 3435.36363636364 3551 0.00793650793650794 2575 1.53872540531875 -1.274160637458 -1 0.570965409607574 3876 3482 3158 2591 3930 2575 3043 4030 3551 3747 3806 3847 M2212 TAKADA_GASTRIC_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKADA_GASTRIC_CANCER_COPY_NUMBER_UP.html Candidate genes in the regions of copy number gain in gastric cancer cell lines. 16103878 4/14 Arthur Liberzon 0.0042963578933001 0.00613615760073279 4275 3401.54545454545 3552 0.000430468697692097 1403 1.49934497260978 -1.49934497260978 -1 1.21234509468582 4275 1403 4171 3293 3130 4055 3914 3020 3934 2670 3552 3848 M7507 CHOI_ATL_STAGE_PREDICTOR http://www.broadinstitute.org/gsea/msigdb/cards/CHOI_ATL_STAGE_PREDICTOR.html Genes used to predict the clinical stages of acute T-cell leukemia (ATL): chronic vs acute. 16909099 34/133 Leona Saunders 0.0839184282471183 0.0965721401684667 3475 3732.18181818182 3552 0.00793650793650794 2646 1.09008601638088 -0.662450695684847 -1 0.404491539486446 3473 4658 3502 4260 4414 3070 2646 3974 3552 4094 3411 3849 M1668 JIANG_AGING_HYPOTHALAMUS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_AGING_HYPOTHALAMUS_UP.html Up-regulated in the hypothalamus of aged (22 months) BALB/c mice, compared to young (2 months) controls 11172053 43/78 John Newman 0.0839184282471183 0.0965721401684667 4225 3199.54545454545 3552 0.00793650793650794 1468 2.10449693975378 -0.795236902867688 -1 0.780902787519821 4223 4224 2889 3552 3665 2555 2485 2560 1468 3964 3610 3850 M113 PID_NFAT_3PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFAT_3PATHWAY.html Role of Calcineurin-dependent NFAT signaling in lymphocytes 18832364 34/74 Pathway Interaction Database 0.0100274167228042 0.0137473594976772 4070 3813.90909090909 3554 0.000915764967126121 3068 1.26955523640285 -1.00897394434748 -1 0.863971421576702 4070 4327 3147 3549 3249 4611 4549 3068 3554 3525 4304 3851 M9648 REACTOME_FORMATION_OF_TUBULIN_FOLDING_INTERMEDIATES_BY_CCT_TRIC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_TUBULIN_FOLDING_INTERMEDIATES_BY_CCT_TRIC.html Genes involved in Formation of tubulin folding intermediates by CCT/TriC 13/26 Reactome 0.0813606842419871 0.0965721401684667 3670 3549.45454545455 3555 0.00768501883391154 2626 0.790921182427634 -0.696147849109298 -1 0.293482276946552 3669 3716 3104 3077 3555 3042 2626 4141 4207 4374 3533 3852 M868 REACTOME_CHROMOSOME_MAINTENANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHROMOSOME_MAINTENANCE.html Genes involved in Chromosome Maintenance 78/251 Reactome 0.161385165508919 0.18131164842359 2015 3490.36363636364 3555 0.0158730158730159 2012 1.20462174969951 -0.916628472072855 -1 0.326531147983705 2012 4134 3024 3506 4065 3043 3555 3587 3827 4101 3540 3853 M2510 ZHANG_RESPONSE_TO_CANTHARIDIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_RESPONSE_TO_CANTHARIDIN_DN.html Genes down-regulated in HL-60 cells (promyeloid leukemia) by cantharidin [PubChem=6708701]. 14639605 49/114 John Newman 0.161385165508919 0.18131164842359 3345 3607.09090909091 3555 0.0158730158730159 3100 0.908057753091332 -0.848263651567654 -1 0.246142940797405 3345 3506 3620 3555 3947 3100 3307 4361 3797 3929 3211 3854 M1022 REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER.html Genes involved in RNA Polymerase III Transcription Initiation From Type 3 Promoter 13/30 Reactome 0.0079173254471773 0.0109700139105479 1445 2637.54545454545 3559 0.000722360234576685 706 0.91343148314624 -0.91343148314624 -1 0.654342890853761 1442 3977 3559 4305 4180 758 706 1439 3619 3678 1350 3855 M15150 ZHANG_BREAST_CANCER_PROGENITORS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_BREAST_CANCER_PROGENITORS_UP.html Genes up-regulated in cancer stem cells isolated from mammary tumors compared to the non-tumorigenic cells. 18559513 315/696 Leona Saunders 0.0839184282471183 0.0965721401684667 1835 3431.45454545455 3559 0.00793650793650794 1833 1.50667307854393 1.83486366047891 1 0.559071949032872 1833 4552 3281 3559 4002 3955 3598 2295 3088 4161 3422 3856 M2508 KINNEY_DNMT1_METHYLATION_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KINNEY_DNMT1_METHYLATION_TARGETS.html Hypomethylated genes in prostate tissue from mice carrying hypomorphic alleles of DNMT1 [GeneID=1786]. 20584988 5/18 Arthur Liberzon 0.308831892710425 0.338760826133205 2680 3507.18181818182 3559 0.0362633635139739 2171 1.22001810681507 -1.22001810681507 -1 0.209643823509014 2678 3559 4678 4464 3803 2171 2491 4622 4498 2922 2693 3857 M720 REACTOME_METABOLISM_OF_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_PROTEINS.html Genes involved in Metabolism of proteins 260/627 Reactome 0.0839184282471183 0.0965721401684667 2890 3279.27272727273 3560 0.00793650793650794 1695 1.22345515960155 -0.793091527725514 -1 0.453980010570643 2887 4422 3772 3560 4124 1695 2097 3641 2694 4200 2980 3858 M1968 MIKKELSEN_IPS_HCP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_HCP_WITH_H3_UNMETHYLATED.html Genes with high-CpG-density promoters (HCP) without H3 methylation marks at either H3K4 or H3K27 in MCV8.1 cells (induced pluripotent cells, iPS). 18509334 38/162 Jessica Robertson 6.78711827208776e-05 0.000131913878983838 3565 3152.36363636364 3561 6.17029787943564e-06 1463 1.76299489314883 -1.96761464961027 -1 2.50016985121313 3561 3963 1463 3975 2290 3989 2740 3693 2917 1835 4250 3859 M17694 REACTOME_BRANCHED_CHAIN_AMINO_ACID_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BRANCHED_CHAIN_AMINO_ACID_CATABOLISM.html Genes involved in Branched-chain amino acid catabolism 11/20 Reactome 0.0839184282471183 0.0965721401684667 4535 3580.63636363636 3562 0.00793650793650794 2589 3.50695760765811 3.50695760765811 1 1.30130527743813 4531 4043 2589 3207 4040 3562 3717 3528 2705 3558 3907 3860 M84 PID_ATM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATM_PATHWAY.html ATM pathway 18832364 29/48 Pathway Interaction Database 0.562716732527621 0.599157148062811 2295 3423.27272727273 3563 0.0724398585335632 2292 0.798157919392846 -0.798157919392846 -1 0.0649020693830504 2292 4151 3563 4199 3945 2448 2787 2829 4519 4054 2869 3861 M19742 REACTOME_COPI_MEDIATED_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COPI_MEDIATED_TRANSPORT.html Genes involved in COPI Mediated Transport 10/14 Reactome 0.150879289072304 0.170489594548545 3330 3559.45454545455 3564 0.0147585475148211 1549 0.199217386977583 0.23723197214492 1 0.0559472196592252 3327 4205 3564 4438 4209 3474 1549 2238 4480 4316 3354 3862 M12469 REACTOME_HIV_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HIV_INFECTION.html Genes involved in HIV Infection 131/285 Reactome 0.0839184282471183 0.0965721401684667 3755 3531.27272727273 3564 0.00793650793650794 2513 1.18302209042024 -1.11643012141358 -1 0.438976759243506 2513 4307 3752 3752 4331 2710 3074 3564 3538 4134 3169 3863 M3592 GOLDRATH_HOMEOSTATIC_PROLIFERATION http://www.broadinstitute.org/gsea/msigdb/cards/GOLDRATH_HOMEOSTATIC_PROLIFERATION.html Up-regulated in CD8+ [GeneID=925] T lymphocytes undergoing homeostatic proliferation (HP) versus the naive cells; these genes are not up-regulated versus effector or memory cell population. 15548615 112/249 Kate Stafford 3.66914270401659e-05 7.66544926929191e-05 3565 3483.90909090909 3564 3.33563990829e-06 2112 1.14367540555942 -0.838811543171445 -1 1.72044450600366 3564 4019 3619 4262 2112 2559 3246 4099 3481 4056 3306 3864 M8692 NIKOLSKY_BREAST_CANCER_19Q13.1_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_19Q13.1_AMPLICON.html Genes within amplicon 19q13.1 identified in a copy number alterations study of 191 breast tumor samples. 19010930 26/126 Jessica Robertson 0.143841754033468 0.16308794081801 2610 3307.27272727273 3565 0.0140189924151489 1872 0.779576726202303 -0.779576726202303 -1 0.22442527781667 2607 3928 3565 4563 4093 1872 2594 2225 4047 4560 2326 3865 M2589 SESTO_RESPONSE_TO_UV_C2 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C2.html Cluster 2: genes changed in primary keratinocytes by UVB irradiation. 11867738 56/103 John Newman 0.0839184282471183 0.0965721401684667 3490 3657.45454545455 3565 0.00793650793650794 2767 1.31914493014333 -1.14404112645089 -1 0.489487027622368 3487 4181 2998 3933 3864 4617 2767 3995 3285 3540 3565 3866 M15884 NIKOLSKY_BREAST_CANCER_7P22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_7P22_AMPLICON.html Genes within amplicon 7p22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 32/58 Jessica Robertson 0.00012148863175905 0.000220400978870657 4655 3281.45454545455 3567 1.10450310123441e-05 755 1.82104451861461 -0.778154786546457 -1 2.43410560289334 4654 3670 2355 4366 2458 3567 3944 2985 755 3014 4328 3867 M15096 REACTOME_MITOCHONDRIAL_TRNA_AMINOACYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOCHONDRIAL_TRNA_AMINOACYLATION.html Genes involved in Mitochondrial tRNA aminoacylation 16/27 Reactome 0.221942971740142 0.247036761419075 1980 3186.81818181818 3569 0.0225558579112799 1692 0.544117130935331 -0.544117130935331 -1 0.120773285634122 1976 4037 3569 4621 4025 1792 1692 2380 4293 4365 2305 3868 M2048 KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_DN.html Genes down-regulated in response to hydorgen peroxyde [PubChem=784] in CS-B cells (Cockaine syndrome fibroblast, CS) with defficient ERCC6 [GeneID=2074]. 12606941 37/81 Arthur Liberzon 0.271231819869783 0.299268261810644 2135 3251.90909090909 3570 0.0283538650603272 1646 0.75749606614099 0.781052873098363 1 0.145071010018246 2131 3570 3593 4323 3942 2411 1646 3042 4133 4657 2323 3869 M15114 DAZARD_UV_RESPONSE_CLUSTER_G5 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G5.html Cluster G5: genes up-regulated in NHEK cells (normal keratinocyte) at 3 h and 24 h time points after UV-B irradiation. 12771951 11/33 Arthur Liberzon 0.657359884574151 0.695347272937804 2755 3633.63636363636 3570 0.0927801075834161 2687 0.606119283272796 -0.606119283272796 -1 0.0349606497946348 2751 4238 3230 4099 4216 3038 2687 3570 4610 4660 2871 3870 M201 PID_ERBB_NETWORK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB_NETWORK_PATHWAY.html ErbB receptor signaling network 18832364 7/18 Pathway Interaction Database 9.70793500818826e-07 4.65147070024235e-06 4465 2591.27272727273 3571 9.70793924917097e-08 54 3.33192239129493 -2.87886812572994 -1 6.49437912733939 4461 1074 3902 215 748 3571 4136 4523 54 1495 4325 3871 M1832 MATZUK_SPERMATID_DIFFERENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_SPERMATID_DIFFERENTIATION.html Genes important for spermatid differentiation, based on mouse models with male reproductive defects. 18989307 24/62 Jessica Robertson 0.00746481676037024 0.0103660094496953 4495 3641.72727272727 3572 0.000680933326983409 2901 1.77950026809171 -1.10852863441705 -1 1.2907555091135 4493 3929 3279 3774 3201 3650 4672 3215 2901 3373 3572 3872 M3682 FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN.html Genes down-regulated in peripheral blood lymphocytes (PBL) from patients with acute transplant rejection compared to those from patients with well functioning kidneys more than 1-year post transplant. 15307835 43/112 Jean Junior 0.0622492421973839 0.0779529526822397 1380 2982.63636363636 3573 0.00582578951862981 1377 0.931397410947354 1.10354954814075 1 0.377276415037344 1377 3992 3573 4180 4139 1617 1648 2603 4081 3806 1793 3873 M1060 REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM.html Genes involved in Cytokine Signaling in Immune system 157/406 Reactome 2.97157761269277e-06 9.75453261746592e-06 4330 3412.72727272727 3574 2.70143784223732e-07 1215 1.30850434518129 -1.31340402234212 -1 2.39662964967388 4330 3728 3329 2905 1215 3554 4090 3908 3079 3574 3828 3874 M10914 STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN http://www.broadinstitute.org/gsea/msigdb/cards/STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN.html Genes down-regulated in prefrontal cortex (PFC) of mice carrying a hemizygotic microdeletion in the 22q11.2 region. 18469815 362/707 Jessica Robertson 9.29656979094399e-05 0.000172803355971295 2460 3318.90909090909 3574 8.45178423690443e-06 2313 1.00706171518729 -0.854374577252553 -1 1.38498740027708 2459 4089 3782 3961 2391 2313 2755 3940 3574 4222 3022 3875 M6515 SPIRA_SMOKERS_LUNG_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/SPIRA_SMOKERS_LUNG_CANCER_DN.html Down-regulated genes that distinguished smokers with and without lung cancer. 17334370 24/87 Jessica Robertson 0.00475866599078688 0.00675935399600707 3605 3291.45454545455 3576 0.000433544582404862 2163 0.819674397963277 0.910077169343546 1 0.650188565866294 3375 3603 3605 3734 3131 2163 2367 3576 3816 3990 2846 3876 M202 YOSHIOKA_LIVER_CANCER_EARLY_RECURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/YOSHIOKA_LIVER_CANCER_EARLY_RECURRENCE_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) samples from patients with early recurrence (within 2 years after surgery) after resection. 19167881 19/52 Yujin Hoshida 0.0839184282471183 0.0965721401684667 4010 3272.72727272727 3577 0.00793650793650794 1688 1.72859967337039 2.55943516777314 1 0.641420891266921 4007 3515 1688 3700 3577 3929 3765 2887 2412 2431 4089 3877 M2482 BIOCARTA_ARAP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARAP_PATHWAY.html ADP-Ribosylation Factor 14/22 BioCarta 0.00149916171245354 0.00225451597707231 4580 2969.72727272727 3581 0.000136380388417637 528 0.587105613826234 0.587105613826234 1 0.5680422980567 2035 4340 3581 4445 4576 1357 528 2074 4578 4261 892 3878 M11701 CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_UP.html Selected genes up-regulated during invasion of lymphatic vessels during metastasis. 18794116 12/35 Jessica Robertson 0.0909930749417042 0.104431435017591 3930 3556.54545454545 3581 0.00863545896392455 1939 1.01224913398983 -1.01490843377678 -1 0.363036567069897 3927 2927 1939 3581 3575 4181 3410 3875 4141 2972 4594 3879 M3694 LIN_MELANOMA_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIN_MELANOMA_COPY_NUMBER_DN.html Candidate genes in significant regions of chromosomal copy number losses in a panel of melanoma samples. 18245465 25/59 Jessica Robertson 0.0839184282471183 0.0965721401684667 3205 3674.18181818182 3581 0.00793650793650794 2832 1.09486806997813 -1.09486806997813 -1 0.406265986824529 3203 4391 3526 4584 3975 3581 3886 3050 3383 4005 2832 3880 M13088 KEGG_PPAR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PPAR_SIGNALING_PATHWAY.html PPAR signaling pathway 26/91 KEGG 0.0705008397040666 0.0878635465035256 3655 3609.36363636364 3584 0.00662426899083708 1691 1.4689119345312 -1.04548111117268 -1 0.567097303823798 3655 3543 1691 3584 3536 4429 4646 4237 3553 3021 3808 3881 M7952 GALLUZZI_PREVENT_MITOCHONDIAL_PERMEABILIZATION http://www.broadinstitute.org/gsea/msigdb/cards/GALLUZZI_PREVENT_MITOCHONDIAL_PERMEABILIZATION.html Proteins acting on mitochondria to prevent membrane permeabilization. 16892093 20/38 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4325 3356 3584 0.00793650793650794 1532 1.87892653377828 -2.01022412869476 -1 0.697201758601165 4322 4335 2905 3789 4051 3405 2856 2053 1532 3584 4084 3882 M16533 SILIGAN_TARGETS_OF_EWS_FLI1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/SILIGAN_TARGETS_OF_EWS_FLI1_FUSION_DN.html Genes bound by EWSR1-FLT1 [GeneID=2130;2321] fusion and down-regulated in STA-ET-7.2 cells (Ewing's sarcoma) after knockdown of EWSR1-FLT1 by RNAi. 15735734 12/32 Arthur Liberzon 0.000396599840728285 0.000653469357824453 4355 3581.45454545455 3585 3.6061032262183e-05 2723 1.03683125855972 -0.729968775730031 -1 1.20699662655164 4351 2789 3132 3299 2723 4175 4120 3585 3061 3617 4544 3883 M7218 FAELT_B_CLL_WITH_VH3_21_DN http://www.broadinstitute.org/gsea/msigdb/cards/FAELT_B_CLL_WITH_VH3_21_DN.html Genes down-regulated in samples from B-CLL (B-cell chronic lymphocytic leukemia) with the immunoglobulin heavy chain VH3-21 gene. 15817677 35/74 Kevin Vogelsang 0.0839184282471183 0.0965721401684667 2275 3268.09090909091 3585 0.00793650793650794 2272 1.05108777284119 1.09167151804108 1 0.390020700121786 2272 4144 3585 4014 3598 3050 2327 2541 3649 3816 2953 3884 M2548 HOLLEMAN_PREDNISOLONE_RESISTANCE_B_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_PREDNISOLONE_RESISTANCE_B_ALL_DN.html Genes distinguishing prednisolone [PubChem=5755] resistant and sensitive B-lineage ALL; here - genes down-regulated in the drug resistant samples. 15295046 8/32 Arthur Liberzon 0.10515950899669 0.120306996864866 3885 3592.27272727273 3586 0.0110494809382074 2198 0.873024488952447 -0.873024488952447 -1 0.293491930119094 3884 3586 4680 3528 3612 3296 3803 3266 4344 3318 2198 3885 M3630 REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT.html Genes involved in Abortive elongation of HIV-1 transcript in the absence of Tat 11/27 Reactome 0.554247560328463 0.591913776891902 2975 3524.90909090909 3587 0.0708209059307053 1988 0.201284369015622 -0.213638667699401 -1 0.0167560454546746 2975 4081 3587 4318 3962 2515 1988 3367 4543 4432 3006 3886 M14427 DODD_NASOPHARYNGEAL_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/DODD_NASOPHARYNGEAL_CARCINOMA_DN.html Genes down-regulated in nasopharyngeal carcinoma (NPC) compared to the normal tissue. 17119049 841/1982 Arthur Liberzon 0.0173062074863546 0.0229736227425093 1645 3470.18181818182 3587 0.00174424806813228 1642 1.4658082008766 1.85176928802474 1 0.878040479642796 1642 4479 4150 3754 3354 4090 3587 2511 2997 4192 3416 3887 M1528 INGRAM_SHH_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/INGRAM_SHH_TARGETS.html Genes up-regulated by in C3H/10T1/2 cells (embryonic pluripotent cell) in response to SSH [GeneID=6469]. 12444557 3/8 John Newman 0.000824356371448491 0.00129281591586601 3510 3504.90909090909 3587 8.24662334743886e-05 1761 0.753512178383234 -0.753512178383234 -1 0.795566304840314 3510 1761 4402 3625 2873 3101 3328 3731 4053 4583 3587 3888 M16024 KEGG_ALZHEIMERS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALZHEIMERS_DISEASE.html Alzheimer's disease 89/213 KEGG 0.0124323572908308 0.0168424476047509 4340 3697.72727272727 3589 0.00113665221247461 3194 1.38356432451678 1.44713337194066 1 0.896959864464116 4339 4175 3445 4017 3282 3589 3337 3683 3194 3522 4092 3889 M13844 GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN.html Genes down-regulated in the A673 cells (Ewing sarcoma) after double knockdown of both FLI1 and DAX1 [GeneID=2313;190] by RNAi. 18591936 114/270 Jessica Robertson 0.0252637095944813 0.032903208215603 2790 3576.81818181818 3589 0.00232350700965086 2748 0.818923782861894 -0.793514866498592 -1 0.443847837497828 2786 4093 3694 4573 3396 2748 3139 3589 4048 4194 3085 3890 M496 REACTOME_RNA_POL_I_TRANSCRIPTION_TERMINATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_I_TRANSCRIPTION_TERMINATION.html Genes involved in RNA Polymerase I Transcription Termination 10/20 Reactome 0.0879563859340169 0.101045262193382 2055 3009.18181818182 3590 0.00833484077684078 1148 0.203261228901119 -0.219610866971311 -1 0.0739619053836501 2053 3784 3590 4247 3829 1306 1148 2307 4402 4308 2127 3891 M4732 BIOCARTA_LECTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LECTIN_PATHWAY.html Lectin Induced Complement Pathway 7/15 BioCarta 0.0915364345330242 0.105003606419033 4170 3501.45454545455 3591 0.00955411622930335 2250 0.944503264501834 -0.949770503685069 -1 0.337920704476642 4168 2250 3846 3457 3591 3240 2934 2955 3783 4276 4016 3892 M629 GRAHAM_CML_QUIESCENT_VS_CML_DIVIDING_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_CML_DIVIDING_DN.html Genes down-regulated in quiescent (G0) vs dividing (M) CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients. 17717066 9/35 Arthur Liberzon 0.386086746459241 0.418893839756426 2740 3441 3591 0.0476190476190476 2385 1.84170278005217 -1.4279092562854 -1 0.254396490902219 2738 3747 4146 3591 4497 3105 2385 3701 4038 2573 3330 3893 M6046 BARRIER_CANCER_RELAPSE_TUMOR_SAMPLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_CANCER_RELAPSE_TUMOR_SAMPLE_UP.html Up-regulated genes in tumor samples from colon cancer patients who developed recurrence of the disease. 16091735 11/19 Leona Saunders 0.0193810438197463 0.0255469961573365 3065 3442.54545454545 3591 0.00177762893787453 2290 0.547800581811333 -0.547800581811333 -1 0.318907588151156 3063 3743 3591 4369 3357 2290 2529 3651 3703 4488 3084 3894 M136 PID_FOXO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FOXO_PATHWAY.html FoxO family signaling 18832364 31/65 Pathway Interaction Database 0.726270090971166 0.762046942743144 2885 3619.45454545455 3594 0.111111111111111 2312 0.893752647410819 -0.497689907257513 -1 0.0385554551078975 2881 4662 3594 3885 4278 3241 2312 3076 4230 4071 3584 3895 M858 REACTOME_RNA_POL_I_RNA_POL_III_AND_MITOCHONDRIAL_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_I_RNA_POL_III_AND_MITOCHONDRIAL_TRANSCRIPTION.html Genes involved in RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription 69/143 Reactome 0.0256679847363993 0.033383340681312 435 2694.63636363636 3595 0.00236113134581219 432 0.898921220226891 -0.898921220226891 -1 0.485138307989545 432 3732 3627 3679 3595 1159 1451 1875 4155 4107 1829 3896 M1531 HU_GENOTOXIC_DAMAGE_24HR http://www.broadinstitute.org/gsea/msigdb/cards/HU_GENOTOXIC_DAMAGE_24HR.html Genes most consistently regulated at 24 h by all six genotoxins tested: cisplatin, methyl methanesulfonate, mitomycin C, taxol, hydroxyurea and etoposide [PubChem=2767;4156;5746;4666;3657;36462]. 15120960 36/88 John Newman 0.0839184282471183 0.0965721401684667 3385 3732.72727272727 3595 0.00793650793650794 2543 1.21680773394237 -0.958763430110963 -1 0.451513391047009 3381 3361 2722 2543 4474 4608 4252 4191 3530 3595 4403 3897 M11268 WHITE_NEUROBLASTOMA_WITH_1P36.3_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/WHITE_NEUROBLASTOMA_WITH_1P36.3_DELETION.html Genes within the smallest region of consistend deletion (SRD) within 1p36.3 area across a large collection of neuroblastoma cell lines and biopsy samples. 15829979 11/23 Leona Saunders 0.00333789512215625 0.00482163271961288 3830 3556 3596 0.000303906385789765 2222 0.899697051737832 -0.940787506052822 -1 0.761912664769857 3829 3189 3051 4609 3081 3729 2222 4529 3596 2829 4452 3898 M4786 OKAWA_NEUROBLASTOMA_1P36_31_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/OKAWA_NEUROBLASTOMA_1P36_31_DELETION.html Genes in the smallest region of deletion (SRD) in 1p36.3 area in neuroblastoma samples. 17667943 11/25 Jessica Robertson 0.00333789512215625 0.00482163271961288 3830 3556.27272727273 3597 0.000303906385789765 2223 0.899697051737832 -0.940787506052822 -1 0.761912664769857 3830 3190 3052 4610 3082 3730 2223 4521 3597 2831 4453 3899 M739 REACTOME_RNA_POL_III_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_III_TRANSCRIPTION.html Genes involved in RNA Polymerase III Transcription 16/37 Reactome 0.0068792683757096 0.00960269633856872 1240 2586.63636363636 3601 0.000627352189031438 681 0.830650140752728 -0.830650140752728 -1 0.612595674909693 1239 3850 3601 4243 3788 681 713 1551 3632 3798 1357 3900 M11458 WONG_PROTEASOME_GENE_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/WONG_PROTEASOME_GENE_MODULE.html Genes that comprise the proteasome gene module 18199530 42/72 Jessica Robertson 0.936539905830794 0.959682046517188 3030 3736.81818181818 3602 0.221718999750027 2790 0.887224038158413 -0.805632508845417 -1 0.00579616680697536 3028 4508 3602 4267 4303 3066 2790 3383 4421 4142 3595 3901 M5736 BARRIER_COLON_CANCER_RECURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_COLON_CANCER_RECURRENCE_DN.html Down-regulated genes from the 70-gene prognosis predictor for stage 2 colon cancer, based on non-neoplastic mucosa gene expression profiles. 17043639 27/56 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3745 3620.81818181818 3603 0.00793650793650794 2846 1.31690657300102 -0.981300001391985 -1 0.48865645414759 3743 3738 2846 3603 3827 3138 4058 4365 3563 3538 3410 3902 M9752 RICKMAN_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_METASTASIS_UP.html Genes up-regulated in metastatic vs non-metastatic HNSCC (head and neck squamous cell carcinoma) samples. 18679425 216/504 Jessica Robertson 2.1305658032375e-06 7.68035277277066e-06 3605 3342.18181818182 3603 1.93687987869392e-07 1060 1.18172799821191 1.43830799228701 1 2.20927637698975 3603 3756 3607 3930 1060 2650 4297 3600 2889 3966 3406 3903 M497 REACTOME_PROCESSING_OF_INTRONLESS_PRE_MRNAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROCESSING_OF_INTRONLESS_PRE_MRNAS.html Genes involved in Processing of Intronless Pre-mRNAs 13/18 Reactome 0.342005771280511 0.373488474532854 4315 3565.36363636364 3604 0.0373359915696145 2539 0.568582587762199 -0.568582587762199 -1 0.0888945619598063 3265 4403 3604 4382 3809 2612 2539 3099 4312 4311 2883 3904 M1067 REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX.html Genes involved in Nonsense Mediated Decay Enhanced by the Exon Junction Complex 81/218 Reactome 0.0839184282471183 0.0965721401684667 3250 3471.90909090909 3605 0.00793650793650794 1762 1.41532112062756 -0.508850371010823 -1 0.525174537542802 3250 4367 3778 3511 4263 1762 1966 4652 3605 4217 2820 3905 M1620 SARTIPY_BLUNTED_BY_INSULIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SARTIPY_BLUNTED_BY_INSULIN_RESISTANCE_DN.html Genes down-regulated in 3T3-L1 cells (adipocyte) by insulin [GeneID=3630] but displayed blunted response to insulin the insulin resistant cells. 14530283 16/28 John Newman 0.0839184282471183 0.0965721401684667 3605 3531.45454545455 3605 0.00793650793650794 2652 1.34157802483672 1.04970204955136 1 0.49781113866675 3605 4001 2652 4230 3901 4117 3179 2921 3570 2735 3935 3906 M6591 REACTOME_CYTOSOLIC_TRNA_AMINOACYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYTOSOLIC_TRNA_AMINOACYLATION.html Genes involved in Cytosolic tRNA aminoacylation 20/29 Reactome 0.525329892985188 0.562159369383099 1705 3390.45454545455 3606 0.0654961816955768 1701 0.573327091053275 -0.573327091053275 -1 0.0524210594603109 1701 4155 3606 4325 3992 2126 2593 3218 4431 4366 2782 3907 M17500 CHESLER_BRAIN_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_QTL_CIS.html Best cis-regulated quantitative trait loci (QTLs) in the mouse genome which modulate transcription in brain tissue. 15711545 44/108 Jean Junior 0.0189916695002431 0.025061944037775 3815 3539.90909090909 3606 0.00174160233911752 2476 1.28446393321036 1.38526685279003 1 0.751672207516763 3812 3639 2906 4079 3353 4334 3005 2476 3228 3606 4501 3908 M4910 ST_ERK1_ERK2_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_ERK1_ERK2_MAPK_PATHWAY.html ERK1/ERK2 MAPK Pathway 15/41 Signaling Transduction KE 0.000303471170998451 0.000509883796091338 4670 3755.18181818182 3607 2.75920945759216e-05 2663 0.913908321851325 -1.04553207433853 -1 1.09989559549633 4670 3607 3410 3545 2663 3822 4241 4670 3548 3253 3878 3909 M12653 HUTTMANN_B_CLL_POOR_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUTTMANN_B_CLL_POOR_SURVIVAL_DN.html Down-regulated genes in B-CLL (B-cell chronic leukemia) patients expressing high levels of ZAP70 and CD38 [GeneID=7535;952], which are associated with poor survival. 16932341 47/112 Leona Saunders 3.54393639924034e-05 7.41709958322475e-05 3610 3504.27272727273 3607 3.22181226281541e-06 2104 1.34413947717786 1.42037677603886 1 2.02903257556134 3607 4442 2625 4597 2104 3710 3236 3986 3104 3136 4000 3910 M18073 THUM_MIR21_TARGETS_HEART_DISEASE_DN http://www.broadinstitute.org/gsea/msigdb/cards/THUM_MIR21_TARGETS_HEART_DISEASE_DN.html Genes down-regulated in a mouse model of heart disease whose expression reverted to normal by silencing of MIR21 [GeneID=406991] microRNA. 19043405 6/16 Jessica Robertson 0.0140539897572473 0.0189026969008211 2200 3048.36363636364 3608 0.00141436706126813 725 0.72888579324872 -0.72888579324872 -1 0.459181129789535 2197 3753 4505 4294 3608 1160 725 2899 4371 4611 1409 3911 M18631 ROME_INSULIN_TARGETS_IN_MUSCLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROME_INSULIN_TARGETS_IN_MUSCLE_DN.html Genes down-regulated by 3 h of euglycemic hyperinsulinemic clamp in the vastus lateralis muscle of healthy lean subjects. 12621037 102/353 Jessica Robertson 3.98872870984861e-06 1.21687387593428e-05 4335 3281.72727272727 3609 3.62612358333225e-07 1339 1.58104735350136 -1.41924822154398 -1 2.84031136084091 4333 3760 2427 3973 1339 2963 4626 3855 2614 2600 3609 3912 M1 PID_FANCONI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FANCONI_PATHWAY.html Fanconi anemia pathway 18832364 34/62 Pathway Interaction Database 0.871464739922876 0.901674491339942 1740 3611.90909090909 3610 0.170145362123632 1738 0.557371730526661 -0.553416803561991 -1 0.00915789987319762 1738 4148 3497 4032 4101 3005 3400 3610 4511 4296 3393 3913 M530 REACTOME_NEGATIVE_REGULATION_OF_FGFR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEGATIVE_REGULATION_OF_FGFR_SIGNALING.html Genes involved in Negative regulation of FGFR signaling 11/49 Reactome 0.0839184282471183 0.0965721401684667 3895 3639.27272727273 3610 0.00793650793650794 2892 1.08907572921207 -1.25629400695494 -1 0.404116658414762 3893 3614 2923 4235 3565 2912 4322 4511 3610 3555 2892 3914 M570 REACTOME_PI3K_EVENTS_IN_ERBB2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_EVENTS_IN_ERBB2_SIGNALING.html Genes involved in PI3K events in ERBB2 signaling 24/47 Reactome 0.0839184282471183 0.0965721401684667 3610 3229.45454545455 3610 0.00793650793650794 880 2.21573069103286 -1.93320626396721 -1 0.822177614296304 3610 3710 2658 1849 3606 4370 3413 3935 880 3745 3748 3915 M15662 WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_DN.html Genes down-regulated in non-neoplastic rectal mucosa samples from patients having cancer associated with ulcerative collitis, compared to those who did not have the cancer. 17255260 10/27 Arthur Liberzon 0.114594993841393 0.130877928623146 3060 3360.72727272727 3610 0.0110035679122614 1854 1.96097570412719 -1.96097570412719 -1 0.633020630829521 3060 3744 2329 3842 3610 2864 1854 3820 4143 3488 4214 3916 M1948 YAMANAKA_GLIOBLASTOMA_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAMANAKA_GLIOBLASTOMA_SURVIVAL_DN.html Genes whose expression most strongly and consistently associated with the short term survival of patients with high grade glioma tumors. 16652150 6/12 Arthur Liberzon 0.0230879506052974 0.0302038348789569 3790 3727.09090909091 3610 0.00233313919799567 2646 0.351808281895477 0.339956387817367 1 0.195456966200069 3788 2646 4569 3589 3397 3610 3047 3316 4236 4636 4164 3917 M10688 PAL_PRMT5_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PAL_PRMT5_TARGETS_UP.html Genes up-regulated in NIH-3T3 cells (fibroblast) after knockdown of PRMT5 [GeneID=10419] by RNAi. 15485929 151/323 John Newman 0.0839184282471183 0.0965721401684667 2305 3582.18181818182 3611 0.00793650793650794 2302 1.3110166653533 1.6861985802255 1 0.48647092219264 2302 4490 3611 3132 3580 4299 3918 2837 3378 3953 3904 3918 M7928 MITSIADES_RESPONSE_TO_APLIDIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/MITSIADES_RESPONSE_TO_APLIDIN_UP.html Genes up-regulated in the MM1S cells (multiple myeloma) after treatment with aplidin [PubChem=44152164], a marine-derived compound with potential anti-cancer properties. 18593922 305/742 Jessica Robertson 6.61675589017351e-05 0.000129030870167928 3910 3596.36363636364 3611 6.01541355016637e-06 2282 1.34849520880164 1.43176992951684 1 1.91708254653902 3909 3951 3044 4270 2282 3611 3539 3877 3119 3280 4678 3919 M17753 BENPORATH_MYC_MAX_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_MYC_MAX_TARGETS.html Set 'Myc targets2': targets of c-Myc [GeneID=4609] and Max [GeneID=4149] identified by ChIP on chip in a Burkitt's lymphoma cell line; overlap set. 18443585 547/1222 Jessica Robertson 0.0765897756730953 0.0944224385172651 2810 3434.90909090909 3612 0.00793650793650794 2091 1.13751789479949 -0.988981267124231 -1 0.426156859130577 2806 4123 4338 4047 3712 2091 2723 3612 3508 4231 2593 3920 M783 REACTOME_PROCESSING_OF_CAPPED_INTRONLESS_PRE_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROCESSING_OF_CAPPED_INTRONLESS_PRE_MRNA.html Genes involved in Processing of Capped Intronless Pre-mRNA 16/30 Reactome 0.240225405322955 0.265870630454267 2820 3422.36363636364 3613 0.024666456426573 2289 0.648879905527032 -0.648879905527032 -1 0.136458412541358 2816 4599 3613 4524 3802 2341 2289 2407 4232 4381 2642 3921 M1095 REACTOME_RNA_POL_I_TRANSCRIPTION_INITIATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_I_TRANSCRIPTION_INITIATION.html Genes involved in RNA Polymerase I Transcription Initiation 12/25 Reactome 0.079543315338426 0.0965721401684667 1890 3038.90909090909 3614 0.00750671334681482 1119 0.205464600219325 -0.219041883305682 -1 0.0762404889286867 1886 3941 3614 4439 3801 1273 1119 2326 4443 4464 2122 3922 M19630 ZHU_CMV_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_ALL_UP.html Up-regulated at any timepoint following infection of primary human foreskin fibroblasts with CMV 9826724 122/272 John Newman 0.0839184282471183 0.0965721401684667 2645 3495.90909090909 3614 0.00793650793650794 2470 1.22715556721623 1.27768716567699 1 0.455353098159097 2644 4092 3322 2908 4021 3987 2470 3614 3592 3954 3851 3923 M14314 KEGG_PURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PURINE_METABOLISM.html Purine metabolism 77/171 KEGG 2.00680593585557e-06 7.38508907946837e-06 4585 3618 3615 1.82437069675929e-07 1031 1.16728960167952 1.43823270335336 1 2.18954769288461 4583 3266 3171 4478 1031 3615 4059 4228 3363 3547 4457 3924 M17669 XU_CREBBP_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_CREBBP_TARGETS_UP.html Genes up-regulated in pro-B lymphocytes after knockout of CREBBP [GeneID=1387]. 16424387 19/34 Kevin Vogelsang 0.000166869783721391 0.000294631426721341 4460 3375 3617 1.51711311020269e-05 2213 1.34547410708114 -1.38469579263349 -1 1.73643282415918 4457 2749 2213 4281 2525 3780 4639 2648 3617 2427 3789 3925 M4911 JISON_SICKLE_CELL_DISEASE_DN http://www.broadinstitute.org/gsea/msigdb/cards/JISON_SICKLE_CELL_DISEASE_DN.html Genes down-regulated in peripheral blood mononuclear cells (PBMC) from sickle cell disease patients compared to those from healthy subjects. 15031206 130/300 Jessica Robertson 0.0802021314724107 0.0965721401684667 3350 3378.09090909091 3619 0.00757131402805337 1278 1.2159435422505 -1.19973198928449 -1 0.45119272072911 3350 4218 3718 3619 4009 1278 3607 3496 3682 4102 2080 3926 M16817 KEGG_OOCYTE_MEIOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OOCYTE_MEIOSIS.html Oocyte meiosis 55/119 KEGG 0.0569750084991689 0.0716353340024431 1145 3007.54545454545 3621 0.00531875909797999 1008 1.24530562954963 1.37463757009664 1 0.521137594263043 1144 4317 3319 4388 4309 1208 1008 3621 4004 3892 1873 3927 M557 REACTOME_DEFENSINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEFENSINS.html Genes involved in Defensins 10/110 Reactome 0.751805273588896 0.78691488633587 3625 3849.90909090909 3622 0.118989385509359 3013 0.226152535166383 -0.325862000471131 -1 0.00860311083776155 3622 4607 3278 4447 4508 3013 3622 3062 4531 4325 3334 3928 M13626 MCCABE_HOXC6_TARGETS_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCCABE_HOXC6_TARGETS_CANCER_DN.html Genes whose promoters were bound by HOXC6 [GeneID=3223] in LNCaP cells (prostate cancer) and which were down-regulated in comparison of tumor vs normal prostate tissue samples. 18339881 12/32 Jessica Robertson 0.00012903745039548 0.000232207946449009 3875 3516.54545454545 3622 1.17313654091344e-05 2477 0.847123152144478 -0.847123152144478 -1 1.12529247383776 3872 2670 2951 3701 2477 4361 4237 4054 3614 3622 3123 3929 M272 PID_CD8_TCR_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CD8_TCR_DOWNSTREAM_PATHWAY.html Downstream signaling in naïve CD8+ T cells 18832364 35/117 Pathway Interaction Database 0.0839184282471183 0.0965721401684667 3980 3477.72727272727 3626 0.00793650793650794 2860 1.49697985370674 -1.41270754499991 -1 0.555475143463878 3979 3707 2938 2860 3965 2900 4147 3769 3140 3224 3626 3930 M14804 REACTOME_EXTENSION_OF_TELOMERES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EXTENSION_OF_TELOMERES.html Genes involved in Extension of Telomeres 13/29 Reactome 0.982136631026588 0.996167154326968 4455 3722 3628 0.306434344980658 2722 0.71112730430769 -0.71112730430769 -1 0.000433514944159221 2722 3582 3381 4174 4455 3196 3159 3687 4503 4455 3628 3931 M18567 ZHAN_MULTIPLE_MYELOMA_MS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_MS_DN.html Top 50 down-regulated genes in cluster MS of multiple myeloma samples with characteristic expression spike of WHSC1 [GeneID=7468]. 16728703 29/96 Kevin Vogelsang 0.00975382729159359 0.013380103831501 4690 3726.54545454545 3628 0.000890667434873222 3248 0.915699662290248 -0.835516288190264 -1 0.627097966950067 4686 3735 3401 3784 3248 3266 3766 3461 3524 3628 4493 3932 M745 REACTOME_MRNA_CAPPING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_CAPPING.html Genes involved in mRNA Capping 13/31 Reactome 0.359137193838789 0.391142014809659 2500 3334.54545454545 3629 0.0396419349446585 1839 0.196269352505037 -0.190610693687133 -1 0.0292466216349904 2496 4040 3629 4184 4062 1900 1839 3216 4486 4361 2467 3933 M771 REACTOME_TRANSCRIPTION_COUPLED_NER_TC_NER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSCRIPTION_COUPLED_NER_TC_NER.html Genes involved in Transcription-coupled NER (TC-NER) 24/49 Reactome 0.687384767461946 0.724816611234626 2505 3447.90909090909 3630 0.10031220177164 2354 0.660827756295423 -0.690198913010384 -1 0.0337619291930984 2501 3843 3630 4186 3993 2354 2360 3304 4346 4372 3038 3934 M2884 WANG_RESPONSE_TO_PACLITAXEL_VIA_MAPK8_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_PACLITAXEL_VIA_MAPK8_UP.html Genes specifically up-regulated via JNK (MAPK8) [GeneID=5599] signaling pathway activated by paclitaxel [PubChem=4666] in BR cells (ovarian cancer). 16547493 21/35 Arthur Liberzon 0.0818277138617808 0.0965721401684667 3825 3414.72727272727 3630 0.00773089178084385 2348 1.43002444414451 1.63711905681483 1 0.530630409741861 3823 2589 2901 2348 3557 3850 4097 3670 2851 3630 4246 3935 M770 REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE.html Genes involved in p53-Dependent G1 DNA Damage Response 36/69 Reactome 0.0839184282471183 0.0965721401684667 3155 3449.09090909091 3631 0.00793650793650794 1575 2.34860109888451 -0.74351706699215 -1 0.871481022701893 3155 4272 3452 3676 4374 2793 3209 3689 1575 4114 3631 3936 M4535 CHEOK_RESPONSE_TO_HD_MTX_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_HD_MTX_DN.html Genes specifically down-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by high-dose methotrexate (HDMTX) [PubChem=4112]. 12704389 19/42 Jean Junior 0.273899271996569 0.302069190062584 2145 3348.27272727273 3631 0.0286777168564081 1706 0.747935725139911 -0.747935725139911 -1 0.142133996671405 2143 4035 3501 4246 4210 2191 1706 3631 4268 4570 2330 3937 M4671 BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_DN.html Down-regulated genes in non-neoplastic mucosa samples from colon cancer patients who developed recurrence of the disease. 16091735 29/54 Leona Saunders 0.466738071388703 0.50186659075894 3230 3579.27272727273 3632 0.0555555555555556 2544 0.886434035855581 -0.944805535602056 -1 0.0970140094003238 3228 4069 3542 4008 4231 2544 3632 3456 4082 3891 2689 3938 M3141 RASHI_RESPONSE_TO_IONIZING_RADIATION_4 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_4.html Cluster 4: genes repressed by ionizing radiation regardless of ATM [GeneID=472] status. 16314843 49/108 Arthur Liberzon 0.000282416547421446 0.000477074239804216 4500 3732.18181818182 3632 2.5677528007052e-05 2644 1.28832680679446 -1.31938934394586 -1 1.56411366328471 4496 3700 3303 4314 2644 4349 3490 4224 3628 3274 3632 3939 M2338 KIM_TIAL1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KIM_TIAL1_TARGETS.html Top scoring genes whose transcripts bound TIAR1 [GeneID=7073] in extracts from RKO cells (colon cancer). 17682065 23/66 Arthur Liberzon 0.00363523124906074 0.00523178551385092 4180 3432.72727272727 3633 0.000331022905191979 1271 1.47126834458359 1.67213546971946 1 1.2268827857814 4177 3740 2608 3163 4475 4502 3633 1271 2306 3326 4559 3940 M19979 CASORELLI_APL_SECONDARY_VS_DE_NOVO_DN http://www.broadinstitute.org/gsea/msigdb/cards/CASORELLI_APL_SECONDARY_VS_DE_NOVO_DN.html Genes down-regulated in secondary APL (acute promyelocytic leukemia) compared to the de novo tumors. 16990782 9/15 Leona Saunders 0.00105361986215265 0.00162945962839846 4125 3547.36363636364 3634 0.000105411974742088 1020 1.70041323933138 1.70041323933138 1 1.73284494912933 3634 3556 4122 3413 4123 4151 4455 1020 3843 3409 3295 3941 M2524 VANOEVELEN_MYOGENESIS_SIN3A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/VANOEVELEN_MYOGENESIS_SIN3A_TARGETS.html Loci bound exclusively by SIN3A [GeneID=25942] in myotubules. 20956564 149/323 Arthur Liberzon 2.92821526760193e-06 9.64273840055e-06 3905 3267.09090909091 3634 2.66201742280367e-07 1210 1.17639718815891 -0.886389995738702 -1 2.15681753565823 3901 4359 3634 4529 1210 1546 3142 3806 3039 4044 2728 3942 M7435 HOEBEKE_LYMPHOID_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOEBEKE_LYMPHOID_STEM_CELL_DN.html Genes down-regulated in the common lymphoid progenitor (CLP, defined as CD34+CD38-CD7+ [GeneID=947;952;924]) compared to a multipotent cord blood cell (defined as CD34+CD38+CD7-). 17170726 61/150 Arthur Liberzon 0.0755340177841117 0.0939114904049741 2865 3694.54545454545 3635 0.00711448272515313 2861 1.20191288199632 1.19000529020527 1 0.451316911464469 2861 4369 3449 3670 3546 4251 3327 4374 3635 3696 3462 3943 M11984 FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_DN.html Genes down-regulated in genomically unstable Ewing's sarcoma tumors compared to the stable ones. 17952124 65/142 Jessica Robertson 0.0002054480784072 0.000356302625986729 3030 3393.90909090909 3635 1.86788424350399e-05 2278 1.51514343036536 1.54154906744661 1 1.90969076921138 3029 3635 3330 4309 2569 4379 3651 2278 2664 3785 3704 3944 M964 REACTOME_DESTABILIZATION_OF_MRNA_BY_TRISTETRAPROLIN_TTP http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DESTABILIZATION_OF_MRNA_BY_TRISTETRAPROLIN_TTP.html Genes involved in Destabilization of mRNA by Tristetraprolin (TTP) 11/20 Reactome 0.0839184282471183 0.0965721401684667 4260 3666.45454545455 3636 0.00793650793650794 2105 1.56675263701753 -2.43571715753574 -1 0.581365302806259 4260 4468 3186 3260 4243 3974 4685 2952 2105 3562 3636 3945 M4710 ZHU_CMV_8_HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_8_HR_UP.html Up-regulated at 8 h following infection of primary human foreskin fibroblasts with CMV 9826724 54/121 John Newman 0.0028348020106723 0.00414473704274896 4575 3607.81818181818 3637 0.000258041944327265 2390 1.33590686089594 -1.17886132633889 -1 1.16339954495384 4575 3637 2390 3037 3052 4139 3738 4259 3485 2850 4524 3946 M19489 REACTOME_SOS_MEDIATED_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SOS_MEDIATED_SIGNALLING.html Genes involved in SOS-mediated signalling 8/20 Reactome 0.124172428640009 0.141505836723513 3105 3293.45454545455 3639 0.0131710962538748 1640 0.676971934891053 -0.676971934891053 -1 0.210142073284361 3101 3811 4077 2542 3639 1640 2023 4406 4375 4430 2184 3947 M18058 WILCOX_RESPONSE_TO_PROGESTERONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WILCOX_RESPONSE_TO_PROGESTERONE_UP.html Genes up-regulated in primary cultures of ovarian surface epithlium cells exposed to progesterone [PubChem=5994] for 5 days. 18070364 88/235 Arthur Liberzon 0.0503392603540064 0.063685144173562 2555 3512.45454545455 3642 0.0046844910511883 2542 1.53131652792659 -1.4886370857654 -1 0.6694244196339 2555 3990 2542 4018 3493 3596 2937 4041 3642 3794 4029 3948 M11048 RIZ_ERYTHROID_DIFFERENTIATION_CCNE1 http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_CCNE1.html Selected gradually up-regulated genes whose expression profile follows that of CCNE1 [GeneID=898] in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). 17213805 28/57 Leona Saunders 0.0839184282471183 0.0965721401684667 2450 3269.45454545455 3642 0.00793650793650794 1466 0.816462596211848 0.973943354952337 1 0.302959772917402 2449 3642 3539 4380 3734 2255 1466 4053 3676 3865 2905 3949 M14520 REACTOME_CYCLIN_E_ASSOCIATED_EVENTS_DURING_G1_S_TRANSITION_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYCLIN_E_ASSOCIATED_EVENTS_DURING_G1_S_TRANSITION_.html Genes involved in Cyclin E associated events during G1/S transition 38/79 Reactome 0.552659305586952 0.590460899676347 1735 3363.09090909091 3644 0.0705204153778628 1734 1.12297765274693 -1.12297765274693 -1 0.0939211033983306 1734 4384 3644 3948 4593 2155 2233 3091 4284 4127 2801 3950 M2314 DELPUECH_FOXO3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DELPUECH_FOXO3_TARGETS_DN.html Genes down-regulated in DL23 cells (colon cancer) upon expression of an activated form of FOXO3 [GeneID=2309]. 17452451 27/50 Arthur Liberzon 0.0368369933943407 0.0471634292475084 4140 3445.45454545455 3644 0.00340624118299287 2070 1.44554377461657 -1.63151745252316 -1 0.700847051370481 4139 3644 2070 3648 3451 3617 4401 3823 3198 2154 3755 3951 M1041 REACTOME_SIGNALING_BY_TGF_BETA_RECEPTOR_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_TGF_BETA_RECEPTOR_COMPLEX.html Genes involved in Signaling by TGF-beta Receptor Complex 37/100 Reactome 0.0839184282471183 0.0965721401684667 4095 3753.45454545455 3645 0.00793650793650794 2980 0.997709306228418 0.754218308457126 1 0.370213879460773 4093 4025 3599 4528 3832 2980 3552 3420 3645 4010 3604 3952 M13486 KEGG_HUNTINGTONS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HUNTINGTONS_DISEASE.html Huntington's disease 92/233 KEGG 0.0839184282471183 0.0965721401684667 2455 3291.36363636364 3646 0.00793650793650794 2118 1.4479842168657 -1.10261188326294 -1 0.537294632601272 2455 4633 3646 3953 4003 2118 2530 4263 2198 4154 2252 3953 M3909 UDAYAKUMAR_MED1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/UDAYAKUMAR_MED1_TARGETS_UP.html Genes up-regulated in HeLa cells after knockdown of MED1 [GeneID=5469] by RNAi. 16574658 85/176 Leona Saunders 0.00611179066216232 0.00858508724307333 3595 3869.63636363636 3647 0.000557166916213861 3166 1.06181607199682 -1.05258038586791 -1 0.801959658401007 4408 3989 3595 4552 3166 3507 4384 4302 3422 3594 3647 3954 M4203 LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_UP.html Genes with copy number gains in primary neuroblastoma tumors. 17533364 113/279 Arthur Liberzon 0.0484653247695477 0.0614304873870978 3665 3644.72727272727 3647 0.00450610329692231 2584 1.1910575764441 -1.14200846651379 -1 0.527493386444543 3665 4362 3647 4409 3485 2584 3504 3364 3973 4160 2939 3955 M11545 KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN http://www.broadinstitute.org/gsea/msigdb/cards/KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN.html Down-regulated genes predicting response of patients with hepatocellular carcinoma (HCC) to combination chemotherapy with 5-fluorouracil (5-FU) [PubChem=3385] and IFN1@ [GeneID=3438]. 15447987 30/68 Yujin Hoshida 0.0839184282471183 0.0965721401684667 2890 3609.18181818182 3649 0.00793650793650794 2537 1.50470611517283 1.84504878212359 1 0.558342079982477 2889 4388 3071 3719 4415 3526 4303 3804 2537 3649 3400 3956 M2336 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 17. 12554760 143/259 Arthur Liberzon 3.58631828062101e-05 7.49910194689427e-05 3685 3384.45454545455 3651 3.26034249466516e-06 1961 1.33553355692974 -0.996971606776702 -1 2.01371049318108 3685 3877 3651 4027 2108 3124 3841 3211 1961 4124 3620 3957 M14524 GRADE_COLON_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_CANCER_UP.html Up-regulated genes in colon carcinoma tumors compared to the matched normal mucosa samples. 17210682 643/1490 Jessica Robertson 0.000198166759926972 0.000344823407730335 3620 3540.81818181818 3652 1.981844336743e-05 2591 1.32046120215046 -1.05409465693986 -1 1.67117736006048 3620 4122 4494 3812 2591 2610 3652 3671 2881 4182 3314 3958 M14691 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AMINOACYL_TRNA_BIOSYNTHESIS.html Aminoacyl-tRNA biosynthesis 26/41 KEGG 0.215815519302997 0.240387811612513 1450 3182.18181818182 3654 0.0218585603825527 1449 0.562612425943529 -0.562612425943529 -1 0.127315312090764 1449 4102 3654 4592 3973 1613 1947 2849 4338 4245 2242 3959 M7189 CHESLER_BRAIN_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_QTL_TRANS.html Best trans-regulated quantitative trait loci (QTLs) in the mouse genome which modulate transcription in brain tissue. 15711545 7/19 Jean Junior 0.033323023125061 0.0428988149351747 3885 3057.36363636364 3654 0.0033833521215249 173 3.77280927396465 -1.53661420241997 -1 1.88594407046281 3885 3690 4373 3149 3654 2708 3851 1801 173 2271 4076 3960 M2609 ZWANG_EGF_PERSISTENTLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_EGF_PERSISTENTLY_UP.html Genes persistently induced by EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 13/40 Yaara Zwang 0.743584314537147 0.778818975842886 4685 3832.09090909091 3654 0.116375620196362 3092 0.707449903846191 -0.707449903846191 -1 0.0280736352398238 4002 3611 3223 3654 3985 3092 3593 4684 4256 4685 3368 3961 M4138 REACTOME_ORC1_REMOVAL_FROM_CHROMATIN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ORC1_REMOVAL_FROM_CHROMATIN.html Genes involved in Orc1 removal from chromatin 43/79 Reactome 0.737224187655136 0.772675585630053 1585 3369.36363636364 3655 0.114405246069877 1582 1.12297765274693 -1.12297765274693 -1 0.0459747383515937 1582 4269 3655 3747 4291 2442 2457 3219 4259 4148 2994 3962 M1244 WIEMANN_TELOMERE_SHORTENING_AND_CHRONIC_LIVER_DAMAGE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WIEMANN_TELOMERE_SHORTENING_AND_CHRONIC_LIVER_DAMAGE_DN.html Genes down-regulated by telomere shortening due to the knockout of TERC [GeneID=7012] in the presence of chronic liver damage. 15608677 3/9 Leona Saunders 0.305816234227365 0.335531461856575 3645 3810 3655 0.03584369570931 2535 0.545982848479264 -0.727535403773816 -1 0.0946500660525196 3641 3529 4273 3714 4665 3440 3655 2535 4447 4535 3476 3963 M456 REACTOME_TRNA_AMINOACYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRNA_AMINOACYLATION.html Genes involved in tRNA Aminoacylation 27/43 Reactome 0.2977792757305 0.32771105826048 1440 3220.54545454545 3657 0.0316261384570286 1438 0.548176922797332 -0.548176922797332 -1 0.0970826792846571 1438 3932 3657 4489 4018 1780 2139 2860 4363 4369 2381 3964 M5126 PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN.html Down-regulated genes in head and neck cancer compared to cervical carcinoma samples. 17510386 12/83 Arthur Liberzon 0.0440340796691689 0.0560259835269415 3815 3602.27272727273 3657 0.00408554180505014 2491 1.5541194140407 1.5541194140407 1 0.711005297930207 3815 3657 2491 4219 3470 4548 3069 3373 4057 2977 3949 3965 M5193 SIG_CHEMOTAXIS http://www.broadinstitute.org/gsea/msigdb/cards/SIG_CHEMOTAXIS.html Genes related to chemotaxis 22/63 Signaling Gateway 0.0834932806540812 0.0965721401684667 4430 3720.36363636364 3658 0.00789466128012517 2745 0.873638843624217 -0.96197618462431 -1 0.324175812838182 4428 2745 3267 3210 3558 4070 3275 4548 4075 3658 4090 3966 M848 REACTOME_MITOTIC_G1_G1_S_PHASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOTIC_G1_G1_S_PHASES.html Genes involved in Mitotic G1-G1/S phases 77/159 Reactome 0.298735036746822 0.327992591892129 1685 3504.90909090909 3658 0.0317460317460317 1681 1.31129416853429 -0.991799426646498 -1 0.232052752192964 1681 4366 3621 3957 4339 2635 2832 3658 3977 4169 3319 3967 M1026 REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX.html Genes involved in Formation of the HIV-1 Early Elongation Complex 16/36 Reactome 0.35261842204812 0.38462987097707 2325 3310.72727272727 3658 0.0387579568051721 1716 0.192775909893333 -0.198415064670515 -1 0.0292398453385646 2322 4196 3658 4391 3902 1888 1716 2968 4455 4435 2487 3968 M14781 REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE.html Genes involved in Late Phase of HIV Life Cycle 58/125 Reactome 0.0839184282471183 0.0965721401684667 2490 3553.45454545455 3658 0.00793650793650794 2486 1.0669569549073 -1.14064405362159 -1 0.39590918031176 2486 4440 3717 4570 3746 2974 3207 3035 3658 4099 3156 3969 M6782 BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP.html Genes up-regulated in T24 (bladder cancer) cells in response to the photodynamic therapy (PDT) stress. 17952126 568/1329 Jessica Robertson 3.44122311582337e-05 7.24419205783841e-05 2590 3602.63636363636 3659 3.44127640605919e-06 2120 1.28046270097206 1.4409279428076 1 1.93770463134822 2590 4546 4311 4461 2120 4210 3218 3143 3302 4069 3659 3970 M3254 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_FLI1 http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_FLI1.html Genes whose expression is coregulated with that of FLI1 [GeneID=2313] in hematopoietic stem cells (HSC). 15711547 6/9 Jean Junior 0.257360584809538 0.28429790203147 3540 3594.45454545455 3659 0.0293161599553208 2737 1.02232791192267 -1.02232791192267 -1 0.20411837765137 3536 3659 4379 4069 3776 2737 3368 3976 4076 3056 2907 3971 M7927 REACTOME_NUCLEOTIDE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEOTIDE_EXCISION_REPAIR.html Genes involved in Nucleotide Excision Repair 28/54 Reactome 0.389292455834066 0.422176451756175 2320 3347.81818181818 3660 0.0438406006790295 1992 0.599319973831381 -0.577895556665327 -1 0.0820420996797003 2316 4027 3660 4394 3835 1992 2015 3141 4380 4384 2682 3972 M16256 ZHAN_EARLY_DIFFERENTIATION_GENES_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_EARLY_DIFFERENTIATION_GENES_UP.html B lymphocyte early differentiation genes (EDG): top genes up-regulated in tonsil B lymphocytes (TBC) compared to the tonsil plasma cells (TPC). 12393520 5/7 Arthur Liberzon 0.0436489815508954 0.0555661851528106 2750 3566.09090909091 3660 0.00445308142077259 2221 0.901398622933675 -0.901398622933675 -1 0.413566553183458 2747 3660 4556 3833 3483 2221 2811 4643 4387 4631 2255 3973 M2615 ZWANG_DOWN_BY_2ND_EGF_PULSE http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_DOWN_BY_2ND_EGF_PULSE.html Genes down-regulated by second pulse of EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 138/454 Yaara Zwang 1.13658834091505e-05 2.80318577133049e-05 4255 3414.36363636364 3660 1.03326746629633e-06 1732 1.23248268277775 1.44371118880479 1 2.05085776522151 4253 2411 3340 3660 1732 2778 4077 4435 3284 3906 3682 3974 M6222 GRABARCZYK_BCL11B_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRABARCZYK_BCL11B_TARGETS_UP.html Genes up-regulated in Jurkat cells (transformed T lymphocytes) after knockdown of BCL11B [GeneID=64919] by RNAi. 17173069 44/127 Arthur Liberzon 2.40140844912664e-06 8.34792284318061e-06 4675 3441.27272727273 3661 2.1831009730785e-07 1114 1.33658782291518 -0.940952455497311 -1 2.48110703671674 4675 4065 3323 2852 1114 3667 4272 3661 2818 3354 4053 3975 M15247 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS.html Ubiquitin mediated proteolysis 77/154 KEGG 0.0709919422193694 0.0884050601222336 2950 3417.81818181818 3662 0.00667199425488052 1828 0.892385878756427 -0.932967769782354 -1 0.343649651630595 2947 4365 3662 4449 4273 1875 3603 2450 4005 4139 1828 3976 M135 PID_IL5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL5_PATHWAY.html IL5-mediated signaling events 18832364 11/23 Pathway Interaction Database 0.015571981957501 0.0207715079569741 3420 3461.81818181818 3663 0.00142575526382882 1585 0.705993215184734 -0.705993215184734 -1 0.434193284599245 3419 3940 3274 3663 3742 3094 3694 1585 4395 4300 2974 3977 M17857 KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT.html SNARE interactions in vesicular transport 21/39 KEGG 0.00842165993470682 0.0116275481597042 3715 3725.45454545455 3664 0.000768552010595697 2725 0.705641235913326 -0.705641235913326 -1 0.498970185106552 3715 3805 3626 3664 3221 3514 4624 2725 4226 4257 3603 3978 M15866 BIDUS_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BIDUS_METASTASIS_UP.html Genes up-regulated in endometroid endometrial tumors from patients with lymph node metastases compared to those without the metastases. 16397028 128/314 Arthur Liberzon 0.298735036746822 0.327992591892129 1455 3571.45454545455 3664 0.0317460317460317 1453 1.12708703922074 1.26372622536817 1 0.199454596350072 1453 4561 3664 4275 4557 3121 2489 3491 3975 4186 3514 3979 M784 REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE.html Genes involved in Citric acid cycle (TCA cycle) 12/23 Reactome 0.0759198502466399 0.0943411345149177 3685 3897 3666 0.007152161495727 3369 0.229058163064548 -0.193383929130203 -1 0.0858450995947613 3683 3616 3506 3666 3548 3369 4319 4675 4569 4382 3534 3980 M17283 REACTOME_G1_S_TRANSITION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G1_S_TRANSITION.html Genes involved in G1/S Transition 62/126 Reactome 0.741135864772821 0.776428048809622 1475 3469.09090909091 3668 0.115611882987508 1475 0.98570922725755 -0.98570922725755 -1 0.0395968774726685 1475 4320 3668 4039 4292 2588 2682 3374 4415 4191 3116 3981 M1886 CHAN_INTERFERON_PRODUCING_DENDRITIC_CELL http://www.broadinstitute.org/gsea/msigdb/cards/CHAN_INTERFERON_PRODUCING_DENDRITIC_CELL.html Genes up-regulated in spleen interferon-producing dendritic cells (IKDC) compared to plasmacytoid dendritic cells (PDC) and conventional dendritic cells (cDC). 16444266 3/24 Jessica Robertson 0.142531260035249 0.161680339996411 2675 3560.36363636364 3668 0.0152594322986947 1504 0.445193217470341 0.512533627863121 1 0.128775258852215 2673 3469 4538 3910 3668 3262 1504 3919 4379 4625 3217 3982 M18937 KEGG_NUCLEOTIDE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NUCLEOTIDE_EXCISION_REPAIR.html Nucleotide excision repair 30/47 KEGG 0.170882099910491 0.191751321882318 2570 3433.27272727273 3670 0.0168914321217283 2199 0.599319973831381 -0.577895556665327 -1 0.157128729328214 2566 4071 3670 4263 3689 2199 2524 3163 4393 4253 2975 3983 M1704 HOWLIN_CITED1_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOWLIN_CITED1_TARGETS_2_UP.html Genes up-regulated in mammary glands from the CITED1 [GeneID=4435] knockout mice: homozygotic vs wild type (WT) animals. 16278680 9/27 Arthur Liberzon 9.29205075322116e-07 4.52518701432489e-06 4590 3132 3670 9.29205463862275e-08 730 1.61148259506317 -1.85185663268286 -1 3.14804445259244 4589 2176 4436 1583 730 4589 3866 4245 2751 1817 3670 3984 M510 REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES.html Genes involved in Cross-presentation of soluble exogenous antigens (endosomes) 30/55 Reactome 0.561816033874586 0.598470092006436 2165 3464.90909090909 3671 0.0722663344422855 2164 0.74351706699215 -0.74351706699215 -1 0.0605943818748235 2164 4513 3671 3945 4675 2169 2315 3041 4427 4317 2877 3985 M4076 REACTOME_HIV_LIFE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HIV_LIFE_CYCLE.html Genes involved in HIV Life Cycle 64/144 Reactome 0.0839184282471183 0.0965721401684667 2425 3577.18181818182 3671 0.00793650793650794 2424 1.0669569549073 -1.14064405362159 -1 0.39590918031176 2424 4371 3734 4534 3714 3025 3332 3161 3671 4133 3250 3986 M518 REACTOME_ANTIGEN_PROCESSING_CROSS_PRESENTATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANTIGEN_PROCESSING_CROSS_PRESENTATION.html Genes involved in Antigen processing-Cross presentation 60/132 Reactome 0.0839184282471183 0.0965721401684667 3110 3683.63636363636 3672 0.00793650793650794 2505 1.30134144854136 -0.973303405386469 -1 0.482880798751278 3108 4640 3572 4202 4533 2505 2662 4388 3672 4046 3192 3987 M243 PID_ARF_3PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF_3PATHWAY.html Arf1 pathway 18832364 21/33 Pathway Interaction Database 0.0839184282471183 0.0965721401684667 3290 3502.18181818182 3673 0.00793650793650794 1156 0.902830970805648 -1.10978688217852 -1 0.335007956668589 3288 3845 3549 4315 4681 2883 1156 3950 3673 3942 3242 3988 M13748 REACTOME_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCONEOGENESIS.html Genes involved in Gluconeogenesis 20/48 Reactome 0.0839184282471183 0.0965721401684667 4595 3758.18181818182 3675 0.00793650793650794 2958 1.1868662796603 -1.31323832209308 -1 0.440403198999023 4592 3675 2958 3418 4190 4576 3758 3460 3404 3582 3727 3989 M895 REACTOME_ASSEMBLY_OF_THE_PRE_REPLICATIVE_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ASSEMBLY_OF_THE_PRE_REPLICATIVE_COMPLEX.html Genes involved in Assembly of the pre-replicative complex 40/76 Reactome 0.789733150894136 0.82365669821721 1715 3525.18181818182 3677 0.132171897270583 1711 0.74351706699215 -0.74351706699215 -1 0.0228981015806341 1711 4271 3677 4109 4205 2537 2788 3332 4570 4415 3162 3990 M7847 REACTOME_SIGNALING_BY_WNT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_WNT.html Genes involved in Signaling by Wnt 38/79 Reactome 0.338328746605638 0.36990399127252 2010 3318.36363636364 3678 0.0368481757621532 1864 0.74351706699215 -0.74351706699215 -1 0.117382791499993 2008 4185 3726 3678 4336 1864 2305 3024 4463 4313 2600 3991 M2035 BAUS_TFF2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BAUS_TFF2_TARGETS_UP.html Genes up-regulated in pyloric atrium with knockout of TFF2 [GeneID=7032]. 16121031 18/53 Arthur Liberzon 0.270030100421902 0.298012494248006 2860 3428.45454545455 3678 0.0282083178683603 2302 0.974662854590541 -0.974662854590541 -1 0.187312072525464 2857 3678 3096 4615 3771 2302 2469 4095 4039 3880 2911 3992 M525 REACTOME_ENDOSOMAL_VACUOLAR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENDOSOMAL_VACUOLAR_PATHWAY.html Genes involved in Endosomal/Vacuolar pathway 17/38 Reactome 0.0839184282471183 0.0965721401684667 4270 3654.36363636364 3679 0.00793650793650794 2753 2.15698207673666 -1.63551345799698 -1 0.800378125826745 4269 4002 2753 2906 4142 3655 3679 3775 3537 3385 4095 3993 M1195 PATIL_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/PATIL_LIVER_CANCER.html Genes up-regulated in hepatocellular carcinoma (HCC) compared to normal liver samples. 15735714 473/1154 Arthur Liberzon 3.00557959179369e-06 9.81473586560644e-06 4415 3569.90909090909 3679 2.73234881631078e-07 1226 1.37064825673469 1.58742528991192 1 2.5091123892493 3480 3950 2995 3618 1226 4411 4259 3679 3227 4012 4412 3994 M11507 IIZUKA_LIVER_CANCER_PROGRESSION_L1_G1_UP http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_L1_G1_UP.html Genes up-regulated during transition from L1 (non-tumor, infected with HCV) to G1 (well differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 13/37 Yujin Hoshida 0.620107782005373 0.658469310327935 2905 3572.36363636364 3681 0.084228109383557 2895 0.965994035634979 -0.965994035634979 -1 0.0640745062177548 2905 4237 3086 4164 3982 2935 3977 2895 4377 3681 3057 3995 M9162 UZONYI_RESPONSE_TO_LEUKOTRIENE_AND_THROMBIN http://www.broadinstitute.org/gsea/msigdb/cards/UZONYI_RESPONSE_TO_LEUKOTRIENE_AND_THROMBIN.html Genes up-regulated in HUVEC cells (primary endothelium) after stimulation with leukotriene LTD4 [PubChem=3908] or thrombin (F2) [GeneID=2147] for 1 h. 16606835 23/80 Arthur Liberzon 0.232850105696956 0.258012673278774 3840 3515.27272727273 3681 0.0238095238095238 2363 1.58684116612722 -1.67371063683778 -1 0.341267616739794 3837 3934 2363 3669 4349 2978 3681 3464 3905 2792 3696 3996 M5321 VERRECCHIA_RESPONSE_TO_TGFB1_C3 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C3.html Cluster 3: ECM related genes up-regulated in dermal fibroblasts within 30 min after TGFB1 [GeneID=7040] addition; returned rapidly to basal level after that. 11279127 13/28 John Newman 0.0030567508422628 0.00444566556388687 3780 3121.09090909091 3683 0.000278273297299797 211 2.9773273479949 -0.944298028513588 -1 2.55973393533933 3776 3655 2594 2897 3877 4477 4210 1221 211 3683 3731 3997 M19805 LI_CYTIDINE_ANALOGS_CYCTOTOXICITY http://www.broadinstitute.org/gsea/msigdb/cards/LI_CYTIDINE_ANALOGS_CYCTOTOXICITY.html Genes whose expression in a panel of lymphoblastoid cell lines was associated with cytotoxicity of the anti-cancer analogs of cytidine, gemcitabine and cytarabine [PubChem=596;3461;6253]. 18757419 13/18 Jessica Robertson 0.161385165508919 0.18131164842359 3685 3591.18181818182 3684 0.0158730158730159 2828 1.03353247835868 -1.48921713775208 -1 0.280154784199833 3949 3682 3438 3793 3749 3161 4180 2828 3777 3684 3262 3998 M608 REACTOME_SIGNALING_BY_THE_B_CELL_RECEPTOR_BCR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_THE_B_CELL_RECEPTOR_BCR.html Genes involved in Signaling by the B Cell Receptor (BCR) 72/158 Reactome 0.0839184282471183 0.0965721401684667 3535 3478.09090909091 3687 0.00793650793650794 1567 1.16878647211608 -1.11957092924874 -1 0.433694435553044 3533 4568 3687 3377 4359 1567 2758 4234 3692 4157 2327 3999 M18607 REACTOME_STEROID_HORMONES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_STEROID_HORMONES.html Genes involved in Steroid hormones 10/44 Reactome 0.623485940159888 0.661773253111308 3165 3552.09090909091 3687 0.084971429771463 2077 0.965095750317657 0.965095750317657 1 0.0632481200990399 3162 3809 3151 4160 4191 3687 2077 4207 4187 3483 2959 4000 M19661 WANG_ESOPHAGUS_CANCER_PROGRESSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_ESOPHAGUS_CANCER_PROGRESSION_UP.html Candidate progression biomarkers up-regulated in transition from non-tumor-risk associated to tumor-risk associated Barrett's esophagus and then to esophageal adenocarcinoma (EAC). 16449976 8/11 Arthur Liberzon 0.386086746459241 0.418893839756426 2990 3571 3687 0.0476190476190476 1956 1.07253519204246 0.642138258118915 1 0.148150500068734 2989 3687 4173 3710 4312 2870 1956 4613 4033 3305 3633 4001 M7603 BOHN_PRIMARY_IMMUNODEFICIENCY_SYNDROM_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOHN_PRIMARY_IMMUNODEFICIENCY_SYNDROM_UP.html Genes up-regulated in B lymphocytes from patients with primary immunodefiency syndrom. 17195838 35/84 Jessica Robertson 0.507614874938545 0.544570353471159 3690 3694.90909090909 3688 0.0623781479059005 1923 1.06287355394423 -0.954351137679289 -1 0.102545342039097 3688 4510 3121 4443 4288 2852 1923 4576 4195 3551 3497 4002 M2090 NOUSHMEHR_GBM_GERMLINE_MUTATED http://www.broadinstitute.org/gsea/msigdb/cards/NOUSHMEHR_GBM_GERMLINE_MUTATED.html Genes with significantl germline mutation differences in proneural G-CIMP (a CpG island methylator phenotype) GBM (glyoblastoma multiforme) tumors. 20399149 3/17 Arthur Liberzon 0.214139132665174 0.238577264781028 3455 3728.72727272727 3688 0.0238095238095238 2474 1.3533733545236 -1.3533733545236 -1 0.30788333300476 3455 3471 4619 3636 4138 3688 4571 3816 3846 2474 3302 4003 M207 PID_RETINOIC_ACID_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RETINOIC_ACID_PATHWAY.html Retinoic acid receptors-mediated signaling 18832364 15/42 Pathway Interaction Database 0.0253023417316243 0.0329443660334514 2660 3205.36363636364 3690 0.00232710174131379 1532 0.739545092679389 0.817835236730913 1 0.400678684294366 2658 4463 3197 3932 3778 1786 2186 3690 4270 3767 1532 4004 M3158 REACTOME_S_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_S_PHASE.html Genes involved in S Phase 63/124 Reactome 0.724094273802006 0.760956664506885 1460 3433.18181818182 3691 0.110471095043625 1457 1.02046213722794 -1.02046213722794 -1 0.0442534914921878 1457 4375 3691 4038 4236 2530 2502 3302 4366 4166 3102 4005 M640 REACTOME_P53_INDEPENDENT_G1_S_DNA_DAMAGE_CHECKPOINT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P53_INDEPENDENT_G1_S_DNA_DAMAGE_CHECKPOINT.html Genes involved in p53-Independent G1/S DNA damage checkpoint 34/65 Reactome 0.711113159730664 0.74815362965826 2145 3577.09090909091 3692 0.106745421744572 2141 0.685423548468324 -0.74351706699215 -1 0.0315704334916709 2141 4273 3692 4106 4390 2393 2874 3529 4494 4335 3121 4006 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 0.0705752982922187 0.0879329560748038 2765 3449.81818181818 3692 0.00729223017584033 1098 0.621313702232092 0.621313702232092 1 0.239790357340795 2764 2966 4647 4349 3692 2551 1098 4042 4308 4671 2860 4007 M13696 DAUER_STAT3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAUER_STAT3_TARGETS_DN.html Top 50 genes down-regulated in A549 cells (lung cancer) expressing STAT3 [GeneID=6774] off an adenovirus vector. 15735721 35/106 Arthur Liberzon 5.72761858872674e-05 0.000113151857954357 4355 3630.72727272727 3694 5.20706155508407e-06 2247 0.998774735978182 -0.919302464660074 -1 1.44072506542645 4354 3215 2867 3026 2247 4016 4503 4306 3694 3225 4485 4008 M14702 KIM_GASTRIC_CANCER_CHEMOSENSITIVITY http://www.broadinstitute.org/gsea/msigdb/cards/KIM_GASTRIC_CANCER_CHEMOSENSITIVITY.html Genes up-regulated in gastric cancer patients refractory to chemotherapy treatment with 5-fluorouracil and cisplatin [PubChem=3385;2767] compared to the sensitive state. 15033468 73/169 John Newman 8.64265526860194e-05 0.000162844722913827 3695 3483.54545454545 3694 7.85726801111955e-06 2363 1.62870968862457 1.54395516491154 1 2.2552715750927 3694 3954 2485 3863 2363 4185 2987 4503 2685 3175 4425 4009 M14449 BIOCARTA_ETS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ETS_PATHWAY.html METS affect on Macrophage Differentiation 14/27 BioCarta 0.0839184282471183 0.0965721401684667 4000 3646.09090909091 3695 0.00793650793650794 2847 0.98799600024656 0.98799600024656 1 0.366609622504426 3998 2847 3220 3257 3695 4004 3995 3365 3660 3718 4348 4010 M5283 REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS.html Genes involved in Host Interactions of HIV factors 94/201 Reactome 0.0839184282471183 0.0965721401684667 3125 3652.72727272727 3695 0.00793650793650794 3084 1.26582676322319 -1.19859014938966 -1 0.469702581998963 3124 4310 3695 3616 3819 3084 3733 3937 3419 4039 3404 4011 M5224 REACTOME_SYNTHESIS_OF_DNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_DNA.html Genes involved in Synthesis of DNA 56/105 Reactome 0.624302868337792 0.662473560016054 1340 3380.27272727273 3696 0.0851520944879281 1337 1.02001506563712 -1.02001506563712 -1 0.0666760285071 1337 4321 3696 3955 4164 2451 2444 3242 4362 4181 3030 4012 M762 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_29 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_29.html Amplification hot spot 29: colocolized fragile sites and cancer genes in the 7p22-p13 region. 16751803 2/11 Arthur Liberzon 0.122380535032444 0.139531675708524 3415 3466.4 3697 0.0144000016064786 1289 0.489212633538302 -0.224593689418514 -1 0.152949896496361 3412 3071 4222 NA 3940 3769 1289 2659 4166 4511 3625 4013 M16490 GALI_TP53_TARGETS_APOPTOTIC_UP http://www.broadinstitute.org/gsea/msigdb/cards/GALI_TP53_TARGETS_APOPTOTIC_UP.html Apoptosis genes up-regulated by TP53 [GeneID=7157] in HCT116 cells (colon cancer) treated with thymoquinone [PubChem=10281]. 18632613 11/14 Jessica Robertson 0.338769586250428 0.370299575733498 3270 3419.36363636364 3697 0.0369065299463045 1822 0.341026055858139 -0.322951578054746 -1 0.0537816393410704 3267 4112 3130 3736 4242 1865 1822 3697 4459 4605 2678 4014 M15555 CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP.html Protein biosynthesis, transport or catabolism genes up-regulated in hyperploid multiple myeloma (MM) compared to the non-hyperploid MM samples. 17409404 43/115 Jessica Robertson 0.030526471452688 0.0393960466062506 1575 2997.81818181818 3697 0.00281440565056399 1032 0.907493984228086 -0.907493984228086 -1 0.465907166485519 1572 4446 3735 4494 3979 1157 1032 3138 3697 4149 1577 4015 M709 REACTOME_CDK_MEDIATED_PHOSPHORYLATION_AND_REMOVAL_OF_CDC6 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CDK_MEDIATED_PHOSPHORYLATION_AND_REMOVAL_OF_CDC6.html Genes involved in CDK-mediated phosphorylation and removal of Cdc6 30/60 Reactome 0.657833210383991 0.695690910372237 1995 3543.09090909091 3698 0.0928941101716567 1992 0.74351706699215 -0.74351706699215 -1 0.0428273682314085 1992 4456 3698 3946 4623 2307 2544 3556 4528 4343 2981 4016 M3656 REACTOME_UNWINDING_OF_DNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_UNWINDING_OF_DNA.html Genes involved in Unwinding of DNA 6/11 Reactome 0.973370896858386 0.990062084366919 3005 3696.09090909091 3699 0.304117918283208 3003 0.349865034147003 -0.392875086370006 -1 0.000554708705872074 3003 3257 4084 3117 4253 3365 3045 3699 4561 4442 3831 4017 M1034 REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC_C http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC_C.html Genes involved in Autodegradation of Cdh1 by Cdh1:APC/C 37/74 Reactome 0.818712644531662 0.851417543780597 2940 3801.27272727273 3699 0.143792821072504 2916 0.74351706699215 -0.74351706699215 -1 0.0189855246022682 2937 4512 3699 4336 4528 2916 3365 3157 4602 4444 3318 4018 M10080 REACTOME_M_G1_TRANSITION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_M_G1_TRANSITION.html Genes involved in M/G1 Transition 49/91 Reactome 0.878419944179737 0.908068797358537 1755 3637.81818181818 3700 0.17433159325913 1754 0.74351706699215 -0.74351706699215 -1 0.0113822921679039 1754 4325 3680 4112 4198 2867 2991 3700 4592 4377 3420 4019 M1030 REACTOME_APC_C_CDH1_MEDIATED_DEGRADATION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_PROTEINS_IN_LATE_MITOSIS_EARLY_G1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APC_C_CDH1_MEDIATED_DEGRADATION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_PROTEINS_IN_LATE_MITOSIS_EARLY_G1.html Genes involved in APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 40/82 Reactome 0.918471293267848 0.943643166027875 4440 3921 3700 0.20378889208827 3202 0.74351706699215 -0.74351706699215 -1 0.00684661946740969 3273 4509 3700 4535 4439 3202 3605 3333 4575 4440 3520 4020 M1536 HASLINGER_B_CLL_WITH_CHROMOSOME_12_TRISOMY http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_CHROMOSOME_12_TRISOMY.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with trisomy of chromosome 12. 15459216 16/33 Kevin Vogelsang 0.511220791520882 0.54818778697182 3615 3697.54545454545 3700 0.063004467238494 2776 0.868305884304399 -0.849289601596288 -1 0.0828609725421837 3611 4399 3127 4551 4289 3023 3700 2776 4479 3802 2916 4021 M14594 LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN.html Genes with copy number losses in primary neuroblastoma tumors. 17533364 505/1145 Arthur Liberzon 1.47918119586739e-06 6.06956487200929e-06 3460 3369.63636363636 3701 1.47918218045797e-07 921 1.32433524674484 1.6467268875742 1 2.52536936983044 3456 3913 4198 3434 921 3727 3701 3295 2524 4156 3741 4022 M8144 KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_UP.html Genes up-regulated in HL-60 cells (acute promyelocytic leukemia, APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 6 h. 18701491 588/1374 Jessica Robertson 8.0584056301732e-07 4.14508109582784e-06 3755 3317.36363636364 3702 8.05840855238024e-08 672 1.24488004763741 1.4162850702305 1 2.44922187653756 3755 3590 4422 3943 672 1935 4131 3323 2994 3702 4024 4023 M805 REACTOME_FORMATION_OF_RNA_POL_II_ELONGATION_COMPLEX_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_RNA_POL_II_ELONGATION_COMPLEX_.html Genes involved in Formation of RNA Pol II elongation complex 24/48 Reactome 0.510071825155696 0.547080927598899 3025 3628.36363636364 3703 0.0628044461291812 2375 0.852049796352599 0.852049796352599 1 0.0815830636652933 3025 4518 3703 4568 3894 2529 2375 3653 4336 4393 2918 4024 M3323 KANG_DOXORUBICIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_DOXORUBICIN_RESISTANCE_DN.html Genes down-regulated in gastric cancer cell lines: doxorubicin [PubChem=31703] resistant vs sensitive. 14734480 9/32 John Newman 0.0765897756730953 0.0944224385172651 4450 3658.36363636364 3703 0.00793650793650794 1993 2.30091178329391 -3.44290412638092 -1 0.862007837659807 4450 3459 4412 3693 3703 4377 4065 2901 1993 2581 4608 4025 M1308 GROSS_HYPOXIA_VIA_HIF1A_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_HIF1A_UP.html Genes up-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of HIF1A [GeneID=3091] by RNAi. 17704799 70/154 Jessica Robertson 0.0839184282471183 0.0965721401684667 3860 3811.54545454545 3704 0.00793650793650794 3400 1.01687527947649 -0.945021497298785 -1 0.377325679761676 3859 4177 3570 3435 3584 3400 4276 4216 3704 4052 3654 4026 M13240 WAGNER_APO2_SENSITIVITY http://www.broadinstitute.org/gsea/msigdb/cards/WAGNER_APO2_SENSITIVITY.html Genes whose expression most significantly correlated with cancer cell line sensitivity to the proapoptotic ligand APO2 [GeneID=8797]. 17767167 12/28 Jessica Robertson 0.161385165508919 0.18131164842359 3705 3667.63636363636 3704 0.0158730158730159 2520 0.995080030687733 -1.05458135084614 -1 0.26973166013371 3704 4285 3404 4237 4333 2520 3289 4007 3820 3623 3122 4027 M54 PID_IL12_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL12_2PATHWAY.html IL12-mediated signaling events 18832364 42/119 Pathway Interaction Database 0.0333367793381589 0.0429047371542468 4525 3511.09090909091 3705 0.00307753796104459 2194 1.59911720534394 1.72579071923691 1 0.799328346716713 3777 3769 2620 2194 3436 4522 3705 3857 3366 2854 4522 4028 M1018 REACTOME_APOPTOSIS_INDUCED_DNA_FRAGMENTATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOSIS_INDUCED_DNA_FRAGMENTATION.html Genes involved in Apoptosis induced DNA fragmentation 6/16 Reactome 0.105677592359708 0.120870197168072 3015 3340.63636363636 3705 0.0111067528601239 1214 1.00861198548302 -1.00861198548302 -1 0.338325711536346 3011 3948 3957 4296 3705 2547 1214 4131 4223 3042 2673 4029 M17094 GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN http://www.broadinstitute.org/gsea/msigdb/cards/GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN.html Genes down-regulated in non-metastatic breast cancer tumors having type 1 amplification in the 20q13 region; involves ZNF217 [GeneID=7764] locus only. 16899599 210/460 Leona Saunders 0.00462862283652446 0.00659262207050262 3990 3737.90909090909 3705 0.00042167180609398 3094 1.24192354187308 -0.993587457310664 -1 0.990052420141758 3990 4304 3705 4567 3123 3154 4429 3203 3094 4013 3535 4030 M13327 VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_DN.html Genes down-regulated in uterine fibroids with deletions in the 7q region vs those without the deletion. 15940248 17/68 Leona Saunders 0.0586324098782227 0.0736599122491559 3705 3508.09090909091 3705 0.00547781248983355 2281 1.9927109521212 -2.89638015375592 -1 0.825096675383183 3705 4158 2461 4297 3515 4343 3748 2920 2281 2804 4357 4031 M14735 REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY.html Genes involved in Resolution of AP sites via the single-nucleotide replacement pathway 10/13 Reactome 0.69418173799595 0.731325455091957 3295 3730.27272727273 3706 0.102108320921347 3171 0.654162550255648 -0.654162550255648 -1 0.0324930289605678 3295 3297 3351 4152 3968 3330 3802 3706 4501 4460 3171 4032 M6979 GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_DN.html Genes down-regulated in myeloid progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 35/110 Arthur Liberzon 0.0567802846660583 0.0714288359584294 4495 3576.36363636364 3706 0.00530008900884971 1996 1.18488959617619 -0.745690294314644 -1 0.496397587141816 4492 3706 3345 4006 3511 2843 4154 1996 3396 3979 3912 4033 M8224 ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_DN.html Genes in discrete regions of loss within 16q region detected in individual invasive breast cancer tumors. 16702952 11/64 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4040 3689.27272727273 3706 0.00793650793650794 2157 1.1799946069258 -1.41654306777924 -1 0.437853369486668 4039 4407 2975 4546 4644 3218 2157 3754 3706 3563 3573 4034 M14 PID_AURORA_B_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AURORA_B_PATHWAY.html Aurora B signaling 18832364 23/52 Pathway Interaction Database 0.298735036746822 0.327992591892129 2905 3605.27272727273 3707 0.0317460317460317 2502 1.95924006074214 1.95924006074214 1 0.34671629019317 2903 3547 2502 3610 4607 4281 3861 2733 3950 3707 3957 4035 M10294 REACTOME_UNFOLDED_PROTEIN_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_UNFOLDED_PROTEIN_RESPONSE.html Genes involved in Unfolded Protein Response 54/108 Reactome 0.726270090971166 0.762046942743144 3195 3731.81818181818 3707 0.111111111111111 2673 0.786771369622283 0.882589687285816 1 0.0339404063499067 3193 4137 3707 4330 4083 3604 2673 3339 4233 4175 3576 4036 M5813 WU_HBX_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_1_DN.html Genes down-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] in SK-Hep-1 cells (hepatocellular carcinoma). 11439330 17/40 John Newman 0.178422011743748 0.19997262545592 2805 3295.36363636364 3707 0.0177075646387434 2212 1.41342468170464 -1.41342468170464 -1 0.361149811994205 3707 4193 2803 3788 3952 2719 3771 2304 3995 2805 2212 4037 M730 REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE_ODC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE_ODC.html Genes involved in Regulation of ornithine decarboxylase (ODC) 31/55 Reactome 0.726270090971166 0.762046942743144 3145 3702.09090909091 3708 0.111111111111111 2803 0.800724562291382 -0.74351706699215 -1 0.0345423309653971 3144 3964 3708 3941 4218 2803 3287 3572 4228 4353 3505 4038 M1782 POS_RESPONSE_TO_HISTAMINE_UP http://www.broadinstitute.org/gsea/msigdb/cards/POS_RESPONSE_TO_HISTAMINE_UP.html Genes gradually up-regulated by histamine [PubChem=774] in B16-F10 melanoma tumors. 18339882 9/17 Jessica Robertson 0.089705808743256 0.102979279708696 3045 3493.63636363636 3708 0.00935471431413666 1167 1.08724531851145 1.08724531851145 1 0.392350313046308 3044 4083 4457 4240 3708 3217 1167 4170 3862 3417 3065 4039 M528 REACTOME_ER_PHAGOSOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ER_PHAGOSOME_PATHWAY.html Genes involved in ER-Phagosome pathway 47/109 Reactome 0.232850105696956 0.258012673278774 1920 3366.90909090909 3709 0.0238095238095238 1919 1.36466523987606 -1.03621887597599 -1 0.293486243993496 1919 4578 3648 3889 4566 2058 1980 3709 3897 4009 2783 4040 M1062 REACTOME_ANTIGEN_PRESENTATION_FOLDING_ASSEMBLY_AND_PEPTIDE_LOADING_OF_CLASS_I_MHC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANTIGEN_PRESENTATION_FOLDING_ASSEMBLY_AND_PEPTIDE_LOADING_OF_CLASS_I_MHC.html Genes involved in Antigen Presentation: Folding, assembly and peptide loading of class I MHC 27/62 Reactome 0.232850105696956 0.258012673278774 3710 3773.81818181818 3709 0.0238095238095238 2993 1.3161850474642 1.30981722871639 1 0.283060046234228 3709 4665 3003 2993 4464 4606 3524 3231 3882 3122 4313 4041 M8411 LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q.html Genes down-regulated in urothelial cell carcinoma (UCC) tumors with LOH on 9q as compared to the tumors showing retention. 16532037 85/181 Arthur Liberzon 3.58208686490491e-06 1.12504417218126e-05 4525 3408.18181818182 3709 3.25644790668031e-07 1293 1.09374018860149 1.1298261343441 1 1.97849972015729 4523 2686 3152 3765 1293 3389 4056 3887 3276 3754 3709 4042 M17621 CHEN_HOXA5_TARGETS_9HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_HOXA5_TARGETS_9HR_UP.html Genes up-regulated 9 h after induction of HoxA5 [GeneID=3205] expression in a breast cancer cell line. 15757903 141/394 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2570 3539.18181818182 3709 0.00793650793650794 1893 1.0714597537142 -0.947411964412169 -1 0.397580006285237 2567 4558 3709 4537 4251 1893 2786 3922 3701 4081 2926 4043 M748 REACTOME_RECRUITMENT_OF_MITOTIC_CENTROSOME_PROTEINS_AND_COMPLEXES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RECRUITMENT_OF_MITOTIC_CENTROSOME_PROTEINS_AND_COMPLEXES.html Genes involved in Recruitment of mitotic centrosome proteins and complexes 39/115 Reactome 0.133464841818457 0.151836913998856 1975 3305.18181818182 3710 0.0129385313760149 1263 0.737214843071506 0.746054062236876 1 0.220595711249327 1974 4382 3640 3952 4317 1724 1263 3710 4405 4364 2626 4044 M7970 PENG_GLUCOSE_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/PENG_GLUCOSE_DEPRIVATION_DN.html Genes down-regulated in BJAB cells (B-lymphoma) after glucose [PubChem=206] deprivation. 12101249 124/285 Broad Institute 0.00315982786607431 0.00458419609301059 3710 3520.18181818182 3710 0.000287670493413688 2545 1.48489615131656 1.65713925702915 1 1.26939470792447 3710 3730 2856 3927 3071 4096 4175 3462 2877 2545 4273 4045 M17456 CALVET_IRINOTECAN_SENSITIVE_VS_RESISTANT_UP http://www.broadinstitute.org/gsea/msigdb/cards/CALVET_IRINOTECAN_SENSITIVE_VS_RESISTANT_UP.html Genes up-regulated in neuroblastoma xenografts: sensitive vs resistant to the topoisomerase inhibitor irinotecan [GeneID=3750]. 16501609 2/6 Arthur Liberzon 0.932721327533986 0.956605852664535 3760 3903.3 3711.5 0.259092216801042 3041 0.159910241055816 -0.159910241055816 -1 0.00112618094579196 3760 3663 4286 NA 4411 3041 3629 3566 4643 4536 3498 4046 M4866 FLOTHO_PEDIATRIC_ALL_THERAPY_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FLOTHO_PEDIATRIC_ALL_THERAPY_RESPONSE_DN.html Down-regulated genes significantly associated with positive minimal residual disease (MRD) on day 46 after chemotherapy treatment of children with acute lymphoblastic leukemia (ALL). 16627760 17/38 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3245 3469.18181818182 3712 0.00793650793650794 2378 1.14329639995154 -0.736628287162217 -1 0.42423599060254 3242 3741 3175 4362 3775 2378 2424 3831 3684 3837 3712 4047 M17095 REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1.html Genes involved in SCF-beta-TrCP mediated degradation of Emi1 33/63 Reactome 0.675057511022657 0.712459346092831 2260 3565.54545454545 3713 0.0971434086605179 2259 0.74351706699215 -0.74351706699215 -1 0.0400161887080373 2259 4274 3713 3951 4585 2338 2488 3611 4521 4446 3035 4048 M4953 REACTOME_CDT1_ASSOCIATION_WITH_THE_CDC6_ORC_ORIGIN_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CDT1_ASSOCIATION_WITH_THE_CDC6_ORC_ORIGIN_COMPLEX.html Genes involved in CDT1 association with the CDC6:ORC:origin complex 34/67 Reactome 0.66573106398459 0.703725640837308 1810 3453 3715 0.0948178071580479 1810 0.74351706699215 -0.74351706699215 -1 0.041472011621791 1810 4231 3715 4028 4379 2319 2461 3169 4470 4398 3003 4049 M10828 SHEPARD_CRUSH_AND_BURN_MUTANT_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHEPARD_CRUSH_AND_BURN_MUTANT_UP.html Human orthologs of genes up-regulated in the crb ('crash and burn') zebrafish mutant that represents a loss-of-function mutation in BMYB [GeneID=4605]. 16150706 137/269 Jennifer Shepard 9.8560579832609e-07 4.69842194400413e-06 4335 3380.45454545455 3715 8.96005672618512e-08 711 1.51912168864465 -1.09942036779459 -1 2.95855700761785 4335 4256 3070 3939 711 2790 3715 4565 2337 3572 3895 4050 M2107 KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_UP.html Genes whose expression significantly and positively correlated with oligodendrocyte density in layer VI of BA9 brain region in patients with bipolar disorder. 18762803 461/1054 Jessica Robertson 6.381843973578e-06 1.75274889991363e-05 3735 3474.81818181818 3716 5.80169316940889e-07 1525 1.32463966286742 1.56345639959082 1 2.30294966350841 3733 3591 3716 2467 1525 3606 4560 3904 2383 4100 4638 4051 M7870 HEIDENBLAD_AMPLIFIED_IN_BONE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLIFIED_IN_BONE_CANCER.html Genes from selected recurrently amplified regions in bone tissue tumors with supernumerary ring chromosomes. 16732325 5/11 Arthur Liberzon 0.13255316750163 0.150836363019096 3690 3610.63636363636 3717 0.0141194775648871 2226 1.02225042359124 -1.02225042359124 -1 0.306959384609302 3690 3439 4240 3717 4030 4179 3256 2226 4247 2899 3794 4052 M970 REACTOME_ACTIVATION_OF_IRF3_IRF7_MEDIATED_BY_TBK1_IKK_EPSILON http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_IRF3_IRF7_MEDIATED_BY_TBK1_IKK_EPSILON.html Genes involved in Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon 8/31 Reactome 0.00524840018141907 0.00741900550531817 4225 3682.45454545455 3719 0.000526083710855347 2398 0.876705674048579 -0.779247816802233 -1 0.682467822381923 4222 3719 4065 3245 3160 3264 4449 4601 3526 2398 3858 4053 M1370 COURTOIS_SENESCENCE_TRIGGERS http://www.broadinstitute.org/gsea/msigdb/cards/COURTOIS_SENESCENCE_TRIGGERS.html Genes that trigger senescence in vitro and in vivo. 18193093 3/8 Jessica Robertson 0.554271799616233 0.591913776891902 3720 3753.72727272727 3719 0.0776260877447054 2636 0.758479313772085 0.758479313772085 1 0.0631400983658669 3229 3470 4332 3716 3926 3719 2636 3900 4294 4551 3518 4054 M15434 REACTOME_DNA_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_REPAIR.html Genes involved in DNA Repair 66/127 Reactome 0.481054735475818 0.516321873941592 1300 3298.54545454545 3720 0.0578892499370203 1296 0.592951192335154 -0.58439443516953 -1 0.062221478878377 1296 4095 3720 4407 4043 2084 2226 2958 4392 4411 2652 4055 M8887 LEE_METASTASIS_AND_RNA_PROCESSING_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_METASTASIS_AND_RNA_PROCESSING_UP.html Components of RNA post-transcriptional modification machinery up-regulated in MDA-MB-435 cells (breast cancer) whose metastatic potential has been reduced by expression of NME1 [GeneID=4830]. 18245461 15/29 Jessica Robertson 0.879870950666333 0.908967212262442 3280 3832.18181818182 3721 0.175232308571757 2819 0.568582587762199 -0.568582587762199 -1 0.00861501270921886 3280 4467 3503 4395 4482 3004 2819 3721 4660 4600 3223 4056 M15356 PUJANA_BREAST_CANCER_LIT_INT_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BREAST_CANCER_LIT_INT_NETWORK.html Genes constituting the LIT-Int network of proteins interacting with breast cancer reference proteins BRCA1, BRCA2, ATM, and CHEK2 [GeneID=672;675;472;11200]; the interactions were manually curated from the literature. 17922014 69/143 Leona Saunders 0.0839184282471183 0.0965721401684667 3505 3720 3722 0.00793650793650794 3184 1.32325933199268 -1.06055093147485 -1 0.49101373351575 3505 4222 3360 3278 3941 3301 3735 4564 3184 4108 3722 4057 M5488 REACTOME_TRAFFICKING_OF_GLUR2_CONTAINING_AMPA_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAFFICKING_OF_GLUR2_CONTAINING_AMPA_RECEPTORS.html Genes involved in Trafficking of GluR2-containing AMPA receptors 7/16 Reactome 0.689819510773092 0.727220298646278 2775 3655.72727272727 3723 0.110468262861399 2771 0.804644505039319 0.804644505039319 1 0.0406866786834235 2771 3587 4011 4144 4050 3080 3723 3013 4356 4391 3087 4058 M6831 BIOCARTA_KREB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_KREB_PATHWAY.html The Citric Acid Cycle 4/11 BioCarta 0.368641624979729 0.400615643472868 2750 3434 3724 0.0449467329037957 1742 0.23633830942975 -0.23633830942975 -1 0.0343195365374589 2749 3911 3879 3724 3928 2677 1742 3301 4619 4289 2955 4059 M597 REACTOME_ACTIVATION_OF_NF_KAPPAB_IN_B_CELLS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_NF_KAPPAB_IN_B_CELLS.html Genes involved in Activation of NF-kappaB in B Cells 39/77 Reactome 0.34170650127321 0.373248639852276 1625 3297.45454545455 3724 0.0372961961222239 1624 0.788258687556946 -0.788258687556946 -1 0.123320015710121 1624 4383 3724 3887 4510 1874 1899 3090 4434 4330 2517 4060 M11025 HOEGERKORP_CD44_TARGETS_TEMPORAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOEGERKORP_CD44_TARGETS_TEMPORAL_DN.html Genes temporally down-regulated by CD44 [GeneID=960] stimulation of B lymphocytes. 12411303 14/40 Kevin Vogelsang 0.0216994048516337 0.0284668004296629 3775 3574.09090909091 3727 0.00199240335766962 2352 1.23549442493584 1.46117436092289 1 0.698030477043166 3774 3000 2352 3253 3368 4523 4238 3027 3946 3727 4107 4061 M16336 PODAR_RESPONSE_TO_ADAPHOSTIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/PODAR_RESPONSE_TO_ADAPHOSTIN_UP.html Up-regulated genes in MM1.S cells (multiple myeloma) treated with adaphostin [PubChem=387042], a tyrosine kinase inhibitor with anticancer properties. 17308109 107/252 Jessica Robertson 5.62190852723031e-05 0.00011129811304859 3730 3642.27272727273 3727 5.11095654122697e-06 2241 1.18772681646814 1.23295393081542 1 1.71640153954526 3727 4172 3216 2726 2241 4060 4126 4412 3531 3447 4407 4062 M668 BIOCARTA_BARR_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BARR_MAPK_PATHWAY.html Role of fl-arrestins in the activation and targeting of MAP kinases 5/26 BioCarta 0.0464989415174804 0.0590818980344124 3485 3756.90909090909 3728 0.00475015653518674 3040 0.676971934891053 -0.676971934891053 -1 0.304005317263595 3485 3466 3866 4080 3496 3040 3728 4139 4235 4285 3506 4063 M12967 REACTOME_MRNA_3_END_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_3_END_PROCESSING.html Genes involved in mRNA 3'-end processing 28/71 Reactome 0.919404229051485 0.944394611428159 3215 3809.45454545455 3729 0.204621511097738 2894 0.568582587762199 -0.568582587762199 -1 0.00516390053984312 3213 4594 3729 4457 4150 2986 2894 3605 4567 4394 3315 4064 M1757 SANSOM_APC_TARGETS_REQUIRE_MYC http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_APC_TARGETS_REQUIRE_MYC.html Genes up-regulated after Cre-lox knockout of APC [GeneID=324] in the small intestine that require functional MYC [GeneID=4609]. 17377531 151/287 Jessica Robertson 8.2060973710091e-05 0.000155683288585217 3900 3464.36363636364 3729 7.46036679823477e-06 1943 1.69761558931189 2.07968348036583 1 2.36280534500003 3898 3729 2557 3421 2343 4192 4366 3990 1943 3113 4556 4065 M10680 KEGG_PROTEASOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROTEASOME.html Proteasome 28/48 KEGG 0.638083453995918 0.675261758226033 2345 3498 3730 0.0882547814868856 2276 0.679448832342462 -0.679448832342462 -1 0.0423517433410487 2344 4100 3730 3884 4268 2276 2590 3577 4407 4250 3052 4066 M938 REACTOME_CIRCADIAN_CLOCK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CIRCADIAN_CLOCK.html Genes involved in Circadian Clock 29/72 Reactome 0.0426476869134051 0.0543505740756639 3730 3695.90909090909 3730 0.00395432571200363 2744 1.72459574301471 1.96788157277144 1 0.797309605540961 4515 3927 2744 3730 3465 3415 4386 3730 3211 3271 4261 4067 M1019 REACTOME_CLEAVAGE_OF_GROWING_TRANSCRIPT_IN_THE_TERMINATION_REGION_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CLEAVAGE_OF_GROWING_TRANSCRIPT_IN_THE_TERMINATION_REGION_.html Genes involved in Cleavage of Growing Transcript in the Termination Region 31/83 Reactome 0.723070292861301 0.760051007704813 2895 3696.18181818182 3731 0.110171477661404 2492 0.648879905527032 -0.648879905527032 -1 0.0282620759661313 2894 4591 3731 4532 4507 2825 2492 3010 4499 4428 3149 4068 M5415 BIOCARTA_IL4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL4_PATHWAY.html IL 4 signaling pathway 11/20 BioCarta 0.415320710913563 0.448741722697937 3735 3613.18181818182 3732 0.0476190476190476 2533 1.07994822337051 -1.24068267816973 -1 0.137374413871673 3732 3783 2810 3727 4361 2533 3847 4073 4031 3552 3296 4069 M250 ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN.html Genes down-regulated in macrophages by P.gingivalis FimA pathogen. 18025224 164/510 Arthur Liberzon 0.000709730803317979 0.00112092974194407 4185 3603.18181818182 3733 6.45418063112728e-05 2744 1.37985888584199 -1.11377770069803 -1 1.48812017522184 4183 4489 3082 4491 2837 3733 2744 3120 3036 3793 4127 4070 M17225 BROWNE_HCMV_INFECTION_14HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_14HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 14 h time point that were not up-regulated at the previous time point, 12 h. 11711622 143/312 John Newman 0.0006373786499785 0.00101383447175806 4395 3850.18181818182 3734 5.79603077004158e-05 2819 1.4846384423468 1.76003092744925 1 1.62478734146506 4394 4493 3338 3224 2819 3734 4675 4248 3374 3544 4509 4071 M502 REACTOME_METABOLISM_OF_NON_CODING_RNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_NON_CODING_RNA.html Genes involved in Metabolism of non-coding RNA 32/58 Reactome 0.0839184282471183 0.0965721401684667 3105 3877.18181818182 3736 0.00793650793650794 3104 1.54668507782595 -1.54668507782595 -1 0.573918956531547 3104 4515 3603 4595 4368 3736 4061 3291 3691 4078 3607 4072 M10236 BORCZUK_MALIGNANT_MESOTHELIOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/BORCZUK_MALIGNANT_MESOTHELIOMA_UP.html Genes up-regulated in biphasic (mixed) vs epithelial subtypes of malignant peritoneal mesothelioma. 16862182 230/473 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2365 3684.09090909091 3736 0.00793650793650794 2363 1.19855529537738 1.48467122460261 1 0.444740570465526 2363 4622 3736 3753 4299 3767 3345 3158 3622 4170 3690 4073 M595 REACTOME_DOWNSTREAM_SIGNALING_EVENTS_OF_B_CELL_RECEPTOR_BCR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNSTREAM_SIGNALING_EVENTS_OF_B_CELL_RECEPTOR_BCR.html Genes involved in Downstream Signaling Events Of B Cell Receptor (BCR) 56/111 Reactome 0.20148367129228 0.225012508025649 2515 3421.54545454545 3737 0.0202467580359854 1583 0.78081384411073 -0.788258687556946 -1 0.184885660764919 2512 4644 3737 3956 4584 1583 2134 3368 4456 4329 2334 4074 M1081 REACTOME_SCFSKP2_MEDIATED_DEGRADATION_OF_P27_P21 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SCFSKP2_MEDIATED_DEGRADATION_OF_P27_P21.html Genes involved in SCF(Skp2)-mediated degradation of p27/p21 34/69 Reactome 0.75785878230136 0.792706753094681 2350 3675.90909090909 3738 0.120964838061774 2348 0.74351706699215 -0.74351706699215 -1 0.0274187262047347 2348 4589 3688 4107 4650 2475 2614 3738 4580 4458 3188 4075 M772 REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING.html Genes involved in RNA Polymerase II Transcription Pre-Initiation And Promoter Opening 19/47 Reactome 0.823070286135157 0.855379765098546 3015 3636.36363636364 3739 0.145684566155283 2597 0.697164433872166 -0.826105627352758 -1 0.0172880833101929 3012 4107 3649 4194 4132 2634 2597 3739 4453 4373 3110 4076 M1239 JOHANSSON_BRAIN_CANCER_EARLY_VS_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOHANSSON_BRAIN_CANCER_EARLY_VS_LATE_UP.html Genes up-regulated in early vs late brain tumors induced by retroviral delivery of PDGFB [GeneID=5155]. 15750623 6/20 Leona Saunders 0.216081862518008 0.240627283212782 3395 3662.09090909091 3739 0.024051117136669 2193 0.684163046089497 -0.684163046089497 -1 0.154713239042022 3395 3404 4271 4145 3739 3436 2193 3007 4180 4534 3979 4077 M3644 BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_DN http://www.broadinstitute.org/gsea/msigdb/cards/BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_DN.html Genes down-regulated in pre B lymphocyte after induction of physiological DNA double-strand breaks (DSB) by RAG2 [GeneID=5897]; the changes depend on ATM [GeneID=472] but not NFKB signaling. 18849970 32/85 Jessica Robertson 0.0839184282471183 0.0965721401684667 4105 3628.63636363636 3739 0.00793650793650794 2357 2.13634282380472 -1.26433361577449 -1 0.792719644657442 4104 3926 2357 3216 4206 3036 4413 3626 3353 3739 3939 4078 M19148 TOMLINS_PROSTATE_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/TOMLINS_PROSTATE_CANCER_UP.html Genes up-regulated in prostate cancer vs benign prostate tissue, based on a meta-analysis of five gene expression profiling studies. 17173048 30/64 Leona Saunders 0.144233670567188 0.16349273833523 3945 3781.18181818182 3740 0.0140600322673347 3123 1.43968673210953 -1.22105409466753 -1 0.413891801658275 3942 3540 3123 3592 3653 3897 4062 3934 3740 3648 4462 4079 M2188 LI_DCP2_BOUND_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/LI_DCP2_BOUND_MRNA.html Genes encoding mRNA transcripts specifically bound by DCP2 [GeneID=167227]. 18039849 70/114 Arthur Liberzon 0.415320710913563 0.448741722697937 3090 3611.18181818182 3740 0.0476190476190476 2432 1.11145802337961 -1.22431778664901 -1 0.141382606366838 3090 4637 3740 4618 3891 2432 3027 3144 4036 4115 2993 4080 M17998 CAFFAREL_RESPONSE_TO_THC_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_DN.html Genes down-regulated in EVSA-T cells (breast cancer) treated THC (delta-9-tetrahydrocannabinol) [PubChem=6610319]. 18454173 35/72 Jessica Robertson 0.0839184282471183 0.0965721401684667 3960 3757.63636363636 3741 0.00793650793650794 2812 1.05093737742549 -1.24906227891344 -1 0.38996489381606 3959 4068 3056 2812 4445 3741 4355 3662 3680 3981 3575 4081 M4552 TARTE_PLASMA_CELL_VS_B_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TARTE_PLASMA_CELL_VS_B_LYMPHOCYTE_UP.html Genes up-regulated in plasma cells compared with B lymphocytes. 12663452 63/118 Kate Stafford 0.00198593077927111 0.00294973945229014 4645 3741 3741 0.00018070233995421 2978 1.2639021809946 -1.22861119024965 -1 1.16893502004111 4641 2978 3163 3482 3009 3759 4370 4597 3634 3741 3777 4082 M824 REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX.html Genes involved in Formation of transcription-coupled NER (TC-NER) repair complex 15/33 Reactome 0.63389956273523 0.671137223447195 3635 3716.36363636364 3742 0.0873015873015873 2838 0.644061240291334 0.631456599580462 1 0.0407723628435696 3633 3742 3597 3799 4032 2838 3094 4101 4170 4397 3477 4083 M676 REACTOME_PI_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI_METABOLISM.html Genes involved in PI Metabolism 27/51 Reactome 0.238510484564987 0.26409738437418 3370 3778 3744 0.0244665279756625 2920 0.864915111871027 -0.847597580439112 -1 0.182809088444909 3366 4394 3583 4259 3744 2920 4641 3625 4193 3824 3009 4084 M795 REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRONLESS_TRANSCRIPT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRONLESS_TRANSCRIPT.html Genes involved in Transport of Mature mRNA Derived from an Intronless Transcript 24/59 Reactome 0.0839184282471183 0.0965721401684667 3265 3883.54545454545 3744 0.00793650793650794 3054 1.54668507782595 -1.54668507782595 -1 0.573918956531547 3264 4672 3484 4623 4354 3744 4443 3054 3626 3987 3468 4085 M12484 REACTOME_GAMMA_CARBOXYLATION_TRANSPORT_AND_AMINO_TERMINAL_CLEAVAGE_OF_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAMMA_CARBOXYLATION_TRANSPORT_AND_AMINO_TERMINAL_CLEAVAGE_OF_PROTEINS.html Genes involved in Gamma-carboxylation, transport, and amino-terminal cleavage of proteins 5/13 Reactome 0.00513016569194313 0.0072628267167509 3885 3485 3745 0.000514204768600496 1861 1.03053279582563 -1.0832724893101 -1 0.805694490225037 3882 2675 3925 3385 3158 4209 4496 3745 3249 1861 3750 4086 M1357 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX2_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX2_DN.html Early prostate development genes (down-regulated at 6 hr dihydrotestosterone [PubChem=10635]) which are also down-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 8/11 Jessica Robertson 0.263404209747799 0.290836976172994 3675 3853.81818181818 3745 0.0301090136527772 2878 0.577847818965278 0.577847818965278 1 0.113287322953444 4529 2878 4327 3535 3783 3251 3675 3674 4446 4549 3745 4087 M14942 WANG_RESPONSE_TO_FORSKOLIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_FORSKOLIN_UP.html Genes up-regulated in LNCaP cells (prostate cancer) treated with forskolin [PubChem=47936], an activator of PKA pathway. 16751804 24/50 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4105 3622.63636363636 3746 0.00793650793650794 2814 1.19232517688554 -1.39210568541521 -1 0.442428798556455 4105 2814 2854 4466 3768 3943 3434 3832 3317 3746 3570 4088 M5290 BIOCARTA_MEF2D_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MEF2D_PATHWAY.html Role of MEF2D in T-cell Apoptosis 9/26 BioCarta 0.0429876098419508 0.0547688797496958 4655 3582.18181818182 3748 0.00438425504416435 1802 1.4533863902646 -1.39703925928365 -1 0.670156041340269 4653 3193 3863 2890 3480 4578 4124 2626 3748 1802 4447 4089 M13194 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_23 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_23.html Amplification hot spot 23: colocolized fragile sites and cancer genes in the 11q12-q25 region. 16751803 8/28 Arthur Liberzon 0.0634211850075439 0.0793357375721705 2035 3083.90909090909 3749 0.0065307415579629 1067 0.855249835097963 -0.855249835097963 -1 0.344044470032416 2031 3749 4226 4005 4377 1607 1067 1988 4418 4515 1940 4090 M5374 BIOCARTA_SARS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SARS_PATHWAY.html The SARS-coronavirus Life Cycle 8/14 BioCarta 0.227807332521451 0.253383612673989 3410 3682.54545454545 3750 0.0255208141696627 3066 1.36107150257004 -1.77869685906771 -1 0.29662503635139 3410 3066 3881 3401 3750 3978 3937 4165 3982 3295 3643 4091 M998 REACTOME_DESTABILIZATION_OF_MRNA_BY_AUF1_HNRNP_D0 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DESTABILIZATION_OF_MRNA_BY_AUF1_HNRNP_D0.html Genes involved in Destabilization of mRNA by AUF1 (hnRNP D0) 36/72 Reactome 0.588102127895887 0.625759893578593 2315 3557.09090909091 3750 0.0774692139723952 2202 0.74351706699215 -0.74351706699215 -1 0.0553313764842706 2314 4389 3711 3750 4613 2202 2389 3787 4564 4425 2984 4092 M17193 MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN.html Down-regulated genes distinguishing in multiple myeloma (MM) samples with lower expression of TACI [GeneID=23495]. 15827134 101/217 Kevin Vogelsang 0.67950230170086 0.716988918209915 2795 3717 3750 0.0982731691896039 2792 0.74188386366319 -0.719847608088443 -1 0.0391819100314205 2792 4363 3750 4205 3960 2794 3513 3518 4304 4207 3481 4093 M9193 MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_DN.html Genes down-regulated in normal bone marrow plasma cells (BMPC) compared to polyclonal plasmablasts (PPC) that also distinguished multiple myeloma (MM) samples by expression of levels of TACI [GeneID=23495]. 15827134 39/89 Kevin Vogelsang 0.905433829002461 0.933418416623429 2315 3714.54545454545 3751 0.192978559155283 2311 0.533678805929573 -0.515899953184024 -1 0.00583731884459136 2311 4386 3628 4201 4088 2800 3009 3751 4628 4575 3483 4094 M787 REACTOME_POL_SWITCHING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POL_SWITCHING.html Genes involved in Polymerase switching 7/14 Reactome 0.916790038294834 0.942122394616138 2990 3727.81818181818 3752 0.220138407556357 2921 0.71112730430769 -0.71112730430769 -1 0.00673043866598671 2986 3752 4004 4236 4514 2921 2942 3405 4500 4383 3363 4095 M1479 MA_MYELOID_DIFFERENTIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/MA_MYELOID_DIFFERENTIATION_UP.html Genes up-regulated during myeloid differentiation induced by tretinoin (ATRA) [PubChem=444795] and IL3 [GeneID=3652] in the EML cell line (myeloid progenitor). 12130493 24/86 Kevin Vogelsang 0.145655857557882 0.165057055069206 3885 3626.36363636364 3752 0.0142091013519222 1910 1.4666137160397 -1.35552491590679 -1 0.41941591741318 3752 3842 3222 3609 3657 3884 1910 3858 3883 3748 4525 4096 M17580 ST_IL_13_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_IL_13_PATHWAY.html Interleukin 13 (IL-13) Pathway 3/7 Signaling Transduction KE 0.110959602804144 0.126756874388157 2745 3291.18181818182 3754 0.011692367066289 1676 0.307005441107918 -0.307005441107918 -1 0.100663388751021 2743 3754 3884 4576 4318 1676 2246 2163 4401 4293 2149 4097 M1870 REACTOME_GLUCOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCOSE_METABOLISM.html Genes involved in Glucose metabolism 36/81 Reactome 0.0839184282471183 0.0965721401684667 3755 3789.36363636364 3754 0.00793650793650794 2940 1.25956483174498 -1.17305689970572 -1 0.467379005439892 3754 3704 3348 3871 4655 4217 2940 3510 3326 3840 4518 4098 M2328 BILANGES_SERUM_AND_RAPAMYCIN_SENSITIVE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_SERUM_AND_RAPAMYCIN_SENSITIVE_GENES.html Genes translationally regulated in MEF cells (embryonic fibroblasts) in response to serum starvation and by rapamycin (sirolimus) [PubChem=6610346]. 17562867 46/117 Arthur Liberzon 0.87261178779014 0.90246277589596 2980 3707.18181818182 3755 0.170821346599105 2520 0.721223866229138 -0.604708514949914 -1 0.0117500239863375 2978 4268 3755 3681 4343 2711 2520 4189 4408 4672 3254 4099 M311 KEGG_ALPHA_LINOLENIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALPHA_LINOLENIC_ACID_METABOLISM.html alpha-Linolenic acid metabolism 2/21 KEGG 0.905639444912904 0.933418416623429 3600 3882.9 3756.5 0.23071399473488 3357 0.205793660848157 -0.205793660848157 -1 0.00225094684682704 3599 3625 3795 NA 4193 3357 4265 3407 4627 4243 3718 4100 M18264 MOOTHA_VOXPHOS http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_VOXPHOS.html Genes involved in oxidative phosphorylation; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 50/111 Vamsi Mootha 0.820342268759519 0.852922980121391 2100 3561.63636363636 3757 0.144495387223695 2096 0.621197773005905 -0.621197773005905 -1 0.0156879227584735 2096 4580 3757 3893 4171 2608 2494 3450 4452 4571 3106 4101 M18742 SENGUPTA_EBNA1_ANTICORRELATED http://www.broadinstitute.org/gsea/msigdb/cards/SENGUPTA_EBNA1_ANTICORRELATED.html Genes whose reduced expression in nasopharyngeal carinoma (NPC) correlated most with the increased expression of EBNA1 [GeneID=3783774], a latent gene of Epstein-Barr virus (EBV). 16912175 105/254 Arthur Liberzon 2.74722117971604e-05 5.96270423721602e-05 4270 3572.36363636364 3759 2.49750498716399e-06 2017 1.28462594263465 1.38429992374435 1 1.98370498694926 4268 3759 3131 4507 2017 2720 4450 4645 3175 2492 4132 4102 M13917 BIOCARTA_PARKIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PARKIN_PATHWAY.html Role of Parkin in the Ubiquitin-Proteasomal Pathway 4/15 BioCarta 7.8308553325015e-06 2.06501902577952e-05 3960 3125.81818181818 3760 7.83088292767123e-07 1569 1.18909638530534 -0.883469480558986 -1 2.03635243440279 3957 1569 3864 2034 1640 3867 4346 2350 3760 2658 4339 4103 M11063 REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE.html Genes involved in mRNA Decay by 5' to 3' Exoribonuclease 10/14 Reactome 0.954055814075282 0.975923498091415 3615 3937.72727272727 3760 0.24423879215208 3172 0.64621637343787 -0.64621637343787 -1 0.00250009182738752 3612 4531 3415 4436 4515 3172 3760 3429 4608 4401 3436 4104 M19849 HAHTOLA_MYCOSIS_FUNGOIDES_CD4_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_CD4_DN.html Genes down-regulated in T helper cells (defines as CD4+) isolated from patients with mucosis fungoides compared to those from normal control donors. 16914566 84/191 Arthur Liberzon 0.514011397665828 0.550424453716195 3140 3866.18181818182 3761 0.0634920634920635 2817 0.882860554926589 1.00620167095699 1 0.0836792328791507 3138 4312 3681 4493 4667 3712 2817 3655 4109 4183 3761 4105 M1507 ZAMORA_NOS2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZAMORA_NOS2_TARGETS_UP.html Up-regulated in hepatocytes upon expression of NOS2 [GeneID=4843]. 12381414 64/123 John Newman 0.0839184282471183 0.0965721401684667 3445 3693.36363636364 3761 0.00793650793650794 2241 1.70664452009889 -1.1134611014378 -1 0.633274127018553 3442 4059 2651 3437 4605 4598 4521 3025 2241 3761 4287 4106 M1380 DEN_INTERACT_WITH_LCA5 http://www.broadinstitute.org/gsea/msigdb/cards/DEN_INTERACT_WITH_LCA5.html Proteins shown to interact with LCA5 [GeneID=167691] in vivo. 17546029 20/41 Jessica Robertson 0.726270090971166 0.762046942743144 2295 3698.27272727273 3762 0.111111111111111 2291 0.999626045461133 1.29544971895009 1 0.0431227112136078 2291 4459 3447 3547 4023 3407 3762 4334 4225 3926 3260 4107 M734 REACTOME_RNA_POL_II_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_II_TRANSCRIPTION.html Genes involved in RNA Polymerase II Transcription 62/152 Reactome 0.727810371687008 0.763492142763672 2550 3599.18181818182 3765 0.11156698612725 2522 0.708827695030199 -0.707955146135607 -1 0.0303648102875533 2548 4643 3765 4411 4149 2527 2522 3303 4394 4356 2973 4108 M7715 FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_DN.html Top 100 genes negatively associated with T-cell acute lymphoblastic leukemia MLL T-ALL) expressing MLL-ENL fusion [GeneID=4297;4298]. 12637319 62/152 Kevin Vogelsang 0.0102253105339428 0.0139859326217326 3995 3820.45454545455 3765 0.000933922545635622 2374 1.36523054862774 -1.13085199854535 -1 0.925352606139435 3995 3765 2374 3321 3253 4621 4522 4646 3200 3712 4616 4109 M2199 THILLAINADESAN_ZNF217_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/THILLAINADESAN_ZNF217_TARGETS_DN.html Genes bound and repressed by ZNF217 [GeneID=7764] in MCF7 cells (breast cancer). 18625718 8/15 Arthur Liberzon 0.244977546705123 0.271002073621389 4665 3627.18181818182 3766 0.027709624657369 1860 1.51607467592118 1.51607467592118 1 0.31422727295442 4665 3461 4627 3990 3766 2014 1860 4264 4248 3317 3687 4110 M6438 WONG_IFNA2_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WONG_IFNA2_RESISTANCE_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) cell lines resistant to IFNA2 [GeneID=3440]. 15709204 28/93 Yujin Hoshida 0.0604135749462278 0.0757554220492437 3390 3481.72727272727 3767 0.00564902698184921 1785 1.72435641334671 1.53731345973536 1 0.706303870543175 3390 4072 2483 4303 3767 4101 2981 4082 3468 3867 1785 4111 M189 KEGG_RIBOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIBOSOME.html Ribosome 60/184 KEGG 0.135751763645295 0.154288810196909 2765 3387 3768 0.0131756350018378 1267 0.508850371010823 -0.508850371010823 -1 0.150968543462906 2761 4378 3768 3509 4272 1575 1267 4625 4587 4246 2269 4112 M19927 TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C http://www.broadinstitute.org/gsea/msigdb/cards/TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C.html Genes down-regulated in HCT116 cells (colon cancer) upon expression of MIR34B or MIR34C [GeneID=407041;407042] microRNAs. 18519671 311/723 Leona Saunders 9.41893460808669e-06 2.40006131449126e-05 3770 3643 3768 8.56270448539324e-07 1669 1.21348358723962 -1.04929908744933 -1 2.04915227087279 3768 4302 3701 4203 1669 2907 4219 4512 3380 4153 3259 4113 M8229 REACTOME_TRANSLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSLATION.html Genes involved in Translation 98/283 Reactome 0.121310824525448 0.138379387469876 2380 3294.18181818182 3769 0.0116878919706721 1286 0.506387309662844 -0.506387309662844 -1 0.158986087196362 2378 4364 3769 3563 4117 1390 1286 4347 4517 4305 2200 4114 M7559 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_15 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_15.html Amplification hot spot 15: colocalized fragile sites and cancer genes in the 6p25-p11.1 region. 16751803 9/23 Arthur Liberzon 0.246460155903422 0.27257783586581 2910 3735.54545454545 3769 0.0279007185826275 2496 0.682979643455143 -0.886595230691497 -1 0.140928305303751 2907 4007 4221 4432 3769 2941 2496 3623 4485 4510 3700 4115 M2394 JUBAN_TARGETS_OF_SPI1_AND_FLI1_DN http://www.broadinstitute.org/gsea/msigdb/cards/JUBAN_TARGETS_OF_SPI1_AND_FLI1_DN.html Genes down-regulated in 745A cells (erythroleukemia) upon knockdown of FLI1 [GeneID=2313] by RNAi and down-regulation of SPI1 [GeneID=6688] by HMBA [PubChem=3616]. 19289502 70/161 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4610 3787.09090909091 3769 0.00793650793650794 2829 1.58537277355552 -1.0938621944056 -1 0.588274562822418 4608 4315 2829 3940 3704 3478 3769 3618 2878 3885 4634 4116 M567 REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE.html Genes involved in SRP-dependent cotranslational protein targeting to membrane 75/217 Reactome 0.194538822004164 0.217463959902556 2900 3438.27272727273 3770 0.0194751579940287 1412 0.506387309662844 -0.506387309662844 -1 0.122648380656289 2900 4264 3770 3510 4116 1870 1412 4647 4512 4327 2493 4117 M1045 REACTOME_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IMMUNE_SYSTEM.html Genes involved in Immune System 498/1251 Reactome 8.84693315184467e-07 4.3730726529055e-06 4115 3612 3770 8.04266973590303e-08 671 1.26298001829472 -1.18568658215326 -1 2.47409728719846 3946 4351 3554 4111 671 3770 3608 4683 3171 4113 3754 4118 M1752 VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP.html Genes up-regulated in uterine fibroids with deletions in the 7q region vs those without the deletion. 15940248 46/102 Leona Saunders 0.878859116702268 0.908122121470083 3770 3934.18181818182 3770 0.174603174603175 3165 0.737545362518905 -0.641216436753837 -1 0.0112839978357158 3770 4650 3663 4530 4274 3165 3467 3694 4315 4155 3593 4119 M14455 TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA.html Genes with hypermethylated DNA in all four esophageal squamous cell carcinoma (ESCC) lines analyzed. 17438526 57/177 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4395 3775 3770 0.00793650793650794 1821 1.66636741405054 2.00688991527195 1 0.618328747975882 4395 4372 1821 4557 3770 3482 4144 3744 3288 3334 4618 4120 M13642 REACTOME_PEPTIDE_CHAIN_ELONGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PEPTIDE_CHAIN_ELONGATION.html Genes involved in Peptide chain elongation 60/185 Reactome 0.282379124102025 0.311201452385252 2995 3468.36363636364 3771 0.0297144777318779 1574 0.508850371010823 -0.508850371010823 -1 0.0942934765633805 2993 4377 3771 3508 4264 1778 1574 4479 4549 4360 2499 4121 M18919 LIU_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LIU_LIVER_CANCER.html Low abundance transcripts specific to hepatocellular carcinoma (HCC). 18332864 20/62 Jessica Robertson 0.0839184282471183 0.0965721401684667 3820 3587.36363636364 3771 0.00793650793650794 2174 1.47525176200636 -1.27776820177446 -1 0.547412633561945 3816 3450 2939 4467 3845 3771 4197 4172 3519 3111 2174 4122 M6177 REACTOME_NOTCH_HLH_TRANSCRIPTION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NOTCH_HLH_TRANSCRIPTION_PATHWAY.html Genes involved in Notch-HLH transcription pathway 4/14 Reactome 0.00454130856605502 0.00647219341257112 4375 3650.63636363636 3773 0.000455061591423899 2586 0.86944359238865 -1.29214926568553 -1 0.695658678077612 4373 3171 3989 3773 3139 4196 3670 2586 3917 2664 4679 4123 M6423 REACTOME_LOSS_OF_NLP_FROM_MITOTIC_CENTROSOMES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LOSS_OF_NLP_FROM_MITOTIC_CENTROSOMES.html Genes involved in Loss of Nlp from mitotic centrosomes 37/107 Reactome 0.191336279887967 0.213986111588308 1985 3318.36363636364 3773 0.0191213786021955 1406 0.737214843071506 0.746054062236876 1 0.180442198519525 1985 4228 3616 3950 4310 1740 1406 3773 4396 4368 2730 4124 M781 REACTOME_3_UTR_MEDIATED_TRANSLATIONAL_REGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_3_UTR_MEDIATED_TRANSLATIONAL_REGULATION.html Genes involved in 3' -UTR-mediated translational regulation 72/229 Reactome 0.0491542955206799 0.0622364303728468 2370 3287.54545454545 3773 0.00457165214434548 1117 0.508850371010823 -0.508850371010823 -1 0.224305830230914 2366 4370 3773 3687 4226 1117 1240 4599 4510 4380 1895 4125 M16843 REACTOME_METABOLISM_OF_RNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_RNA.html Genes involved in Metabolism of RNA 184/402 Reactome 0.161385165508919 0.18131164842359 2640 3568.36363636364 3775 0.0158730158730159 2205 1.21496078297854 -1.08500482032893 -1 0.329333701088081 2638 4627 3775 4280 4571 2205 2458 3723 3825 4238 2912 4126 M4669 REACTOME_INFLUENZA_LIFE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INFLUENZA_LIFE_CYCLE.html Genes involved in Influenza Life Cycle 90/257 Reactome 0.351459064880124 0.383454523405881 2770 3443.90909090909 3776 0.0386015903026294 2015 0.88595422995905 -0.88595422995905 -1 0.134810114293272 2766 4435 3776 3815 4493 2015 2039 3713 4159 4219 2453 4127 M13354 KONDO_COLON_CANCER_HCP_WITH_H3K27ME1 http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_COLON_CANCER_HCP_WITH_H3K27ME1.html Genes with high levels of histone H3 monomethylation mark at K27 (H3K27me1) in SW48 cells (colon cancer) by ChIP-chip assay on a 12K CpG array (CpG promoters only, HCP=high-CpG-density promoters). 18488029 15/37 Jessica Robertson 0.0404590477430637 0.0516315625610012 4380 3816.45454545455 3776 0.00374753164807167 3067 1.04108883277265 -0.72488063963407 -1 0.489794806059824 4380 3973 3116 4074 3461 3468 4591 3391 3067 3776 4684 4128 M2055 DAZARD_UV_RESPONSE_CLUSTER_G28 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G28.html Cluster G28: genes differentially up-regulated in NHEK (normal keratinocyte) compared to SCC12B2 cells (squamous cell carcinoma) by UV-B radiation. 12771951 21/41 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3795 3547.90909090909 3776 0.00793650793650794 2157 1.42299771945169 -1.1062175689697 -1 0.528023046049035 3793 4154 2237 2157 4330 4273 4310 3756 3611 2630 3776 4129 M7636 REACTOME_INFLUENZA_VIRAL_RNA_TRANSCRIPTION_AND_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INFLUENZA_VIRAL_RNA_TRANSCRIPTION_AND_REPLICATION.html Genes involved in Influenza Viral RNA Transcription and Replication 67/206 Reactome 0.115776181483483 0.132162530190402 4375 3368.54545454545 3777 0.0111235848269703 1419 0.565524304672362 -0.565524304672362 -1 0.181679473213624 2777 4374 3777 3562 4344 1474 1419 4375 4525 4431 1996 4130 M5650 REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE.html Genes involved in Cytochrome P450 - arranged by substrate type 10/99 Reactome 0.00547726404588575 0.00772620689916334 3780 3311.54545454545 3779 0.000499177120170589 1344 1.48493693140327 1.68309632916755 1 1.14637866568362 3779 2210 1344 3969 3152 4478 3235 4120 3936 1961 4243 4131 M2066 WHITFIELD_CELL_CYCLE_LITERATURE http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_LITERATURE.html A list of known cell cycle regulated genes that was compiled from the literature by the authors. 12058064 21/52 Jessica Robertson 0.999118518351607 0.999999893590849 3660 3914.90909090909 3779 0.472415393005568 2459 0.664881003189227 -0.600668938262926 -1 9.4344183290032e-09 3656 3779 2459 3375 4633 3700 3759 4405 4598 4662 4038 4132 M16066 SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN http://www.broadinstitute.org/gsea/msigdb/cards/SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN.html Genes down-regulated in lymphoblastoid cells from the European population compared to those from the Asian population. 17206142 444/989 Leona Saunders 0.000417283517432269 0.00068466056116513 4455 3715.54545454545 3780 3.79420624023533e-05 2376 1.11704802487233 -0.982322701440938 -1 1.29211028443637 4455 4124 3780 4042 2734 2376 3680 4562 3348 4226 3544 4133 M11961 PUJANA_CHEK2_PCC_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_CHEK2_PCC_NETWORK.html Genes constituting the CHEK2-PCC network of transcripts whose expression positively correlates (Pearson correlation coefficient, PCC >= 0.4) with that of CHEK2 [GeneID=11200]. 17922014 487/1174 Leona Saunders 0.0839184282471183 0.0965721401684667 2705 3741.90909090909 3781 0.00793650793650794 2702 1.18635125564149 -1.06713734771386 -1 0.440212092190901 2702 4550 3781 3967 4470 3008 3319 3916 3653 4234 3561 4134 M1923 MIKKELSEN_PLURIPOTENT_STATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_PLURIPOTENT_STATE_DN.html Genes down-regulated in the induced pluripotent cells (iPS) and embryonic stem cells (ES) compared to the parental lineage-committed and partially reprogrammed cell lines. 18509334 10/17 Jessica Robertson 0.751985672431077 0.78691488633587 3785 3913 3781 0.119047619047619 3212 1.02225042359124 -1.02225042359124 -1 0.0388876256552008 3781 4604 3212 4586 4448 3279 3311 4520 4243 3496 3563 4135 M18855 VECCHI_GASTRIC_CANCER_EARLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/VECCHI_GASTRIC_CANCER_EARLY_UP.html Up-regulated genes distinguishing between early gastric cancer (EGC) and normal tissue samples. 17297478 280/656 Arthur Liberzon 0.0755039081881855 0.0938989686225683 3440 3537.90909090909 3785 0.0071115429504147 1199 1.69361781216999 -1.44644775039486 -1 0.635987401178799 3439 4217 1199 3439 3785 4137 4565 4180 2904 2654 4398 4136 M15565 ZHU_CMV_24_HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_24_HR_UP.html Up-regulated at 24 h following infection of primary human foreskin fibroblasts with CMV 9826724 92/221 John Newman 0.0839184282471183 0.0965721401684667 2505 3557.81818181818 3785 0.00793650793650794 2098 1.17793264609607 1.18442626715518 1 0.437088250311161 2502 4132 3537 3131 4356 3803 2098 4077 3633 4082 3785 4137 M1731 GAVIN_FOXP3_TARGETS_CLUSTER_T7 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_T7.html Cluster T7 of genes with similar expression profiles in thymic T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 72/151 Jessica Robertson 0.0839184282471183 0.0965721401684667 4075 3777.27272727273 3786 0.00793650793650794 2956 1.00243551266338 -0.923863052528699 -1 0.371967603934414 4071 3502 3624 4258 3786 3355 2956 4552 3470 4121 3855 4138 M17309 GALI_TP53_TARGETS_APOPTOTIC_DN http://www.broadinstitute.org/gsea/msigdb/cards/GALI_TP53_TARGETS_APOPTOTIC_DN.html Apoptosis genes down-regulated by TP53 [GeneID=7157] in HCT116 cells (colon cancer) treated with thymoquinone [PubChem=10281]. 18632613 9/13 Jessica Robertson 5.63640893847396e-06 1.59109712564391e-05 4375 3383.27272727273 3786 5.63642323462257e-07 1511 1.43565538257413 -1.15082268762976 -1 2.51800826249542 4375 3194 4476 2782 1511 3881 3849 3786 2766 2582 4014 4139 M18260 HEIDENBLAD_AMPLICON_8Q24_UP http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLICON_8Q24_UP.html Up-regulated genes whose expression is associated with amplification of the 8q24 chromosome region in pancreatic cancer cell lines. 15688027 26/65 Arthur Liberzon 4.66678597293799e-06 1.37126688371108e-05 4375 3300.63636363636 3787 4.24254170223949e-07 1402 1.10698139635913 -1.19471928393032 -1 1.96767309680064 4371 1836 2890 1834 1402 4255 3787 4506 3262 3812 4352 4140 M19735 CHANG_POU5F1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_POU5F1_TARGETS_DN.html Genes down-regulated by POU5F1 [GeneID=5460] in bladder cancer cell lines. 18676852 5/9 Jessica Robertson 0.00618634822442365 0.00868200891873292 3185 3869.27272727273 3787 0.000620363791127166 3184 0.767209070431772 0.767209070431772 1 0.578084051675119 3787 3661 4370 4058 3184 3184 3548 4567 4152 4567 3484 4141 M82 PID_RET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RET_PATHWAY.html Signaling events regulated by Ret tyrosine kinase 18832364 28/63 Pathway Interaction Database 0.0839184282471183 0.0965721401684667 3385 3855 3788 0.00793650793650794 3384 0.868273252399874 -0.945133350001948 -1 0.322184835767 3384 4452 3489 3612 4459 3870 3788 3410 3696 4041 4204 4142 M13148 CHEN_HOXA5_TARGETS_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_HOXA5_TARGETS_6HR_DN.html Genes down-regulated 6 h after induction of HoxA5 [GeneID=3205] expression in a breast cancer cell line. 15757903 5/14 Arthur Liberzon 0.283409517838358 0.312263578789218 2765 3840.54545454545 3789 0.0327759124858957 2762 0.964626333722432 0.964626333722432 1 0.178230157845777 2762 4210 4503 4375 3789 3061 3369 3695 4381 4610 3491 4143 M9746 SU_TESTIS http://www.broadinstitute.org/gsea/msigdb/cards/SU_TESTIS.html Genes up-regulated specifically in human testis tissue. 11904358 41/176 John Newman 2.96627126485851e-06 9.74750851832185e-06 3790 3646.18181818182 3790 2.69661387664072e-07 1214 1.27254683870825 -1.03154944809151 -1 2.33091613862496 3790 3923 3047 4368 1214 4639 4287 3752 3095 3519 4474 4144 M865 REACTOME_RNA_POL_II_PRE_TRANSCRIPTION_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_II_PRE_TRANSCRIPTION_EVENTS.html Genes involved in RNA Polymerase II Pre-transcription Events 33/69 Reactome 0.795262495417409 0.829215612535644 3110 3764.36363636364 3791 0.134271764137992 2741 0.74879288803231 0.710136518372086 1 0.0222610275023014 3109 4590 3723 4596 4010 2845 2741 3791 4351 4412 3240 4145 M12972 MATHEW_FANCONI_ANEMIA_GENES http://www.broadinstitute.org/gsea/msigdb/cards/MATHEW_FANCONI_ANEMIA_GENES.html Genes identified with the Fanconi anemia (FA) and the FA pathway. 16998502 7/11 Arthur Liberzon 0.798408458127762 0.831594139761435 2530 3758.45454545455 3791 0.147985019760266 2527 0.527065563706588 -0.527065563706588 -1 0.0154295917275283 2527 3791 4210 4508 4428 3248 3185 3253 4563 4504 3126 4146 M1453 NADLER_HYPERGLYCEMIA_AT_OBESITY http://www.broadinstitute.org/gsea/msigdb/cards/NADLER_HYPERGLYCEMIA_AT_OBESITY.html Genes correlated with the development of hyperglycemia in obese mice. 11027337 34/86 Kevin Vogelsang 0.000239957162879409 0.000410829106778558 4600 3709.72727272727 3791 2.18166672135799e-05 2609 1.10128066453982 -1.05262861901702 -1 1.36316262559188 4599 4583 3384 4092 2609 2818 3259 4360 3444 3791 3868 4147 M1831 MATZUK_SPERMATOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_SPERMATOCYTE.html Genes important for spermatocyte, based on mouse models with male reproductive defects. 18989307 55/225 Jessica Robertson 0.0839184282471183 0.0965721401684667 3205 3789.09090909091 3792 0.00793650793650794 3133 1.04629908009503 -0.800724944518883 -1 0.388243789235383 3205 4376 3511 4024 4554 3462 3133 3792 3677 3994 3952 4148 M3042 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_KERATAN_SULFATE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_KERATAN_SULFATE.html Glycosaminoglycan biosynthesis - keratan sulfate 8/15 KEGG 0.000320222332325015 0.000535131451351787 4065 3439.18181818182 3793 3.20268485739501e-05 2387 1.72150251672971 -1.4966207182888 -1 2.0586337267321 4061 2458 3793 3690 2697 4436 3843 3928 2663 2387 3875 4149 M1868 MIKI_COEXPRESSED_WITH_CYP19A1 http://www.broadinstitute.org/gsea/msigdb/cards/MIKI_COEXPRESSED_WITH_CYP19A1.html Nuclear receptors whose expression correlated with that of aromatase (CYP19A1) [GeneID=1588] in a panel of breast cancer biopsies. 17440110 5/9 Jessica Robertson 0.32115702407422 0.351786305472602 3255 3536.09090909091 3794 0.0379958780948218 1998 0.617946635740603 -0.617946635740603 -1 0.102484730578397 3252 3794 4516 4292 4371 1998 2379 2551 4285 4617 2842 4150 M1371 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX3 http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX3.html Early prostate development genes (up-regulated at 6 hr dihydrotestosterone [PubChem=10635]) which are also up-regulated in lower grade vs higher grade locally invasive prostate cancers. 18794802 3/12 Jessica Robertson 0.359312159962296 0.391142014809659 3800 3846.45454545455 3796 0.0435447658957987 2595 0.381956309982055 -0.457497694703761 -1 0.0569163339574173 3796 3497 4333 4291 4325 3506 3761 2595 4217 4552 3438 4151 M712 REACTOME_MICRORNA_MIRNA_BIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MICRORNA_MIRNA_BIOGENESIS.html Genes involved in MicroRNA (miRNA) Biogenesis 10/27 Reactome 0.951984457238593 0.974229999261858 3440 3900.63636363636 3797 0.241202970546165 3269 0.168787778562545 -0.164723305711463 -1 0.00069954360583534 3437 4240 3571 4486 4203 3269 3510 3797 4632 4344 3418 4152 M8535 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GANGLIO_SERIES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GANGLIO_SERIES.html Glycosphingolipid biosynthesis - ganglio series 5/16 KEGG 0.0765897756730953 0.0944224385172651 4265 3380.09090909091 3798 0.00793650793650794 1843 1.84955840494846 -1.52785069628539 -1 0.692913936136116 4264 3105 3798 2826 3964 4198 4168 4103 1843 1856 3056 4153 M1743 MARSON_BOUND_BY_FOXP3_UNSTIMULATED http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_BOUND_BY_FOXP3_UNSTIMULATED.html Genes with promoters bound by FOXP3 [GeneID=50943] in unstimulated hybridoma cells. 17237765 830/1812 Jessica Robertson 1.55766304998777e-06 6.28159126699027e-06 3800 3703.18181818182 3798 1.55766414183023e-07 947 1.24458040579449 1.36157609034038 1 2.36650126324873 3798 4613 4440 4538 947 3692 3418 3644 3256 4193 4196 4154 M5244 KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM.html Glyoxylate and dicarboxylate metabolism 8/18 KEGG 0.093241225875967 0.106906871655195 4110 3803.54545454545 3799 0.00974013702241383 2826 1.28946856674414 -0.867029780836157 -1 0.457663970967936 4108 2826 3799 4212 3593 4114 4332 4250 3765 3290 3550 4155 M4072 REACTOME_OLFACTORY_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OLFACTORY_SIGNALING_PATHWAY.html Genes involved in Olfactory Signaling Pathway 16/764 Reactome 0.514011397665828 0.550424453716195 3145 3680.09090909091 3799 0.0634920634920635 2789 1.17302356200135 1.17302356200135 1 0.111181445122969 3145 4194 2789 4582 3943 3499 3040 3433 4111 3799 3946 4156 M194 BIOCARTA_PROTEASOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PROTEASOME_PATHWAY.html Proteasome Complex 22/35 BioCarta 0.49851924531325 0.534935008824797 2975 3650.90909090909 3800 0.0608166423762381 1909 0.21211799048364 -0.248316627017514 -1 0.0210661282473221 2974 4152 3684 4265 4582 2626 1909 3800 4398 4280 3490 4157 M14897 REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN.html Genes involved in Regulation of Glucokinase by Glucokinase Regulatory Protein 16/32 Reactome 0.0839184282471183 0.0965721401684667 3540 3861.09090909091 3800 0.00793650793650794 2799 1.54668507782595 -1.54668507782595 -1 0.573918956531547 3537 4400 3168 4587 4544 4121 4466 2799 3509 3800 3541 4158 M4648 ZEMBUTSU_SENSITIVITY_TO_NIMUSTINE http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_NIMUSTINE.html Top genes associated with chemosensitivity to nimustine [PubChem=39214] across 85 tumor xenografts. 11809704 8/30 Arthur Liberzon 0.147859119791321 0.167157499479404 4155 3840.63636363636 3800 0.0158730158730159 2411 1.93814972080921 -2.21687155405543 -1 0.550373144260151 4152 3557 4613 3979 3765 3985 3800 3794 3755 2411 4436 4159 M18086 DAIRKEE_CANCER_PRONE_RESPONSE_BPA_E2 http://www.broadinstitute.org/gsea/msigdb/cards/DAIRKEE_CANCER_PRONE_RESPONSE_BPA_E2.html 'Cancer prone response profile' (CPRP): genes common to estradiol and bisphenol A [PubChem=5757;6623] response of epithelial cell cultures from patients at high risk of breast cancer. 18381411 89/217 Jessica Robertson 0.0430488659070091 0.0548320156673673 3590 3797.54545454545 3801 0.00399227780221967 2513 1.51501250061208 1.87547286290486 1 0.698294738462556 3590 4260 3081 3801 3468 4642 4505 4273 2513 3690 3950 4160 M4781 PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_DN.html Down-regulated genes in angioimmunoblastic lymphoma (AILT) compared to normal T lymphocytes. 18006812 97/221 Arthur Liberzon 0.000405796703585293 0.000667215211579187 3805 3823.36363636364 3802 3.68974157598564e-05 2727 1.30571684757336 1.30931700258551 1 1.51569697888602 3802 4563 3386 3880 2727 4664 3669 3807 3339 3704 4516 4161 M12243 SCHUHMACHER_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHUHMACHER_MYC_TARGETS_UP.html Genes up-regulated in P493-6 cells (Burkitt's lymphoma) induced to express MYC [GeneID=4609]. 11139609 61/115 Yujin Hoshida 8.1132293753027e-06 2.12396737148495e-05 4560 3731.90909090909 3802 7.37569026880029e-07 1618 0.911565727722269 -0.947822320800022 -1 1.55700239151846 4557 2836 3589 3802 1618 3800 4398 4533 3670 3967 4281 4162 M1158 CROSBY_E2F4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CROSBY_E2F4_TARGETS.html Putative E2F4 [GeneID=1874] target genes identified as mitotic genes down-regulated in the LNCaP C4-2 cells (prostate cancer) at both 6 and 24 h following irradiation. 17043659 6/10 Leona Saunders 0.984615780328036 0.997736449858204 2670 3861.18181818182 3804 0.341269841269841 2667 0.569236511420671 0.569236511420671 1 0.000204773902446005 2667 3438 4195 3792 4595 3401 3832 3776 4476 4497 3804 4163 M151 PID_AR_TF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AR_TF_PATHWAY.html Regulation of Androgen receptor activity 18832364 43/92 Pathway Interaction Database 0.000674840961313117 0.00107015388991989 4215 3778.63636363636 3805 6.13680049950952e-05 2828 1.17871183734101 -1.4009454029317 -1 1.27986544082037 4211 3888 2979 3602 2828 4479 3650 4396 3516 3805 4211 4164 M16929 REACTOME_PI3K_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_CASCADE.html Genes involved in PI3K Cascade 33/105 Reactome 0.0839184282471183 0.0965721401684667 3095 3782.81818181818 3806 0.00793650793650794 2824 0.968597908790672 0.801400996559551 1 0.359411691521882 3092 4270 3356 3806 4583 3552 2824 4428 3683 3962 4055 4165 M14796 MAYBURD_RESPONSE_TO_L663536_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAYBURD_RESPONSE_TO_L663536_DN.html Genes down-regulated in H720 cells (lung cancer) after treatment with L663536 (MK886) [PubChem=105049], an inhibitor of leukotriene biosynthesis. 16551867 48/107 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4525 3618.72727272727 3807 0.00793650793650794 1365 2.07136513832849 -1.40921979621272 -1 0.768608772898387 4524 4183 2612 3373 4187 4074 4612 3558 1365 3511 3807 4166 M138 PID_THROMBIN_PAR4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_THROMBIN_PAR4_PATHWAY.html PAR4-mediated thrombin signaling events 18832364 12/29 Pathway Interaction Database 0.161385165508919 0.18131164842359 4410 3847.09090909091 3808 0.0158730158730159 2327 2.49872111272945 -2.49872111272945 -1 0.677316573405236 4409 3808 2327 3599 4245 4492 4679 3397 3784 3613 3965 4167 M1157 KONG_E2F3_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KONG_E2F3_TARGETS.html Genes up-regulated in MEF cells (embryonic fibroblasts) at 16 hr after serum stimulation and knockdown of E2F3 [GeneID=1871] by RNAi. 16909124 74/175 Arthur Liberzon 0.909848641179835 0.936716520211616 1865 3645.72727272727 3808 0.196478540764276 1863 1.05264800508063 -0.997530073303439 -1 0.0109243495855804 1863 4502 2163 3442 4540 3501 3808 4061 4451 4132 3640 4168 M1353 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX1_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX1_UP.html Early prostate development genes (up-regulated at 6 h dihydrotestosterone [PubChem=10635]) which are also up-regulated in normal epithelium vs high grade prostatic intraepithelial neoplasia (PIN). 18794802 12/30 Jessica Robertson 0.000241453754798507 0.000413240429140176 4265 3765.72727272727 3809 2.19527508029717e-05 2483 0.611960564543746 -0.474464392839445 -1 0.756914826689272 4262 2483 3313 3777 2610 4186 3483 4481 3809 4548 4471 4169 M10994 BIOCARTA_SRCRPTP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SRCRPTP_PATHWAY.html Activation of Src by Protein-tyrosine phosphatase alpha 9/18 BioCarta 0.559703729706801 0.596491170663195 3175 3726.36363636364 3810 0.0787563641850154 2868 0.754639173726346 0.754639173726346 1 0.0618975781930851 3174 4291 3810 4249 4024 3171 3257 2868 4530 4260 3356 4170 M8801 NICK_RESPONSE_TO_PROC_TREATMENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/NICK_RESPONSE_TO_PROC_TREATMENT_DN.html Genes down-regulated in neutrophils upon treatment with activated protein C (PROC) [GeneID=5624] of pulmonary inflammation induced by bacterial lipopolysaccharide (LPS). 15339848 21/68 Arthur Liberzon 0.342174872627849 0.373586079481385 3520 3719.18181818182 3810 0.0373584851076316 2374 0.782482083390574 -0.683331254262175 -1 0.122304040121161 3517 4235 3527 4384 3810 2374 4387 3666 4168 3943 2900 4171 M5467 BIOCARTA_GRANULOCYTES_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GRANULOCYTES_PATHWAY.html Adhesion and Diapedesis of Granulocytes 7/21 BioCarta 4.74941251407492e-05 9.57236431869035e-05 4390 3360.09090909091 3811 4.74951402326481e-06 1320 2.00637776324548 -2.83367012658679 -1 2.9474597664891 4390 1320 3811 2507 2218 4625 3557 4174 3984 2255 4120 4172 M5570 HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_DN.html Genes down-regulated in lesional skin biopsies from mycosis fundoides patients compared to the normal skin samples. 16914566 15/50 Arthur Liberzon 0.161385165508919 0.18131164842359 4510 3459.54545454545 3811 0.0158730158730159 1994 1.42801045928177 -1.74406924037379 -1 0.387084074415651 4508 4108 2472 4063 3976 4511 1994 2773 3811 3257 2582 4173 M14151 DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP http://www.broadinstitute.org/gsea/msigdb/cards/DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP.html Genes up-regulated in HEK293 cells (embryonic kidney) at 6 h, 12 h or 24 h after infection with reovirus strain T3A (known as a strong inducer of apoptosis). 12885910 218/530 John Newman 0.0277613209174197 0.0359860442099665 3975 3845.45454545455 3811 0.00255617740532172 2983 1.21360019516185 -1.14758215943255 -1 0.640503849121424 3975 4623 3666 4278 3409 2983 3753 3958 3679 4165 3811 4174 M6752 TENEDINI_MEGAKARYOCYTE_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/TENEDINI_MEGAKARYOCYTE_MARKERS.html Genes essential to the development of megakaryocytes, as expressed in normal cells and essential thrombocythemic cells (ET). 15271793 43/96 Kate Stafford 0.311450798260223 0.341473664166449 3640 3782.90909090909 3812 0.0333554286828031 2502 1.39939352387255 -1.0476729633867 -1 0.23869518734631 3637 4381 2584 3745 3812 4659 4211 2502 4070 3591 4420 4175 M2168 FIGUEROA_AML_METHYLATION_CLUSTER_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_3_UP.html Cluster 3 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 113/343 Arthur Liberzon 2.66051206532531e-05 5.79598304886769e-05 3875 3509.45454545455 3812 2.41867658188372e-06 2008 1.32372603795942 1.54322506160951 1 2.0500421815457 3593 3878 3273 3875 2008 3871 4119 3057 3173 3945 3812 4176 M19016 GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN.html Genes down-regulated in erythroid progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 362/930 Arthur Liberzon 1.08477854431623e-05 2.68956204162215e-05 4260 3305.90909090909 3813 9.86167175628862e-07 1540 1.5281638195289 -1.29502815812324 -1 2.55291070102625 4258 4483 3287 3891 1717 1540 3819 4065 2800 3813 2692 4177 M6387 WINNEPENNINCKX_MELANOMA_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WINNEPENNINCKX_MELANOMA_METASTASIS_UP.html Genes from the 254-gene classifier which were up-regulated in melanoma patients with a reported distant metastasis within 4 years. 16595783 121/263 Arthur Liberzon 0.161385165508919 0.18131164842359 1965 3672.18181818182 3813 0.0158730158730159 1961 1.40529148470897 1.66857690090982 1 0.380925748874092 1961 4494 2712 3683 4629 3981 3648 3594 3818 4061 3813 4178 M11592 MAHADEVAN_RESPONSE_TO_MP470_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAHADEVAN_RESPONSE_TO_MP470_UP.html Top genes up-regulated in the GIST (gastrointestinal stromal tumor) cell line resistant to imatinib [PubChem=5291] after treatment with MP470, a protein kinase inhibitor. 17325667 11/29 Arthur Liberzon 0.000389792279534415 0.000643157261231785 4210 3359.90909090909 3814 3.54419417642875e-05 1517 1.76390517525185 -1.57895655856017 -1 2.05785234946677 4210 3857 1969 3203 2719 4195 4258 3814 2762 1517 4455 4179 M12942 MAINA_VHL_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAINA_VHL_TARGETS_UP.html Genes up-regulated in RCC4 cells (renal cell carcinoma) engineered to stably express VHL [GeneID=7428] off a plasmid vector. 15824735 6/18 Leona Saunders 0.0765897756730953 0.0944224385172651 3830 3606.27272727273 3815 0.00793650793650794 1849 1.45870599758865 -2.34985618113092 -1 0.546485967162738 3826 1849 4274 3630 3815 3898 3020 4661 3303 3055 4338 4180 M1701 HOWLIN_CITED1_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOWLIN_CITED1_TARGETS_1_UP.html Genes up-regulated in mammary glands from the CITED1 [GeneID=4435] knockout mice: homozygotic vs. heterozygotic animals. 16278680 25/50 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4600 3784.63636363636 3815 0.00793650793650794 2283 1.54520467329616 1.42281991025163 1 0.573369631890207 4598 3771 2283 4127 3724 3815 4098 4279 3503 3437 3996 4181 M19283 REACTOME_METABOLISM_OF_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_MRNA.html Genes involved in Metabolism of mRNA 155/349 Reactome 0.232850105696956 0.258012673278774 2725 3420.36363636364 3817 0.0238095238095238 1728 1.14124427301244 -0.931111401163259 -1 0.245437111591184 2725 4428 3774 3817 4531 1728 1932 3854 3909 4236 2690 4182 M16584 LIU_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LIU_BREAST_CANCER.html Low abundance transcripts specific for breast cancer. 18332864 20/57 Jessica Robertson 0.161385165508919 0.18131164842359 4055 3702.72727272727 3817 0.0158730158730159 2509 1.04618050748156 -1.15869630884985 -1 0.28358322594346 4053 3711 2842 3365 4248 3539 4508 4213 3817 3925 2509 4183 M8525 KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_DN.html Genes down-regulated in HL-60 cells (acute promyelocytic leukemia, APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 24 h. 18701491 616/1371 Jessica Robertson 1.7377724952663e-06 6.74664615809268e-06 3820 3473.45454545455 3817 1.73777385420175e-07 1002 1.33049807226524 -1.09480095750931 -1 2.51478379106345 3817 4169 4424 4408 1002 2474 3278 4353 2502 4106 3675 4184 M16154 NICK_RESPONSE_TO_PROC_TREATMENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/NICK_RESPONSE_TO_PROC_TREATMENT_UP.html Genes up-regulated in neutrophils upon treatment with activated protein C (PROC) [GeneID=5624] of pulmonary inflammation induced by bacterial lipopolysaccharide (LPS). 15339848 4/6 Arthur Liberzon 0.358781804477507 0.390988729251534 3350 3532.18181818182 3817 0.0434656208911825 2125 0.172941021499642 -0.327744152254314 -1 0.0257811653884128 3349 3817 4532 3917 4250 2244 2125 3165 4325 4624 2506 4185 M7738 PYEON_HPV_POSITIVE_TUMORS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PYEON_HPV_POSITIVE_TUMORS_UP.html Up-regulated genes in cervical carcinoma and head and neck tumors positive for human papilloma virus (HPV) compared to those negative for HPV. 17510386 44/125 Arthur Liberzon 0.466738071388703 0.50186659075894 3680 3835.63636363636 3820 0.0555555555555556 3226 1.02798954016306 -1.03525590532645 -1 0.1125062702166 3676 4324 3302 4399 4427 3226 3575 3941 4087 3820 3415 4186 M12002 MAYBURD_RESPONSE_TO_L663536_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAYBURD_RESPONSE_TO_L663536_UP.html Genes up-regulated in H720 cells (lung cancer) after treatment with L663536 (MK886) [PubChem=105049], an inhibitor of leukotriene biosynthesis. 16551867 19/42 Arthur Liberzon 0.357596461540877 0.389878319865182 3575 3806.54545454545 3820 0.0394322687115057 2673 1.31704079454117 -1.39076995187711 -1 0.196932355327746 4110 3574 2673 4469 3820 4503 3572 2852 4101 3530 4668 4187 M1172 IWANAGA_E2F1_TARGETS_INDUCED_BY_SERUM http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_E2F1_TARGETS_INDUCED_BY_SERUM.html Genes up-regulated in REF52 cells (embryonic fibroblast) by expression of E2F1 [GeneID=1869] that were also induced at 16 hr after serum stimulation. 16288221 14/37 Arthur Liberzon 0.698152987361708 0.734848360012795 2965 3829.90909090909 3820 0.103174603174603 2964 1.0317175520583 1.0317175520583 1 0.0504595691493037 2964 4080 3010 4509 4442 3690 3820 3939 4210 3725 3740 4188 M1272 WANG_RESPONSE_TO_PACLITAXEL_VIA_MAPK8_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_PACLITAXEL_VIA_MAPK8_DN.html Genes specifically down-regulated via JNK (MAPK8) [GeneID=5599] signaling pathway activated by paclitaxel [PubChem=4666] in BR cells (ovarian cancer). 16547493 2/5 Arthur Liberzon 0.55063552393403 0.588432854083207 3710 3786.5 3821.5 0.085044736963889 2733 0.294703377262048 -0.516463611109392 -1 0.0248087048173222 3708 3530 4290 NA 3935 2733 3254 4211 4547 4538 3119 4189 M17541 REACTOME_REGULATION_OF_BETA_CELL_DEVELOPMENT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_BETA_CELL_DEVELOPMENT.html Genes involved in Regulation of beta-cell development 7/32 Reactome 0.333635069996361 0.364857395099871 3205 3725.54545454545 3823 0.0397789701132477 2136 0.758479313772085 0.758479313772085 1 0.121398960184263 3204 4535 3984 4585 3823 3106 2136 3512 4514 4357 3225 4190 M17860 TAKAO_RESPONSE_TO_UVB_RADIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKAO_RESPONSE_TO_UVB_RADIATION_DN.html Genes down-regulated in primary tissue culture of epidermal kerationcytes after UVB irradiation. 11982916 65/173 John Newman 0.0839184282471183 0.0965721401684667 4430 3888.27272727273 3823 0.00793650793650794 3183 1.19660761468167 -0.819409605646687 -1 0.444017856519383 4427 4572 3183 3744 3946 3386 3688 4327 3669 4006 3823 4191 M934 REACTOME_DESTABILIZATION_OF_MRNA_BY_BRF1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DESTABILIZATION_OF_MRNA_BY_BRF1.html Genes involved in Destabilization of mRNA by Butyrate Response Factor 1 (BRF1) 14/22 Reactome 0.0839184282471183 0.0965721401684667 4180 3753.90909090909 3825 0.00793650793650794 2278 1.29732819593571 0.728133715135702 1 0.481391625688214 4176 4402 3357 2807 4275 4640 3596 3825 2278 3722 4215 4192 M14665 SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP http://www.broadinstitute.org/gsea/msigdb/cards/SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP.html Genes up-regulated in lymphoblastoid cells from the European population compared to those from the Asian population. 17206142 373/882 Leona Saunders 1.89858033594684e-05 4.3251081449912e-05 4295 3692.36363636364 3825 1.72599701883946e-06 1908 1.23523409555137 -0.915041277548697 -1 1.9703962139695 4293 4248 3727 4206 1908 2858 3817 4448 3065 4221 3825 4193 M8813 SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN.html Top 50 down-regulated markers distinguishing diffuse large B-cell lymphoma (DLBCL) from follicular lymphoma (FL) samples. 11786909 46/124 Jean Junior 0.0839184282471183 0.0965721401684667 3955 3392.36363636364 3825 0.00793650793650794 1543 1.98496984758089 2.09034354181974 1 0.736550601534871 3952 4504 1543 2677 3825 3885 4634 2791 3324 2019 4162 4194 M810 REACTOME_ELONGATION_ARREST_AND_RECOVERY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ELONGATION_ARREST_AND_RECOVERY.html Genes involved in Elongation arrest and recovery 17/37 Reactome 0.578951381542626 0.616163110131444 3620 3765.45454545455 3827 0.0756245855444399 2645 0.852049796352599 0.852049796352599 1 0.0654986549921963 3616 4461 3631 4564 3921 2990 2645 3827 4269 4396 3100 4195 M508 REACTOME_SIGNALING_BY_SCF_KIT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_SCF_KIT.html Genes involved in Signaling by SCF-KIT 47/107 Reactome 0.0839184282471183 0.0965721401684667 3830 3707.18181818182 3828 0.00793650793650794 2680 1.00127993842077 1.0330470718709 1 0.371538812078143 3828 3886 3466 2680 3931 4357 2910 3431 3641 4008 4641 4196 M15371 BIOCARTA_ETC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ETC_PATHWAY.html Electron Transport Reaction in Mitochondria 6/16 BioCarta 0.892924910838528 0.921437157496001 2590 3678.81818181818 3830 0.200223121650696 2586 0.148179158412708 0.205355537286577 1 0.00192465756678822 2586 4242 3830 3929 4369 2979 3098 3357 4509 4268 3300 4197 M3548 REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY.html Genes involved in NEP/NS2 Interacts with the Cellular Export Machinery 17/34 Reactome 0.0839184282471183 0.0965721401684667 3570 3895.54545454545 3831 0.00793650793650794 2815 1.54668507782595 -1.54668507782595 -1 0.573918956531547 3567 4526 3264 4591 4617 4091 4480 2815 3515 3831 3554 4198 M7357 LEE_EARLY_T_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_EARLY_T_LYMPHOCYTE_UP.html Genes up-regulated at early stages of progenitor T lymphocyte maturation compared to the late stages. 15210650 55/177 Arthur Liberzon 0.146089983289993 0.165476833864372 3545 3738.09090909091 3831 0.0142546499623682 1316 1.55973781495995 -1.15844173620249 -1 0.44541823699873 3542 3831 1316 2948 4666 4650 4305 4079 3810 3516 4456 4199 M18184 REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS.html Genes involved in Transport of Ribonucleoproteins into the Host Nucleus 17/33 Reactome 0.0839184282471183 0.0965721401684667 3775 3951.72727272727 3832 0.00793650793650794 2997 1.54668507782595 -1.54668507782595 -1 0.573918956531547 3771 4525 3236 4589 4543 4338 4363 2997 3539 3832 3736 4200 M1177 KOINUMA_COLON_CANCER_MSI_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOINUMA_COLON_CANCER_MSI_DN.html Genes down-regulated in colorectal carcinoma samples positive for MSI (microsatellite instability) compared to the MSI negative ones. 16247484 6/12 Arthur Liberzon 0.0158958809180461 0.0211854658651775 3140 3605.18181818182 3832 0.00160107445580578 1621 0.919310432764863 0.919310432764863 1 0.562505830241627 3137 3436 4163 3912 4682 3832 3032 1621 4077 4487 3278 4201 M1654 SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_DN.html Genes down-regulated in 3T3-L1 cells (adipocyte) by insulin [GeneID=3630] which continued to respond normally to insulin in the insulin resistant cells. 14530283 13/28 John Newman 0.161385165508919 0.18131164842359 4480 3829.90909090909 3833 0.0158730158730159 2899 1.09137119673266 1.13493905584388 1 0.295832853450365 4476 2899 2925 4465 3833 3592 3878 4583 3819 3086 4573 4202 M3845 GALE_APL_WITH_FLT3_MUTATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/GALE_APL_WITH_FLT3_MUTATED_UP.html Genes up-regulated in acute promyelocytic leukemia (APL) patients with mutated FLT3 [GeneID=2322]. 16105978 40/92 Kevin Vogelsang 0.344199161927256 0.375708658931078 4650 3975.54545454545 3834 0.0376281610825745 3445 0.943041164816152 1.05850066402349 1 0.146551696103716 4646 3834 3468 4487 3813 3984 3729 4482 4165 3445 3678 4203 M262 AMUNDSON_RESPONSE_TO_ARSENITE http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_RESPONSE_TO_ARSENITE.html Genes discriminating responses to sodium arsenite [PubChem=26435] from other stresses. 15824734 157/376 Arthur Liberzon 2.54561208609736e-05 5.58200198196173e-05 4680 3577.27272727273 3835 2.31421958341854e-06 1576 1.23648175462878 1.47112360306581 1 1.92231161597857 4680 3986 3498 3671 1992 1576 4621 3835 3456 3949 4086 4204 M14648 CAFFAREL_RESPONSE_TO_THC_8HR_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_8HR_3_DN.html Genes down-regulated in EVSA-T cells (breast cancer) treated with 3 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 8 h. 18454173 17/40 Jessica Robertson 0.0100753721007271 0.0138090651254774 2150 3136.18181818182 3835 0.000920164769142429 615 1.35448193627119 1.35448193627119 1 0.920803692849098 2147 4280 3383 4254 4053 1824 615 3988 4337 3835 1782 4205 M11563 KAUFFMANN_DNA_REPAIR_GENES http://www.broadinstitute.org/gsea/msigdb/cards/KAUFFMANN_DNA_REPAIR_GENES.html Genes involved in DNA repair, compiled manually by the authors. 17891185 144/260 Jessica Robertson 0.0839184282471183 0.0965721401684667 3130 3911.27272727273 3835 0.00793650793650794 3127 0.950347712981906 -0.718100176770988 -1 0.352639703146215 3127 4559 3721 4499 4215 3417 3835 4143 3698 4227 3583 4206 M1952 MEISSNER_BRAIN_HCP_WITH_H3K4ME2 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_HCP_WITH_H3K4ME2.html Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation mark (H3K4me2) in brain. 18600261 5/29 Arthur Liberzon 0.0146683897586183 0.0196782348722833 4360 3758.45454545455 3836 0.00147661216625409 1756 0.824278998312121 -0.824278998312121 -1 0.514015291361353 4360 1756 4572 2737 3323 4439 4484 3492 3836 4639 3705 4207 M6231 BIOCARTA_NO2IL12_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NO2IL12_PATHWAY.html NO2-dependent IL 12 Pathway in NK cells 5/23 BioCarta 0.341070750141018 0.372641066719704 4030 3761.81818181818 3837 0.0408558580957633 2851 1.43277247975609 1.43277247975609 1 0.224522241061039 4030 2851 3850 3644 3828 4641 3837 3305 4287 2883 4224 4208 M12605 CHEOK_RESPONSE_TO_MERCAPTOPURINE_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_DN.html Genes specifically down-regulated in pediadric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490]. 12704389 11/25 Jean Junior 0.0839184282471183 0.0965721401684667 3840 3767 3840 0.00793650793650794 2782 1.20993540766736 1.57776914341181 1 0.448963319029381 3840 3942 2782 4505 3736 4157 3712 4323 3629 2833 3978 4209 M11629 MONTERO_THYROID_CANCER_POOR_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/MONTERO_THYROID_CANCER_POOR_SURVIVAL_UP.html Up-regulated genes predicting poor survival of patients with thyroid carcinoma. 17873908 7/14 Arthur Liberzon 0.959899380041551 0.9804028977495 2940 3728.72727272727 3840 0.275038224124613 2937 0.743402933014126 -0.684163046089497 -1 0.00233566189408005 2938 2959 4570 2937 4157 3421 3057 3998 4502 4637 3840 4210 M18501 DANG_REGULATED_BY_MYC_UP http://www.broadinstitute.org/gsea/msigdb/cards/DANG_REGULATED_BY_MYC_UP.html Genes up-regulated by MYC [GeneID=4609], according to the MYC Target Gene Database. 14519204 58/109 Chi Dang 0.0839184282471183 0.0965721401684667 3770 3887.27272727273 3840 0.00793650793650794 2381 1.35969941078349 1.78800330023918 1 0.504535330355894 3767 4373 3063 4190 3840 4551 4456 3798 2381 3792 4549 4211 M1180 OHASHI_AURKA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/OHASHI_AURKA_TARGETS.html Candidate substrate proteins of AURKA [GeneID=6790]. 16785988 2/8 Arthur Liberzon 0.893507331299124 0.921799119856477 2970 3711.3 3840.5 0.220305604869966 2820 0.417565949485973 0.417565949485973 1 0.00539761636818714 2966 3260 4241 NA 4104 3014 2820 4024 4505 4522 3657 4212 M628 REACTOME_DOWNREGULATION_OF_TGF_BETA_RECEPTOR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNREGULATION_OF_TGF_BETA_RECEPTOR_SIGNALING.html Genes involved in Downregulation of TGF-beta receptor signaling 14/31 Reactome 0.253300068237906 0.279944367868591 3145 3882.72727272727 3841 0.0262043541827116 3141 0.789722803877716 0.789722803877716 1 0.159610962327948 3141 4284 3442 4485 3756 4269 3450 3470 4240 4332 3841 4213 M8406 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_21 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_21.html Amplification hot spot 21: colocolized fragile sites and cancer genes in the 12q13-q21 region. 16751803 3/10 Arthur Liberzon 0.199339822025045 0.222671372111885 4650 3690.36363636364 3844 0.0219865602004738 2371 1.02225042359124 -1.02225042359124 -1 0.243751690521106 4648 3224 4228 3524 4168 3844 3532 2371 4161 2457 4437 4214 M9291 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_16 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_16.html Amplification hot spot 16: colocolized fragile sites and cancer genes in the 8q11.1-q24.3 region. 16751803 3/15 Arthur Liberzon 0.785941684398692 0.819884847081984 3660 3882.81818181818 3845 0.142857142857143 3164 0.544925320904729 -0.133563370895195 -1 0.0171791193373576 3660 3873 4224 3845 4182 3828 3349 3164 4275 4513 3798 4215 M1256 INAMURA_LUNG_CANCER_SCC_SUBTYPES_UP http://www.broadinstitute.org/gsea/msigdb/cards/INAMURA_LUNG_CANCER_SCC_SUBTYPES_UP.html Up-regulated genes discriminating between two subtypes of squamous cell carcinoma (SCC) type of non-small cell lung cancer: SSC-A vs SSC-B. 16007138 9/17 Arthur Liberzon 0.435369722646862 0.469537979360919 4280 3711.18181818182 3848 0.0555555555555556 2450 1.2876396622878 -1.11502078858096 -1 0.154533697700522 3848 3489 4277 4234 4478 3740 2450 3387 4065 2577 4278 4216 M2558 HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_UP.html Genes distinguishing prednisolone [PubChem=5755] resistant and sensitive ALL (B- and T-lineage ALL); here - genes up-regulated in the drug resistant samples. 15295046 15/27 Arthur Liberzon 0.833311749085373 0.865447441536804 3850 3825.81818181818 3849 0.150302990121973 2762 0.599791225856082 -0.599791225856082 -1 0.0137593337241993 3849 4338 3521 4317 4227 2762 3106 3676 4467 4682 3139 4217 M983 REACTOME_INTERFERON_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERFERON_SIGNALING.html Genes involved in Interferon Signaling 98/246 Reactome 0.0839184282471183 0.0965721401684667 3555 3873.63636363636 3850 0.00793650793650794 3330 1.35271789434703 -1.41827914724932 -1 0.501944741813848 3554 4309 3358 3494 3934 4451 3449 4293 3330 3850 4588 4218 M4735 WANG_LMO4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_LMO4_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) engineered to conditionally express LMO4 [GeneID=8543] by a Tet Off system. 17452977 254/584 Arthur Liberzon 7.02579836666132e-07 3.81051980858506e-06 4010 3187.09090909091 3853 6.38709146398404e-08 577 1.3698692779465 -1.16047577968109 -1 2.71343105761825 4009 2730 2990 2388 577 3853 3909 4210 2137 3983 4272 4219 M17421 DACOSTA_LOW_DOSE_UV_RESPONSE_VIA_ERCC3_XPCS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_LOW_DOSE_UV_RESPONSE_VIA_ERCC3_XPCS_UP.html Genes up-regulated in fibroblasts expressing the XP/CS mutant form of ERCC3 [GeneID=2071], after low dose UVC irradiation. 15608684 18/35 Arthur Liberzon 0.869787339807015 0.900137693095334 2860 3641.09090909091 3853 0.169166635961542 2774 0.807089268139954 -0.823354058980645 -1 0.0134794422359547 2860 3853 2774 3218 4418 3164 3957 4157 4573 3877 3201 4220 M18854 PENG_RAPAMYCIN_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/PENG_RAPAMYCIN_RESPONSE_DN.html Genes down-regulated in BJUB cells (B-lymphoma) in response to rapamycin (sirolimus) [PubChem=6610346] treatment. 12101249 173/354 Broad Institute 0.0839184282471183 0.0965721401684667 3930 3938.63636363636 3853 0.00793650793650794 2991 1.04827503171036 -1.00323204144742 -1 0.388976993498508 3930 4555 3748 4574 4485 2991 3703 3853 3620 4195 3671 4221 M3977 WEBER_METHYLATED_ICP_IN_SPERM_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_ICP_IN_SPERM_UP.html Methylated germline-specific genes with intermediate-CpG-density promoters (ICP) in sperm. 17334365 7/27 Arthur Liberzon 0.214139132665174 0.238577264781028 4335 3793.45454545455 3853 0.0238095238095238 2806 1.33308548244905 -2.09693445347743 -1 0.303267978572472 4332 3435 4582 3985 4237 3578 3628 2806 3853 3214 4078 4222 M6669 HEDENFALK_BREAST_CANCER_BRACX_UP http://www.broadinstitute.org/gsea/msigdb/cards/HEDENFALK_BREAST_CANCER_BRACX_UP.html Up-regulated genes distinguishing between two groups of non-BRCA1/BRCA2 [GeneID=672;675] breast tumors (BRACx): group A vs group B. 12610208 14/33 John Newman 0.161385165508919 0.18131164842359 4315 3958.45454545455 3854 0.0158730158730159 3476 1.20444518001043 1.20444518001043 1 0.326483286068871 4314 3854 3515 4173 3967 3804 3476 4346 3764 3728 4602 4223 M16479 FLOTHO_PEDIATRIC_ALL_THERAPY_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FLOTHO_PEDIATRIC_ALL_THERAPY_RESPONSE_UP.html Up-regulated genes significantly associated with positive minimal residual disease (MRD) on day 46 after chemotherapy treatment of children with acute lymphoblastic leukemia (ALL). 16627760 30/75 Arthur Liberzon 0.410984406092562 0.445185604935216 3010 3475.36363636364 3854 0.0469790763823069 1968 0.820977950444232 -0.875019074408241 -1 0.105469106240205 3010 3996 3633 3881 3854 1968 2381 4401 4330 4067 2708 4224 M9224 SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_UP.html Selected genes up-regulated in peripheral blood monocytes (PBMC) of patients with hepatocellular carcinoma (HCC) compared to those with chronic hepatitis. 19074895 61/146 Arthur Liberzon 0.298735036746822 0.327992591892129 3090 3831.18181818182 3854 0.0317460317460317 3011 1.27294240140095 -1.32695197798049 -1 0.225265843963506 3086 4501 3369 4025 4625 3649 3011 3812 3964 3854 4247 4225 M251 PID_SYNDECAN_3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_3_PATHWAY.html Syndecan-3-mediated signaling events 18832364 8/26 Pathway Interaction Database 0.0158121199286355 0.0210798275919163 4555 3838.09090909091 3855 0.00159257701357738 3196 0.754639173726346 0.754639173726346 1 0.462345949622635 4551 3196 3906 3855 3336 3749 3710 3296 3958 4304 4358 4226 M6924 BIOCARTA_EIF2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF2_PATHWAY.html Regulation of eIF2 4/16 BioCarta 0.184764197403027 0.206784100556624 4285 3699.90909090909 3857 0.0202205541730488 2349 0.554170537432062 -0.554170537432062 -1 0.138651717372208 3888 2967 3857 3353 4479 3418 4282 2349 4177 4281 3648 4227 M10922 WANG_RECURRENT_LIVER_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RECURRENT_LIVER_CANCER_UP.html Genes up-regulated in samples from patients with recurrent hepatocellular carcinoma (HCC). 17975138 17/28 Yujin Hoshida 0.0163806365884891 0.0217881530098382 3610 3699.81818181818 3857 0.00150035357592714 2404 0.904378795632191 -0.904378795632191 -1 0.549342297281304 3609 3971 3557 3857 3328 3957 4559 2404 3894 4635 2927 4228 M19888 KEGG_ACUTE_MYELOID_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ACUTE_MYELOID_LEUKEMIA.html Acute myeloid leukemia 28/71 KEGG 6.86535308673556e-06 1.8595979517019e-05 4230 3374.09090909091 3860 6.24124955541205e-07 1549 1.09812383906526 -0.741675073486765 -1 1.89882546615112 4228 2278 2840 1762 1549 4333 4146 4106 3387 3860 4626 4229 M1926 REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS_VIA_7ALPHA_HYDROXYCHOLESTEROL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS_VIA_7ALPHA_HYDROXYCHOLESTEROL.html Genes involved in Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol 9/28 Reactome 2.43549737926157e-05 5.38336826378288e-05 4410 3471.63636363636 3860 2.43552407208698e-06 1850 1.70305236673079 2.14334357342294 1 2.65746714912776 4407 2794 3911 3341 2011 3860 4557 4209 1850 2563 4685 4230 M1645 LI_ADIPOGENESIS_BY_ACTIVATED_PPARG http://www.broadinstitute.org/gsea/msigdb/cards/LI_ADIPOGENESIS_BY_ACTIVATED_PPARG.html Adipocyte genes induced in 3T3-L1 cells (adipocyte) by constitutively active PPARG [GeneID=5468] or its agonist, TZD [PubChem=5437]. 11981038 11/22 John Newman 0.267245516976451 0.295008832167644 3065 3488.63636363636 3860 0.0278718962378203 1962 2.07493235299091 -0.569912029070816 -1 0.402100144788413 3061 3860 1962 4227 4026 3863 3343 2433 4050 3567 3983 4231 M1976 OKAMOTO_LIVER_CANCER_MULTICENTRIC_OCCURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/OKAMOTO_LIVER_CANCER_MULTICENTRIC_OCCURRENCE_DN.html Genes down-regulated in both the patients in the multicentric hepatocellular carcinoma (HCC) group and those with multicentric recurrence. 16788756 2/13 Yujin Hoshida 0.669294716995167 0.706695593474392 3840 3792.2 3860 0.115689930447971 2263 0.294307421788627 -0.576551338545617 -1 0.0162191647879909 3838 3724 4575 NA 4128 3230 2263 3118 4523 4641 3882 4232 M13104 REACTOME_VIF_MEDIATED_DEGRADATION_OF_APOBEC3G http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_VIF_MEDIATED_DEGRADATION_OF_APOBEC3G.html Genes involved in Vif-mediated degradation of APOBEC3G 32/64 Reactome 0.817244010949131 0.850267636613594 2410 3676.63636363636 3861 0.143164562854988 2410 0.779694643445633 -0.74351706699215 -1 0.0200765892871701 2410 4186 3712 4020 4598 2597 3082 3861 4345 4462 3170 4233 M2480 ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_UP.html Genes up-regulated in normal tissue adjacent to liver tumor, compared to the normal liver samples. 18413731 138/382 Jessica Robertson 0.0839184282471183 0.0965721401684667 3865 3732.45454545455 3861 0.00793650793650794 2739 1.46597976256452 -1.05320555430355 -1 0.543972129520385 3861 4091 2903 4400 3680 3910 4517 2739 2888 3439 4629 4234 M9372 KAUFFMANN_DNA_REPLICATION_GENES http://www.broadinstitute.org/gsea/msigdb/cards/KAUFFMANN_DNA_REPLICATION_GENES.html Genes involved in DNA replication, compiled manually by the authors. 17891185 87/171 Jessica Robertson 0.978142492010033 0.992975675381069 3100 3925.72727272727 3863 0.293593634327669 3097 0.776021655906608 -0.704228466498908 -1 0.000868382122233179 3097 4634 3689 4338 4173 3372 3604 3863 4445 4205 3763 4235 M10154 SA_G2_AND_M_PHASES http://www.broadinstitute.org/gsea/msigdb/cards/SA_G2_AND_M_PHASES.html Cdc25 activates the cdc2/cyclin B complex to induce the G2/M transition. 6/13 SigmaAldrich 0.988218300718606 0.999176814272271 2820 3759.09090909091 3864 0.358612054521202 2817 0.569236511420671 0.569236511420671 1 7.44153399665611e-05 2817 3864 3890 2944 4476 3442 3210 4166 4533 4295 3713 4236 M7062 ELVIDGE_HIF1A_AND_HIF2A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HIF1A_AND_HIF2A_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) after knockdown of both HIF1A and HIF2A [GeneID=3091;2034] by RNAi. 16565084 28/59 Arthur Liberzon 0.0250020990609022 0.0325805996105082 3480 3866.18181818182 3864 0.00229916748069248 3246 0.794391836624656 -0.640441698670338 -1 0.431794337758611 4216 3449 3476 4087 3392 3246 4528 4680 4110 3864 3480 4237 M1681 BURTON_ADIPOGENESIS_PEAK_AT_16HR http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_PEAK_AT_16HR.html Cluster 4: genes maximally expressed at 16 h time point during differentiation of 3T3-L1 fibroblasts into adipocytes in response to adipogenic hormones. 12137940 31/73 John Newman 0.0839184282471183 0.0965721401684667 2440 3623.18181818182 3864 0.00793650793650794 2436 2.24167690154478 2.76084818669655 1 0.831805315709513 2437 4232 2436 3266 4587 4168 3871 3991 3304 3699 3864 4238 M11197 HSIAO_HOUSEKEEPING_GENES http://www.broadinstitute.org/gsea/msigdb/cards/HSIAO_HOUSEKEEPING_GENES.html Housekeeping genes identified as expressed across 19 normal tissues. 11773596 326/786 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4325 3609.09090909091 3864 0.00793650793650794 2099 1.49915228987601 -1.12304860755466 -1 0.556281256046961 4321 4420 3733 2909 4179 3332 3864 2099 2378 4174 4291 4239 M4280 REACTOME_EARLY_PHASE_OF_HIV_LIFE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EARLY_PHASE_OF_HIV_LIFE_CYCLE.html Genes involved in Early Phase of HIV Life Cycle 6/19 Reactome 0.730349845308875 0.765813241243542 3760 3842.81818181818 3865 0.122837478371219 3008 0.282099085761082 -0.41063994557409 -1 0.0119486431137584 3757 3008 4078 4143 3995 3445 3429 3819 4299 4433 3865 4240 M8991 ZERBINI_RESPONSE_TO_SULINDAC_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZERBINI_RESPONSE_TO_SULINDAC_UP.html Selected genes up-regulated in DU145 and PC-3 cells (prostate cancer) after treatment with the NSAID (non-steroid anti-inflammatory drug) sulindac [PubChem=5352]. 17178890 7/12 Arthur Liberzon 0.00409890401739332 0.00586666592104615 3990 3559.54545454545 3865 0.000410648415900716 1898 1.3864847115573 1.73887143509413 1 1.13097334523467 3989 3463 4114 3837 3121 4094 4166 1898 3865 2264 4344 4241 M17423 LAIHO_COLORECTAL_CANCER_SERRATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/LAIHO_COLORECTAL_CANCER_SERRATED_DN.html Genes down-regulated in serrated vs conventional colorectal carcinoma (CRC) samples. 16819509 64/154 Arthur Liberzon 1.38624294076502e-05 3.30413754853759e-05 4125 3628.36363636364 3865 1.260228796094e-06 1805 1.10187744204695 -0.738093452295881 -1 1.80476995925374 4125 3564 3420 4175 1805 4054 3908 3865 3100 3576 4320 4242 M11031 CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_LD_MTX_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_LD_MTX_UP.html Genes specifically up-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490] and low-dose methotrexate (LDMTX) [PubChem=4112]. 12704389 7/18 Jean Junior 0.172746205639593 0.193750291916499 3340 3525.54545454545 3865 0.0187856821758214 1474 0.191231556136674 -0.218216465434771 -1 0.0498219443022386 3338 3721 4372 3865 4622 1605 1474 4573 4474 4568 2169 4243 M261 PID_P53_REGULATION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P53_REGULATION_PATHWAY.html p53 pathway 18832364 43/90 Pathway Interaction Database 0.0750445031332883 0.0933524135074565 3185 3598.90909090909 3866 0.00706669935865625 1995 1.43554656604156 1.86768763762995 1 0.54040681537805 3181 4651 3375 4029 4604 3966 3314 1995 2460 4147 3866 4244 M16962 IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN.html Genes down-regulated during transition from L0 (non-tumor, not infected with HCV) to L1 (non-tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 28/61 Yujin Hoshida 0.0839184282471183 0.0965721401684667 4580 3911 3866 0.00793650793650794 3120 1.29841681663351 -1.04635769077969 -1 0.481795573502707 4580 3736 3120 3171 4102 4491 4605 3434 3517 3866 4399 4245 M14966 REACTOME_REGULATION_OF_GENE_EXPRESSION_IN_BETA_CELLS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_GENE_EXPRESSION_IN_BETA_CELLS.html Genes involved in Regulation of gene expression in beta cells 5/22 Reactome 0.110562001328738 0.126364277616211 2240 3245.72727272727 3867 0.0116481763282338 1578 0.758479313772085 0.758479313772085 1 0.249069744482941 2236 4294 3986 3867 3959 2262 1578 2161 4349 4358 2653 4246 M643 REACTOME_ACYL_CHAIN_REMODELLING_OF_PC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACYL_CHAIN_REMODELLING_OF_PC.html Genes involved in Acyl chain remodelling of PC 5/23 Reactome 0.329950249161416 0.361164883805279 4340 3570.27272727273 3868 0.0392493100850901 2319 0.315427973889895 -0.3120916703762 -1 0.0509953954314095 3681 3868 3944 3998 4235 2923 2319 2563 4340 4336 3066 4247 M18954 MANN_RESPONSE_TO_AMIFOSTINE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MANN_RESPONSE_TO_AMIFOSTINE_UP.html Genes up-regulated in HCT116 cells (colon cancer) after treatment with amifostine [PubChem=2141] depending on the presence of TP53 [GeneID=7157]: TP53-positive vs TP53-null cells. 15750621 17/28 Leona Saunders 0.00254687512560943 0.00374479348559956 3985 3652.36363636364 3868 0.000231802577760244 2923 0.810214150167253 -0.815818841718213 -1 0.718641475057702 3982 2923 3014 3165 3039 3868 4039 3999 4194 3388 4565 4248 M9703 BIOCARTA_ATRBRCA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ATRBRCA_PATHWAY.html Role of BRCA1, BRCA2 and ATR in Cancer Susceptibility 18/27 BioCarta 0.0839184282471183 0.0965721401684667 4115 3523 3869 0.00793650793650794 1284 2.21506016817542 3.06400283704495 1 0.821928807486572 4115 3848 2291 3934 3970 3840 4069 3116 1284 3869 4417 4249 M1091 REACTOME_DIGESTION_OF_DIETARY_CARBOHYDRATE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DIGESTION_OF_DIETARY_CARBOHYDRATE.html Genes involved in Digestion of dietary carbohydrate 2/13 Reactome 0.874881645992573 0.904610633963194 3345 3902.4 3869 0.206216009010389 3344 0.126943148382808 0.126943148382808 1 0.00202022485472044 3344 4245 4101 NA 4222 3428 3637 3344 4642 4463 3598 4250 M13059 ZHAN_V2_LATE_DIFFERENTIATION_GENES http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_V2_LATE_DIFFERENTIATION_GENES.html The v2LDG set: 50 most variable late differentiation genes (LDG) with similar expression patterns in bone marrow plasma cells (BPC) and multiple myeloma (MM) samples. 12393520 34/77 Kevin Vogelsang 0.000377990807522235 0.000625225882121141 3925 3605.81818181818 3869 3.43687061147325e-05 2689 0.992589818137774 1.20497678001726 1 1.16245611145462 3921 2890 3237 3476 2710 4487 3869 2689 4001 3968 4416 4251 M13597 GRADE_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_METASTASIS_DN.html Down-regulated genes in colon carcinoma tumors with lymph node metastases. 17210682 30/64 Jessica Robertson 0.157644012788832 0.177876196467244 4180 3864.45454545455 3869 0.0154747048713571 2990 0.80691496023696 -0.914140682277819 -1 0.221177038885148 4179 2990 3617 3869 3670 3632 4531 4297 3891 4066 3767 4252 M12707 MILI_PSEUDOPODIA_HAPTOTAXIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MILI_PSEUDOPODIA_HAPTOTAXIS_UP.html Transcripts enriched in pseudopodia of NIH/3T3 cells (fibroblast) in response to haptotactic migratory stimulus by fibronectin, FN1 [GeneID=2335]. 18451862 333/805 Jessica Robertson 0.0839184282471183 0.0965721401684667 3625 3904.18181818182 3870 0.00793650793650794 2980 1.15155763333241 1.4338679944659 1 0.427301435872832 2980 4355 3763 3622 4109 4442 3870 3736 3624 4213 4232 4253 M6917 BIOCARTA_EPONFKB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPONFKB_PATHWAY.html Erythropoietin mediated neuroprotection through NF-kB 7/18 BioCarta 0.0765897756730953 0.0944224385172651 3875 3521.54545454545 3872 0.00793650793650794 2350 2.13231238342611 2.13231238342611 1 0.798844179900766 4166 2406 3833 2794 3872 3917 4299 4037 2350 3190 3873 4254 M13022 BIOCARTA_PTC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PTC1_PATHWAY.html Sonic Hedgehog (SHH) Receptor Ptc1 Regulates cell cycle 3/16 BioCarta 0.978688564809742 0.993314839657451 3665 3993.18181818182 3872 0.319448070290485 3662 0.31022489200211 0.398501178047359 1 0.000330328004560689 3836 3662 3872 3715 4197 3773 3664 4201 4490 4286 4229 4255 M1389 BIOCARTA_SPRY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SPRY_PATHWAY.html Sprouty regulation of tyrosine kinase signals 9/30 BioCarta 0.00604345399409154 0.00849928733982982 4295 3649 3873 0.000605995267952999 2292 0.7158055543087 -0.676971934891053 -1 0.541769049581468 4292 2292 3873 2855 3180 3996 3660 3271 3952 4287 4481 4256 M15262 YAGI_AML_RELAPSE_PROGNOSIS http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_RELAPSE_PROGNOSIS.html Genes associated with clinical prognosis of pediatric AML (acute myeloid leukemia): good prognosis=no relapse > 3 years; poor prognosis=relapse < 1 year or no response to therapy. 12738660 26/57 Kate Stafford 0.299227000842514 0.328455780264235 3725 3442.81818181818 3873 0.0318078029968734 1783 0.873409486178706 -0.857935920426018 -1 0.154366966191581 3723 3931 3500 3873 3912 1783 2055 4105 4042 4015 2932 4257 M5395 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_GRANULOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_GRANULOCYTE_UP.html Genes up-regulated by RUNX1-RUNX1T1 [GeneID=861;862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing granulocytes. 17898786 7/36 Arthur Liberzon 0.313653458643614 0.343808212211457 3875 3778 3874 0.0369377828591234 2546 2.34985618113092 -2.34985618113092 -1 0.398274417706431 3874 4536 4134 4483 4399 3208 3496 2546 4025 3201 3656 4258 M1442 STONER_ESOPHAGEAL_CARCINOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/STONER_ESOPHAGEAL_CARCINOGENESIS_UP.html Genes up-regulated in esophagus by the carcinogen NMBA [PubChem=13643] and brought back to normal by a diet with PEITC [PubChem=16741] or black raspberries. 18676871 19/57 Jessica Robertson 0.104819903495019 0.119947757699062 4585 3829.18181818182 3874 0.0100158993998204 2783 0.761276536512712 -0.833365797479417 -1 0.256286087777431 4582 4153 3416 4602 3597 3253 3826 2783 4134 3901 3874 4259 M3985 KEGG_CITRATE_CYCLE_TCA_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CITRATE_CYCLE_TCA_CYCLE.html Citrate cycle (TCA cycle) 17/33 KEGG 0.763837962269928 0.798426208163481 2945 3645 3877 0.122960610358499 2489 0.240243862189443 -0.221334598237816 -1 0.00858530689482807 2944 3899 3574 3877 4064 2489 3131 4197 4582 4241 3097 4260 M16374 IIZUKA_LIVER_CANCER_PROGRESSION_G1_G2_DN http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_G1_G2_DN.html Genes down-regulated during transition from G1 (well differentiated tumor, infected with HCV) to G2 (moderately differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 35/76 Yujin Hoshida 0.00051178359776013 0.000824980371208795 4505 3366 3878 4.65366083825624e-05 935 2.20655912504463 -0.695472145745689 -1 2.48706258091493 4503 3889 2776 3878 2773 4100 4164 1752 935 3815 4441 4261 M3686 SA_REG_CASCADE_OF_CYCLIN_EXPR http://www.broadinstitute.org/gsea/msigdb/cards/SA_REG_CASCADE_OF_CYCLIN_EXPR.html Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases. 8/24 SigmaAldrich 0.795417024828793 0.829215612535644 2555 3611.54545454545 3881 0.146729071848553 2551 1.02225042359124 -1.02225042359124 -1 0.0303907070284135 2551 4115 3893 4550 4393 2611 2653 3881 4475 3296 3309 4262 M2562 HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_DN.html Genes distinguishing vincristine [PubChem=5978] resistant and sensitive ALL (B- and T-lineage ALL); here - genes down-regulated in the drug resistant samples. 15295046 18/48 Arthur Liberzon 0.00221127925947032 0.00326981843164339 2730 3490.81818181818 3881 0.000201227728042912 1160 1.50112990491585 1.50112990491585 1 1.36378894022986 2729 4462 3246 4193 4520 4045 3034 1160 4150 3881 2979 4263 M5731 BIOCARTA_AKAP95_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKAP95_PATHWAY.html AKAP95 role in mitosis and chromosome dynamics 8/20 BioCarta 0.980479820544289 0.994917375285954 4555 4049.45454545455 3882 0.325396825396825 3347 0.681378109929211 0.681378109929211 1 0.000551168500698415 4555 3347 3813 3479 4645 3801 3882 3750 4468 4262 4542 4264 M4170 ST_INTERFERON_GAMMA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_INTERFERON_GAMMA_PATHWAY.html Interferon gamma pathway. 5/15 Signaling Transduction KE 0.202934516006912 0.22657878055954 4275 3915.90909090909 3883 0.0224265448832241 2758 1.84092616749431 1.84092616749431 1 0.433878063274444 4274 2758 3883 3530 3726 4582 4686 4525 3830 2886 4395 4265 M16161 LOPEZ_MESOTHELIOMA_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_UP.html Top genes associated with favorable survival after surgery of patients with epithelioid mesothelioma. 16540645 9/17 Arthur Liberzon 0.000268519468158528 0.000455569235260993 4280 3765.81818181818 3887 2.68551919894632e-05 1892 0.931063488247177 -0.977979284252346 -1 1.13718976578081 4279 1892 4587 3514 2656 4433 3781 4294 3887 3424 4677 4266 M16563 BIOCARTA_MTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MTOR_PATHWAY.html mTOR Signaling Pathway 18/32 BioCarta 0.460164356349748 0.495708085943659 3660 3705 3888 0.0545030298621518 2038 0.697706624490691 -0.636933935209298 -1 0.0777266584924584 3658 4396 3582 4103 4548 2038 2939 3888 4425 4277 2901 4267 M5042 CHANG_CORE_SERUM_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_CORE_SERUM_RESPONSE_UP.html Up-regulated genes in the canonical gene expression signature of the fibroblast core serum response (CSR) defined by the Stanford group. 14737219 143/318 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2155 3687.18181818182 3888 0.00793650793650794 2154 1.18008897419937 1.53167732170989 1 0.437888385772869 2154 4361 3374 4110 4401 3888 3573 3243 3408 4123 3924 4268 M41 PID_ER_NONGENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ER_NONGENOMIC_PATHWAY.html Plasma membrane estrogen receptor signaling 18832364 29/69 Pathway Interaction Database 0.298735036746822 0.327992591892129 3685 3695.81818181818 3890 0.0317460317460317 2231 1.19527623519542 0.754474158326386 1 0.21152167565079 3682 3836 2231 2903 4151 4261 2868 4363 3954 3890 4515 4269 M13585 CAFFAREL_RESPONSE_TO_THC_24HR_5_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_24HR_5_UP.html Genes up-regulated in EVSA-T cells (breast cancer) treated with 5 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 24 h. 18454173 33/76 Jessica Robertson 1.14353636408408e-05 2.8173561525226e-05 4165 3660.81818181818 3891 1.03958391646045e-06 1735 1.08613011235862 0.946777245402849 1 1.8064569062769 4163 3891 2839 3938 1735 4537 3600 3472 3788 3963 4343 4270 M11672 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP.html Genes from the blue module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 77/193 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2900 3863.90909090909 3892 0.00793650793650794 2898 1.11495526876141 1.06480712360225 1 0.413719620642242 2898 4056 3155 3872 4293 4441 4038 4469 3521 3868 3892 4271 M1783 POS_RESPONSE_TO_HISTAMINE_DN http://www.broadinstitute.org/gsea/msigdb/cards/POS_RESPONSE_TO_HISTAMINE_DN.html Genes gradually down-regulated by histamine [PubChem=774] in B16-F10 melanoma tumors. 18339882 5/14 Jessica Robertson 0.469326541376493 0.504534107109485 3285 3822.72727272727 3892 0.0613952737800557 2725 0.519587577273908 0.519587577273908 1 0.0564279782027409 3285 3465 4458 4541 3892 2951 2725 4312 4252 4602 3567 4272 M42 PID_DNA_PK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_DNA_PK_PATHWAY.html DNA-PK pathway in nonhomologous end joining 18832364 8/19 Pathway Interaction Database 0.196677821691126 0.219802592998954 3060 3451.72727272727 3894 0.0216618799932002 1790 0.407978698483221 -0.407978698483221 -1 0.0981207745083061 3056 3491 3894 4302 4553 1790 2278 3930 4157 4297 2221 4273 M10179 REACTOME_FORMATION_OF_THE_TERNARY_COMPLEX_AND_SUBSEQUENTLY_THE_43S_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_THE_TERNARY_COMPLEX_AND_SUBSEQUENTLY_THE_43S_COMPLEX.html Genes involved in Formation of the ternary complex, and subsequently, the 43S complex 34/99 Reactome 0.634457400939775 0.671576096861031 3825 3796.81818181818 3894 0.0874281027615768 2292 0.410389528650757 -0.410389528650757 -1 0.025937162670879 3825 4455 3759 3894 4261 2292 2853 4642 4626 4309 2849 4274 M18635 CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_DN.html Genes down-regulated in APL (acute promyeolocytic leukemia) blasts expressing PML-RARA fusion [GeneID=5371;5914] compared to normal promyeloblasts. 16990782 477/1119 Leona Saunders 4.44428221554092e-05 9.03510041736431e-05 2985 3654.63636363636 3895 4.04033818025638e-06 2176 1.50373850265687 1.82573643584446 1 2.22284875570187 2983 4549 2988 3895 2176 4654 3921 3772 3051 4051 4161 4275 M8659 IIZUKA_LIVER_CANCER_PROGRESSION_L1_G1_DN http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_L1_G1_DN.html Genes down-regulated during transition from L1 (non-tumor, infected with HCV) to G1 (well differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 5/15 Yujin Hoshida 0.214139132665174 0.238577264781028 4390 3745.81818181818 3899 0.0238095238095238 2447 0.819191846053495 0.819191846053495 1 0.186360632955008 4388 2528 4368 3694 3846 2969 2447 4300 3899 4566 4199 4276 M790 REACTOME_ACTIVATION_OF_CHAPERONE_GENES_BY_XBP1S http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_CHAPERONE_GENES_BY_XBP1S.html Genes involved in Activation of Chaperone Genes by XBP1(S) 35/65 Reactome 0.232850105696956 0.258012673278774 4250 3958.45454545455 3901 0.0238095238095238 3271 0.802850120352287 -0.659013612737573 -1 0.172661733015091 4250 3271 3669 3608 3790 4658 3809 3909 3901 4104 4574 4277 M977 REACTOME_KINESINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KINESINS.html Genes involved in Kinesins 16/32 Reactome 0.807426962686765 0.840427087327894 2005 3500.81818181818 3902 0.139079150635621 2005 0.617635170442549 -0.575655026609274 -1 0.0170450365319532 2005 3902 2571 4176 4258 2905 2376 4020 4548 4423 3325 4278 M14242 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS.html Genes trans-regulated by the same QTL (quantitative trait loci) in brain and hematopoietic stem cells (HSC). 15711547 93/280 Jean Junior 0.0839184282471183 0.0965721401684667 4350 3501.90909090909 3903 0.00793650793650794 2088 1.77029912675313 2.30654919426816 1 0.656894052023034 4350 4496 3133 4326 4090 2088 2736 2684 2750 3965 3903 4279 M6682 BIOCARTA_MCM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MCM_PATHWAY.html CDK Regulation of DNA Replication 12/19 BioCarta 0.865412014258462 0.896005457095703 4310 3877.18181818182 3904 0.166666666666667 2910 1.55517194746902 1.55517194746902 1 0.0271093431954112 3963 3904 2910 3486 4308 3891 3768 4322 4306 3609 4182 4280 M10175 ELVIDGE_HYPOXIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HYPOXIA_DN.html Genes down-regulated in MCF7 cells (breast cancer) under hypoxia conditions. 16565084 102/212 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4295 3852.18181818182 3904 0.00793650793650794 3130 1.41880959293454 -1.49227129269345 -1 0.526468983594738 4291 4259 3393 4322 3904 4203 3130 4433 3152 3521 3766 4281 M16463 MANN_RESPONSE_TO_AMIFOSTINE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MANN_RESPONSE_TO_AMIFOSTINE_DN.html Genes down-regulated in HCT116 cells (colon cancer) after treatment with amifostine [PubChem=2141] depending on the presence of TP53 [GeneID=7157]: TP53-positive vs TP53-null cells. 15750621 9/24 Leona Saunders 0.00524279463577036 0.00741331794303558 3910 3779.72727272727 3905 0.000525520496636196 2577 0.682770578009354 -0.684163046089497 -1 0.531582990858635 3910 3004 4267 3723 3159 3905 2577 3852 4350 4532 4298 4282 M1483 SCHURINGA_STAT5A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHURINGA_STAT5A_TARGETS_DN.html Genes down-regulated in hematopoietic stem cells (HSC) overexpressing a constitutively active form of STAT5 [GeneID=6776] off retroviral vector. 15353555 9/96 Kevin Vogelsang 0.940634982288152 0.963035946471986 4420 3965.36363636364 3905 0.246031746031746 3414 1.10153946517136 -1.10153946517136 -1 0.00658621912743772 4420 3905 4393 4361 4137 3696 3876 3520 4385 3414 3512 4283 M18562 MANALO_HYPOXIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/MANALO_HYPOXIA_DN.html Genes down-regulated in response to both hypoxia and overexpression of an active form of HIF1A [GeneID=3091]. 15374877 190/395 Kate Stafford 0.232850105696956 0.258012673278774 4070 3686.09090909091 3906 0.0238095238095238 1935 1.0388042705559 -0.867897179730483 -1 0.223406264126754 1935 4305 3722 4207 4069 3156 3541 4067 3906 4199 3440 4284 M1051 REACTOME_INTEGRATION_OF_PROVIRUS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTEGRATION_OF_PROVIRUS.html Genes involved in Integration of provirus 5/13 Reactome 0.214139132665174 0.238577264781028 3970 3816.36363636364 3907 0.0238095238095238 2905 0.27309585765708 0.153558225948074 1 0.0621274688637717 3970 2905 4088 3838 3907 3572 3358 4058 3892 4450 3942 4285 M13038 CHASSOT_SKIN_WOUND http://www.broadinstitute.org/gsea/msigdb/cards/CHASSOT_SKIN_WOUND.html List of the transcription factors up-regulated 1 hr after wounding HDF cells (dermal fibroblasts). 17404577 7/13 Leona Saunders 0.540779504477699 0.578427929235905 2925 3745.72727272727 3907 0.0748713593689329 2882 0.647704822195356 0.647704822195356 1 0.056288315809316 2924 3907 4197 3483 3917 3221 2882 4379 4364 4498 3431 4286 M4230 ZHAN_LATE_DIFFERENTIATION_GENES_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_LATE_DIFFERENTIATION_GENES_DN.html B lymphocyte late differentiation genes (LDG): top genes down-regulated in plasma cells from tonsils (TPC) compared to those from bone marrow (BPC). 12393520 9/37 Arthur Liberzon 0.026032404512282 0.0338291313212849 4465 3815.72727272727 3908 0.00263424880259167 2077 1.23868786843974 -0.858440606458081 -1 0.665898335364946 4463 3718 4559 3908 3415 4312 4553 2077 3177 3421 4370 4287 M2138 SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_DN.html Cluster 6: genes down-regulated in B493-6 cells (B lymphocytes) by MYC [GeneID=4609] in combination with serum but not affected by serum alone; they are also up-regulated by MYC alone. 15516975 30/92 Leona Saunders 0.514011397665828 0.550424453716195 2435 3811.72727272727 3910 0.0634920634920635 2434 1.91515516455502 1.91515516455502 1 0.181522116913073 2434 4275 3475 3735 4305 4193 3799 4038 4104 3910 3661 4288 M4939 MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP.html Genes correlated with the early tumor onset in the Emu-myc transgenic mouse lymphoma model. 18922927 81/151 Jessica Robertson 0.0839184282471183 0.0965721401684667 3295 3925.54545454545 3910 0.00793650793650794 3185 1.31200147973681 1.5068156859084 1 0.486836351233906 3292 4133 3185 4091 3910 4574 3836 4497 3542 3645 4476 4289 M16991 BIOCARTA_IGF1MTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IGF1MTOR_PATHWAY.html Skeletal muscle hypertrophy is regulated via AKT/mTOR pathway 15/32 BioCarta 0.559531481960197 0.59644324942345 4625 3900.09090909091 3911 0.0718276541197311 3087 0.802330283385049 -0.824255768191531 -1 0.0658195670270118 4625 3608 3242 3733 3911 4036 3087 4568 4242 3766 4083 4290 M40 PID_E2F_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_E2F_PATHWAY.html E2F transcription factor network 18832364 48/115 Pathway Interaction Database 0.0839184282471183 0.0965721401684667 4065 3727.81818181818 3911 0.00793650793650794 2404 1.92043398914862 2.07719358647153 1 0.712603675830815 4064 3887 2404 2987 4351 4290 4604 3444 2429 3911 4635 4291 M1690 YANG_MUC2_TARGETS_DUODENUM_6MO_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_MUC2_TARGETS_DUODENUM_6MO_DN.html Genes down-regulated in duodenum of 6 month old MUC2 [GeneID=4583] knockout mice. 18794118 8/59 Jessica Robertson 0.402022177705894 0.435678983517535 3915 3984.45454545455 3911 0.0501205158444072 3207 0.827273627480229 -0.774583954451289 -1 0.109112659370488 3911 3688 4427 4577 3865 3247 3725 4332 4255 4595 3207 4292 M13404 BIOCARTA_VDR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VDR_PATHWAY.html Control of Gene Expression by Vitamin D Receptor 3/17 BioCarta 0.89366909976696 0.921799119856477 3855 3933.45454545455 3913 0.200780725498758 3257 0.142686664592223 -0.142686664592223 -1 0.00184442094326107 3853 4297 3824 4158 4081 3257 3292 3913 4594 4267 3732 4293 M17842 REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS_VIA_24_HYDROXYCHOLESTEROL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS_VIA_24_HYDROXYCHOLESTEROL.html Genes involved in Synthesis of bile acids and bile salts via 24-hydroxycholesterol 5/20 Reactome 0.110656812202227 0.126441800043803 4025 3961.18181818182 3913 0.0116587123065829 2887 1.08804497814992 1.08804497814992 1 0.357186721394049 4023 3867 3913 4221 3621 4663 3692 3836 4319 2887 4531 4294 M944 REACTOME_REGULATION_OF_MRNA_STABILITY_BY_PROTEINS_THAT_BIND_AU_RICH_ELEMENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_MRNA_STABILITY_BY_PROTEINS_THAT_BIND_AU_RICH_ELEMENTS.html Genes involved in Regulation of mRNA Stability by Proteins that Bind AU-rich Elements 57/115 Reactome 0.597318307603006 0.634989471285773 3165 3763.36363636364 3921 0.0793650793650794 2774 1.07580374435829 -1.30758376384001 -1 0.0775591284244327 3165 4648 3732 3958 4364 2774 3225 3921 4156 4184 3270 4295 M12820 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_18 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_18.html Amplification hot spot 18: colocolized fragile sites and cancer genes in the 18q11.2-q23 region. 16751803 3/5 Arthur Liberzon 0.481063017846562 0.516321873941592 3505 3823.09090909091 3921 0.0634920634920635 2760 0.811385032410593 -0.811385032410593 -1 0.0851428881524379 3502 2760 4234 4131 4486 3921 3892 3009 4092 4518 3509 4296 M2422 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_MAGENTA_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_MAGENTA_UP.html Genes from the magenta module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 20/117 Arthur Liberzon 0.232850105696956 0.258012673278774 4330 3855.63636363636 3923 0.0238095238095238 3219 0.926314734775619 -1.13677928937128 -1 0.199214154162962 4327 4076 3219 3595 3797 3312 4123 4184 3903 3923 3953 4297 M1756 SANSOM_APC_MYC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_APC_MYC_TARGETS.html Genes down-regulated after double Cre-lox knockout of both APC and MYC [GeneID=324;4609] in small intestine. 17377531 143/308 Arthur Liberzon 4.81612930889208e-06 1.40554697243813e-05 4240 3552.45454545455 3925 4.37830895650214e-07 1416 1.51604099975528 -1.03571684622851 -1 2.6888391939821 4240 4360 3091 4015 1416 3469 4308 4002 2463 3788 3925 4298 M514 REACTOME_SPRY_REGULATION_OF_FGF_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SPRY_REGULATION_OF_FGF_SIGNALING.html Genes involved in Spry regulation of FGF signaling 7/24 Reactome 0.385539379182179 0.418590716137093 4540 3947.18181818182 3926 0.0475341670392668 3347 0.7158055543087 -0.676971934891053 -1 0.0989572875945515 4539 3381 3918 3658 3853 3347 4250 3926 4208 4318 4021 4299 M1744 MARSON_BOUND_BY_E2F4_UNSTIMULATED http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_BOUND_BY_E2F4_UNSTIMULATED.html Genes with promoters bound by E2F4 [GeneID=1874] in unstimulated hybridoma cells. 17237765 457/969 Jessica Robertson 0.0839184282471183 0.0965721401684667 4180 3849.63636363636 3926 0.00793650793650794 2401 1.09208182493576 -0.912532454613945 -1 0.405232111942507 2401 4551 3743 4344 4177 3395 3926 4177 3707 4230 3695 4300 M10198 FUNG_IL2_SIGNALING_2 http://www.broadinstitute.org/gsea/msigdb/cards/FUNG_IL2_SIGNALING_2.html Genes up-regulated by IL2 [GeneID=3558] in T1 cells (primary thymocytes immortalized by Tax, an HTLV-1 encoded gene). 15735688 5/15 Arthur Liberzon 0.423961536401932 0.457655784284601 3050 3718.27272727273 3929 0.0536644647038135 1840 0.313538410266078 0.296948106473789 1 0.038904507819823 3048 4011 4261 4612 3929 2996 1840 3580 4579 4528 3517 4301 M19907 KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN.html Genes down-regulated in HL-60 cells (acute promyelocytic leukemia, APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 6 h. 18701491 544/1244 Jessica Robertson 4.22830352594974e-06 1.27748744826567e-05 4160 3538.45454545455 3930 4.22831157131911e-07 1398 1.3883233804817 -1.14290665549617 -1 2.48337441972954 4157 3985 4423 4335 1398 2606 3310 4649 2328 3930 3802 4302 M565 REACTOME_BETA_DEFENSINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BETA_DEFENSINS.html Genes involved in Beta defensins 8/55 Reactome 0.757064576645444 0.792052825666567 3645 3933.63636363636 3931 0.131941319068492 3105 0.265647639466202 -0.454706941723143 -1 0.00983110587530243 3644 4537 3931 4179 4457 3305 3726 3105 4515 4326 3545 4303 M580 REACTOME_ASSOCIATION_OF_LICENSING_FACTORS_WITH_THE_PRE_REPLICATIVE_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ASSOCIATION_OF_LICENSING_FACTORS_WITH_THE_PRE_REPLICATIVE_COMPLEX.html Genes involved in Association of licensing factors with the pre-replicative complex 7/19 Reactome 0.941537725897953 0.963749625067236 3390 3873.72727272727 3932 0.24718620201376 3277 0.336863157047989 -0.430359669537828 -1 0.00197452393397825 3386 4085 3932 4169 4158 3277 3567 3437 4591 4328 3681 4304 M12627 REACTOME_DOPAMINE_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOPAMINE_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Dopamine Neurotransmitter Release Cycle 4/20 Reactome 0.345634281806152 0.377187294956597 3665 3748.45454545455 3932 0.0415222097907273 2579 0.363473629043601 -0.302330314932311 -1 0.0562583570024938 3661 3494 3990 4217 4041 3806 3021 2579 4129 4363 3932 4305 M93 REACTOME_ACETYLCHOLINE_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACETYLCHOLINE_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Acetylcholine Neurotransmitter Release Cycle 4/18 Reactome 0.357966648633322 0.390191141078332 3665 3750.90909090909 3933 0.0433440898899737 2593 0.363473629043601 -0.302330314932311 -1 0.0543026208165727 3662 3495 3991 4218 4042 3807 3022 2593 4130 4367 3933 4306 M16542 YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP.html Up-regulated genes distinguishing hepatocellular carcinoma (HCC) samples positive for EPCAM [GeneID=4072] from the negative ones. 18316609 35/108 Yujin Hoshida 0.0839184282471183 0.0965721401684667 4385 3505.54545454545 3933 0.00793650793650794 1056 2.97453992642614 -2.45573865056236 -1 1.10374430954042 4383 3890 2618 2569 4302 3933 4081 4206 1056 3226 4297 4307 M602 REACTOME_REGULATION_OF_COMPLEMENT_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_COMPLEMENT_CASCADE.html Genes involved in Regulation of Complement cascade 4/20 Reactome 0.0821221129379263 0.0965721401684667 4485 3829.72727272727 3935 0.00853248176309561 2295 0.9392360253186 0.9392360253186 1 0.34851655726447 4483 2295 3935 3518 3572 4274 3478 3545 4071 4331 4625 4308 M1403 PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN.html Genes down-regulated in long term hematopoietic stem cells (LT-HSC) compared to multipotent progenitor (MPP) cells. 11781229 15/32 Kate Stafford 0.64348410221232 0.680823324219221 4320 3848.09090909091 3936 0.0895001049630974 2860 2.29929928430081 2.29929928430081 1 0.140327143459558 4319 3936 2860 3795 4591 3970 3294 2922 4221 3772 4649 4309 M7488 PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_UP.html Antigen processing and presentation genes up-regulated in JY cells (B lymphocytes) treated with TSA [PubChem=5562]. 18829567 52/89 Jessica Robertson 0.000680804566843693 0.00107924566990174 4290 3871.81818181818 3936 6.19104852404137e-05 2829 0.861077293263568 -0.812623157892737 -1 0.933816023180074 4289 3956 3697 3668 2829 3643 4680 3936 4108 4131 3653 4310 M1789 WORSCHECH_TUMOR_REJECTION_DN http://www.broadinstitute.org/gsea/msigdb/cards/WORSCHECH_TUMOR_REJECTION_DN.html Down-regulated genes defining rejection of mammary carcinoma (MMC) tumors. 18381452 9/13 Jessica Robertson 0.275742742869669 0.304030704255827 4360 3945.90909090909 3939 0.0317460317460317 2888 0.885177717035442 -0.651496647261806 -1 0.167305263515492 4357 3906 4462 3989 3794 3893 4248 2888 3939 3418 4511 4311 M182 PID_IL3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL3_PATHWAY.html IL3-mediated signaling events 18832364 21/41 Pathway Interaction Database 0.0192974324626146 0.0254439416206562 4530 3779 3941 0.00176989175662266 2162 0.776235535368111 -0.807854677181078 -1 0.452391365141004 4526 4520 3534 4195 3356 4132 3193 2162 4273 3941 3737 4312 M12591 ROME_INSULIN_TARGETS_IN_MUSCLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROME_INSULIN_TARGETS_IN_MUSCLE_UP.html Genes up-regulated by 3 h of euglycemic hyperinsulinemic clamp in the vastus lateralis muscle of healthy lean subjects. 12621037 313/722 Jessica Robertson 0.0839184282471183 0.0965721401684667 3590 3877.45454545455 3941 0.00793650793650794 2975 1.29227415244699 -0.926063260551675 -1 0.479516252727048 3589 4617 3745 4114 3837 3941 4312 2975 3017 4197 4308 4313 M9473 RAMALHO_STEMNESS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMALHO_STEMNESS_UP.html Genes enriched in embryonic, neural and hematopoietic stem cells. 12228720 134/297 John Newman 0.0872720719565037 0.100308297568844 4155 3821.27272727273 3943 0.00826722249931196 3064 1.06065261833865 -0.725020170110328 -1 0.387178682640773 4151 4017 3667 3376 3567 3516 4043 3064 3943 4120 4570 4314 M2077 WHITFIELD_CELL_CYCLE_G2_M http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_G2_M.html Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the G2/M phase of cell cycle. 12058064 153/356 Jessica Robertson 0.000919659361855549 0.00143173547164621 3945 3821.63636363636 3943 8.36403663113168e-05 2877 1.27362412609824 1.22153688514714 1 1.32407038618795 3943 4254 3412 3949 2877 4165 4018 3743 3452 3823 4402 4315 M3621 MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_DN.html Genes correlated with the late tumor onset in the Emu-myc transgenic mouse lymphoma model. 18922927 18/33 Jessica Robertson 2.58032211498027e-05 5.64490636358428e-05 4020 3726.45454545455 3947 2.34577489036035e-06 1997 0.975722742407656 -1.04529659286923 -1 1.51518365760203 4017 3897 3206 2537 1997 4638 3947 4681 4145 3457 4469 4316 M5316 MODY_HIPPOCAMPUS_PRENATAL http://www.broadinstitute.org/gsea/msigdb/cards/MODY_HIPPOCAMPUS_PRENATAL.html Genes highly expressed in prenatal hippocampus (cluster 1). 11438693 32/88 John Newman 0.0839184282471183 0.0965721401684667 3385 3746.18181818182 3947 0.00793650793650794 2484 1.99511100064377 -0.814184853432016 -1 0.740313617086996 3382 4664 3142 3279 4653 4673 4243 2484 2585 3947 4156 4317 M4772 CAIRO_HEPATOBLASTOMA_CLASSES_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_HEPATOBLASTOMA_CLASSES_UP.html Genes up-regulated in robust Cluster 2 (rC2) of hepatoblastoma samples compared to those in the robust Cluster 1 (rC1). 19061838 386/821 Arthur Liberzon 0.232850105696956 0.258012673278774 3630 4065.81818181818 3948 0.0238095238095238 3473 1.10099261947894 -0.90435976975593 -1 0.236780551478703 3629 4616 3784 4343 4490 3473 3718 4575 3911 4237 3948 4318 M125 PID_IGF1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IGF1_PATHWAY.html IGF1 pathway 18832364 28/54 Pathway Interaction Database 0.0689727849746511 0.086027806864843 4640 4015.72727272727 3956 0.0064759193638741 3249 1.07972344193912 -1.0153571254289 -1 0.420463822466857 4636 4390 3249 3431 3530 3609 4586 4657 3956 3863 4266 4319 M543 REACTOME_CELL_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CYCLE.html Genes involved in Cell Cycle 258/635 Reactome 0.0839184282471183 0.0965721401684667 3705 3926.90909090909 3956 0.00793650793650794 3300 1.19137593105193 -0.942615092359509 -1 0.44207656771914 3300 4251 3704 3818 4340 3585 3997 4310 3702 4233 3956 4320 M6509 PARK_HSC_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/PARK_HSC_MARKERS.html Genes in a cCDNA library from hematopoietic stem cells (HSC) after subtraction of lineage-specific markers. 11781229 26/59 Kevin Vogelsang 0.549961512769057 0.587846635227145 3615 3717.63636363636 3956 0.0700122210929839 2726 0.746586045060099 -0.68770613922741 -1 0.0629672021701255 3613 3998 3403 4192 4035 3198 3474 3956 4283 4016 2726 4321 M1247 CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP http://www.broadinstitute.org/gsea/msigdb/cards/CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP.html Genes up-regulated in K562 cells (chronic myelogenous leukemia, CML) expressing TP53 and MYC [GeneID=7157;4609]. 15856024 22/43 Arthur Liberzon 0.667434366415499 0.704890115173097 4185 3928.81818181818 3957 0.0952380952380952 3263 0.830099673459886 -0.690217107874347 -1 0.0460835581102867 4195 3775 3263 4007 4184 3599 3745 4464 4185 3957 3843 4322 M6794 BUSA_SAM68_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BUSA_SAM68_TARGETS_UP.html Genes up-regulated in LNCaP cells (prostate cancer) after knockdown of SAM68 [GeneID=10657] by RNAi. 17237817 2/10 Arthur Liberzon 0.203571739022014 0.22723610506364 4120 3855 3958 0.0249737775265676 2761 1.1462327696857 -0.994589521643861 -1 0.269622365387372 4119 2761 4177 NA 3748 3708 3397 3815 4234 4490 4101 4323 M16104 ZHAN_VARIABLE_EARLY_DIFFERENTIATION_GENES_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_VARIABLE_EARLY_DIFFERENTIATION_GENES_DN.html The vEDG down-regulated set: most variable early differentiation genes (EDG) with similar expression patterns in tonsil B lymphocytes (TBC) and multiple myeloma (MM) cells compared to the plasma cells from tonsil (TPC) and bone marrow (BPC). 12393520 22/48 Arthur Liberzon 0.667434366415499 0.704890115173097 3510 3884.09090909091 3959 0.0952380952380952 3402 0.613481341547116 -0.659263875046779 -1 0.0340578409646991 3508 4029 3579 4177 4523 3448 3895 4014 4191 3959 3402 4324 M721 REACTOME_ACTIVATION_OF_THE_MRNA_UPON_BINDING_OF_THE_CAP_BINDING_COMPLEX_AND_EIFS_AND_SUBSEQUENT_BINDING_TO_43S http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_THE_MRNA_UPON_BINDING_OF_THE_CAP_BINDING_COMPLEX_AND_EIFS_AND_SUBSEQUENT_BINDING_TO_43S.html Genes involved in Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S 41/112 Reactome 0.412671711857184 0.446910016584877 3475 3689.63636363636 3960 0.0472275858315008 1970 0.410389528650757 -0.410389528650757 -1 0.0524699161421836 3471 4655 3766 3960 4316 1970 2386 4571 4581 4350 2560 4325 M14670 DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER http://www.broadinstitute.org/gsea/msigdb/cards/DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER.html The lung adenocarcinoma TSP (tumor sequencing project) genes showing strong correlation between DNA copy number variation and gene expression. 18948947 60/141 Jessica Robertson 0.415320710913563 0.448741722697937 3810 3793.63636363636 3960 0.0476190476190476 2987 1.0219485692195 -0.944683854603771 -1 0.12999658924495 3808 4135 3575 4387 4280 3215 4326 2987 4026 3960 3031 4326 M17905 ELVIDGE_HIF1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HIF1A_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) after knockdown of HIF1A [GeneID=3091] by RNAi. 16565084 44/93 Arthur Liberzon 0.298735036746822 0.327992591892129 4085 3874.63636363636 3961 0.0317460317460317 3036 1.11670938964835 1.40247000423516 1 0.19761811890588 4083 3961 3367 4328 4092 4062 3036 3506 3955 3821 4410 4327 M17138 BYSTRYKH_SCP2_QTL http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_SCP2_QTL.html Genes that physically map to the hematopoietic stem cell (HSC) proliferation QTL (quantitative trait locus) Scp2. 15711547 4/8 Jean Junior 0.415589331959574 0.448928448492983 3590 4051.54545454545 3961 0.0522979642930111 3586 0.717773725536766 0.717773725536766 1 0.0912567370704238 3880 3589 4363 3586 3871 4644 3839 3961 4121 4565 4148 4328 M3889 ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_UP.html Genes commonly up-regulated in CD-1 and CD-2 clusters of multiple myeloma samples and which were higher expressed in the CD-1 group. 16728703 60/158 Kevin Vogelsang 0.0486797820203615 0.0616856296775052 4345 3669.54545454545 3961 0.00452650218651635 2189 1.75605064051075 -1.10708219638345 -1 0.776561058223368 4344 4368 3305 4250 3486 2189 3462 4033 2830 3961 4137 4329 M2531 REACTOME_MRNA_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_PROCESSING.html Genes involved in mRNA Processing 91/233 Reactome 0.878859116702268 0.908122121470083 3860 4085 3962 0.174603174603175 3684 1.08968442361181 -0.99818423851241 -1 0.0166715132861454 3860 4635 3754 4413 4473 3684 3858 3962 4318 4209 3769 4330 M1577 BURTON_ADIPOGENESIS_3 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_3.html Strongly up-regulated at 16-24 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 69/152 John Newman 0.239396866193938 0.265016233164374 4140 3566.81818181818 3962 0.0245698127252999 1412 1.34824212531789 1.36977566997828 1 0.284222083040615 1827 4136 1412 3501 4600 3962 3519 4251 4136 3856 4035 4331 M19590 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_DN.html Genes from the turquoise module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphocholine (oxPAPC). 16912112 35/90 Arthur Liberzon 0.514011397665828 0.550424453716195 3405 3861.81818181818 3963 0.0634920634920635 3228 1.17051956326086 -0.960224359841556 -1 0.110944111268755 3401 4387 3228 4013 4163 3344 3611 4444 4112 3814 3963 4332 M540 LOPEZ_MESOTELIOMA_SURVIVAL_TIME_UP http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTELIOMA_SURVIVAL_TIME_UP.html Top genes higher expressed in short term mesothelioma survivors. 16540645 14/57 Arthur Liberzon 0.667434366415499 0.704890115173097 3855 3977 3963 0.0952380952380952 2471 1.54870939107535 1.54870939107535 1 0.0859776756847591 4285 3855 2471 3807 3963 4528 3852 4585 4189 3723 4489 4333 M16639 KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_DN.html Genes down-regulated in MEWO cells (melanoma) after 48h of methionine [PubChem=876] deprivation. 16908595 42/93 Arthur Liberzon 8.85111143058564e-06 2.27891803097386e-05 4115 3756.45454545455 3964 8.04649730987737e-07 1648 0.921436923448363 0.834530803196618 1 1.5635629770254 4514 3269 3196 4440 1648 4111 4464 4114 3815 3786 3964 4334 M9585 PUJANA_ATM_PCC_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_ATM_PCC_NETWORK.html Genes constituting the ATM-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient, PCC >= 0.4) with that of ATM [GeneID=472] across a compendium of normal tissues. 17922014 861/2334 Leona Saunders 4.79388252255227e-06 1.40050707610224e-05 4245 3673.18181818182 3965 4.79389286417301e-07 1453 1.46064451519401 -1.21304777585829 -1 2.59142131694972 4241 4612 4296 3965 1453 2717 4556 3509 2942 4178 3936 4335 M3155 GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_UP.html Genes up-regulated in quiescent CD34+ [GeneID=8842] cells isolated from peripheral blood of normal donors compared to the dividing cells from CML (chronic myeloid leukemia) patients. 17717066 127/341 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4020 3542.36363636364 3968 0.00793650793650794 1666 1.41998567410953 1.67289106137519 1 0.5269053848328 2319 4018 1666 3176 4298 4287 3968 4093 3652 3470 4019 4336 M5611 PUJANA_BRCA1_PCC_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BRCA1_PCC_NETWORK.html Genes constituting the BRCA1-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient, PCC >= 0.4) with that of BRCA1 [GeneID=672] across a compendium of normal tissues. 17922014 1002/2578 Leona Saunders 0.0765897756730953 0.0944224385172651 3880 3984.72727272727 3968 0.00793650793650794 3118 1.32999765291583 -1.03215863931022 -1 0.498266994615853 3878 4610 4295 3968 4501 3118 3676 4467 3333 4240 3746 4337 M11932 REACTOME_TIE2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TIE2_SIGNALING.html Genes involved in Tie2 Signaling 9/24 Reactome 0.00620162682792144 0.00869824104029927 4475 3874 3972 0.000621900219089647 3074 0.79421835211995 -0.636933935209298 -1 0.598199763393547 4475 3379 3972 3074 3185 4425 3296 3760 4313 4351 4384 4338 M851 REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE.html Genes involved in Regulation of mitotic cell cycle 49/99 Reactome 0.997486100429051 0.999999893590849 4410 4049 3973 0.419679392225336 3542 0.74351706699215 -0.74351706699215 -1 1.07627432806378e-08 3722 4581 3702 4040 4409 3542 3713 3973 4635 4406 3816 4339 M1735 GAVIN_FOXP3_TARGETS_CLUSTER_P6 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_P6.html Cluster P6 of genes with similar expression profiles in peripheral T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 48/126 Jessica Robertson 0.0839184282471183 0.0965721401684667 4190 3596.27272727273 3973 0.00793650793650794 1414 1.50304976375298 -1.14949190371679 -1 0.557727467806324 4188 3393 1414 2713 4429 3973 4110 4639 3209 3220 4271 4340 M11184 REACTOME_ENDOGENOUS_STEROLS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENDOGENOUS_STEROLS.html Genes involved in Endogenous sterols 3/15 Reactome 0.481063017846562 0.516321873941592 3625 3585.18181818182 3974 0.0634920634920635 2160 1.08804497814992 1.08804497814992 1 0.11417426828951 3621 2829 3985 3974 3918 4194 2160 4218 4102 2448 3988 4341 M731 WEBER_METHYLATED_ICP_IN_FIBROBLAST http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_ICP_IN_FIBROBLAST.html Germline-specific genes with intermediate-CpG-density promoters (ICP) that are methylated in primary fibroblasts. 17334365 14/105 Arthur Liberzon 0.298735036746822 0.327992591892129 3565 3977 3974 0.0317460317460317 3201 1.21026576620684 0.766931422571552 1 0.214174293221798 3565 3974 3201 4379 4047 3579 4283 4493 3944 3732 4550 4342 M16091 DISTECHE_ESCAPED_FROM_X_INACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/DISTECHE_ESCAPED_FROM_X_INACTIVATION.html Genes that escape X inactivation. 12900543 14/53 Broad Institute 0.417457952198059 0.450843043097512 4355 4046.18181818182 3976 0.0479360602330827 3481 0.276512143429315 -0.288185387449314 -1 0.0349685550826096 4353 3976 3544 4178 3855 3481 4461 3869 4386 4569 3836 4343 M16647 REACTOME_CELL_CYCLE_CHECKPOINTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CYCLE_CHECKPOINTS.html Genes involved in Cell Cycle Checkpoints 71/137 Reactome 0.0839184282471183 0.0965721401684667 3980 4036.45454545455 3977 0.00793650793650794 3555 1.90375995201855 -0.74351706699215 -1 0.706416543002023 3977 4574 3610 3813 4311 3782 3946 4474 3555 4204 4155 4344 M16909 PARENT_MTOR_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/PARENT_MTOR_SIGNALING_UP.html Genes up-regulated in HepaRG cells (liver cancer) expressing constituvely active form of MTOR [GeneID=2475]. 17483347 387/856 Arthur Liberzon 1.70986017668335e-06 6.67110992728605e-06 3980 3590.45454545455 3977 1.55441955054892e-07 946 1.35535926025021 -1.18949298583018 -1 2.56419662131886 4614 4125 3578 4446 946 2523 4371 3981 2958 3976 3977 4345 M1392 SHIN_B_CELL_LYMPHOMA_CLUSTER_8 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_8.html Cluster 8 of genes distinguishing among different B lymphocyte neoplasms. 19010892 21/65 Jessica Robertson 0.709866532920871 0.747009785148709 4150 3842.54545454545 3978 0.106395685288257 2929 0.820496907858653 0.830117338700678 1 0.0379911698297364 4148 4331 2929 4098 3978 3033 3420 4660 4320 3631 3720 4346 M1494 REACTOME_BASE_FREE_SUGAR_PHOSPHATE_REMOVAL_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BASE_FREE_SUGAR_PHOSPHATE_REMOVAL_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY.html Genes involved in Base-free sugar-phosphate removal via the single-nucleotide replacement pathway 8/11 Reactome 0.614921670109158 0.653258432584792 3110 3678.54545454545 3979 0.0910187854798449 2866 0.654162550255648 -0.654162550255648 -1 0.0442157499010127 3106 3104 3979 4077 4156 2948 4014 3328 4532 4354 2866 4347 M12455 JAZAG_TGFB1_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/JAZAG_TGFB1_SIGNALING_DN.html Genes down-regulated in PANC-1-puro cells (pancreatic cancer) stimulated by TGF1B [GeneID=7040] for 2 h. 15592526 35/68 Leona Saunders 0.0839184282471183 0.0965721401684667 3710 3883.18181818182 3980 0.00793650793650794 2585 1.32781717791711 -0.799035861827213 -1 0.492704985485962 3706 4586 2585 3739 4072 4306 3899 4059 3667 3980 4116 4348 M9565 AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_UP.html Up-regulated genes whose expression correlates with copy number gains in pancreatic adenocarcinoma cell lines and primary tumor specimens. 15199222 189/425 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4290 3869.18181818182 3980 0.00793650793650794 2740 1.44327301445846 -0.974917428514387 -1 0.535546475580299 4287 4252 3528 4261 3980 3229 4360 3347 2740 3970 4607 4349 M1934 MEISSNER_NPC_ICP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_ICP_WITH_H3K4ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in neural precursor cells (NPC). 18600261 13/32 Jessica Robertson 0.298735036746822 0.327992591892129 4000 3937.72727272727 3980 0.0317460317460317 3202 1.87560319275937 1.87560319275937 1 0.331915518546199 3997 3980 3202 3659 4434 4234 4256 3704 3951 3686 4212 4350 M732 REACTOME_SLBP_DEPENDENT_PROCESSING_OF_REPLICATION_DEPENDENT_HISTONE_PRE_MRNAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SLBP_DEPENDENT_PROCESSING_OF_REPLICATION_DEPENDENT_HISTONE_PRE_MRNAS.html Genes involved in SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs 5/14 Reactome 0.296402019780051 0.326271990765638 3520 3844.90909090909 3982 0.0345440610955885 2520 0.729177223291865 -0.729177223291865 -1 0.129647440539098 3519 4413 3982 4579 4581 3351 3148 2520 4432 4355 3414 4351 M1025 REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_.html Genes involved in Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. 48/117 Reactome 0.623501688537435 0.661773253111308 1860 3544.72727272727 3983 0.0849749091753622 1856 0.567855231057917 -0.567855231057917 -1 0.0372147272716099 1856 4505 3756 4204 4166 2434 2078 3983 4559 4434 3017 4352 M1874 LUDWICZEK_TREATING_IRON_OVERLOAD http://www.broadinstitute.org/gsea/msigdb/cards/LUDWICZEK_TREATING_IRON_OVERLOAD.html Genes changed in liver in response to nifedipine [PubChem=4485] treatment of iron overload. 17293870 6/10 Jessica Robertson 0.0765897756730953 0.0944224385172651 3985 3735.63636363636 3983 0.00793650793650794 2064 1.30534865338687 -1.23996398678939 -1 0.48903255504151 3983 3622 4521 2615 3956 4408 4486 4634 2817 2064 3986 4353 M1742 MARSON_BOUND_BY_FOXP3_STIMULATED http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_BOUND_BY_FOXP3_STIMULATED.html Genes with promoters bound by FOXP3 [GeneID=50943] in hybridoma cells stimulated by PMA [PubChem=4792] and ionomycin [PubChem=3733]. 17237765 684/1510 Jessica Robertson 8.29993181105845e-07 4.21381153484506e-06 4040 3405.09090909091 3984 8.29993491105912e-08 682 1.22015583108849 -1.07992026781326 -1 2.39739319807339 4040 3984 4439 4572 682 1503 3863 4612 3005 4177 2579 4354 M725 REACTOME_TRANSPORT_OF_MATURE_TRANSCRIPT_TO_CYTOPLASM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_MATURE_TRANSCRIPT_TO_CYTOPLASM.html Genes involved in Transport of Mature Transcript to Cytoplasm 38/92 Reactome 0.466738071388703 0.50186659075894 3220 3881.27272727273 3985 0.0555555555555556 3218 1.54668507782595 -1.54668507782595 -1 0.169273872388093 3218 4585 3676 4200 4512 3535 3985 3290 4074 4126 3493 4355 M1032 REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_MITOTIC_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_MITOTIC_PROTEINS.html Genes involved in APC/C:Cdc20 mediated degradation of mitotic proteins 44/85 Reactome 0.998447053758475 0.999999893590849 3745 4108.90909090909 3987 0.444542821459445 3651 0.74351706699215 -0.74351706699215 -1 1.07627432806378e-08 3741 4582 3685 4272 4491 3651 3873 3987 4611 4443 3862 4356 M2479 SUZUKI_CTCFL_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SUZUKI_CTCFL_TARGETS_UP.html Genes up-regulated in testis tissue upon knockout of CTCFL [GeneID=140690]. 20231363 6/17 Arthur Liberzon 0.822436702569706 0.854910911322458 3190 3912.72727272727 3988 0.158730158730159 3010 0.626092328563209 0.626092328563209 1 0.0155801503209778 3186 3383 4675 3988 4516 3010 3471 4539 4296 4677 3299 4357 M8780 MUELLER_COMMON_TARGETS_OF_AML_FUSIONS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MUELLER_COMMON_TARGETS_OF_AML_FUSIONS_DN.html Down-regulated target genes shared by acute myeloid leukemia (AML) translocation products PML RARA [GeneID=5371;5914], AML1 ETO [GeneID=861;862], and PLZF RARA [GeneID=5914;7704]. 15024077 22/71 Arthur Liberzon 0.232850105696956 0.258012673278774 4430 3813.36363636364 3989 0.0238095238095238 2509 1.21814061000641 -1.13275139295871 -1 0.261974513292302 4429 4334 2509 4385 3989 4082 3690 3363 3910 3246 4010 4358 M13158 BIOCARTA_LONGEVITY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LONGEVITY_PATHWAY.html The IGF-1 Receptor and Longevity 11/25 BioCarta 0.0730217621623932 0.090860323285442 4440 3933.45454545455 3991 0.0068694954533257 3239 0.697706624490691 -0.636933935209298 -1 0.265646311525454 4437 3612 3295 3548 3542 3239 4618 4307 4389 4290 3991 4359 M10450 REACTOME_GAB1_SIGNALOSOME http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAB1_SIGNALOSOME.html Genes involved in GAB1 signalosome 25/46 Reactome 0.0839184282471183 0.0965721401684667 3995 3800.81818181818 3991 0.00793650793650794 2937 0.877117161977081 -0.997675080204945 -1 0.325466491124557 3994 3646 3531 2949 4492 4241 3991 2937 3699 4003 4326 4360 M6520 BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_UP.html Genes up-regulated in patients at the incipient stage of Alzheimer's disease. 14769913 290/826 John Newman 1.37178444260259e-05 3.27801218665768e-05 4640 3563.54545454545 3995 1.24708454207253e-06 1801 1.43069797824806 -1.16276753717199 -1 2.34514950526402 4637 4249 2576 3743 1801 2386 4084 4440 3279 3995 4009 4361 M2536 ABRAMSON_INTERACT_WITH_AIRE http://www.broadinstitute.org/gsea/msigdb/cards/ABRAMSON_INTERACT_WITH_AIRE.html Proteins interacting with AIRE [GeneID=326], based on massspectroscopy analysis of co-immunoprecipitates in 293T cells (embryonic kidney). 20085707 41/101 Arthur Liberzon 0.998891390156452 0.999999893590849 3275 4055.18181818182 3997 0.461304285072356 3271 0.800386288607798 -0.800386288607798 -1 1.17233814712957e-08 3271 4660 3316 3811 4496 3924 4479 3997 4622 4137 3894 4362 M6729 REACTOME_RECRUITMENT_OF_NUMA_TO_MITOTIC_CENTROSOMES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RECRUITMENT_OF_NUMA_TO_MITOTIC_CENTROSOMES.html Genes involved in Recruitment of NuMA to mitotic centrosomes 5/13 Reactome 0.971282091030123 0.988581207334309 2885 3886.27272727273 3998 0.298842988241517 2884 0.160608230087116 0.19851084120622 1 0.000292806233848793 2884 4415 3998 4170 4380 3263 3440 3620 4647 4370 3562 4363 M7982 ISHIKAWA_STING_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/ISHIKAWA_STING_SIGNALING.html Prmary innate immune response genes induced in 293T cells (embryonic kidney) by overexpression of STING (TMEM173) [GeneID=340061]. 18724357 6/9 Jessica Robertson 0.257116726491607 0.284095491709425 2335 3551 4000 0.0292842906047973 1981 0.865959434211689 0.865959434211689 1 0.172995695189782 2331 4538 4513 4547 4000 2252 1981 3742 4199 4615 2343 4364 M1249 YU_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/YU_MYC_TARGETS_UP.html Genes up-regulated in B cell lymphoma tumors expressing an activated form of MYC [GeneID=4609]. 16382050 15/54 Kevin Vogelsang 0.514011397665828 0.550424453716195 3845 3886.90909090909 4001 0.0634920634920635 1986 1.98003947840864 -1.98003947840864 -1 0.187671977947691 3843 4199 1986 4248 4465 4335 3856 4001 4099 3773 3951 4365 M2289 MUELLER_COMMON_TARGETS_OF_AML_FUSIONS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MUELLER_COMMON_TARGETS_OF_AML_FUSIONS_UP.html Up-regulated target genes shared by acute myeloid leukemia (AML) translocation products PML RARA [GeneID=5371;5914], AML1 ETO [GeneID=861;862], and PLZF RARA [GeneID=5914;7704]. 15024077 8/22 Arthur Liberzon 0.0525071377525905 0.0662310760453941 3035 3431.81818181818 4001 0.0053790682523755 1672 0.855249835097963 -0.855249835097963 -1 0.36855582834393 3033 4345 4540 4312 4001 1672 2391 1912 4562 4626 2356 4366 M780 REACTOME_CDC6_ASSOCIATION_WITH_THE_ORC_ORIGIN_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CDC6_ASSOCIATION_WITH_THE_ORC_ORIGIN_COMPLEX.html Genes involved in CDC6 association with the ORC:origin complex 6/11 Reactome 0.98844183711053 0.999176814272271 4380 3950 4002 0.359839488462719 3214 0.287480783599851 -0.337979157892313 -1 3.75809941216351e-05 3445 4211 4002 4377 4324 3383 3214 3767 4618 4376 3733 4367 M109 REACTOME_VIRAL_MESSENGER_RNA_SYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_VIRAL_MESSENGER_RNA_SYNTHESIS.html Genes involved in Viral Messenger RNA Synthesis 5/17 Reactome 0.896424399613729 0.924437662101658 4085 3886.72727272727 4002 0.202876255545448 3158 0.183726748754181 -0.161803213600227 -1 0.00229155603037187 3730 3869 4081 4002 4085 3290 3158 4156 4623 4437 3323 4368 M13133 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS.html Genes associated with the same cis-regulatory QTL (quantitative trait loci) in both brain and hematopoietic stem cells (HSC). 15711547 48/91 Jean Junior 0.0839184282471183 0.0965721401684667 4340 3913.90909090909 4003 0.00793650793650794 3136 1.1444484855792 -1.24323122568601 -1 0.42466348795983 4337 4138 3553 4003 4387 3937 4194 3874 3469 4025 3136 4369 M16036 CHANDRAN_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANDRAN_METASTASIS_UP.html Genes up-regulated in metastatic tumors from the whole panel of patients with prostate cancer. 17430594 119/361 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3470 3818.45454545455 4004 0.00793650793650794 2666 1.26467258523616 1.30571915724634 1 0.469274308242697 3467 4258 3414 4450 4004 4293 2666 4148 3392 3441 4470 4370 M18394 ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP.html Genes in discrete regions of gain within 16q region detected in individual invasive breast cancer tumors. 16702952 30/97 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4005 4014.90909090909 4005 0.00793650793650794 2926 1.3188209130246 -1.12707623418764 -1 0.48936679657474 4005 4661 2926 4617 4535 4563 3784 3818 3267 3647 4341 4371 M6740 SABATES_COLORECTAL_ADENOMA_SIZE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SABATES_COLORECTAL_ADENOMA_SIZE_UP.html A selection of genes whose expression displayed significant positive correlation with size of colorectal adenoma. 18171984 9/20 Leona Saunders 0.97720699251571 0.992240946246721 4205 4010 4006 0.314858674865387 3214 0.783759958321005 0.783759958321005 1 0.000969136429664532 4205 4006 4142 3790 4436 3214 3901 3781 4520 4480 3635 4372 M1316 GROSS_HYPOXIA_VIA_ELK3_ONLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_ONLY_DN.html Genes specifically down-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of ELK3 [GeneID=2004] by RNAi. 17704799 32/59 Jessica Robertson 0.35943518917414 0.391142014809659 4150 3872.90909090909 4006 0.0396825396825397 2478 1.05120758670762 -1.09100496566985 -1 0.156643264432355 4149 3419 2478 4421 4082 4609 3988 3202 4006 3738 4510 4373 M646 REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS.html Genes involved in TGF-beta receptor signaling activates SMADs 15/38 Reactome 0.0129971865759241 0.017572076253543 3995 4007.36363636364 4007 0.00118860115090222 3289 0.852076727437729 0.789722803877716 1 0.546661957963356 3993 4195 3402 4433 3289 4216 4264 3893 4007 3768 4621 4374 M1811 MATZUK_FERTILIZATION http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_FERTILIZATION.html Genes important for fertilization, based on mouse models with female fertility defects. 18989307 2/11 Jessica Robertson 0.818558128959145 0.851417543780597 3480 3949.7 4007.5 0.172748617268684 2947 0.202121822540088 -0.384329532559157 -1 0.00516112949127097 3477 3874 4486 NA 4055 2947 3960 4109 4552 4607 3430 4375 M2202 JAZAERI_BREAST_CANCER_BRCA1_VS_BRCA2_UP http://www.broadinstitute.org/gsea/msigdb/cards/JAZAERI_BREAST_CANCER_BRCA1_VS_BRCA2_UP.html Up-regulated genes distinguishing between breast cancer tumors with mutated BRCA1 [GeneID=672] from those with mutated BRCA2 [GeneID=675]. 12096084 36/77 John Newman 0.0839184282471183 0.0965721401684667 3590 4048.90909090909 4008 0.00793650793650794 3248 1.04554982903808 -0.974878328884859 -1 0.387965769234867 4569 4507 3509 4593 4008 3586 4659 4277 3586 3996 3248 4376 M1873 VILIMAS_NOTCH1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VILIMAS_NOTCH1_TARGETS_DN.html Genes down-regulated in bone marrow progenitors by constitutively active NOTCH1 [GeneID=4851]. 17173050 7/42 Jessica Robertson 0.363403930694681 0.395106918616073 4280 4164.18181818182 4009 0.0441573713524459 3705 0.616177591342105 -0.616177591342105 -1 0.0908317339221287 4276 4009 4520 4601 3839 3705 3720 3971 4583 4621 3961 4377 M8463 DAZARD_UV_RESPONSE_CLUSTER_G3 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G3.html Cluster G3: genes increasingly up-regulated in NHEK cells (normal keratinocyte) after 6 h time point upon UV-B irradiation. 12771951 9/27 John Newman 0.0984494602353744 0.112768069093856 4190 3919.09090909091 4010 0.0103103972642358 2374 0.699307209898384 -0.826567861519588 -1 0.242275950747785 4187 2374 4397 3637 3601 4067 3662 4010 4000 4582 4593 4378 M679 REICHERT_G1S_REGULATORS_AS_PI3K_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/REICHERT_G1S_REGULATORS_AS_PI3K_TARGETS.html G1 to S phase regulators significantly changed in DanG cells (pancreatic cancer) treated with Ly294002 [PubChem=3973], a phosphoinositide 3-kinase (PI3K) inhibitor. 17483325 3/11 Jessica Robertson 0.771300967838773 0.805328951714013 3620 3958.90909090909 4012 0.137167624134479 2366 0.172666744179911 0.172666744179911 1 0.00593442924700868 3617 4012 4519 3123 4652 3837 2366 4232 4661 4620 3909 4379 M4493 REN_BOUND_BY_E2F http://www.broadinstitute.org/gsea/msigdb/cards/REN_BOUND_BY_E2F.html Genes whose promoters were bound by E2F1 and E2F4 [GeneID=1869;1874] in the primary fibroblasts WI-38, by ChIP on chip assay. 11799067 59/110 Yujin Hoshida 0.161385165508919 0.18131164842359 2645 3672.90909090909 4013 0.0158730158730159 2075 1.568520850276 -0.970328055568418 -1 0.425171564981795 2642 4267 2075 2818 4433 3830 4094 4315 3805 4110 4013 4380 M3900 MUNSHI_MULTIPLE_MYELOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/MUNSHI_MULTIPLE_MYELOMA_DN.html Genes down-regulated in multiple myeloma (MM) compared to normal plasma cells from the patient's identical twin. 12969976 6/14 Kevin Vogelsang 0.006267030068979 0.00878471519689966 3165 3839.63636363636 4013 0.000628477458933575 2707 0.921065653530816 0.921065653530816 1 0.692293837007321 3163 2707 4387 3823 3187 4170 4622 4463 4013 4576 3125 4381 M13893 GARY_CD5_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARY_CD5_TARGETS_DN.html Genes down-regulated in Daudi cells (B lymphocytes) stably expressing CD5 [GeneID=921] off a plasmid vector. 17878328 276/626 Arthur Liberzon 0.232850105696956 0.258012673278774 4015 4070 4015 0.0238095238095238 3294 1.00507950538697 -0.713493292417268 -1 0.216153383031544 4015 4620 3779 4342 4575 3294 3634 4453 3907 4235 3916 4382 M1168 SHIRAISHI_PLZF_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHIRAISHI_PLZF_TARGETS_UP.html Genes up-regulated in A375 and 397 cells (melanoma) by forced expression of PLZF [GeneID=7704] off adenovirus vector. 16862184 9/17 Arthur Liberzon 0.000473929082976915 0.000768719862523303 4080 3672.63636363636 4015 4.74030187274264e-05 2129 1.02555597131856 -0.985013623756859 -1 1.16742655073568 4076 2129 4184 3567 2777 4462 4015 4331 3845 2574 4439 4383 M17902 BIOCARTA_CASPASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CASPASE_PATHWAY.html Caspase Cascade in Apoptosis 19/39 BioCarta 0.0361142808694868 0.04630137350326 4400 3880.90909090909 4016 0.00333828277660558 2753 1.51084000090833 1.51084000090833 1 0.736929176062191 3728 4398 3258 4565 3449 4400 4121 2753 4016 3896 4106 4384 M910 REACTOME_SYNTHESIS_SECRETION_AND_INACTIVATION_OF_GIP http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_SECRETION_AND_INACTIVATION_OF_GIP.html Genes involved in Synthesis, Secretion, and Inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) 7/17 Reactome 0.910330139360585 0.936716520211616 4020 3974.72727272727 4019 0.214285714285714 3224 0.501461186966887 -0.501461186966887 -1 0.00520414829384465 4019 3788 4050 3997 4484 3224 4027 3882 4360 4419 3472 4385 M66 PID_MYC_ACTIV_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MYC_ACTIV_PATHWAY.html Validated targets of C-MYC transcriptional activation 18832364 57/136 Pathway Interaction Database 0.0839184282471183 0.0965721401684667 4005 3930 4020 0.00793650793650794 2415 2.2029711837126 -0.805618364669518 -1 0.817443022067407 4001 4642 3000 3947 4662 4128 4684 3298 2415 4020 4433 4386 M18669 MOOTHA_TCA http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_TCA.html Tricarboxylic acid related genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 10/21 Vamsi Mootha 0.0163208452795415 0.0217209545526644 4320 3962.09090909091 4020 0.00149483592499015 3327 0.224336262347295 -0.176445718410028 -1 0.136377459648355 4318 3619 3566 3485 3327 3798 4382 4062 4388 4618 4020 4387 M620 REACTOME_INSULIN_RECEPTOR_SIGNALLING_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INSULIN_RECEPTOR_SIGNALLING_CASCADE.html Genes involved in Insulin receptor signalling cascade 42/127 Reactome 0.139070793954084 0.157946131960455 4265 3977.90909090909 4023 0.0135207622133066 3543 0.93214466205322 -1.06288832754689 -1 0.273087120128824 4265 4444 3543 3614 3645 4046 3801 4488 3824 4064 4023 4388 M4864 KEGG_BASAL_TRANSCRIPTION_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASAL_TRANSCRIPTION_FACTORS.html Basal transcription factors 16/38 KEGG 0.290046004777202 0.319500606108596 3785 3849.54545454545 4024 0.0306614752155335 2469 0.911836455445393 0.940413398142939 1 0.165159922980778 3782 4078 3467 4306 4408 4110 3619 2469 4024 3796 4286 4389 M14690 REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION.html Genes involved in Mitochondrial Fatty Acid Beta-Oxidation 10/17 Reactome 0.905730589071005 0.933418416623429 3300 3842.27272727273 4028 0.193209118287285 2867 0.254465837100047 -0.364682488972151 -1 0.00278331780842301 4028 4201 3462 4245 4389 3297 2867 3299 4529 4362 3586 4390 M8180 SAKAI_TUMOR_INFILTRATING_MONOCYTES_DN http://www.broadinstitute.org/gsea/msigdb/cards/SAKAI_TUMOR_INFILTRATING_MONOCYTES_DN.html Selected genes down-regulated in inflammatory monocytes infiltrating hepatocellular carcinoma (HCC). 19074895 58/137 Jessica Robertson 0.0839184282471183 0.0965721401684667 4455 3908.81818181818 4028 0.00793650793650794 2933 1.27119653921814 1.67555956814284 1 0.47169511188734 4452 4223 3425 4023 4352 3098 2933 4199 3609 4028 4655 4391 M1490 GREENBAUM_E2A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GREENBAUM_E2A_TARGETS_UP.html Genes up-regulated in pre-B lymphocytes upon Cre-Lox knockout of E2A [GeneID=6929]. 15310760 25/58 Kevin Vogelsang 0.0839184282471183 0.0965721401684667 3690 3741.27272727273 4028 0.00793650793650794 1964 1.72390483776827 -2.14482318064945 -1 0.639678807376078 3686 4028 1964 2581 4505 4454 4225 4140 3545 3435 4591 4392 M17363 KIM_LRRC3B_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KIM_LRRC3B_TARGETS.html Immune response genes up-regulated in zenograft tumors formed by SNU-601 cells (gastric cancer) made to express LRRC3B [GeneID=116135]. 18757430 35/111 Jessica Robertson 0.0839184282471183 0.0965721401684667 4620 3815.27272727273 4029 0.00793650793650794 2421 1.45384084127185 -1.33448035008495 -1 0.539467814347632 4620 3733 2421 2463 4441 4029 4619 4666 3550 2778 4648 4393 M7272 KEGG_PARKINSONS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PARKINSONS_DISEASE.html Parkinson's disease 56/151 KEGG 0.415320710913563 0.448741722697937 3700 3897.45454545455 4030 0.0476190476190476 3123 0.873829353950382 -0.511877979964026 -1 0.111155139065644 3698 4441 3741 4030 4241 3416 3123 4117 4035 4146 3884 4394 M17830 TOMIDA_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TOMIDA_METASTASIS_UP.html Up-regulated genes associated with the acquision of metastatic potential in LNM35 cells (large cell lung cancer). 17260014 27/61 Arthur Liberzon 0.0220441983647712 0.0288948569335154 4265 3863.27272727273 4030 0.00202438476088755 3150 0.967973122888826 -1.08577338258556 -1 0.544592686358499 4261 3541 3198 3430 3374 4561 4381 3150 4147 4030 4423 4395 M1152 RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_MAPK1_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_MAPK1_UP.html Apoptotic genes dependent on MAPK1 [GeneID=5594] and up-regulated in AML12 cells (hepatocytes) after stimulation with TGFB1 [GeneID=7040]. 16909112 6/12 Arthur Liberzon 0.33296556889208 0.364210237121449 4370 3779.81818181818 4030 0.0396825396825397 2054 1.51104553864695 -1.76355639142255 -1 0.242277345513992 4369 3814 4189 2229 4016 4030 4451 4084 3992 2054 4350 4396 M889 REACTOME_DCC_MEDIATED_ATTRACTIVE_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DCC_MEDIATED_ATTRACTIVE_SIGNALING.html Genes involved in DCC mediated attractive signaling 8/22 Reactome 0.0765897756730953 0.0944224385172651 4400 3860.45454545455 4031 0.00793650793650794 2951 1.22421531399904 -1.69379145427173 -1 0.458636963562778 4396 4292 4046 4241 4155 3865 3782 4031 2951 3303 3403 4397 M9694 REACTOME_ACTIVATION_OF_THE_PRE_REPLICATIVE_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_THE_PRE_REPLICATIVE_COMPLEX.html Genes involved in Activation of the pre-replicative complex 18/30 Reactome 0.999496534166694 0.999999893590849 3080 3907.90909090909 4033 0.498606047788819 3078 0.240473945938494 -0.282701809373748 -1 2.26530969700422e-09 3078 4163 3262 3677 4391 3706 3649 4098 4620 4310 4033 4398 M1069 REACTOME_PIP3_ACTIVATES_AKT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PIP3_ACTIVATES_AKT_SIGNALING.html Genes involved in PIP3 activates AKT signaling 15/30 Reactome 0.836574911095424 0.868066880733648 3325 3771.63636363636 4033 0.151828801616084 2664 0.758479313772085 0.758479313772085 1 0.0170357912026232 3323 4039 3558 4189 4033 4063 2664 3346 4302 4452 3519 4399 M864 REACTOME_MITOTIC_G2_G2_M_PHASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOTIC_G2_G2_M_PHASES.html Genes involved in Mitotic G2-G2/M phases 44/128 Reactome 0.382825359068099 0.415740355178009 2170 3552.90909090909 4034 0.0429245231139068 1730 0.737214843071506 0.746054062236876 1 0.102716670264686 2166 4380 3637 4034 4281 2441 1730 4429 4437 4409 3138 4400 M17316 WU_HBX_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_2_UP.html Genes up-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] in primary hepatocytes. 11439330 22/42 John Newman 0.415320710913563 0.448741722697937 3745 3931.90909090909 4034 0.0476190476190476 3161 1.29149896861628 -1.47465525656265 -1 0.164284648439831 3742 4234 3161 3551 4269 4322 4070 3685 4034 3663 4520 4401 M17157 REACTOME_PYRUVATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRUVATE_METABOLISM.html Genes involved in Pyruvate metabolism 8/19 Reactome 0.117428655697494 0.133983608619055 3870 4042.09090909091 4035 0.0124138692561953 3393 0.274765939317111 -0.192413936590474 -1 0.0876739705919582 3868 3810 4035 4162 3633 4119 3393 3942 4604 4405 4492 4402 M11189 SHAFFER_IRF4_TARGETS_IN_ACTIVATED_B_LYMPHOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/SHAFFER_IRF4_TARGETS_IN_ACTIVATED_B_LYMPHOCYTE.html IRF4 [GeneID=3662] target genes induced after activation of primary B lymphocytes by anti-IgM crosslinking. 18568025 56/132 Jessica Robertson 0.0507943005835551 0.0642434797664074 4525 3947.45454545455 4036 0.00472785651582274 3282 1.17326723016107 -1.1611693579879 -1 0.511275194435207 4521 4266 3282 4101 3495 3896 4410 4070 3589 3756 4036 4403 M17204 CHIARETTI_T_ALL_RELAPSE_PROGNOSIS http://www.broadinstitute.org/gsea/msigdb/cards/CHIARETTI_T_ALL_RELAPSE_PROGNOSIS.html Genes whose expression predicted relapse in less than 2 years after chemotherapy for adult patients with T-ALL (T cell lymphoblastic leukemia). 14684422 22/68 Arthur Liberzon 0.415320710913563 0.448741722697937 4600 3985.45454545455 4037 0.0476190476190476 1889 1.68788950471526 2.22877461543649 1 0.214707360468705 4003 4597 1889 3882 4346 4614 4564 3642 4037 3666 4600 4404 M13962 REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS.html Genes involved in Activation of the AP-1 family of transcription factors 6/10 Reactome 0.460527967665402 0.495985763383148 3170 3966.63636363636 4039 0.0598505561732171 3166 0.504674660524815 -0.504674660524815 -1 0.0561774399599696 4346 3169 4039 3166 3886 4294 4648 3582 4278 4408 3817 4405 M14560 CHO_NR4A1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CHO_NR4A1_TARGETS.html Genes up-regulated in RKO cells (colon cancer) after treatment with the NR4A1 [GeneID=3164] agonist, DIM-C-pPhOCH3. 17234778 22/54 Jessica Robertson 0.00639559345666079 0.00895421300804077 4325 3759.18181818182 4039 0.000583114730293775 2173 1.76585221514989 -2.31620442213401 -1 1.32189738015381 4325 4190 2173 4084 3174 3764 4145 4039 3565 3665 4227 4406 M2340 DALESSIO_TSA_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/DALESSIO_TSA_RESPONSE.html Top genes up-regulated in HEK293 cells (fibroblast) in response to trichostatin A (TSA) [PubChem=5562]. 17709385 24/59 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4675 3816.36363636364 4039 0.00793650793650794 2547 1.2859362870099 -1.25589714786417 -1 0.477164499818957 4674 4104 2547 2678 4096 4039 4524 3851 3681 3375 4411 4407 M11318 MITSIADES_RESPONSE_TO_APLIDIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/MITSIADES_RESPONSE_TO_APLIDIN_DN.html Genes down-regulated in the MM1S cells (multiple myeloma) after treatment with aplidin [PubChem=44152164], a marine-derived compound with potential anti-cancer properties. 18593922 152/406 Jessica Robertson 0.0839184282471183 0.0965721401684667 2905 3878.09090909091 4040 0.00793650793650794 2904 1.16286542944163 1.23861599044498 1 0.431497350514431 2904 4491 3290 3890 4362 4452 3359 4040 3625 4093 4153 4408 M794 REACTOME_ACTIVATION_OF_CHAPERONES_BY_ATF6_ALPHA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_CHAPERONES_BY_ATF6_ALPHA.html Genes involved in Activation of Chaperones by ATF6-alpha 10/20 Reactome 0.423587023235753 0.457356864258695 3605 3824.81818181818 4041 0.0488510721868734 2651 0.795848744087966 -0.901398622933675 -1 0.0988331401905609 3602 3861 3017 2856 4461 4521 4041 2651 4488 4388 4187 4409 M9880 ABRAHAM_ALPC_VS_MULTIPLE_MYELOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ABRAHAM_ALPC_VS_MULTIPLE_MYELOMA_DN.html Genes down-regulated in immunoglobulin light chain amyloidosis plasma cells (ALPC) compared to multiple myeloma (MM) cells. 15388584 12/26 Kevin Vogelsang 0.929545109497602 0.953765794417728 4205 3915.63636363636 4041 0.214285714285714 2818 0.681821563523922 -1.02225042359124 -1 0.00512361067969292 4201 4041 3362 4252 4489 3460 2818 4640 4359 3621 3829 4410 M19909 AMIT_EGF_RESPONSE_40_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_40_MCF10A.html Genes whose expression peaked at 40 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 11/22 Leona Saunders 0.00135928824443776 0.00206161930831912 3940 3995.81818181818 4042 0.000123648074467313 2946 0.888636063834641 0.862135849146308 1 0.872399651718301 3940 4042 3057 4083 2946 4534 4623 4682 3974 3565 4508 4411 M15709 ACEVEDO_LIVER_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) compared to normal liver samples. 18413731 644/1528 Jessica Robertson 0.0765897756730953 0.0944224385172651 4680 3966.18181818182 4042 0.00793650793650794 2895 1.3761249912368 -1.1415929284566 -1 0.515548025350994 4679 4545 4465 3897 3753 2895 4042 4204 3202 4172 3774 4412 M12457 LY_AGING_MIDDLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LY_AGING_MIDDLE_DN.html Genes down-regulated in fibroblasts from middle-age individuals, compared to those from the young donors. 10741968 12/36 John Newman 0.999419364322855 0.999999893590849 3375 3901.09090909091 4043 0.492063492063492 2530 0.606119283272796 -0.606119283272796 -1 8.44181194725986e-09 3374 4164 2530 3174 4358 4043 3691 4015 4576 4591 4396 4413 M1017 REACTOME_DNA_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_REPLICATION.html Genes involved in DNA Replication 119/224 Reactome 0.988515516638124 0.999176814272271 2470 3882.81818181818 4044 0.333735771719465 2466 0.983005423565778 -1.04064690139522 -1 0.000128507965971751 2466 4430 3690 4044 4446 3387 3627 4161 4478 4211 3771 4414 M16789 SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY.html Cluster 3: genes strongly up-regulated in B493-6 cells (B lymphocytes) by a combination of MYC [GeneID=4609] and serum but not by each of them alone. 15516975 26/50 Leona Saunders 4.40803118551116e-05 8.9691854690861e-05 4350 3766.45454545455 4044 4.00738137229942e-06 2173 1.18723069619411 -0.983503041569833 -1 1.75636217832042 4348 3338 3435 4299 2173 4330 4288 4126 3546 3504 4044 4415 M1162 BAKER_HEMATOPOESIS_STAT1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BAKER_HEMATOPOESIS_STAT1_TARGETS.html STAT1 [GeneID=6772] targets in hematopoetic signaling. 17934481 5/11 Arthur Liberzon 0.0841574788195652 0.0968234583227308 2405 3336.90909090909 4045 0.00875255631803266 1678 0.811385032410593 -0.811385032410593 -1 0.300740908941009 2403 4045 4208 4472 4532 2150 1678 2067 4423 4502 2226 4416 M18506 CROONQUIST_IL6_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_IL6_DEPRIVATION_DN.html Genes down-regulated in the ANBL-6 cell line (multiple myeloma, MM) after withdrawal of IL6 [GeneID=3569]. 12791645 63/145 Arthur Liberzon 0.415320710913563 0.448741722697937 3620 3791.45454545455 4045 0.0476190476190476 1861 1.37367600357491 -1.31480499017071 -1 0.174737947880035 3619 3593 1861 2952 4664 4123 4627 4509 4045 3542 4171 4417 M2560 HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_DN.html Genes distinguishing prednisolone [PubChem=5755] resistant and sensitive ALL (B- and T-lineage ALL); here - genes down-regulated in the drug resistant samples. 15295046 10/16 Arthur Liberzon 0.0755900372983306 0.0939562108169701 3765 3627.63636363636 4045 0.00711995246734151 2000 2.50346982391423 2.50346982391423 1 0.939860851631697 3764 3163 2273 4222 4175 4446 4045 2000 4140 3498 4178 4418 M18436 BOYAULT_LIVER_CANCER_SUBCLASS_G3_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G3_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G3, defined by unsupervised clustering. 17187432 145/323 Yujin Hoshida 0.161385165508919 0.18131164842359 4050 4033.90909090909 4046 0.0158730158730159 3548 0.996059578975923 1.12594221096621 1 0.26999718167928 4046 4090 3661 4036 4140 3548 4428 4413 3822 4196 3993 4419 M73 TAKAO_RESPONSE_TO_UVB_RADIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKAO_RESPONSE_TO_UVB_RADIATION_UP.html Genes up-regulated in primary tissue culture of epidermal kerationcytes after UVB irradiation. 11982916 60/160 John Newman 0.0839184282471183 0.0965721401684667 3920 4041.72727272727 4047 0.00793650793650794 3652 0.978222150660282 1.01641009904554 1 0.362982900003618 3919 4179 3706 4396 4574 3652 4444 3686 3661 4047 4195 4420 M18660 ROETH_TERT_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROETH_TERT_TARGETS_UP.html Genes up-regulated in T lymphocytes overexpressing TERT [GeneID=7015] off a retrovirus vector. 15741219 8/19 Kevin Vogelsang 0.379293165668618 0.411999947687331 4050 3912.36363636364 4048 0.046570351928589 3034 0.815289299351509 -0.774094362469265 -1 0.114764536355443 4048 3034 4389 4283 3848 3426 3264 4581 4176 4578 3409 4421 M13596 YANAGISAWA_LUNG_CANCER_RECURRENCE http://www.broadinstitute.org/gsea/msigdb/cards/YANAGISAWA_LUNG_CANCER_RECURRENCE.html Genes defining a 25-signal proteomic signature associated with a high risk of cancer recurrence and poor survival of NSCLC (non-small cell lung cancer) patients. 17551146 13/31 Jessica Robertson 0.999714512065876 0.999999893590849 3640 3989 4050 0.523809523809524 2679 0.692661823509764 -0.692661823509764 -1 9.9036935574929e-09 3638 3618 3118 2679 4435 4050 4468 4648 4585 4642 3998 4422 M13492 REACTOME_DEADENYLATION_OF_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEADENYLATION_OF_MRNA.html Genes involved in Deadenylation of mRNA 15/27 Reactome 0.965659858496735 0.984783916630185 4055 4033.90909090909 4051 0.263977487428412 3073 0.15888698496375 -0.154537978160688 -1 0.000386739044059767 4051 4678 3641 4454 4392 3073 3620 4019 4560 4400 3485 4423 M850 REACTOME_PI_3K_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI_3K_CASCADE.html Genes involved in PI-3K cascade 24/61 Reactome 0.35943518917414 0.391142014809659 4490 4187.54545454545 4052 0.0396825396825397 3494 1.07700977600007 -1.23627500711406 -1 0.160488117968174 4488 4669 3494 4531 4462 3882 4052 4602 4008 3988 3887 4424 M1146 CORRADETTI_MTOR_PATHWAY_REGULATORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CORRADETTI_MTOR_PATHWAY_REGULATORS_DN.html Major antagonists linked to the mTOR [GeneID=2475] signaling network. 17041621 7/29 Leona Saunders 0.210647530761723 0.235022459321294 3735 3945.45454545455 4053 0.0233766643790315 3221 0.606818588177895 0.606818588177895 1 0.139493267479284 3504 3221 4183 3652 3731 4159 4053 4456 4216 4491 3734 4425 M18833 HU_ANGIOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HU_ANGIOGENESIS_DN.html Down-regulated genes that separate angiogenic from non-angiogenic non-small cell lung carcinoma (NSCLC) samples. 15592519 23/71 Leona Saunders 0.463515516703437 0.499088628509261 4210 3994.45454545455 4054 0.0550381233703971 3441 0.605670461735873 0.588442656940275 1 0.0668200803192999 4207 4073 3441 4100 3878 3918 3624 3722 4430 4492 4054 4426 M925 REACTOME_SIGNAL_REGULATORY_PROTEIN_SIRP_FAMILY_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_REGULATORY_PROTEIN_SIRP_FAMILY_INTERACTIONS.html Genes involved in Signal regulatory protein (SIRP) family interactions 8/15 Reactome 0.00270007756066949 0.00395887467124444 4390 3821.90909090909 4055 0.000270336387028841 2855 0.809947021061508 -0.86525486839667 -1 0.711256564068497 4387 3133 4055 3160 3060 4174 2855 4676 3807 4420 4314 4427 M1443 REACTOME_GLUTATHIONE_CONJUGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUTATHIONE_CONJUGATION.html Genes involved in Glutathione conjugation 13/32 Reactome 0.161385165508919 0.18131164842359 4055 3825.90909090909 4055 0.0158730158730159 2208 0.935456052385338 -1.09289641104993 -1 0.253569668874275 4055 2208 2954 3572 4260 4288 4325 4299 3781 3679 4664 4428 M4448 BOYAULT_LIVER_CANCER_SUBCLASS_G23_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G23_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G23, defined by unsupervised clustering. 17187432 29/68 Yujin Hoshida 0.912207156538424 0.938235894543252 3855 4021 4055 0.198412698412698 3184 0.983544052341924 -1.02785928628644 -1 0.00995414323544205 3851 4457 3184 4264 4425 3703 4187 3955 4347 4055 3803 4429 M10739 CROONQUIST_NRAS_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_NRAS_SIGNALING_DN.html Genes down-regulated in ANBL-6 cell line (multiple myeloma, MM) expressing a constantly active form of NRAS [GeneID=4893] off a plasmid vector compared to those grown in the presence of IL6 [GeneID=3569]. 12791645 45/102 Arthur Liberzon 0.912207156538424 0.938235894543252 2090 3709.54545454545 4056 0.198412698412698 2090 1.11935927516644 1.34972726585453 1 0.0113286870826251 2090 4449 2434 2728 4601 4019 3727 4267 4348 4086 4056 4430 M1044 REACTOME_CONVERSION_FROM_APC_C_CDC20_TO_APC_C_CDH1_IN_LATE_ANAPHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CONVERSION_FROM_APC_C_CDC20_TO_APC_C_CDH1_IN_LATE_ANAPHASE.html Genes involved in Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase 11/21 Reactome 0.966629843240334 0.985344234375507 3675 3955.90909090909 4057 0.265892196481389 2943 0.224549252536994 0.196420753141352 1 0.000526288971926842 3671 4469 3169 4526 4550 3065 2943 4057 4670 4448 3947 4431 M15606 MARKEY_RB1_ACUTE_LOF_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARKEY_RB1_ACUTE_LOF_UP.html Genes up-regulated in adult fibroblasts with inactivated RB1 [GeneID=5925] by Cre-lox: acute loss of function (LOF) of RB1. 17452985 159/356 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2740 3774.27272727273 4059 0.00793650793650794 2736 1.44734106341564 1.75686509906552 1 0.537055981589896 2736 4129 2751 3502 4183 4440 3855 4280 3319 4059 4263 4432 M3495 AGARWAL_AKT_PATHWAY_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/AGARWAL_AKT_PATHWAY_TARGETS.html Angiogenic and metastatic genes changed in RKO cells (colorectal cancer) upon perturbation of key components of AKT pathway. 15592509 4/11 Leona Saunders 0.170497471344962 0.191365545083232 4440 3788.45454545455 4061 0.0185192831733684 1632 1.59400497103402 -2.17401461051923 -1 0.41842321461902 4440 3467 4249 4061 3700 4072 4277 4244 3919 1632 3612 4433 M11250 FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_DN.html Genes down-regulated in MCF-7 cells (breast cancer) by selective estrogen receptor modulators (SERM) 4-hydroxytamoxifen, raloxifene, or ICI 182780 but not by estradiol [PubChem=44959;5035;3478439;5757]. 14973112 37/71 Arthur Liberzon 0.997878800752153 0.999999893590849 3250 3946.36363636364 4062 0.428571428571429 3112 0.682366935643231 -0.707376863285772 -1 9.72979171441912e-09 3249 4187 3112 3615 4563 3916 3961 4081 4545 4119 4062 4434 M129 PID_PLK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PLK1_PATHWAY.html PLK1 signaling events 18832364 31/65 Pathway Interaction Database 0.997531259367701 0.999999893590849 4025 4050.36363636364 4063 0.420634920634921 3049 1.09858160097838 1.09858160097838 1 1.67605139869188e-08 3049 4593 3397 4269 4469 4022 4024 4060 4538 4070 4063 4435 M4557 BIOCARTA_NEUROTRANSMITTERS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NEUROTRANSMITTERS_PATHWAY.html Biosynthesis of neurotransmitters 2/9 BioCarta 0.776213004254084 0.810277152580672 4015 3978.4 4063.5 0.153241768215968 3297 0.807081982395523 -0.23263843919783 -1 0.0269540121032666 4013 3302 3818 NA 4038 4220 4089 3297 4439 4266 4302 4436 M792 REACTOME_PERK_REGULATED_GENE_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PERK_REGULATED_GENE_EXPRESSION.html Genes involved in PERK regulated gene expression 16/34 Reactome 0.995144133623056 0.999999893590849 4680 4076.63636363636 4071 0.383886660849784 3231 0.208972196040663 0.262675369403195 1 1.73318031023441e-09 3231 4677 3444 4397 4252 4071 3894 3839 4678 4386 3974 4437 M1648 HU_GENOTOXIC_DAMAGE_4HR http://www.broadinstitute.org/gsea/msigdb/cards/HU_GENOTOXIC_DAMAGE_4HR.html Genes most consistently regulated at 4 h by all six genotoxins tested: cisplatin, methyl methanesulfonate, mitomycin C, taxol, hydroxyurea and etoposide [PubChem=2767;4156;5746;4666;3657;36462]. 15120960 35/65 John Newman 0.962708300639618 0.982843376208551 2550 3766.18181818182 4071 0.258439546607207 2547 0.812563908940295 -0.684086274124321 -1 0.00223226110631989 2547 4230 3028 4266 4551 3186 3492 4071 4482 4105 3470 4438 M5871 MOOTHA_PYR http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_PYR.html Genes involved in pyruvate metabolism; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 2/8 Vamsi Mootha 0.433369674096706 0.467596199128981 3890 4081.1 4073 0.0611658724740414 2969 0.258463246455409 -0.150680722181351 -1 0.0311890203256996 3886 2969 4601 NA 3889 3938 4551 4049 4178 4653 4097 4439 M2441 LE_NEURONAL_DIFFERENTIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/LE_NEURONAL_DIFFERENTIATION_DN.html Genes down-regulated during neuronal differentiation of SH-SY5Y cells (neuroblastoma) in response to stimulation by tretinoin (all-trans retinoic acid, ATRA) [PubChem=444795] and BDNF [GeneID=627]. 19635812 11/25 Arthur Liberzon 0.466738071388703 0.50186659075894 4435 3864.81818181818 4073 0.0555555555555556 2130 1.52856163282491 -1.02225042359124 -1 0.167290387971721 4435 3717 2130 3782 4538 4369 4173 3943 4073 2840 4513 4440 M7813 PETRETTO_BLOOD_PRESSURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_BLOOD_PRESSURE_DN.html Genes that are most strongly negatively correlated with systolic blood pressure (SBP). 18443592 8/14 Jessica Robertson 0.402665650834292 0.436275431169825 4095 4026.72727272727 4075 0.0502227801890923 3433 0.634408439154937 -0.68171126448364 -1 0.0835370654235229 4092 3433 4343 4075 3867 4038 3931 3640 4183 4553 4139 4441 M893 REACTOME_RESPIRATORY_ELECTRON_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESPIRATORY_ELECTRON_TRANSPORT.html Genes involved in Respiratory electron transport 38/93 Reactome 0.696629315183928 0.733739035952324 2355 3645.36363636364 4076 0.102763997028764 2185 0.582845558623966 -0.582845558623966 -1 0.0286457748301375 2354 4451 3739 4271 4259 2625 2185 4076 4595 4414 3130 4442 M14236 REACTOME_SIGNAL_ATTENUATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_ATTENUATION.html Genes involved in Signal attenuation 6/20 Reactome 0.975584103470021 0.991452420052162 3590 4116.18181818182 4076 0.310129987051104 3583 0.294973463860763 -0.128660863822084 -1 0.00040196706263796 3587 4609 4076 4620 4189 3737 3987 3583 4541 4429 3920 4443 M16304 NEBEN_AML_WITH_FLT3_OR_NRAS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NEBEN_AML_WITH_FLT3_OR_NRAS_UP.html Genes up-regulated in acute myeloid leukemia (AML) samples with constitutively activated FLT3 [GeneID=2322] or with activating point mutations within NRAS [GeneID=4893]. 15674343 5/14 Arthur Liberzon 0.888831467201411 0.917819359917544 4255 4063.36363636364 4077 0.197216962586768 2900 1.014057760828 -0.957327669993091 -1 0.0138046069742087 4251 3722 4250 4051 4077 4657 4049 3844 4464 2900 4432 4444 M8397 ELVIDGE_HIF2A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HIF2A_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) after knockdown of HIF2A [GeneID=2034] by RNAi. 16565084 5/9 Arthur Liberzon 0.33296556889208 0.364210237121449 4475 4005.72727272727 4078 0.0396825396825397 2896 1.68597784507015 1.68597784507015 1 0.270325563833818 4473 3909 4144 4078 3948 4227 4359 3505 3981 2896 4543 4445 M19135 REACTOME_POST_CHAPERONIN_TUBULIN_FOLDING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POST_CHAPERONIN_TUBULIN_FOLDING_PATHWAY.html Genes involved in Post-chaperonin tubulin folding pathway 10/22 Reactome 0.00134415220782844 0.00204237913290664 4530 3818.18181818182 4079 0.000122270378071388 2857 0.944027214555154 0.933081182405137 1 0.928183893261527 4530 3457 3177 2857 2943 3716 4330 4357 4179 4375 4079 4446 M516 REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT.html Genes involved in The citric acid (TCA) cycle and respiratory electron transport 66/157 Reactome 0.717787276500701 0.754836440233906 4320 3602.45454545455 4080 0.108641485649419 2016 0.567855231057917 -0.567855231057917 -1 0.025353630751589 2016 4318 3762 4339 4080 2614 2224 4227 4571 4319 3157 4447 M700 REACTOME_ACYL_CHAIN_REMODELLING_OF_PG http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACYL_CHAIN_REMODELLING_OF_PG.html Genes involved in Acyl chain remodelling of PG 4/18 Reactome 0.692766787621851 0.729998913154035 4420 4031.45454545455 4081 0.111317115127661 3398 0.411208267715882 -0.517862694904459 -1 0.020543715272409 4417 3816 3959 4295 3981 4138 3398 3448 4471 4342 4081 4448 M9811 SCHWAB_TARGETS_OF_BMYB_POLYMORPHIC_VARIANTS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHWAB_TARGETS_OF_BMYB_POLYMORPHIC_VARIANTS_UP.html Genes up-regulated in 293 cells (embryonic kidney) expressing polymorphic variants S427G (SNP ID=rs2070235) or I624M (SNP ID=rs11556379) of BMYB [GeneID=4605]. 18026132 8/18 Jessica Robertson 0.827668296980902 0.859967547594791 3570 3858.72727272727 4082 0.161242304136648 2633 0.768796250367993 0.768796250367993 1 0.0184115639596435 3568 3720 4316 4082 4136 4509 2633 3221 4329 4545 3387 4449 M11716 REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING.html Genes involved in Formation of ATP by chemiosmotic coupling 9/21 Reactome 0.719187203542367 0.756138935561933 2790 3708.90909090909 4083 0.119272231507922 2280 0.36003898209569 -0.36003898209569 -1 0.0159765014872477 2788 4472 4083 4256 4091 2620 2280 3923 4638 4439 3208 4450 M796 REACTOME_ACTIVATION_OF_GENES_BY_ATF4 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_GENES_BY_ATF4.html Genes involved in Activation of Genes by ATF4 12/26 Reactome 0.916617566221681 0.942122394616138 3320 4077.81818181818 4084 0.20215988294872 3316 0.217528838328174 0.258720823438328 1 0.00205879258001994 3316 4528 3453 4490 4084 3923 3932 4087 4657 4389 3997 4451 M7963 KEGG_CELL_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CELL_CYCLE.html Cell cycle 75/142 KEGG 0.0839184282471183 0.0965721401684667 3610 4105.36363636364 4085 0.00793650793650794 3156 1.5565686607844 -1.05413902433118 -1 0.577586397122644 3608 4569 3156 3751 4616 4647 4459 4046 3599 4085 4623 4452 M4572 LOCKWOOD_AMPLIFIED_IN_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LOCKWOOD_AMPLIFIED_IN_LUNG_CANCER.html Overexpressed genes with amplified copy number across 27 non-small cell lung cancer (NSCLC) cell lines. 18391978 152/320 Jessica Robertson 0.0839184282471183 0.0965721401684667 3700 3914.18181818182 4085 0.00793650793650794 2410 1.06781671287268 -0.78291128464773 -1 0.396228205433925 3697 4306 3650 4268 4632 4085 4511 2410 3449 3905 4143 4453 M12964 XU_RESPONSE_TO_TRETINOIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_RESPONSE_TO_TRETINOIN_DN.html Genes down-regulated in NB4 cells (acute promyelocytic leukemia, APL) by tretinoin [PubChem=444795] alone. 16140955 4/22 Kevin Vogelsang 0.302882295223533 0.332390265905732 3105 3481.54545454545 4086 0.035436971983329 1753 0.181896383383287 -0.181896383383287 -1 0.0318046495668953 3102 4086 4390 4161 4488 2137 1753 2532 4652 4579 2417 4454 M3905 XU_RESPONSE_TO_TRETINOIN_AND_NSC682994_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_RESPONSE_TO_TRETINOIN_AND_NSC682994_DN.html Genes down-regulated synergistically in NB4 cells (acute promyelocytic leukemia, APL) by tretinoin and NSC682994 [PubChem=444795;388304]. 16140955 5/18 Kevin Vogelsang 0.983642641300207 0.997262963464468 3830 4058.54545454545 4086 0.337217065237382 3147 0.151175157010424 -0.168580266453203 -1 6.57730134428652e-05 3827 4118 4394 4086 4416 3629 3147 3920 4667 4581 3859 4455 M3492 REACTOME_MTORC1_MEDIATED_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MTORC1_MEDIATED_SIGNALLING.html Genes involved in mTORC1-mediated signalling 6/12 Reactome 0.848890247238921 0.880261053012079 3960 3989.63636363636 4089 0.172192704569326 2513 0.209708688957436 -0.210145099748503 -1 0.00424575762178249 3958 4084 4089 4476 4270 3676 2513 3574 4589 4451 4206 4456 M2112 KIM_ALL_DISORDERS_DURATION_CORR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_DURATION_CORR_UP.html Genes whose expression in brain significantly and positively correlated with the duration of all psychiatric disorders studied. 18762803 2/16 Jessica Robertson 0.443656421821505 0.478254886739262 4285 4080.8 4089 0.0630750880175374 2787 0.172611721854415 -0.227138091751529 -1 0.0202116355895815 4282 3723 4622 NA 3896 2787 4485 3872 4616 4664 3861 4457 M3214 KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS.html Primary bile acid biosynthesis 9/26 KEGG 0.0635566421949453 0.0794839672606122 4130 4033.09090909091 4092 0.00654511101716971 3393 1.08804497814992 1.08804497814992 1 0.437369409550201 4130 3746 3788 4363 3532 4413 4092 3980 4262 3393 4665 4458 M7223 REACTOME_TRAFFICKING_OF_AMPA_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAFFICKING_OF_AMPA_RECEPTORS.html Genes involved in Trafficking of AMPA receptors 14/32 Reactome 0.0176158445900169 0.0233515835215896 3805 4000.81818181818 4092 0.00161440908921703 3339 0.769532174982967 -0.751976009954791 -1 0.458967567075286 3803 3580 3353 3922 3339 4092 4430 4557 4222 4387 4324 4459 M1260 WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP.html Genes up-regulated in rectal cancer patients resistant to radiotherapy (non-responders) relative to the sensitive ones (responders). 16585155 67/172 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3985 3957.45454545455 4092 0.00793650793650794 2847 1.4081339717098 -0.918241502027502 -1 0.522507646215428 3985 4180 3577 4403 3987 4318 4637 2847 2862 4092 4644 4460 M1667 VISALA_RESPONSE_TO_HEAT_SHOCK_AND_AGING_DN http://www.broadinstitute.org/gsea/msigdb/cards/VISALA_RESPONSE_TO_HEAT_SHOCK_AND_AGING_DN.html Genes down-regulated after heat shock in peripheral lympocytes from old donors, compared to those from the young ones. 12618007 18/28 John Newman 0.928613457766785 0.953018542070774 4095 3980.90909090909 4093 0.213346817084503 2701 0.599103495223089 0.73686194797464 1 0.00457655996797774 2701 4278 3495 4093 4094 3866 4066 4309 4495 4593 3800 4461 M19988 GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_DN.html Genes down-regulated in metastatic breast cancer tumors having type 2 amplification in the 20q13 region; involves MYBL2, STK6 and ZNF217 [GeneID=4605;6790;7764] 16899599 116/259 Leona Saunders 0.0839184282471183 0.0965721401684667 3735 4017.09090909091 4095 0.00793650793650794 3160 1.20718679556216 -1.00278367447257 -1 0.44794340837085 3731 4560 3632 4456 3861 3809 4095 4409 3160 4145 4330 4462 M11829 MENSSEN_MYC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MENSSEN_MYC_TARGETS.html Genes up-regulated by adenoviral expression of c-MYC [GeneID=4609] in HUVEC cells (umbilical vein endothelium). 11983916 47/88 Yujin Hoshida 0.985023615986936 0.997736449858204 2855 3918.09090909091 4098 0.317460317460317 2854 0.835342264795056 -0.947757548936523 -1 0.000300502111414901 2854 4503 3507 3810 4480 4108 3286 3714 4462 4098 4277 4463 M16399 WEBER_METHYLATED_ICP_IN_SPERM_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_ICP_IN_SPERM_DN.html Unmethylated germline-specific genes with intermediate-CpG-density promoters (ICP) in sperm. 17334365 7/78 Arthur Liberzon 0.626270756850124 0.664260924988611 3955 4150.45454545455 4098 0.0937339560076095 3407 0.964626333722432 0.964626333722432 1 0.0626428016691676 3407 4044 4583 4313 3951 3953 4497 3810 4355 4644 4098 4464 M15347 BIOCARTA_AKAPCENTROSOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKAPCENTROSOME_PATHWAY.html Protein Kinase A at the Centrosome 13/25 BioCarta 0.557443745451391 0.594352990030767 4460 3977.72727272727 4099 0.0714285714285714 3167 1.08171156655751 -1.4820450231858 -1 0.0893415998091716 4458 4161 3167 3926 4099 4248 3550 4036 4132 3669 4309 4465 M1085 REACTOME_APOBEC3G_MEDIATED_RESISTANCE_TO_HIV1_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOBEC3G_MEDIATED_RESISTANCE_TO_HIV1_INFECTION.html Genes involved in APOBEC3G mediated resistance to HIV-1 infection 3/10 Reactome 0.386086746459241 0.418893839756426 4245 3988.36363636364 4100 0.0476190476190476 3107 0.249735374387901 0.121999128317213 1 0.0344962285587705 4244 3107 4100 3835 4395 3915 3486 4150 4020 4461 4159 4466 M17405 ZHAN_MULTIPLE_MYELOMA_SUBGROUPS http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_SUBGROUPS.html Top genes up-regulated in MM4 vs MM1 subgroup of multiple myeloma samples. 11861292 11/37 Kevin Vogelsang 0.934513742648037 0.958024808148917 4315 4059.90909090909 4100 0.219492126878105 3394 0.323586589719987 -0.323586589719987 -1 0.00220274772078578 4315 3617 3394 4482 4100 3584 3480 4414 4633 4574 4066 4467 M1156 KONG_E2F1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KONG_E2F1_TARGETS.html Genes up-regulated in MEF cells (embryonic fibroblast) at 16 h after serum stimulation and knockdown of E2F1 [GeneID=1869] by RNAi. 16909124 8/22 Arthur Liberzon 0.0765897756730953 0.0944224385172651 4575 3984.90909090909 4103 0.00793650793650794 3307 1.50673698853398 -0.606119283272796 -1 0.564480177558963 4573 3522 4194 3854 4103 4278 3772 4424 3430 3307 4377 4468 M7079 WONG_EMBRYONIC_STEM_CELL_CORE http://www.broadinstitute.org/gsea/msigdb/cards/WONG_EMBRYONIC_STEM_CELL_CORE.html The 'core ESC-like gene module': genes coordinately up-regulated in a compendium of mouse embryonic stem cells (ESC) which are shared with the human ESC-like module. 18397753 230/477 Nikolaos Papanikolaou 0.0839184282471183 0.0965721401684667 3795 4030.18181818182 4103 0.00793650793650794 3443 1.38991330622429 -1.01552974115392 -1 0.515746615475939 3795 4624 3682 3443 4366 3834 4115 4541 3623 4206 4103 4469 M1105 GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN.html Genes down-regulated in ME-A cells (breast cancer) undergoing apoptosis in response to doxorubicin [PubChem=31703]. 17160024 1244/2619 Arthur Liberzon 1.62894967076151e-06 6.48828316484466e-06 4375 3523.27272727273 4104 1.6289508648274e-07 968 1.31932677030006 -1.08827333990472 -1 2.5018468849358 4374 4121 4165 3620 968 2449 4442 4104 2715 4129 3669 4470 M2285 CHENG_TAF7L_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CHENG_TAF7L_TARGETS.html Genes down-regulated in testis tissues upon knockout of TAF7L [GeneID=54457]. 17242199 3/8 Arthur Liberzon 0.0777359771792779 0.0957599340331483 4320 3991.72727272727 4105 0.00805971864968193 2853 0.54449468210465 -0.54449468210465 -1 0.202772340935804 4320 2853 4641 4126 3562 4025 3433 3636 4105 4670 4538 4471 M1859 RHEIN_ALL_GLUCOCORTICOID_THERAPY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RHEIN_ALL_GLUCOCORTICOID_THERAPY_DN.html Genes down-regulated in ALL (acute lymphoblastic leukemia) blasts after 1 week of treatment with glucocorticoids. 17330098 262/606 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2785 3806.90909090909 4108 0.00793650793650794 2649 1.26864825612318 1.77550049852778 1 0.470749536087617 2784 4619 3561 3383 4229 4672 4336 2649 3346 4189 4108 4472 M11298 CAFFAREL_RESPONSE_TO_THC_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_UP.html Genes up-regulated in EVSA-T cells (breast cancer) treated THC (delta-9-tetrahydrocannabinol) [PubChem=6610319]. 18454173 34/71 Jessica Robertson 0.965883269670455 0.984797432914655 3850 4131.63636363636 4108 0.264414092672934 3439 0.814993968887916 -0.76524362822269 -1 0.00198196869705352 3847 4514 3439 4108 4639 3824 4490 4398 4607 4095 3487 4473 M123 MUELLER_PLURINET http://www.broadinstitute.org/gsea/msigdb/cards/MUELLER_PLURINET.html Genes constituting the PluriNet protein-protein network shared by the pluripotent cells (embryonic stem cells, embryonical carcinomas and induced pluripotent cells). 18724358 200/443 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4625 4058.90909090909 4109 0.00793650793650794 2986 1.6683167513527 2.02904841151079 1 0.619052076628836 4102 4625 3505 4208 3884 4109 4320 4100 2986 4185 4624 4474 M14954 KIM_RESPONSE_TO_TSA_AND_DECITABINE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_RESPONSE_TO_TSA_AND_DECITABINE_DN.html Genes down-regulated in glioma cell lines treated with both decitabine [PubChem=451668] and TSA [PubChem=5562]. 16885346 7/19 Arthur Liberzon 4.4645430533674e-05 9.07235418390271e-05 4635 3772.18181818182 4112 4.46463275055468e-06 2204 0.646018424659929 -0.819143903010331 -1 0.954532120963235 4632 2562 4112 4056 2204 4555 3078 3457 4120 4466 4252 4475 M16169 ALCALA_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/ALCALA_APOPTOSIS.html Genes able to induce cell death in an expression cDNA library screen. 17621274 79/200 Jessica Robertson 0.0839184282471183 0.0965721401684667 3930 3888.18181818182 4112 0.00793650793650794 2632 1.19850274300344 -1.13963443085067 -1 0.444721070178014 3929 4566 3665 4337 4265 2632 4441 4303 3689 4112 2831 4476 M15305 PUJANA_BRCA_CENTERED_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BRCA_CENTERED_NETWORK.html Genes constituting the BRCA-centered network (BCN). 17922014 79/153 Leona Saunders 0.698152987361708 0.734848360012795 4640 4095.72727272727 4113 0.103174603174603 3522 1.28476249901192 -1.34498595828517 -1 0.0628355720852651 3737 4639 3522 4113 4637 3847 3973 4236 4214 4151 3984 4477 M10504 SEMBA_FHIT_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SEMBA_FHIT_TARGETS_DN.html Genes down-regulated in H1299 cells (non-small cell lung cancer, NSCLC) expressing the Y144F mutant form of FHIT [GeneID=2272]. 16407838 4/9 Leona Saunders 0.147859119791321 0.167157499479404 3960 3934.81818181818 4114 0.0158730158730159 2676 1.27407892517585 -1.27407892517585 -1 0.361798067178555 3960 3041 4280 4122 4467 4344 4114 4617 3802 2676 3860 4478 M10279 HORIUCHI_WTAP_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HORIUCHI_WTAP_TARGETS_DN.html Genes down-regulated in primary endothelial cells (HUVEC) after knockdown of WTAP [GeneID=9589] by RNAi. 17088532 224/539 Leona Saunders 0.0839184282471183 0.0965721401684667 3560 4055.63636363636 4115 0.00793650793650794 2833 1.28626659915283 -1.08218021017752 -1 0.47728706672266 3560 4485 2833 4115 3799 4600 4234 4546 3685 4083 4672 4479 M17096 GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_2 http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_2.html Genes exclusively up-regulated in B lymphocytes from WM (Waldenstroem's macroglobulinemia) but with a similar expression profile in MM (macroglobulinemia) and normal cells. 17252022 5/24 Arthur Liberzon 0.360855022636929 0.392517789247133 3550 3909.18181818182 4117 0.0437753431858435 2599 0.43883028163036 0.421427555119316 1 0.0651466807360481 3549 4117 4592 4155 4172 3410 3568 2599 4399 4650 3790 4480 M2132 WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN.html Genes down-regulated in RS4;11 cells (MLL, mixed lineage leukemia) in response to SB216763 [PubChem=176158], an inhibitor of GSK3B [GeneID=2932]. 20541704 263/609 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4040 4027.45454545455 4117 0.00793650793650794 2666 1.38041671176741 1.53401221309829 1 0.5122227723378 4038 4423 2666 3896 3791 4167 4584 4383 3557 4117 4680 4481 M5336 REACTOME_CELL_CYCLE_MITOTIC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CYCLE_MITOTIC.html Genes involved in Cell Cycle, Mitotic 191/409 Reactome 0.850621352955467 0.881665927880849 3910 4152.90909090909 4118 0.158730158730159 3742 0.978804465626823 -0.940648856879627 -1 0.0195690733581539 3906 4626 3742 4046 4588 3814 4118 4242 4303 4229 4068 4482 M18811 PUJANA_XPRSS_INT_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_XPRSS_INT_NETWORK.html Genes constituting the XPRSS-Int network: intersection of genes whose expression correlates with BRCA1, BRCA2, ATM, and CHEK2 [GeneID=672;675;472;11200] in a compendium of normal tissues. 17922014 122/283 Leona Saunders 0.698152987361708 0.734848360012795 3160 3974.63636363636 4118 0.103174603174603 3160 1.18749443020141 -1.20417489200326 -1 0.0580783543669648 3160 4630 3656 4118 4648 3489 3704 4270 4215 4190 3641 4483 M535 DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_UP.html Genes up-regulated in CD34+ [GeneID=947] cells isolated from bone marrow of CML (chronic myelogenous leukemia) patients, compared to those from normal donors. 17252012 917/1965 Leona Saunders 0.0603296996135507 0.0756907556597319 3765 4101.72727272727 4121 0.00620330054084866 3418 1.16825508795725 1.34757938327606 1 0.478680730426568 3762 4611 4121 4120 3525 3656 4682 4421 3418 4232 4571 4484 M101 PID_HDAC_CLASSI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HDAC_CLASSI_PATHWAY.html Signaling events mediated by HDAC Class I 18832364 38/88 Pathway Interaction Database 0.243504785595724 0.269436464061762 4280 3820.90909090909 4125 0.0250499172964959 2268 1.14803873873798 -1.30877449121866 -1 0.239002689906703 4280 4142 3270 4562 4146 2899 4489 3890 3959 4125 2268 4485 M2433 IM_SREBF1A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/IM_SREBF1A_TARGETS.html Genes differentially expressed in liver tissue upon knockout of the 1a isoform of SREBF1 [GeneID=6720]. 19564420 3/7 Arthur Liberzon 0.4792804412472 0.514998428728361 4130 3967.18181818182 4126 0.0631708641405317 2759 0.54074175336308 -0.606070604945799 -1 0.0569631793884179 4126 2759 4667 4347 3898 3408 4600 3511 4276 4675 3372 4486 M121 PID_MTOR_4PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MTOR_4PATHWAY.html mTOR signaling pathway 18832364 51/104 Pathway Interaction Database 0.751985672431077 0.78691488633587 4060 4077.18181818182 4128 0.119047619047619 3575 0.972535609023229 -1.15326602213631 -1 0.0369964147120215 4059 4576 3659 4033 4225 3856 4232 3575 4241 4128 4265 4487 M7997 SA_CASPASE_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/SA_CASPASE_CASCADE.html Apoptosis is mediated by caspases, cysteine proteases arranged in a proteolytic cascade. 13/30 SigmaAldrich 0.0441457695275424 0.0561528436498544 4535 3901.27272727273 4129 0.00409612029669059 2995 0.732205411146527 0.732205411146527 1 0.334719038596024 4533 4109 3148 4316 3471 3325 2995 4285 4311 4292 4129 4488 M4397 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_DN.html Genes from the black module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 8/17 Arthur Liberzon 0.614897683158074 0.653258432584792 3160 3685.18181818182 4130 0.0910131234949755 2117 0.741099050280441 0.741099050280441 1 0.0500919082000013 3157 4165 4130 4514 4610 2904 2117 2966 4546 4476 2952 4489 M2343 FEVR_CTNNB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FEVR_CTNNB1_TARGETS_DN.html Genes down-regulated in intestinal crypt cells upon deletion of CTNNB1 [GeneID=1499]. 17785439 395/1027 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3585 3932.63636363636 4130 0.00793650793650794 2920 1.40172863177324 1.51786159204633 1 0.5201308559581 3581 4300 2920 3177 3622 4383 4445 4578 3491 4130 4632 4490 M14532 ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY.html PI3K Pathway 27/55 Signaling Transduction KE 0.964580988386728 0.984112020809974 3560 3999.54545454545 4132 0.261904761904762 3255 0.708552034957567 -0.732391749063172 -1 0.00180142684735674 3558 4188 3545 3672 4660 4214 3255 4132 4406 4029 4336 4491 M17377 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES.html Glycosphingolipid biosynthesis - lacto and neolacto series 8/26 KEGG 0.866750129423296 0.897192645566062 4135 4070 4133 0.182539682539683 3488 0.416381697695757 -0.521916827387356 -1 0.00717073165964923 4133 3862 3796 4353 4609 3488 4174 4032 4328 4244 3751 4492 M504 REACTOME_ANDROGEN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANDROGEN_BIOSYNTHESIS.html Genes involved in Androgen biosynthesis 2/16 Reactome 0.913657080922504 0.939520974589172 4325 4101.6 4133.5 0.238266650850473 3732 0.0975978912345408 -0.162180333293174 -1 0.000966549963328849 4324 3755 3914 NA 4122 3904 3732 4145 4625 4314 4181 4493 M1944 IRITANI_MAD1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IRITANI_MAD1_TARGETS_DN.html Genes down-regulated by overexpression of MAD1 [GeneID=4084] in primary thymocytes from RAG2 [GeneID=5897] knockout mice. 12234922 40/109 Jessica Robertson 0.98087374186238 0.995101613848693 3360 4000.54545454545 4134 0.302113902912065 3039 0.622040753223063 -0.622040753223063 -1 0.000484886014694403 3360 4656 3639 4273 4417 3393 3039 4134 4614 4633 3848 4494 M105 PID_TELOMERASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TELOMERASE_PATHWAY.html Regulation of Telomerase 18832364 41/89 Pathway Interaction Database 0.236469033998112 0.261898816666309 3595 4027 4135 0.0242290650637051 3136 1.27927357103582 0.812219373991887 1 0.272085878837393 4485 4584 3592 4459 3741 3594 4587 3136 4198 4135 3786 4495 M6866 MISSIAGLIA_REGULATED_BY_METHYLATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/MISSIAGLIA_REGULATED_BY_METHYLATION_DN.html Genes down-regulated in PaCa44 and CFPAC1 cells (pancreatic cancer) after treatment with decitabine [PubChem=451668], a DNA hypomethylating agent similar to azacitidine [PubChem=9444]. 15637593 72/203 Leona Saunders 0.557443745451391 0.594352990030767 2605 3990.18181818182 4135 0.0714285714285714 2602 1.26312869985104 1.4311992298473 1 0.104325351252995 2602 4573 3337 3959 4602 4172 3920 4305 4135 4068 4219 4496 M1235 OXFORD_RALA_OR_RALB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_OR_RALB_TARGETS_UP.html Genes up-regulated after knockdown of RALA or RALB [GeneiD=5898;5899], which were also differentially expressed in bladder cancer compared to normal bladder urothelium tissue. 17496927 27/75 Arthur Liberzon 0.796944161638877 0.830253521885233 3500 4001.27272727273 4135 0.134920634920635 3173 0.878886959661843 1.03471748964898 1 0.025954098224915 3496 3997 3248 3173 4565 4494 4135 4345 4266 4031 4264 4497 M1359 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX4_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX4_DN.html Early prostate development genes (down-regulated at 6 hr dihydrotestosterone [PubChem=10635]) which are also down-regulated in localized vs metastatic prostate cancers. 18794802 14/46 Jessica Robertson 0.014329244201612 0.0192508137410418 4135 4005.81818181818 4135 0.00131122134358906 3298 0.719587360236431 -0.618848213589239 -1 0.45123874755273 4135 3553 3333 4140 3298 4519 4051 3718 4192 4550 4575 4498 M11537 CHANG_CYCLING_GENES http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_CYCLING_GENES.html Fibroblast serum response genes showing periodic expression during the cell cycle; excluded from the core serum response signature. 14737219 105/262 Arthur Liberzon 0.557443745451391 0.594352990030767 3735 4014.90909090909 4137 0.0714285714285714 2747 1.27984815656888 -1.19332714576742 -1 0.105706258222408 3734 4433 2747 3382 4642 4125 4538 4276 4137 4163 3987 4499 M9239 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_9 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_9.html Amplification hot spot 9: colocolized fragile sites and cancer genes in the 8p23-q12; 8q23 region. 16751803 2/17 Arthur Liberzon 0.997990948085852 0.999999893590849 4055 4203.3 4137.5 0.498429077785377 3751 0.117111391910668 -0.117111391910668 -1 1.81462277794506e-10 4052 4014 4223 NA 4337 3751 4404 4034 4659 4512 4047 4500 M19381 REACTOME_G2_M_CHECKPOINTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G2_M_CHECKPOINTS.html Genes involved in G2/M Checkpoints 24/46 Reactome 0.999656988059273 0.999999893590849 3575 4040.90909090909 4138 0.515796290112764 3457 0.569236511420671 0.569236511420671 1 7.81878602547152e-09 3573 4397 3457 3556 4350 3838 3764 4281 4640 4456 4138 4501 M1390 SHIN_B_CELL_LYMPHOMA_CLUSTER_6 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_6.html Cluster 6 of genes distinguishing among different B lymphocyte neoplasms. 19010892 2/16 Jessica Robertson 0.872419081245664 0.902462652255449 4090 4186.6 4140 0.204495101292184 3489 0.593132639346561 -0.946898236632457 -1 0.00966320187019762 4477 4087 4349 NA 4087 4140 4132 3489 4409 4556 4140 4502 M80 KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_UP.html Genes up-regulated in TC71 and EWS502 cells (Ewing's sarcoma) by EWSR1-FLI1 [GeneID=2130;2314] as inferred from RNAi knockdown of this fusion protein. 17114343 783/1883 Leona Saunders 0.000507905998951094 0.00081929346336827 4540 3984.36363636364 4141 5.08022122133315e-05 2787 1.31204534964693 -1.04896748645495 -1 1.48027666108195 4537 4480 4141 3814 2787 3553 4333 4659 3218 4212 4094 4503 M2368 GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP.html Genes up-regulated during later stage of differentiation of Oli-Neu cells (oligodendroglial precursor) in response to PD174265 [PubChem=4709]. 19139271 354/745 Arthur Liberzon 0.0839184282471183 0.0965721401684667 2600 3883.72727272727 4141 0.00793650793650794 2596 1.50648540406931 1.7513605316959 1 0.559002309815088 2596 4484 2778 3561 4348 4616 4093 4188 3581 4141 4335 4504 M10169 WU_APOPTOSIS_BY_CDKN1A_VIA_TP53 http://www.broadinstitute.org/gsea/msigdb/cards/WU_APOPTOSIS_BY_CDKN1A_VIA_TP53.html Genes downstream of both CDKN1A and TP53 [GeneID=1026;7157] in 2774qw1 cells (ovarian cancer). 12138103 57/116 Arthur Liberzon 0.955240661249004 0.976922247623927 4220 3961.54545454545 4142 0.246031746031746 2756 1.03427993293329 0.98193054875488 1 0.00383349676825875 4219 4182 2756 2817 4472 3952 4142 4580 4390 4021 4046 4505 M10762 IGARASHI_ATF4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IGARASHI_ATF4_TARGETS_UP.html Genes up-regulated in A549 cells (lung cancer) after knockdown of ATF4 [GeneID=468] by RNAi. 17297441 2/5 Leona Saunders 0.0173193508984456 0.0229845591362549 4650 3911 4142.5 0.00193934873614391 1574 0.34314045241188 -0.320035134094292 -1 0.205520206749412 4649 1574 4116 NA 3365 4158 4127 4169 4049 4469 4434 4506 M12104 PENG_LEUCINE_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/PENG_LEUCINE_DEPRIVATION_DN.html Genes down-regulated in BJAB cells (B-lymphoma) after leucine [PubChem=857] deprivation. 12101249 142/307 Broad Institute 0.0839184282471183 0.0965721401684667 3325 4038.45454545455 4144 0.00793650793650794 3324 1.15134790520488 -1.32248713090216 -1 0.427223613341143 3324 4492 3686 3892 4185 4291 3606 4609 3566 4144 4628 4507 M2325 LEE_BMP2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_BMP2_TARGETS_DN.html Genes down-regulated in uterus upon knockout of BMP2 [GeneID=650]. 17515606 562/1243 Arthur Liberzon 0.0765897756730953 0.0944224385172651 4650 4146.72727272727 4145 0.00793650793650794 3002 1.53763885631661 1.85212511378762 1 0.576057176067072 3751 4614 4649 3964 3874 4145 4636 4130 3002 4203 4646 4508 M3045 CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_UP.html Genes up-regulated in CD4+ [GeneID=920] T lymphocytes after stimulation with prostaglandin E2 [PubChem=5280360]. 16424048 80/192 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4150 4004.90909090909 4146 0.00793650793650794 2527 1.26558671316218 -1.09593811768502 -1 0.469613508093137 4146 4434 2527 3326 4494 4554 4138 4586 3675 3912 4262 4509 M5060 SA_FAS_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/SA_FAS_SIGNALING.html The TNF-type receptor Fas induces apoptosis on ligand binding. 7/11 SigmaAldrich 0.562604368603265 0.599157148062811 4105 4076.36363636364 4148 0.0793650793650794 2563 0.758920512736625 0.73268825289964 1 0.0617114865449428 4101 2563 3887 4128 4134 4453 4214 4483 4148 4294 4435 4510 M1029 REACTOME_INTERACTIONS_OF_VPR_WITH_HOST_CELLULAR_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERACTIONS_OF_VPR_WITH_HOST_CELLULAR_PROTEINS.html Genes involved in Interactions of Vpr with host cellular proteins 20/39 Reactome 0.0839184282471183 0.0965721401684667 4300 4101.81818181818 4148 0.00793650793650794 3313 1.54668507782595 -1.54668507782595 -1 0.573918956531547 4300 4523 3417 4607 4586 4677 4148 3313 3567 3922 4060 4511 M9693 FINETTI_BREAST_CANCERS_KINOME_GRAY http://www.broadinstitute.org/gsea/msigdb/cards/FINETTI_BREAST_CANCERS_KINOME_GRAY.html Genes in the gray cluster of protein kinases distinguishing between luminal A and basal breast cancer subtypes. 18245477 14/32 Jessica Robertson 0.367495256273024 0.399462484550079 4335 3810.90909090909 4151 0.0407873672953528 1704 0.666163048219339 -0.714626316618673 -1 0.0970407765888222 4334 3454 3299 3607 4230 3648 1704 4443 4449 4601 4151 4512 M19745 TARTE_PLASMA_CELL_VS_PLASMABLAST_DN http://www.broadinstitute.org/gsea/msigdb/cards/TARTE_PLASMA_CELL_VS_PLASMABLAST_DN.html Genes down-regulated in mature plasma cells compared with plasmablastic B lymphocytes. 12663452 219/494 Kate Stafford 0.0839184282471183 0.0965721401684667 3225 3979.63636363636 4152 0.00793650793650794 3221 1.43210021242583 1.66051595874339 1 0.531400652363856 3221 4486 3431 3685 4499 4569 4345 3560 3355 4152 4473 4513 M13814 GENTILE_UV_RESPONSE_CLUSTER_D5 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D5.html Cluster d5: genes progressively down-regulated in WS1 cells (fibroblast) through 18 h after irradiation with high dose UV-C. 12907719 26/57 John Newman 0.726270090971166 0.762046942743144 4615 4123 4152 0.111111111111111 3567 0.715394171070442 -0.799339747007882 -1 0.0308612764466664 4615 4101 3567 4096 4207 3673 4152 4439 4229 4585 3689 4514 M12073 HAHTOLA_MYCOSIS_FUNGOIDES_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_DN.html Genes down-regulated in monocytes isolated from peripheral blood samples of patients with mucosis fungoides compared to those from normal healthy donors. 16914566 4/24 Arthur Liberzon 0.76527490244494 0.799749819994868 4155 4144.36363636364 4153 0.134920634920635 3740 0.375789443039403 -0.0997739732101115 -1 0.0133303247971698 3800 3871 4153 4151 4319 4307 4361 3740 4260 4481 4145 4515 M1128 LANG_MYB_FAMILY_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LANG_MYB_FAMILY_TARGETS.html Myb family target genes. 15608679 30/54 Arthur Liberzon 0.597318307603006 0.634989471285773 3730 4026.54545454545 4153 0.0793650793650794 3172 1.00741679008222 -1.07933038353135 -1 0.0726288307563445 3726 4454 3309 3172 4406 4348 3594 4545 4153 3909 4676 4516 M490 REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE.html Genes involved in Pyruvate metabolism and Citric Acid (TCA) cycle 20/44 Reactome 0.0882050085293357 0.101306046560899 4555 4166.18181818182 4154 0.0083594190393116 3569 0.242469266154071 -0.185590073869514 -1 0.0881295614076829 4554 3896 3612 4019 3569 4122 4670 4351 4574 4307 4154 4517 M4455 EGUCHI_CELL_CYCLE_RB1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/EGUCHI_CELL_CYCLE_RB1_TARGETS.html RB1 [GeneID=5925] target genes involved in cell cycle regulation: genes down-regulated by doxorubicin [PubChem=31703] only in cells expressing RB1. 16862181 11/25 Leona Saunders 0.98836997527622 0.999176814272271 3030 3917.27272727273 4154 0.332972568931175 2265 0.38562367213027 0.37273169182921 1 5.04113600783777e-05 3027 3943 2265 3429 4534 4154 3783 4561 4624 4496 4274 4518 M2608 ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_24HR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_24HR.html Cell cycle genes significantly (p =< 0.05) changed in fibroblast cells at 24 h after exposure to ionizing radiation. 17404513 80/213 Itai Pashtan 0.63389956273523 0.671137223447195 2705 3747.90909090909 4160 0.0873015873015873 1953 1.43685787249259 -1.26841537565773 -1 0.0909604371315632 2704 4263 1953 3223 4628 4211 3791 4160 4172 3789 4333 4519 M1070 REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION.html Genes involved in Antigen processing: Ubiquitination & Proteasome degradation 108/234 Reactome 0.0839184282471183 0.0965721401684667 4465 4028.09090909091 4161 0.00793650793650794 3354 1.10740974747272 -0.872304153956382 -1 0.410919750274233 4464 4429 3710 4398 4201 3550 4161 4045 3354 4198 3799 4520 M16834 BERENJENO_TRANSFORMED_BY_RHOA_REVERSIBLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_REVERSIBLY_UP.html Genes up-regulated in NIH3T3 cells (fibroblasts) transformed by expression of contitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector; their expression reverted completely after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins. 17213802 4/10 Leona Saunders 0.982658470084167 0.99648075975209 3975 4099.63636363636 4161 0.333333333333333 3168 0.159718955556257 -0.204890765262209 -1 8.93851813537496e-05 4418 3872 4161 3168 4214 3795 4567 3975 4469 4486 3971 4521 M10501 RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP.html Genes up-regulated in poorly differentiated thyroid carcinoma (PDTC) compared to normal thyroid tissue. 17406368 420/909 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3920 4043.36363636364 4164 0.00793650793650794 3332 1.33954238883941 -1.09829089727405 -1 0.497055787685573 3918 4482 3600 3332 3822 4460 4313 4350 3431 4164 4605 4522 M3058 WALLACE_JAK2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WALLACE_JAK2_TARGETS_UP.html Genes up-regulated more than 7-fold by expressing JAK2 [GeneID=3717] in the JAK2 null cell line. 15189810 19/50 Arthur Liberzon 0.796944161638877 0.830253521885233 4620 4146.54545454545 4164 0.134920634920635 3390 0.832191792694672 -0.832191792694672 -1 0.0245751597611307 4164 3483 3390 4088 4110 4619 4583 3664 4267 4627 4617 4523 M18312 KEGG_MATURITY_ONSET_DIABETES_OF_THE_YOUNG http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MATURITY_ONSET_DIABETES_OF_THE_YOUNG.html Maturity onset diabetes of the young 5/27 KEGG 0.835038782101297 0.866664835642675 4065 4077.72727272727 4167 0.164900573506159 2493 0.268273026791118 0.222163265418698 1 0.00609437324955336 4065 4167 3809 4548 4498 3963 2493 4118 4634 4259 4301 4524 M2076 WHITFIELD_CELL_CYCLE_G2 http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_G2.html Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the G2 phase of cell cycle. 12058064 145/299 Jessica Robertson 0.0839184282471183 0.0965721401684667 3015 3915.81818181818 4168 0.00793650793650794 3014 1.1257970057223 1.16429911064494 1 0.417742597570299 3014 4426 3018 3380 4181 4459 3777 4480 3705 4168 4466 4525 M959 REACTOME_DESTABILIZATION_OF_MRNA_BY_KSRP http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DESTABILIZATION_OF_MRNA_BY_KSRP.html Genes involved in Destabilization of mRNA by KSRP 13/20 Reactome 0.936989803160346 0.959723326253417 3545 4140.81818181818 4171 0.222222222222222 3490 0.758479313772085 0.758479313772085 1 0.0049499080862211 3541 4603 3490 4608 4282 4171 3996 3933 4368 4422 4135 4526 M16010 KOBAYASHI_EGFR_SIGNALING_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOBAYASHI_EGFR_SIGNALING_24HR_DN.html Genes down-regulated in H1975 cells (non-small cell lung cancer, NSCLC) resistant to gefitinib [PubChem=123631] after treatment with EGFR inhibitor CL-387785 [PubChem=2776] for 24h. 17145885 179/370 Arthur Liberzon 0.0839184282471183 0.0965721401684667 3665 3882.09090909091 4171 0.00793650793650794 1761 1.46354884524523 1.68076532943473 1 0.543070103920169 3664 4171 1761 3039 4502 4498 4434 4427 3651 3999 4557 4527 M6506 DANG_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DANG_MYC_TARGETS_UP.html Genes up-regulated by MYC [GeneID=4609] and whose promoters are bound by MYC, according to MYC Target Gene Database. 14519204 100/250 Chi Dang 0.0839184282471183 0.0965721401684667 4445 4110.45454545455 4173 0.00793650793650794 3382 2.04045856128172 -1.04349663172894 -1 0.757140458657515 4441 4631 3653 3686 4663 3992 4279 3801 3382 4173 4514 4528 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 0.674535131409309 0.712068399590904 3980 4124.54545454545 4174 0.106179292999683 2988 0.100858010228133 -0.135229837432379 -1 0.00543697815124192 3976 4542 4356 4511 4174 3432 4083 2988 4673 4561 4074 4529 M15969 VERNELL_RETINOBLASTOMA_PATHWAY_UP http://www.broadinstitute.org/gsea/msigdb/cards/VERNELL_RETINOBLASTOMA_PATHWAY_UP.html Cluster 1: genes up-regulated by RB1, CDNK2A [GeneID=1029;5925], and one of the E2Fs (E2F1, E2F2, or E2F3 [GeneID=1869;1870;1871]). 12923195 46/123 Kevin Vogelsang 0.63389956273523 0.671137223447195 3970 4058.72727272727 4175 0.0873015873015873 2535 1.01826813611435 -0.742511505335801 -1 0.0644615697899956 3968 4023 2535 3742 4279 4455 4543 4432 4175 3998 4496 4530 M2257 SONG_TARGETS_OF_IE86_CMV_PROTEIN http://www.broadinstitute.org/gsea/msigdb/cards/SONG_TARGETS_OF_IE86_CMV_PROTEIN.html Cellular genes up-regulated in forskin fibroblasts by expression of CMV EI86 protein off an adenovirus vector. 11867723 40/80 John Newman 0.726270090971166 0.762046942743144 4175 3979.45454545455 4175 0.111111111111111 2963 0.970869210768409 -0.796116474965184 -1 0.0418821745797611 4175 3705 2963 3175 4466 4147 4176 4451 4231 4045 4240 4531 M10633 BASSO_B_LYMPHOCYTE_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/BASSO_B_LYMPHOCYTE_NETWORK.html Genes which comprise the top 1% of highly interconnected genes (major hubs) that account for most of gene interactions in the reconstructed regulatory networks from expression profiles in B lymphocytes. 15778709 102/235 Jean Junior 0.0839184282471183 0.0965721401684667 4180 4067.18181818182 4176 0.00793650793650794 3378 1.11908709705755 1.1578848104812 1 0.415252792860498 3678 4308 3645 3378 4178 4277 4676 4176 3693 4088 4642 4532 M10243 FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP.html Genes up-regulated in peripheral blood lymphocytes (PBL) from patients with acute transplant rejection compared to those from patients with well functioning kidneys more than 1-year post transplant. 15307835 54/112 Jean Junior 0.956170612539976 0.977446660201206 4070 4183.90909090909 4176 0.24746946389212 3247 0.902627693696124 -0.75915712735977 -1 0.00326863849154148 4067 4577 3247 4035 4129 4636 4005 4254 4400 4176 4497 4533 M2074 WHITFIELD_CELL_CYCLE_G1_S http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_G1_S.html Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the G1/S phase of cell cycle. 12058064 75/193 Jessica Robertson 0.0839184282471183 0.0965721401684667 4180 4031.09090909091 4176 0.00793650793650794 3138 1.36529792808375 1.48074939066341 1 0.506612737879386 3317 4176 3138 4393 4647 4680 3913 4179 3621 3946 4332 4534 M2044 KEGG_SPLICEOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SPLICEOSOME.html Spliceosome 79/188 KEGG 0.99971037388422 0.999999893590849 4165 4222 4177 0.523186126096224 3761 0.578713217742273 -0.578713217742273 -1 7.97886709842355e-09 4162 4641 3761 4045 4363 3887 4177 4431 4653 4249 4073 4535 M2156 DUTERTRE_ESTRADIOL_RESPONSE_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DUTERTRE_ESTRADIOL_RESPONSE_24HR_UP.html Genes up-regulated in MCF7 cells (breast cancer) at 24 h of estradiol [PubChem=5757] treatment. 20406972 194/447 Jessica Robertson 0.0839184282471183 0.0965721401684667 4470 3815.90909090909 4178 0.00793650793650794 1572 1.52264409509014 -1.24375495133922 -1 0.564998216319636 4467 3727 1572 2767 4460 4178 4562 4591 3602 3644 4405 4536 M2478 FU_INTERACT_WITH_ALKBH8 http://www.broadinstitute.org/gsea/msigdb/cards/FU_INTERACT_WITH_ALKBH8.html Proteins identified by mass spectrometry in complexes containing ALKBH8 [GeneID=91801]. 20308323 9/18 Arthur Liberzon 0.555422159131177 0.593007117267874 3420 3859.18181818182 4182 0.0778644159285204 2545 0.561262134236352 -0.561262134236352 -1 0.0465582028361953 3417 4239 4674 4376 3927 2646 2545 4182 4518 4676 3251 4537 M14308 GRASEMANN_RETINOBLASTOMA_WITH_6P_AMPLIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/GRASEMANN_RETINOBLASTOMA_WITH_6P_AMPLIFICATION.html Genes changed in retinoblastoma tumors with respect to chromosome 6p amplifications. 16007192 10/23 Leona Saunders 0.62619104920917 0.664260924988611 2870 3874 4183 0.0855710386088432 2083 0.194360930491498 0.267016056806388 1 0.0126217908545216 2869 4680 3419 4594 4634 3598 2083 4183 4539 4520 3495 4538 M1213 KANG_GIST_WITH_PDGFRA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_GIST_WITH_PDGFRA_DN.html Genes down-regulated in gastrointestinal stromal tumors (GIST) with PDGFRA [GeneID=5156] mutations. 15690055 5/10 Arthur Liberzon 0.147859119791321 0.167157499479404 4645 3924.36363636364 4183 0.0158730158730159 2902 1.53661420241997 -1.53661420241997 -1 0.436349772310731 4643 4010 4259 4288 4400 4237 3578 2932 3736 2902 4183 4539 M10142 KALMA_E2F1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KALMA_E2F1_TARGETS.html DNA replication genes up-regulated in a Rat-1a cell line (fibroblast) by expression of E2F1 [GeneID=1869]. 11313881 8/13 John Newman 0.998604875842613 0.999999893590849 4015 4176.18181818182 4183 0.48184309987688 3569 0.32638827454975 -0.311097723357333 -1 3.7165795200116e-09 4011 4241 4417 4183 4329 3677 3569 4116 4648 4590 4157 4540 M5198 GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_DN.html Genes down-regulated in quiescent vs dividing CD34+ [GeneID=8842] cells isolated from peripheral blood of normal donors. 17717066 52/155 Arthur Liberzon 0.939568126258135 0.962153898523955 2450 3890.72727272727 4184 0.225170752884447 2068 1.22969511172911 1.36607812813902 1 0.00753135029574668 2447 4653 2068 3558 4656 4305 3983 4446 4438 4060 4184 4541 M665 REACTOME_TRANSCRIPTIONAL_ACTIVITY_OF_SMAD2_SMAD3_SMAD4_HETEROTRIMER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSCRIPTIONAL_ACTIVITY_OF_SMAD2_SMAD3_SMAD4_HETEROTRIMER.html Genes involved in Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer 18/61 Reactome 0.777551103547242 0.811493200717678 4620 4058.90909090909 4186 0.127717226140952 3088 0.797539268330461 -0.947373714465565 -1 0.026445449333827 4618 4038 3580 4191 4186 3739 4321 3088 4378 4339 4170 4542 M19957 FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_UP.html Genes up-regulated in genomically unstable Ewing's sarcoma tumors compared to the stable ones. 17952124 139/318 Jessica Robertson 0.466738071388703 0.50186659075894 3390 4166.36363636364 4188 0.0555555555555556 3388 1.29473905093155 1.43349252047691 1 0.141700140237104 3388 4629 3552 4116 4638 4643 4218 3771 4086 4188 4601 4543 M2904 SUNG_METASTASIS_STROMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SUNG_METASTASIS_STROMA_DN.html Genes down-regulated in metastatic vs non-metastatic stromal cells originated from either bone or prostate tissues. 19047182 28/67 Jessica Robertson 0.796944161638877 0.830253521885233 3575 4055.90909090909 4189 0.134920634920635 2993 1.45215877129405 1.45215877129405 1 0.0428831853790253 3574 4189 2993 4452 4240 4602 4031 3808 4271 4042 4413 4544 M13262 SYED_ESTRADIOL_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/SYED_ESTRADIOL_RESPONSE.html Genes responsive to estradiol [PubChem=5757] both in normal and cancer ovarian cell lines. 16116479 12/47 Arthur Liberzon 0.972114443288272 0.989097341632696 4665 4186.45454545455 4189 0.277777777777778 3332 0.771521646895487 -0.745690824888046 -1 0.00134264688394608 4663 3979 3332 3798 4402 4467 4189 4021 4424 4646 4130 4545 M17956 ZERBINI_RESPONSE_TO_SULINDAC_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZERBINI_RESPONSE_TO_SULINDAC_DN.html Selected genes down-regulated in DU145 and PC-3 cells (prostate cancer) after treatment with the NSAID (non-steroid anti-inflammatory drug) sulindac [PubChem=5352]. 17178890 2/8 Arthur Liberzon 0.964525522645257 0.984112020809974 3785 4095.8 4191.5 0.309951595285537 3059 0.159419553765359 0.159419553765359 1 0.000405307815519738 3785 4298 4115 NA 4596 3859 3059 4268 4668 4468 3842 4546 M1400 ZEILSTRA_CD44_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZEILSTRA_CD44_TARGETS_DN.html Genes implicated in apoptosis that were down-regulated in duodenum of CD44 [GeneID=960] knockout mice. 18483247 2/8 Jessica Robertson 0.976490631293578 0.991943442064103 3640 4074.8 4191.5 0.340785465610585 3161 0.243587963017894 -0.0795091924240428 -1 0.000312796428791913 3636 4088 4362 NA 4295 3645 3161 4537 4621 4564 3839 4547 M639 REACTOME_SYNTHESIS_OF_PIPS_AT_THE_EARLY_ENDOSOME_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PIPS_AT_THE_EARLY_ENDOSOME_MEMBRANE.html Genes involved in Synthesis of PIPs at the early endosome membrane 7/15 Reactome 0.75935894145697 0.794098638622486 4340 4107.72727272727 4192 0.132764648426222 3108 0.574762572684831 -0.574762572684831 -1 0.0210354884970104 4336 4412 3942 4583 4192 3628 4037 3108 4651 4334 3962 4548 M5588 HOFFMANN_LARGE_TO_SMALL_PRE_BII_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_LARGE_TO_SMALL_PRE_BII_LYMPHOCYTE_UP.html Genes up-regulated during differentiation from large pre-BII to small pre-BII lymphocyte. 11779835 133/286 Arthur Liberzon 0.0839184282471183 0.0965721401684667 4450 4016.36363636364 4193 0.00793650793650794 2695 1.38704069380897 -1.24168283820446 -1 0.514680692781836 4447 4427 2695 2955 4443 4066 4569 4668 3640 4077 4193 4549 M716 REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX.html Genes involved in Regulation of pyruvate dehydrogenase (PDH) complex 6/13 Reactome 0.662507677047796 0.700476302943585 3970 4238.90909090909 4195 0.102929882941005 3623 0.250134976706551 -0.192413936590474 -1 0.0141358365509576 4590 3623 3967 4154 3969 4532 4195 4490 4646 4347 4115 4550 M6981 KEGG_PROTEIN_EXPORT http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROTEIN_EXPORT.html Protein export 16/39 KEGG 0.985174253839929 0.997736449858204 4200 4195.90909090909 4198 0.318087301053453 3493 0.501461186966887 -0.501461186966887 -1 0.000180392579081236 4456 4342 3493 4198 4196 4051 3673 4655 4649 4251 4191 4551 M17864 GENTILE_UV_LOW_DOSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_LOW_DOSE_UP.html Selected genes up-regulated in WS1 (fibroblast) in response to irradiation with low dose UV-C. 12907719 32/54 John Newman 0.998444025612634 0.999999893590849 4370 4153.45454545455 4200 0.444444444444444 3320 0.824631417846079 -0.68229579013055 -1 1.21329316009096e-08 4366 4663 3320 3500 4345 4133 4438 4200 4558 4080 4085 4552 M9389 FINETTI_BREAST_CANCER_KINOME_RED http://www.broadinstitute.org/gsea/msigdb/cards/FINETTI_BREAST_CANCER_KINOME_RED.html Genes in the red cluster of protein kinases distinguishing between luminal A and basal breast cancer subtypes. 18245477 14/55 Jessica Robertson 0.865412014258462 0.896005457095703 3720 3978.63636363636 4201 0.166666666666667 2117 1.05897295124801 1.05897295124801 1 0.0184597338739266 3720 4004 2117 3876 4396 4520 4201 4473 4309 3730 4419 4553 M532 REACTOME_G0_AND_EARLY_G1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G0_AND_EARLY_G1.html Genes involved in G0 and Early G1 11/29 Reactome 0.991437596273865 0.999999893590849 3320 3950.18181818182 4202 0.351284679455008 2962 0.338650422802654 -0.342845501090869 -1 3.92371243965769e-09 3482 4202 2962 4522 4626 3318 3320 4330 4588 4320 3782 4554 M1862 ZHOU_PANCREATIC_ENDOCRINE_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_PANCREATIC_ENDOCRINE_PROGENITOR.html Transcription factors expressed in progenitors of endocrine pancreatic cells. 18754011 4/16 Jessica Robertson 0.830635172006998 0.862858881849876 4515 4215 4202 0.162697626047167 3776 0.258264139872328 -0.404102845742658 -1 0.00604744179690154 3973 4417 4511 4512 4045 3776 4202 3898 4596 4613 3822 4555 M1197 TERAMOTO_OPN_TARGETS_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_1.html Cluster 1: genes whose up-regulation peaked one day after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 10/19 Arthur Liberzon 0.398753076528776 0.432236159290735 3845 4082.09090909091 4203 0.0451967315205244 3189 0.781031460717116 -0.716234310788259 -1 0.103997235046256 4405 3745 3189 4233 3843 4622 3925 3843 4203 4524 4371 4556 M11153 REACTOME_ACTIVATION_OF_ATR_IN_RESPONSE_TO_REPLICATION_STRESS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_ATR_IN_RESPONSE_TO_REPLICATION_STRESS.html Genes involved in Activation of ATR in response to replication stress 22/40 Reactome 0.999793329844176 0.999999893590849 3750 4093.18181818182 4205 0.537592093222442 3395 0.569236511420671 0.569236511420671 1 7.81878602547152e-09 3746 4337 3395 3748 4378 3927 3872 4339 4637 4441 4205 4557 M10376 MOOTHA_GLYCOGEN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_GLYCOGEN_METABOLISM.html Genes involved in glycogen metabolism; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 8/25 Vamsi Mootha 0.682605025130561 0.719938588287601 4555 3781.63636363636 4207 0.108420642840333 2221 0.289235942983607 0.362262814409296 1 0.0150872217664629 2893 4207 4602 4554 4360 2810 2221 3181 4555 4655 3560 4558 M801 REACTOME_ACTIVATION_OF_CHAPERONE_GENES_BY_ATF6_ALPHA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_CHAPERONE_GENES_BY_ATF6_ALPHA.html Genes involved in Activation of Chaperone Genes by ATF6-alpha 8/18 Reactome 0.965407527043065 0.984740895020419 4035 4082.72727272727 4208 0.285671198626922 2541 0.901398622933675 -0.901398622933675 -1 0.00220031010289531 4031 4208 4012 2541 4176 4465 4389 3530 4568 4392 4598 4559 M29 SHEN_SMARCA2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHEN_SMARCA2_TARGETS_UP.html Genes whose expression positively correlated with that of SMARCA2 [GeneID=6595] in prostate cancer samples. 19074882 248/578 Jessica Robertson 0.0839184282471183 0.0965721401684667 4110 4204.09090909091 4208 0.00793650793650794 3654 1.05963977377532 -0.925143665784038 -1 0.393194038727108 4106 4424 3764 4497 4432 4044 4595 4154 3654 4208 4367 4560 M7634 REACTOME_MITOTIC_M_M_G1_PHASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOTIC_M_M_G1_PHASES.html Genes involved in Mitotic M-M/G1 phases 108/203 Reactome 0.999185469605757 0.999999893590849 3075 4067 4209 0.476190476190476 3071 0.893431811932545 -0.938300436240473 -1 1.32951118491019e-08 3071 4632 3683 4209 4477 3630 3927 4373 4566 4214 3955 4561 M1165 BAKER_HEMATOPOESIS_STAT5_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BAKER_HEMATOPOESIS_STAT5_TARGETS.html STAT5 [GeneID=6777] targets in hematopoietic signaling. 17934481 3/10 Arthur Liberzon 0.729097494342972 0.764671185875373 3905 4062.63636363636 4209 0.122430941905401 3072 0.811385032410593 -0.811385032410593 -1 0.0345594127893278 3903 3384 4209 4135 4423 4415 4420 3072 4317 4503 3908 4562 M13936 PENG_GLUTAMINE_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/PENG_GLUTAMINE_DEPRIVATION_DN.html Genes down-regulated in BJAB cells (B-lymphoma) after glutamine [PubChem=738] deprivation. 12101249 246/542 Broad Institute 0.0839184282471183 0.0965721401684667 4520 4147.63636363636 4210 0.00793650793650794 3403 1.25629892862928 -1.3462214283009 -1 0.466167146774523 4518 4554 3751 4498 4683 3747 4471 3790 3403 4210 3999 4563 M15351 SUZUKI_AMPLIFIED_IN_ORAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SUZUKI_AMPLIFIED_IN_ORAL_CANCER.html High-level amplifications detected in oral squamous cell carcinoma (OSCC) lines by array-CGH analysis. 17599052 6/24 Leona Saunders 0.0330037126280219 0.0425227927893623 3955 4026.36363636364 4212 0.00335043700385632 2960 0.479364056218788 0.479364056218788 1 0.240293465967235 3951 2960 4212 4224 3450 4627 4515 3596 3884 4505 4366 4564 M1201 TERAMOTO_OPN_TARGETS_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_5.html Cluster 5: genes whose up-regulation peaked 5 days after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 3/8 Arthur Liberzon 0.137368636087725 0.156050770595655 2740 3483.54545454545 4212 0.0146681426818103 1296 0.417338764113246 0.417338764113246 1 0.12306608218614 2737 4212 4256 4542 4546 2037 1296 3092 4565 4526 2510 4565 M1664 CHEN_ETV5_TARGETS_TESTIS http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_ETV5_TARGETS_TESTIS.html Genes down-regulated in testis from 4 week old ETV5 [GeneID=2119] knockout mice. 16107850 11/41 John Newman 0.557443745451391 0.594352990030767 4215 3912.63636363636 4212 0.0714285714285714 2193 1.07460506797698 1.14941777809686 1 0.0887546540977421 4212 3345 2193 3206 4419 4447 4617 4348 4126 3568 4558 4566 M19724 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_LIGHTYELLOW_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_LIGHTYELLOW_UP.html Genes from the lightyellow module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 9/18 Arthur Liberzon 0.315222187806214 0.345366184722918 3600 4065.72727272727 4213 0.0371581292634658 3325 0.384949971282521 0.418296398403243 1 0.0649684331716314 3600 3325 4128 4228 3807 3977 4213 4235 4435 4475 4300 4567 M19582 REACTOME_MRNA_DECAY_BY_3_TO_5_EXORIBONUCLEASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_DECAY_BY_3_TO_5_EXORIBONUCLEASE.html Genes involved in mRNA Decay by 3' to 5' Exoribonuclease 7/11 Reactome 0.999700823973171 0.999999893590849 4215 4266.54545454545 4214 0.555785552786015 3785 0.173404312403806 -0.154516944941517 -1 1.13236555645834e-09 4214 4682 4029 4561 4537 3842 3785 4050 4662 4403 4167 4568 M7854 WHITEFORD_PEDIATRIC_CANCER_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/WHITEFORD_PEDIATRIC_CANCER_MARKERS.html Differentially expressed genes in a panel of xenografts representing 8 common pediatric tumors compared to the normal tissues. 17210681 85/222 Jessica Robertson 0.415320710913563 0.448741722697937 4555 4032.63636363636 4216 0.0476190476190476 2340 1.23761798198693 -0.862771268049176 -1 0.157430737396997 4553 4314 2340 3379 4471 4153 4216 4369 4043 4037 4484 4569 M14865 PALOMERO_GSI_SENSITIVITY_DN http://www.broadinstitute.org/gsea/msigdb/cards/PALOMERO_GSI_SENSITIVITY_DN.html Down-regulated genes associated with sensitivity and resistance to gamma-secretase (GSI) in T-cell acute lymphoblastic leukemia (T-ALL) cell lines. 17873882 4/9 Jessica Robertson 0.766863439230724 0.801052625108152 4220 4058.63636363636 4218 0.135507880814763 2987 0.626577689949601 -0.626577689949601 -1 0.022064600078866 4218 4477 4526 4598 4011 2987 3336 3214 4613 4622 4043 4570 M2241 JOHNSTONE_PARVB_TARGETS_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_3_DN.html Genes down-regulated upon overexpression of PARVB [GeneID=29780] in MDA-MB-231 cells (breast cancer) cultured in 3D Matrigel only. 17998334 570/1358 Arthur Liberzon 0.0765897756730953 0.0944224385172651 3535 4140.45454545455 4218 0.00793650793650794 3415 1.23024214088409 -0.877202480094739 -1 0.460894838923183 3531 4547 4633 4117 3882 4474 4374 3799 3415 4218 4555 4571 M6171 TANG_SENESCENCE_TP53_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TANG_SENESCENCE_TP53_TARGETS_DN.html Genes down-regulated in WI-38 cells (senescent primary fibroblasts) after inactivation of TP53 [GeneID=7157] by GSE56 polypeptide. 17533371 37/94 Leona Saunders 0.96855221189793 0.986445482493741 3355 4011.90909090909 4219 0.26984126984127 2431 1.11178409531248 -1.00987648635424 -1 0.00240861753267379 3355 4453 2431 3746 4643 4219 3736 4507 4419 4011 4611 4572 M17370 BIOCARTA_RANMS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RANMS_PATHWAY.html Role of Ran in mitotic spindle regulation 6/15 BioCarta 0.984561117257313 0.997736449858204 4040 4190 4220 0.341036155269348 3824 0.172828968209564 -0.197004103136194 -1 6.21712580004676e-05 4037 4414 3865 4555 4220 3836 4273 3824 4664 4284 4118 4573 M1463 TIEN_INTESTINE_PROBIOTICS_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_24HR_UP.html Genes up-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 24h. 16394013 378/786 Arthur Liberzon 0.0181605444352211 0.0240125031668866 4240 4099.09090909091 4220 0.00166474651499457 3238 1.25293721291556 1.55288541384279 1 0.741730756130605 4237 4615 3753 4119 3347 4081 4608 4430 3238 4220 4442 4574 M18917 MORI_IMMATURE_B_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_IMMATURE_B_LYMPHOCYTE_DN.html Down-regulated genes in the B lymphocyte developmental signature based on expression profiling of lymphomas from the Emu-myc transgenic mice: the immature B stage. 18922927 83/197 Jessica Robertson 0.298735036746822 0.327992591892129 3270 3910.18181818182 4220 0.0317460317460317 2211 1.28079685139752 1.34302808661898 1 0.22665580420013 3270 4220 2211 2595 4649 4572 4328 4596 3972 4022 4577 4575 M2050 VISALA_AGING_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/VISALA_AGING_LYMPHOCYTE_UP.html Genes up-regulated in peripheral lymphocytes from old individuals compared to those from young donors. 12618007 6/14 Arthur Liberzon 0.0389349747326344 0.0497679464258388 3935 4041.27272727273 4222 0.00396344554711475 3167 0.253874446391308 -0.164478400994605 -1 0.120920353230923 3935 3167 4612 3858 3466 4249 3576 4222 4422 4658 4289 4576 M7081 FARMER_BREAST_CANCER_CLUSTER_8 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_8.html Cluster 8: selected ERBB2 [GeneID=2064] amplicon genes clustered together across breast cancer samples. 15897907 5/12 Leona Saunders 0.135740820486158 0.154288810196909 4365 4009.27272727273 4224 0.0144823648104124 3114 0.328331536842144 -0.221956526638158 -1 0.0974112163211675 4362 3405 4239 4360 3660 3114 3678 4502 4224 4521 4037 4577 M5714 WILLIAMS_ESR2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WILLIAMS_ESR2_TARGETS_DN.html Genes uniquely down-regulated in T47D cells (breast cancer) by induction of ESR2 [GeneID=2100] expression in the Tet-Off system. 17700529 10/19 Jessica Robertson 0.765868596165638 0.800191804154332 3075 3853.18181818182 4224 0.123648868495759 2468 0.298195445127419 -0.277441786507176 -1 0.0105516897710858 4224 4471 3072 4525 4287 3429 2468 3075 4297 4543 3994 4578 M5304 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_8 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_8.html Amplification hot spot 8: colocolized fragile sites and cancer genes in the 9q11-34 region. 16751803 5/17 Arthur Liberzon 0.52878652641509 0.565729146753679 4515 3663.45454545455 4225 0.0724832313767492 2001 0.160237454090267 0.160237454090267 1 0.0144899841734455 2810 4295 4225 4515 4233 2531 2001 3590 4617 4514 2967 4579 M1537 MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_8 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_8.html Cluster 8: genes down-regulated in SW260 cells (colon cancer) by sodium butyrate, curcumin, sulindac and TSA [PubChem=5222465;969516;5352;5562]. 10969808 5/19 John Newman 0.976059749259925 0.991720725288813 3300 3980.63636363636 4228 0.311485850978956 3115 0.601131574055522 0.601131574055522 1 0.000793356648403179 3298 4475 4405 4600 4228 3207 3115 3628 4603 4584 3644 4580 M13087 REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA.html Genes involved in Processing of Capped Intron-Containing Pre-mRNA 81/214 Reactome 0.964580988386728 0.984112020809974 4330 4250.54545454545 4230 0.261904761904762 3747 1.06543599231755 -1.06543599231755 -1 0.00270877161768581 4328 4638 3747 4412 4568 4078 4230 4119 4403 4216 4017 4581 M5075 SCHLOSSER_MYC_TARGETS_REPRESSED_BY_SERUM http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_MYC_TARGETS_REPRESSED_BY_SERUM.html Cluster 7: genes up-regulated in B493-6 cells (B lymphocytes) by MYC [GeneID=4609] and down-regulated by the combination of MYC and serum. 15516975 105/226 Leona Saunders 0.63389956273523 0.671137223447195 4520 4251.81818181818 4230 0.0873015873015873 3728 0.97287961994038 -0.882739634423672 -1 0.0615882449939049 4517 4564 3728 4274 4495 3993 4498 4164 4169 4138 4230 4582 M2114 BENPORATH_PROLIFERATION http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_PROLIFERATION.html Set 'Proliferation Cluster': genes defined in human breast tumor expression data. 18443585 97/210 Jessica Robertson 0.161385165508919 0.18131164842359 3770 4105.63636363636 4231 0.0158730158730159 3421 1.33255099826697 1.50580527659652 1 0.361208327468225 3769 4311 3421 3503 4447 4594 4339 4231 3826 4062 4659 4583 M1037 KANG_DOXORUBICIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_DOXORUBICIN_RESISTANCE_UP.html Genes up-regulated in gastric cancer cell lines: doxorubicin [PubChem=31703] resistant vs sensitive. 14734480 24/71 John Newman 0.997132701412606 0.999999893590849 3105 3894.63636363636 4235 0.412698412698413 2503 1.1117488842441 -0.952450796566922 -1 1.69829364997105e-08 3103 4279 2503 3498 4555 4235 4044 4288 4527 3371 4438 4584 M9516 PUJANA_BRCA2_PCC_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BRCA2_PCC_NETWORK.html Genes constituting the BRCA2-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient, PCC >= 0.4) with that of BRCA2 [GeneID=675] across a compendium of normal tissues. 17922014 281/743 Leona Saunders 0.0839184282471183 0.0965721401684667 4625 4163.45454545455 4236 0.00793650793650794 3635 1.23489396903182 -1.03963487567292 -1 0.458224539522822 4622 4618 3635 3816 4323 3965 4412 4381 3650 4140 4236 4585 M669 REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY.html Genes involved in Downregulation of SMAD2/3:SMAD4 transcriptional activity 11/39 Reactome 0.97530599069028 0.991384787933764 3775 4136.45454545455 4239 0.285714285714286 3518 0.947373714465565 -0.947373714465565 -1 0.00130127110152644 3772 4409 3518 4185 4355 4152 3722 4239 4433 4340 4376 4586 M2015 CROONQUIST_STROMAL_STIMULATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_STROMAL_STIMULATION_DN.html Genes down-regulated in ANBL-6 cell line (multiple myeloma, MM) co-cultured with bone marrow stromal cells compared to those grown in the presence of IL6 [GeneID=3569]. 12791645 4/20 Arthur Liberzon 0.891248594863606 0.919909893288735 4240 4024 4239 0.198979764014475 2644 0.353178489796483 -0.485593824314818 -1 0.00468034395180795 4239 3136 4557 3645 4199 4506 2644 4311 4551 4632 3844 4587 M1335 CAFFAREL_RESPONSE_TO_THC_8HR_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_8HR_3_UP.html Genes up-regulated in EVSA-T cells (breast cancer) treated with 3 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 8 h. 18454173 5/10 Jessica Robertson 0.692011014414562 0.729366534760828 3925 4122.09090909091 4242 0.11109874668471 3019 0.29673475847638 0.269104975029989 1 0.0148655117308082 3922 4046 4319 4165 4086 4382 4343 3019 4272 4547 4242 4588 M295 SIG_PIP3_SIGNALING_IN_CARDIAC_MYOCTES http://www.broadinstitute.org/gsea/msigdb/cards/SIG_PIP3_SIGNALING_IN_CARDIAC_MYOCTES.html Genes related to PIP3 signaling in cardiac myocytes 48/93 Signaling Gateway 0.834367499525838 0.866159969600814 3475 4060 4243 0.150793650793651 3129 0.898688287318233 -1.04928550299761 -1 0.0204986871788939 3472 4649 3608 4406 4630 4243 3129 3766 4292 4109 4356 4589 M2498 PHONG_TNF_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PHONG_TNF_TARGETS_DN.html Genes down-regulated in Calu-6 cells (lung cancer) at 1 h time point after TNF [GeneID=7124] treatment. 20516219 4/8 Arthur Liberzon 0.953917243927404 0.975923498091415 4680 4235.72727272727 4244 0.264887437604018 3113 0.192612415296726 -0.267724093312333 -1 0.000745180608383162 4227 4244 4677 4426 4148 4005 3113 4253 4597 4678 4225 4590 M5756 REACTOME_E2F_ENABLED_INHIBITION_OF_PRE_REPLICATION_COMPLEX_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_E2F_ENABLED_INHIBITION_OF_PRE_REPLICATION_COMPLEX_FORMATION.html Genes involved in E2F-enabled inhibition of pre-replication complex formation 5/13 Reactome 0.999400614767787 0.999999893590849 4250 4222.72727272727 4247 0.523820599571527 3618 0.147396296911647 -0.198581851679791 -1 6.93036649974475e-10 4247 4348 3974 4090 4529 4042 3618 4415 4666 4352 4169 4591 M18941 KORKOLA_EMBRYONAL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_EMBRYONAL_CARCINOMA.html Genes predicting the embryonic carcinoma (EC) subtype of nonseminomatous male germ cell tumors (NSGCT). 15870693 3/19 Leona Saunders 0.924851617760192 0.949573768804614 4250 4127 4253 0.228045037206625 2768 0.623181617430001 -0.187137175225315 -1 0.00511872448662667 4249 4120 4253 4544 4290 4087 2768 3533 4374 4523 4656 4592 M1907 CASTELLANO_HRAS_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_HRAS_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) isolated from HRAS [GeneID=3265] knockout mice. 16909116 3/9 Leona Saunders 0.0932683243465792 0.106911782751485 4550 4090.90909090909 4254 0.00974309645213706 2883 0.596291040633515 -0.18599427710763 -1 0.211633943035306 4550 2883 4157 3650 3594 4329 4254 4394 4244 4484 4461 4593 M1815 MATZUK_POST-IMPLANTATION_AND_POST-PARTUM http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_POST-IMPLANTATION_AND_POST-PARTUM.html Genes important for post-implantation and post-partum, based on mouse models with female fertility defects. 18989307 6/25 Jessica Robertson 0.177037762706991 0.198516141671442 4540 4107.63636363636 4254 0.0192959004429872 2331 0.359655898766178 -0.460268273545556 -1 0.0923144818956874 4536 3908 4488 4474 4254 4058 3795 2331 4504 4608 4228 4594 M6382 KEGG_REGULATION_OF_AUTOPHAGY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_REGULATION_OF_AUTOPHAGY.html Regulation of autophagy 18/60 KEGG 0.0248027268360143 0.0323567867354017 4465 4131.27272727273 4258 0.00228062241991968 3307 0.724921007698044 0.709889733028573 1 0.394826497579 4397 3847 3307 4437 3389 4653 4028 4461 4204 4258 4463 4595 M1079 REACTOME_APC_CDC20_MEDIATED_DEGRADATION_OF_NEK2A http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APC_CDC20_MEDIATED_DEGRADATION_OF_NEK2A.html Genes involved in APC-Cdc20 mediated degradation of Nek2A 14/31 Reactome 0.80778104511689 0.84060892236681 4455 3730.27272727273 4258 0.139223177226304 2432 0.217597879260936 0.209705100702527 1 0.00599763054002029 2432 4529 3162 4455 4420 2574 2700 4258 4672 4454 3377 4596 M18448 REACTOME_GLUCOSE_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCOSE_TRANSPORT.html Genes involved in Glucose transport 19/44 Reactome 0.0839184282471183 0.0965721401684667 4670 3951.45454545455 4260 0.00793650793650794 2659 2.07532273754488 -1.54668507782595 -1 0.770077294999179 4668 4522 2785 4560 4286 4646 3874 3677 2659 3529 4260 4597 M2163 FIGUEROA_AML_METHYLATION_CLUSTER_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_2_DN.html Cluster 2 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 2/12 Arthur Liberzon 0.0243225446650467 0.0317657314103704 4305 3896.3 4260 0.0027321744966669 1900 0.533771388773919 -0.533771388773919 -1 0.292279448680008 4301 1900 4623 NA 3420 4396 4367 4219 3980 4665 3092 4598 M808 REACTOME_CYCLIN_A_B1_ASSOCIATED_EVENTS_DURING_G2_M_TRANSITION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYCLIN_A_B1_ASSOCIATED_EVENTS_DURING_G2_M_TRANSITION.html Genes involved in Cyclin A/B1 associated events during G2/M transition 5/17 Reactome 0.999790958676171 0.999999893590849 4265 4187.81818181818 4263 0.571428571428571 3368 0.302393660613187 0.332054493701245 1 3.31126110940733e-09 4263 3468 4013 3368 4592 4526 4009 4195 4600 4395 4637 4599 M2543 GENTLES_LEUKEMIC_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/GENTLES_LEUKEMIC_STEM_CELL_DN.html Genes down-regulated in LSC (leukemic stem) cells compared to LPC (leukemia progenitor) cells from AML (acute myeloid leukemia) tumor samples. 21177505 9/40 Andrew Gentles 0.959475796616814 0.980183907335163 3935 4080.27272727273 4266 0.2742760618094 2952 1.4279092562854 -1.4279092562854 -1 0.0045369186290571 3931 4470 4679 4374 4266 3858 2952 3828 4441 3427 4657 4600 M3075 BIOCARTA_SET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SET_PATHWAY.html Granzyme A mediated Apoptosis Pathway 9/25 BioCarta 0.862730913117456 0.893624460404156 4120 3980.18181818182 4271 0.180106818909554 2745 0.229358270649139 -0.207412879703842 -1 0.00409499290922128 4117 4606 3839 4590 4524 2745 2750 4287 4636 4271 3417 4601 M839 REACTOME_DEADENYLATION_DEPENDENT_MRNA_DECAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEADENYLATION_DEPENDENT_MRNA_DECAY.html Genes involved in Deadenylation-dependent mRNA decay 32/52 Reactome 0.976799932703565 0.992042584449265 3560 4058.45454545455 4271 0.289755117583302 3145 0.64621637343787 -0.64621637343787 -1 0.000819570453666722 3559 4671 3714 4496 4573 3145 3561 4271 4631 4404 3618 4602 M2431 KAUFFMANN_MELANOMA_RELAPSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAUFFMANN_MELANOMA_RELAPSE_UP.html DNA repair and replication genes up-regulated in melanoma patients who will relapse vs patients who will not. 17891185 37/74 Jessica Robertson 0.999910410861216 0.999999893590849 3715 4105.09090909091 4272 0.571428571428571 3205 0.626699778755084 -0.684163046089497 -1 8.78945887087292e-09 3713 4328 3205 3557 4431 3928 4373 4272 4599 4541 4209 4603 M489 REACTOME_INHIBITION_OF_THE_PROTEOLYTIC_ACTIVITY_OF_APC_C_REQUIRED_FOR_THE_ONSET_OF_ANAPHASE_BY_MITOTIC_SPINDLE_CHECKPOINT_COMPONENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INHIBITION_OF_THE_PROTEOLYTIC_ACTIVITY_OF_APC_C_REQUIRED_FOR_THE_ONSET_OF_ANAPHASE_BY_MITOTIC_SPINDLE_CHECKPOINT_COMPONENTS.html Genes involved in Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components 13/22 Reactome 0.800436714769379 0.833336246480629 2530 3700.81818181818 4274 0.136283994242226 2529 0.221162728472604 0.213200578992825 1 0.00640095940061349 2529 4530 3124 4451 4276 2561 2579 4274 4671 4306 3408 4604 M1660 MULLIGAN_NTF3_SIGNALING_VIA_INSR_AND_IGF1R_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGAN_NTF3_SIGNALING_VIA_INSR_AND_IGF1R_DN.html Genes similarly down-regulated in 3T3-L1 cells (fibroblasts able to differentiate to adipocytes) upon stimulation of INSR or IGFR1 by NTF3 [GeneID=3643;3480;4908]. 12213819 4/16 John Newman 0.172716905305213 0.193750291916499 4405 4175.72727272727 4274 0.0187822068881179 3702 0.500318703070681 -0.234466264851729 -1 0.130349047075186 4402 3910 4419 4503 3702 4095 3744 4466 4274 4592 3826 4605 M17122 NUYTTEN_EZH2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NUYTTEN_EZH2_TARGETS_DN.html Genes down-regulated in PC3 cells (prostate cancer) after knockdown of EZH2 [GeneID=2146] by RNAi. 17724462 646/1509 Jessica Robertson 4.06816115144225e-05 8.37215773195361e-05 4630 4006.63636363636 4276 4.06823562806933e-06 2178 1.32184640532245 -1.11108605768778 -1 1.96996393821235 4626 4350 4309 4276 2178 3624 4578 4527 3197 4167 4241 4606 M1080 REACTOME_G2_M_DNA_DAMAGE_CHECKPOINT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G2_M_DNA_DAMAGE_CHECKPOINT.html Genes involved in G2/M DNA damage checkpoint 7/16 Reactome 0.995424174680374 0.999999893590849 4075 4243.54545454545 4277 0.416491826638662 3325 0.569236511420671 0.569236511420671 1 7.81878602547152e-09 4072 3949 4096 3325 4277 4682 4217 4407 4605 4457 4592 4607 M6907 BIOCARTA_RARRXR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RARRXR_PATHWAY.html Nuclear receptors coordinate the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription in carcinoma cells 5/21 BioCarta 0.999841501491681 0.999999893590849 4280 4255.27272727273 4278 0.583128199620296 3851 0.106773129103061 -0.129974296637943 -1 6.82774269980862e-12 4277 4416 3851 4381 4404 3878 3953 4590 4675 4278 4105 4608 M14339 BIOCARTA_ARENRF2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARENRF2_PATHWAY.html Oxidative Stress Induced Gene Expression Via Nrf2 9/19 BioCarta 0.956930203251513 0.978009799877119 4285 4169.72727272727 4279 0.26984126984127 3660 0.504674660524815 -0.504674660524815 -1 0.001781407412326 4284 4532 3853 4182 4353 3900 4439 3965 4420 4279 3660 4609 M1863 ZHOU_PANCREATIC_BETA_CELL http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_PANCREATIC_BETA_CELL.html Transcription factors expressed in adult pancreatic beta cells. 18754011 2/13 Jessica Robertson 0.914138388396787 0.939809672669448 3740 4100 4279.5 0.23873962211347 2807 0.0892124578112421 0.0892124578112421 1 0.000879154485860946 3736 4047 4512 NA 4590 3538 2807 4620 4665 4614 3871 4610 M4791 BIOCARTA_EIF4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF4_PATHWAY.html Regulation of eIF4e and p70 S6 Kinase 21/39 BioCarta 0.936989803160346 0.959723326253417 4315 4161.36363636364 4282 0.222222222222222 3499 0.697706624490691 -0.636933935209298 -1 0.00455329959627416 4313 4519 3499 4021 4153 4163 3763 4321 4369 4282 4372 4611 M4495 COLLIS_PRKDC_SUBSTRATES http://www.broadinstitute.org/gsea/msigdb/cards/COLLIS_PRKDC_SUBSTRATES.html Substrates of PRKDC [GeneID=5591]. 15592499 16/40 Jessica Robertson 0.86218646984916 0.893257969868044 4365 4178.09090909091 4282 0.164870537858266 3496 0.669166489254796 -0.606119283272796 -1 0.0119909651909263 4361 4282 3496 3944 4048 3964 4520 4344 4524 4558 3918 4612 M18789 LY_AGING_OLD_DN http://www.broadinstitute.org/gsea/msigdb/cards/LY_AGING_OLD_DN.html Genes down-regulated in fibroblasts from old individuals, compared to those from young donors. 10741968 39/99 Arthur Liberzon 0.232850105696956 0.258012673278774 4675 4128.72727272727 4283 0.0238095238095238 3240 1.58283561878937 -0.859896986399719 -1 0.340406179798211 4283 4385 3240 3438 4673 4371 4671 3796 3881 4035 4643 4613 M9402 SCIAN_CELL_CYCLE_TARGETS_OF_TP53_AND_TP73_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCIAN_CELL_CYCLE_TARGETS_OF_TP53_AND_TP73_DN.html Cell cycle genes down-regulated in H1299 cells (lung cancer) after overexpression of either P53 or P73 [GeneID=7157;7161]. 17982488 13/31 Jessica Robertson 0.988438980056112 0.999176814272271 3475 4044.27272727273 4289 0.333333333333333 2368 0.383230125084525 0.275158479517971 1 5.00984481089885e-05 3474 4289 2368 3937 4572 4230 3706 4510 4472 4544 4385 4614 M14511 NAKAMURA_BRONCHIAL_AND_BRONCHIOLAR_EPITHELIA http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_BRONCHIAL_AND_BRONCHIOLAR_EPITHELIA.html Differentiation markers for normal bronchiolar and bronchial epithelial cells. 16491115 4/18 Arthur Liberzon 0.987296406208028 0.999176814272271 4300 4239.72727272727 4296 0.353761749894802 3601 0.163403612283359 0.0650752172260069 1 2.13602007589595e-05 4296 4349 4216 3601 4542 4212 4414 3681 4593 4507 4226 4615 M14386 MCCOLLUM_GELDANAMYCIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCCOLLUM_GELDANAMYCIN_RESISTANCE_DN.html Genes down-regulated in A549GARS cells (lung cancer) resistant to the geldanamycin and 17-AAG [PubChem=5476289;6440175]. 18794130 5/13 Jessica Robertson 0.7828502534162 0.816841747385508 4380 4048 4297 0.141627228905041 2909 1.29214926568553 -1.29214926568553 -1 0.041498592692835 4376 3815 4430 4420 4297 4231 4509 3149 4334 2909 4058 4616 M8214 CHNG_MULTIPLE_MYELOMA_HYPERPLOID_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHNG_MULTIPLE_MYELOMA_HYPERPLOID_DN.html Protein biosynthesis, transport or catabolism genes down-regulated in hyperploid multiple myeloma (MM) compared to the non-hyperploid MM samples. 17409404 19/41 Jessica Robertson 0.35664834443824 0.388935104034813 4470 4192.63636363636 4298 0.0393034739528812 3568 0.875914653845502 0.936380202249759 1 0.131309156305203 4466 4336 3568 4431 3818 4298 4507 4112 4282 3904 4397 4617 M2537 MIZUSHIMA_AUTOPHAGOSOME_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/MIZUSHIMA_AUTOPHAGOSOME_FORMATION.html Key proteins in mammalian autophagosome formation. 20144757 16/22 Arthur Liberzon 0.0967937936948857 0.110925829604851 4425 4093.54545454545 4299 0.00921224978557905 3347 1.10141324090085 -1.22684838403304 -1 0.384466097202584 4623 3714 3347 4425 3585 4473 4425 4438 3896 3804 4299 4618 M15216 REACTOME_BOTULINUM_NEUROTOXICITY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BOTULINUM_NEUROTOXICITY.html Genes involved in Botulinum neurotoxicity 7/20 Reactome 0.52360610197077 0.560442712159668 4355 4086.81818181818 4300 0.0714685482189565 2822 0.326205245236796 0.263456754130062 1 0.0299843217116875 4355 3945 3923 4300 4060 4419 3751 2822 4428 4322 4630 4619 M7331 KOBAYASHI_EGFR_SIGNALING_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOBAYASHI_EGFR_SIGNALING_6HR_UP.html Genes up-regulated in H1975 cells (non-small cell lung cancer, NSCLC) resistant to gefitinib [PubChem=123631] after treatment with EGFR inhibitor CL-387785 [PubChem=2776] for 6h. 17145885 4/12 Leona Saunders 0.016202155766399 0.0215752491961767 4070 4116.09090909091 4300 0.00163215117900153 3202 0.793305133041827 0.793305133041827 1 0.483109999899047 4068 3202 4113 4418 3340 4300 4378 4366 4460 4467 4165 4620 M3828 REACTOME_PROTEOLYTIC_CLEAVAGE_OF_SNARE_COMPLEX_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROTEOLYTIC_CLEAVAGE_OF_SNARE_COMPLEX_PROTEINS.html Genes involved in Proteolytic cleavage of SNARE complex proteins 7/18 Reactome 0.52360610197077 0.560442712159668 4360 4087.81818181818 4301 0.0714685482189565 2823 0.326205245236796 0.263456754130062 1 0.0299843217116875 4356 3946 3924 4301 4061 4420 3752 2823 4429 4323 4631 4621 M10412 ZHAN_MULTIPLE_MYELOMA_PR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_PR_DN.html Top 50 down-regulated genes in cluster PR of multiple myeloma samples characterized by increased expression of proliferation and cell cycle genes. 16728703 17/69 Arthur Liberzon 0.97530599069028 0.991384787933764 4540 4121.54545454545 4303 0.285714285714286 2826 0.821093691019749 -0.991958508420229 -1 0.00112781814457848 4538 4077 2826 4516 4672 4384 3522 4221 4440 3838 4303 4622 M1050 REACTOME_PHOSPHORYLATION_OF_THE_APC_C http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHOSPHORYLATION_OF_THE_APC_C.html Genes involved in Phosphorylation of the APC/C 10/24 Reactome 0.609418881716245 0.64770625532373 4685 3747.27272727273 4319 0.0819151086165463 2062 0.195680503958396 0.178361992295147 1 0.0134914580128529 3095 4681 3054 4448 4522 2483 2062 4319 4682 4449 3425 4623 M17072 RUNNE_GENDER_EFFECT_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUNNE_GENDER_EFFECT_UP.html Up-regulated genes detecting gender effects in global expression profiling studies. 17724341 8/40 Arthur Liberzon 0.999630360939744 0.999999893590849 4250 4302.72727272727 4319 0.546290590987824 3939 0.177884695062205 -0.215073829971074 -1 1.20804844024226e-09 4248 4346 4131 4319 4503 3939 4229 4472 4644 4477 4022 4624 M1916 ZHANG_TLX_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_DN.html Genes down-regulated in neural stem cells (NSC) at both 36 h and 60 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 60/112 Jessica Robertson 0.989865950533548 0.999999893590849 4125 4101.09090909091 4322 0.341269841269841 2668 1.29285037887611 -1.4272629205233 -1 2.00421134531871e-08 4122 4322 2668 3684 4513 4079 4400 4408 4473 4116 4327 4625 M18970 CHANDRAN_METASTASIS_TOP50_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANDRAN_METASTASIS_TOP50_UP.html Top 50 genes up-regulated in metastatic vs primary prostate cancer tumors. 17430594 28/90 Arthur Liberzon 0.975266454117946 0.991384787933764 4055 4069.54545454545 4327 0.285610396410995 3135 0.698066780971794 -0.564787004596475 -1 0.000958833528091262 4054 4516 3638 4332 4327 3135 3917 4364 4461 4470 3551 4626 M16458 RIZ_ERYTHROID_DIFFERENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION.html Selected gradually up-regulated genes in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). 17213805 47/104 Leona Saunders 0.96855221189793 0.986445482493741 3925 4255.27272727273 4334 0.26984126984127 3433 0.765301292835915 0.829305561257812 1 0.00165798152439619 3925 4445 3433 4533 4334 4612 4185 4249 4416 4097 4579 4627 M1915 ZHANG_TLX_TARGETS_60HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_60HR_DN.html Genes down-regulated in neural stem cells (NSC) at 60 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 181/374 Jessica Robertson 0.667434366415499 0.704890115173097 4480 4287.63636363636 4334 0.0952380952380952 3432 1.31456365415859 -1.12903750655431 -1 0.0729789124769434 4480 4557 3432 4279 4506 4177 4550 4452 4196 4201 4334 4628 M655 REACTOME_SYNTHESIS_OF_PIPS_AT_THE_LATE_ENDOSOME_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PIPS_AT_THE_LATE_ENDOSOME_MEMBRANE.html Genes involved in Synthesis of PIPs at the late endosome membrane 6/13 Reactome 0.932530327557217 0.956605852664535 3990 4300.45454545455 4338 0.236320979187296 3892 0.138135627678898 -0.115480955639648 -1 0.000972831206278255 3988 4683 3948 4523 4118 4568 4133 3892 4674 4338 4440 4629 M2180 PUJANA_BREAST_CANCER_WITH_BRCA1_MUTATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BREAST_CANCER_WITH_BRCA1_MUTATED_UP.html The XPRSS-Int network genes up-regulated in breast tumors from patients with germline mutations in BRCA1 [GeneID=672] compared to those with the wild type allele. 17922014 33/75 Arthur Liberzon 0.999590520100346 0.999999893590849 4590 4301.90909090909 4338 0.507936507936508 3477 0.879812171797956 -0.879812171797956 -1 1.30650480978389e-08 4586 4668 3477 3954 4657 4286 4368 4338 4577 4087 4323 4630 M14418 MARTINELLI_IMMATURE_NEUTROPHIL_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTINELLI_IMMATURE_NEUTROPHIL_UP.html Neutrophil-specific genes up-regulated in comparison of immature with mature neutrophils. 15302890 4/65 Arthur Liberzon 0.735086912123852 0.770607890427823 4685 4240.90909090909 4341 0.124390748688505 3078 0.328337025069726 -0.459550220686054 -1 0.0135817934764551 4683 4168 4530 4473 4556 3864 4046 3078 4341 4623 4288 4631 M6379 KUMAMOTO_RESPONSE_TO_NUTLIN_3A_DN http://www.broadinstitute.org/gsea/msigdb/cards/KUMAMOTO_RESPONSE_TO_NUTLIN_3A_DN.html Genes down-regulated in response to nutlin-3a [PubChem=216345], an inhibitor of MDM2 [GeneID=4193], in skin fibroblast cultures after knockdown of TP53 [GeneID=7157] by RNAi. 18451145 5/17 Jessica Robertson 0.999812607559328 0.999999893590849 4545 4271.81818181818 4342 0.57608849183496 3650 0.263367485395931 0.250330152099135 1 2.65202869363099e-09 3650 4541 4473 4010 4545 4142 3741 4342 4658 4604 4284 4632 M7239 BIOCARTA_DNAFRAGMENT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DNAFRAGMENT_PATHWAY.html Apoptotic DNA fragmentation and tissue homeostasis 7/18 BioCarta 0.998091937102985 0.999999893590849 3750 4298.09090909091 4347 0.46536268302067 3749 0.335152362755275 0.378784072513931 1 3.8646230064061e-09 3749 4347 3815 4556 4674 4649 4335 3883 4645 4265 4361 4633 M715 REACTOME_REGULATORY_RNA_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATORY_RNA_PATHWAYS.html Genes involved in Regulatory RNA pathways 12/30 Reactome 0.997878800752153 0.999999893590849 4350 4289.81818181818 4347 0.428571428571429 3562 0.216787784419475 -0.164723305711463 -1 1.86520168253121e-09 4572 4200 3562 4444 4365 4313 4347 4385 4542 4346 4112 4634 M18241 NIKOLSKY_BREAST_CANCER_7P15_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_7P15_AMPLICON.html Genes within amplicon 7p15 identified in a copy number alterations study of 191 breast tumor samples. 19010930 3/13 Jessica Robertson 0.998048320609036 0.999999893590849 4685 4325.18181818182 4352 0.464152945703079 3760 0.208195145762642 -0.265475938106092 -1 1.72005433185945e-09 3871 4684 4352 4549 4320 3760 4647 4240 4684 4559 3911 4635 M7721 BIOCARTA_EIF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF_PATHWAY.html Eukaryotic protein translation 10/40 BioCarta 0.960158985072255 0.980454348234601 4515 4155.63636363636 4357 0.253968253968254 3076 0.740761778402115 0.740761778402115 1 0.00232119277010062 4512 4679 3512 4605 4357 3956 3076 3866 4397 4269 4483 4636 M867 MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN.html Genes down-regulated in low grade (LMP and G1) serous ovarian carcinomas vs the higher grade invasive tumors (G2 and G3). 15558012 12/32 Arthur Liberzon 0.837351644117051 0.868680496863516 4120 4202.45454545455 4359 0.152196070339772 3265 0.964626333722432 0.964626333722432 1 0.0215577413839427 4120 4343 3265 4390 4034 4466 3682 4359 4454 4527 4587 4637 M1945 ISHIDA_E2F_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ISHIDA_E2F_TARGETS.html Genes up-regulated in MEF cells (embryonic fibroblast) after expression of E2F1 or E2F2 [GeneID=1869;1870]. 11416145 31/63 Arthur Liberzon 0.990625451453736 0.999999893590849 4345 4120.54545454545 4359 0.345918522017423 2285 1.283030935173 -1.283030935173 -1 1.98762428405035e-08 4345 4458 2285 3130 4679 4359 4669 4505 4534 4072 4290 4638 M2040 GERHOLD_RESPONSE_TO_TZD_UP http://www.broadinstitute.org/gsea/msigdb/cards/GERHOLD_RESPONSE_TO_TZD_UP.html Genes up-regulated in 3T3-L1 cells (fibroblast) induced to differentiate to mature adipocytes and then treated with a TZD derivative AD-5075 [PubChem=128440], a PPARG [GeneID=5468] activator. 12021175 4/8 Arthur Liberzon 0.252599903025638 0.279236410846459 4545 4119.27272727273 4362 0.0286956919294833 2440 0.596690121516254 -0.557854902141481 -1 0.120836953989214 4545 3694 4609 3829 4381 4143 4362 2440 4261 4656 4392 4639 M1175 IWANAGA_E2F1_TARGETS_NOT_INDUCED_BY_SERUM http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_E2F1_TARGETS_NOT_INDUCED_BY_SERUM.html Genes up-regulated in REF52 cells (embryonic fibroblast) by expression of E2F1 [GeneID=1869] that were not induced at all at 16 hr after serum stimulation. 16288221 3/8 Arthur Liberzon 0.25081156366536 0.277324914425644 4525 4182.09090909091 4370 0.0284635332440313 3385 0.268057535257467 0.216984478466023 1 0.0545771829930226 4522 3385 4214 3467 3774 4380 4170 4370 4601 4506 4614 4640 M19443 GUTIERREZ_MULTIPLE_MYELOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_MULTIPLE_MYELOMA_UP.html Genes exclusively up-regulated in plasma cells from MM (multiple myeloma) patients but with a similiar expression pattern in the normal cells and in the cells from WM (Waldenstroem's macroblobulinemia) patients. 17252022 24/48 Arthur Liberzon 0.987774264674235 0.999176814272271 3705 4217.18181818182 4370 0.329936582322025 3615 0.583897205327712 -0.583897205327712 -1 7.63319543114591e-05 3701 4596 3615 4569 4370 4363 3810 3632 4612 4649 4472 4641 M788 REACTOME_REGULATION_OF_THE_FANCONI_ANEMIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_THE_FANCONI_ANEMIA_PATHWAY.html Genes involved in Regulation of the Fanconi anemia pathway 4/13 Reactome 0.999694155654945 0.999999893590849 4385 4266.27272727273 4373 0.554805238455792 3806 0.159084298203371 -0.155027451101413 -1 8.90471045844585e-10 4281 4418 4005 4373 4385 4013 3806 4390 4676 4385 4197 4642 M17333 FARMER_BREAST_CANCER_CLUSTER_2 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_2.html Cluster 2: selected proliferation and 8q amplicon genes clustered together across breast cancer samples. 15897907 24/72 Leona Saunders 0.972211343482757 0.989097341632696 4375 4143.36363636364 4373 0.278006290530298 2162 1.16099993629442 -0.773290481513499 -1 0.00202044058363177 4601 4032 2162 4196 4552 4373 4221 4632 4444 3989 4375 4643 M14033 REACTOME_MRNA_SPLICING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_SPLICING.html Genes involved in mRNA Splicing 63/178 Reactome 0.9999966994683 0.999999893590849 4560 4374.18181818182 4378 0.682539682539683 3744 0.584186906809141 -0.584186906809141 -1 8.07132897168354e-09 4560 4647 3744 4340 4560 4222 4105 4650 4641 4378 4269 4644 M6693 POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN.html Top marker genes in medulloblastoma associated with poor response to treatment (poor outcome). 11807556 32/80 Jean Junior 0.131788552126364 0.150039153368353 3795 4200.36363636364 4384 0.012765097941712 3634 0.650669299741853 -0.603038880238648 -1 0.19592909060159 3794 4229 3652 4392 3634 4448 4426 4384 4213 4572 4460 4645 M10597 WHITEHURST_PACLITAXEL_SENSITIVITY http://www.broadinstitute.org/gsea/msigdb/cards/WHITEHURST_PACLITAXEL_SENSITIVITY.html Genes that reduced viability of NCI-H1155 cells (non-small-cell lung cancer, NSCLC) in the presence of otherwise sublethal concentrations of paclitaxel [PubChem=4666], based on RNAi synthetic lethal screen. 17429401 22/65 Jessica Robertson 0.0435756119568519 0.0554878580515783 4025 4067.27272727273 4386 0.00404213067983185 1852 0.91554776822972 -0.938186356131078 -1 0.420263275591872 4025 4673 3405 4624 4386 4588 4577 1852 3970 3958 4682 4646 M15664 ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER http://www.broadinstitute.org/gsea/msigdb/cards/ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER.html The 'Cervical Cancer Proliferation Cluster' (CCPC): genes whose expression in cervical carcinoma positively correlates with that of the HPV E6 and E7 oncogenes; they are also differentially expressed according to disease outcome. 16007141 88/219 Leona Saunders 0.850621352955467 0.881665927880849 4635 4152.72727272727 4387 0.158730158730159 2353 1.27074171935981 -1.33933667303597 -1 0.0254057263970938 4631 4499 2353 3280 4671 4387 4653 4544 4301 3993 4368 4647 M16075 WANG_RESPONSE_TO_ANDROGEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_ANDROGEN_UP.html Genes up-regulated in LNCaP cells (prostate cancer) treated with synthetic androgen R1881 [PubChem=13766]. 16751804 25/55 Arthur Liberzon 0.726270090971166 0.762046942743144 4475 4217.09090909091 4394 0.111111111111111 3422 0.707491558868149 -0.746221472744836 -1 0.0305203668839561 4220 3709 3422 4475 4394 4399 4500 4008 4227 4471 4563 4648 M1066 REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION.html Genes involved in Class I MHC mediated antigen processing & presentation 148/328 Reactome 0.0839184282471183 0.0965721401684667 4045 4243.09090909091 4398 0.00793650793650794 3501 1.16161788841848 -0.926277259113194 -1 0.431034433108205 4041 4628 3672 4536 4398 4247 4579 4477 3501 4187 4408 4649 M963 KEGG_RNA_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RNA_DEGRADATION.html RNA degradation 41/72 KEGG 0.999997845224247 0.999999893590849 4660 4380.18181818182 4410 0.694610054454328 3679 0.64621637343787 -0.64621637343787 -1 9.11913432046123e-09 4486 4657 3679 4410 4676 4104 4215 4658 4650 4247 4400 4650 M1155 ABDULRAHMAN_KIDNEY_CANCER_VHL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ABDULRAHMAN_KIDNEY_CANCER_VHL_UP.html Genes up-regulated in the RCC4 cells (renal cell carcinoma, RCC) expressing VHL [GeneID=7428] mutants Type 1 and 2B (associated with RCC) but not those of Type 2A and 2C (not associated with RCC). 17001320 3/9 Arthur Liberzon 0.996938775513304 0.999999893590849 4455 4383.45454545455 4410 0.439482059190191 4113 0.130235906808857 -0.173363562723314 -1 4.03162344840796e-10 4451 4543 4193 4428 4296 4113 4372 4410 4680 4495 4237 4651 M6452 KAUFFMANN_MELANOMA_RELAPSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAUFFMANN_MELANOMA_RELAPSE_DN.html DNA repair and replication genes down-regulated in melanoma patients who will relapse vs patients who will not. 17891185 5/9 Jessica Robertson 0.295479702309909 0.325333149676746 4680 4186.90909090909 4411 0.0344175780653053 2519 0.612285198611562 0.612285198611562 1 0.109144169961188 4678 3624 4305 4611 3936 4508 4629 2519 4411 4542 4293 4652 M1692 YANG_MUC2_TARGETS_COLON_3MO_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_MUC2_TARGETS_COLON_3MO_DN.html Genes down-regulated in colon of 3 month old MUC2 [GeneID=4583] knockout mice. 18794118 2/18 Jessica Robertson 0.999888256152389 0.999999893590849 4685 4400.8 4414.5 0.636157241481685 4049 0.125922294223314 -0.125922294223314 -1 3.30296550802306e-10 4401 4685 4428 NA 4453 4049 4181 4324 4681 4596 4210 4653 M2362 TERAO_AOX4_TARGETS_SKIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/TERAO_AOX4_TARGETS_SKIN_UP.html Genes up-regulated in skin upon knockout of AOX4 [GeneID=71872]. 18981221 31/80 Arthur Liberzon 0.99893305574693 0.999999893590849 4675 4274.72727272727 4422 0.463177059990175 3339 0.790269958804531 -0.692661823509764 -1 1.15524958413853e-08 4672 4670 3339 4495 4422 3940 4628 3876 4586 4073 4321 4654 M46 PID_ATR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATR_PATHWAY.html ATR signaling pathway 18832364 29/52 Pathway Interaction Database 0.35943518917414 0.391142014809659 4465 4185.36363636364 4424 0.0396825396825397 3245 1.43822465390602 1.89874956564086 1 0.214313717213481 3980 4667 3245 3675 4463 4424 4537 4532 3999 4053 4464 4655 M5058 FUNG_IL2_TARGETS_WITH_STAT5_BINDING_SITES_T1 http://www.broadinstitute.org/gsea/msigdb/cards/FUNG_IL2_TARGETS_WITH_STAT5_BINDING_SITES_T1.html Genes with putative STAT5 [GeneID=6777] binding sites; up-regulated by IL2 [GeneID=3558] only in T1 cells (primary thymocytes immortalized by Tax, an HTLV-1 encoded gene). 15735688 4/11 Arthur Liberzon 0.927231339356809 0.951808555580725 3910 4288.72727272727 4424 0.2305251349302 3233 0.289889985718279 0.259886772479295 1 0.0022729371619409 3907 4296 4263 4599 4114 4547 3233 4635 4629 4529 4424 4656 M1395 MORI_PRE_BI_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_PRE_BI_LYMPHOCYTE_UP.html Up-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Pre-BI stage. 18922927 72/185 Jessica Robertson 0.557443745451391 0.594352990030767 4030 4136.81818181818 4437 0.0714285714285714 2562 1.25473442975192 1.35366852876566 1 0.103632044868785 4026 4437 2562 3504 4519 4507 4661 4651 4131 3908 4599 4657 M1747 ZHENG_FOXP3_TARGETS_IN_THYMUS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_IN_THYMUS_DN.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are down-regulated only in developing (located in the thymus) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 7/34 Jessica Robertson 0.632279013951316 0.670330194428929 4415 4369.81818181818 4442 0.0952015631915259 3928 0.302106590400564 -0.279217792959621 -1 0.0191825913119955 4411 4534 4442 4619 3954 4180 3928 4202 4590 4598 4610 4658 M1039 REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_CYCLIN_B http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_CYCLIN_B.html Genes involved in APC/C:Cdc20 mediated degradation of Cyclin B 12/32 Reactome 0.853859408794772 0.884826446176979 2875 3820.90909090909 4445 0.160404546479954 2555 0.198231415270347 0.184886788202138 1 0.00385060217381232 2871 4533 3080 4453 4654 2663 2555 4637 4679 4445 3460 4659 M12661 MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN.html Genes commonly down-regulated in SK-N-BE cells (neuroblastoma) after RNAi knockdown of CCND1 and CDK4 [GeneID=595;1019]. 18413728 37/103 Jessica Robertson 0.96855221189793 0.986445482493741 4450 4290.45454545455 4446 0.26984126984127 2582 0.987664583135397 -0.70714217916542 -1 0.00213971940986936 4446 4587 2582 4401 4606 4398 4526 4656 4417 4118 4458 4660 M1587 YIH_RESPONSE_TO_ARSENITE_C4 http://www.broadinstitute.org/gsea/msigdb/cards/YIH_RESPONSE_TO_ARSENITE_C4.html Genes in cluster 4: immediate down-regulation in HFW cells (fibroblast) by sodium arsenite [PubChem=26435]. 12016162 6/28 John Newman 0.910330139360585 0.936716520211616 4275 4420.09090909091 4449 0.214285714285714 3945 0.272178680890818 -0.200336400192999 -1 0.00282466089623766 4271 4539 4410 4518 4449 4317 4542 3945 4358 4586 4686 4661 M2006 MIKKELSEN_ES_LCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_LCP_WITH_H3K27ME3.html Genes with low-CpG-density promoters bearing H3 trimethylation mark at K27 (H3K27me3) in embryonic stem cells (ES). 17603471 5/24 Arthur Liberzon 0.910330139360585 0.936716520211616 4505 4323.72727272727 4449 0.214285714285714 3560 0.402732049743043 -0.348709506826252 -1 0.00417954008530209 4288 3560 4595 4504 4504 4449 4247 3783 4361 4651 4619 4662 M14767 AMUNDSON_GAMMA_RADIATION_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_GAMMA_RADIATION_RESPONSE.html Genes down-regulated across the entire panel of NCI-60 cell lines in response to gamma radiation. 18199535 22/62 Jessica Robertson 0.999927061207498 0.999999893590849 3950 4269.45454545455 4452 0.579365079365079 2885 0.606119283272796 -0.606119283272796 -1 8.44181194725986e-09 3947 4281 2885 3886 4452 4525 4424 4686 4606 4599 4673 4663 M2566 HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_DN.html Genes distinguishing asparaginase resistant and sensitive ALL (B- and T-lineage ALL); here - genes down-regulated in the drug resistant samples. 15295046 15/38 Arthur Liberzon 0.890120801142621 0.918948242818754 4200 4042.27272727273 4456 0.181892265479662 2756 0.697407548399686 -0.601509963757545 -1 0.00935788607493438 4196 4601 3474 4492 4456 2756 2888 4589 4572 4684 3757 4664 M1591 BURTON_ADIPOGENESIS_PEAK_AT_24HR http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_PEAK_AT_24HR.html Cluster 5: genes progressively up-regulated (peak at 24 h time point) during differentiation of 3T3-L1 fibroblasts into adipocytes in response to adipogenic hormones. 12137940 36/99 John Newman 0.340248220034166 0.371829094934725 4090 4104.54545454545 4457 0.0371025161040964 1511 1.69026216716437 -1.73744642586071 -1 0.265457400220666 4090 4588 1511 4031 4599 4678 4457 4636 4197 3842 4521 4665 M4888 ZHAN_MULTIPLE_MYELOMA_PR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_PR_UP.html Top 50 up-regulated genes in cluster PR of multiple myeloma samples characterized by increased expression of proliferation and cell cycle genes. 16728703 21/61 Kevin Vogelsang 0.986789494879683 0.998983148544194 3835 4251.81818181818 4464 0.325200902516343 2248 0.684163046089497 -0.684163046089497 -1 0.000110492939453728 3834 4464 2248 4402 4521 4409 4399 4629 4654 4577 4633 4666 M19287 MORI_LARGE_PRE_BII_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_LARGE_PRE_BII_LYMPHOCYTE_UP.html Up-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Large Pre-BII stage. 18922927 72/203 Jessica Robertson 0.986831624970353 0.998983148544194 4165 4229.09090909091 4466 0.325396825396825 3108 0.958773443861779 1.01846571389266 1 0.00015484348373569 4161 4570 3108 3441 4651 4368 4504 4563 4466 4158 4530 4667 M2008 MIKKELSEN_ES_LCP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_LCP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing the bivalent histone H3 trimethylation mark at K4 and K27 (H3K4me3 and H3K27me3) in embryonic stem cells (ES). 17603471 2/8 Arthur Liberzon 0.955773941727661 0.977254351066074 4655 4360.4 4467 0.292836553517327 3540 0.168536818285089 -0.273738269988326 -1 0.000615576498660112 4612 4013 4596 NA 4382 4256 4552 3540 4655 4652 4346 4668 M2172 FIGUEROA_AML_METHYLATION_CLUSTER_5_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_5_UP.html Cluster 5 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 8/20 Arthur Liberzon 0.910330139360585 0.936716520211616 4570 4410.90909090909 4473 0.214285714285714 3672 0.365231370960214 -0.227027880314526 -1 0.00379035909590797 4570 4473 4624 4519 4372 4584 4416 3672 4354 4666 4270 4669 M1922 MIKKELSEN_PLURIPOTENT_STATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_PLURIPOTENT_STATE_UP.html Genes up-regulated in the induced pluripotent cells (iPS) and embryonic stem cells (ES) compared to the parental lineage-committed and partially reprogrammed cell lines. 18509334 5/22 Jessica Robertson 0.387187771574276 0.419991179999319 3060 3740.09090909091 4474 0.047789990757582 1772 0.237734584344641 -0.284534542366493 -1 0.0327398122115697 3059 4474 4548 4580 4511 2407 1772 3646 4554 4629 2961 4670 M18773 CASTELLANO_HRAS_AND_NRAS_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_HRAS_AND_NRAS_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblasts) isolated from HRAS and NRAS [GeneID=3265;4893] double knockout mice. 16909116 3/10 Leona Saunders 0.9999171262673 0.999999893590849 4625 4407.54545454545 4477 0.609301548421738 3822 0.106368930710257 0.0605963605242832 1 0 4621 4213 4159 4477 4539 4472 3822 4679 4669 4485 4347 4671 M6972 MONTERO_THYROID_CANCER_POOR_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/MONTERO_THYROID_CANCER_POOR_SURVIVAL_DN.html Down-regulated genes predicting poor survival of patients with thyroid carcinoma. 17873908 4/16 Arthur Liberzon 0.998965404797412 0.999999893590849 4045 4366.09090909091 4478 0.497105314585715 3554 0.111430511375024 -0.116145871079343 -1 8.55005142242656e-11 4044 4478 4571 4603 4468 4065 3554 4542 4685 4638 4379 4672 M6792 ODONNELL_TARGETS_OF_MYC_AND_TFRC_DN http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_TARGETS_OF_MYC_AND_TFRC_DN.html Genes up-regulated in P493-6 cells (B lymphocyte, Burkitt's lymphoma model) by MYC [GeneID=4609] and down-regulated by RNAi knockdown of TFRC [GeneID=7037]. 16508012 20/59 Leona Saunders 0.999982770389775 0.999999893590849 4630 4269.63636363636 4479 0.631078358731721 3076 0.650431436885707 -0.517174830436356 -1 9.19033541674851e-09 3854 4236 3076 4102 4619 4629 4582 4181 4630 4479 4578 4673 M4217 REACTOME_MITOTIC_PROMETAPHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOTIC_PROMETAPHASE.html Genes involved in Mitotic Prometaphase 57/108 Reactome 0.992250758218665 0.999999893590849 4450 4401 4484 0.357142857142857 3364 0.953397709908703 -1.06815601573936 -1 1.43080592764876e-08 4462 4645 3364 4571 4658 4450 4681 4556 4484 4091 4449 4674 M1913 ZHANG_TLX_TARGETS_36HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_36HR_DN.html Genes down-regulated in neural stem cells (NSC) at 36 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 122/272 Jessica Robertson 0.597318307603006 0.634989471285773 4495 4190 4492 0.0793650793650794 3049 1.39776791912143 1.67238926014592 1 0.100770854064892 3491 4495 3049 3898 4685 4613 4492 4524 4158 4159 4526 4675 M19946 LI_CYTIDINE_ANALOG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/LI_CYTIDINE_ANALOG_PATHWAY.html The 'cytidine analog pathway': genes involved in transport and metabolism of the anti-cancer analogs of cytidine: gemcitabine and cytarabine [PubChem=596;3461;6253]. 18757419 10/18 Jessica Robertson 0.542307586406221 0.579797707027048 4530 4286.45454545455 4494 0.0685853492803144 3215 0.597366331953697 -0.684163046089497 -1 0.0516893847163569 4527 4408 3215 4517 3905 4285 4649 4494 4553 4594 4004 4676 M2564 HOLLEMAN_DAUNORUBICIN_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_DAUNORUBICIN_ALL_DN.html Genes distinguishing daunorubicin [PubChem=30323] resistant and sensitive ALL (B- and T-lineage ALL); here - genes down-regulated in the drug resistant samples. 15295046 4/10 Arthur Liberzon 0.96926638349084 0.986958338339434 4685 4186.72727272727 4510 0.294070441749943 3157 0.22828425952353 -0.0467497545353828 -1 0.000475727535502299 3318 4540 4683 4510 4347 3157 4022 4543 4544 4683 3707 4677 M10694 SASAI_TARGETS_OF_CXCR6_AND_PTCH1_UP http://www.broadinstitute.org/gsea/msigdb/cards/SASAI_TARGETS_OF_CXCR6_AND_PTCH1_UP.html Up-regulated genes in medulloblastoma tumors from heterozygotic CXCR6 [GeneID=10663] knockout mice compared to those from PTCH1 [GeneID=5727] heterozygotic knockout mice. 17413002 4/19 Jessica Robertson 0.907837394670209 0.935383911922735 4480 4398.54545454545 4513 0.21212834856469 3353 0.214529511724248 -0.280266794864573 -1 0.00227486294921172 4673 4476 4514 4513 4202 4595 4309 3353 4656 4616 4477 4678 M6312 WU_APOPTOSIS_BY_CDKN1A_NOT_VIA_TP53 http://www.broadinstitute.org/gsea/msigdb/cards/WU_APOPTOSIS_BY_CDKN1A_NOT_VIA_TP53.html Genes downstream of CDKN1A [GeneID=1026] in a TP53 [GeneID=7157] independent pathway in 2774qw1 cells (ovarian cancer). 12138103 9/19 Arthur Liberzon 0.992735565696391 0.999999893590849 4360 4433.72727272727 4516 0.388888888888889 4012 0.368174800277096 -0.378771074208172 -1 4.42243993673926e-09 4359 4605 4618 4012 4631 4386 4108 4278 4516 4663 4595 4679 M1198 TERAMOTO_OPN_TARGETS_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_3.html Cluster 3: genes whose up-regulation peaked 3 days after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 2/5 Arthur Liberzon 0.935818577678036 0.959152636701504 4690 4371.8 4532.5 0.26296192076151 2900 0.026677093104047 0.026677093104047 1 0.000176614493519817 4358 4686 4255 NA 4624 4513 2900 4631 4686 4525 4540 4680 M1215 LI_WILMS_TUMOR_ANAPLASTIC_UP http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_ANAPLASTIC_UP.html Selected up-regulated genes distinguishing between Wilms tumors of different histological types: anaplastic vs favorable histology. 15531917 12/24 Leona Saunders 0.999999747857921 0.999999893590849 4530 4345.36363636364 4536 0.748724830013249 2848 0.161245716033405 0.163623302048144 1 9.26981841218794e-10 4278 4608 2848 3883 4614 4536 4527 4624 4677 4530 4674 4681 M3427 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_11 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_11.html Amplification hot spot 11: colocolized fragile sites and cancer genes in the 11q3 region. 16751803 2/3 Arthur Liberzon 0.999652707674244 0.999999893590849 4680 4456.4 4540.5 0.587301587301587 3696 0.148737613133804 -0.188225336231907 -1 7.15694241412265e-10 4676 3696 4227 NA 4641 4549 4446 4672 4609 4516 4532 4682 M2606 ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_6HR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_6HR.html Cell cycle genes significantly (p =< 0.05) changed in fibroblast cells at 6 h after exposure to ionizing radiation. 17404513 54/110 Itai Pashtan 0.921309192177062 0.946143956726213 4565 4228.54545454545 4546 0.206349206349206 2538 1.36305701220956 -1.13339926728004 -1 0.0119789263204591 4393 4579 2538 3682 4608 4546 4561 4619 4352 4075 4561 4683 M5583 REACTOME_MRNA_SPLICING_MINOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_SPLICING_MINOR_PATHWAY.html Genes involved in mRNA Splicing - Minor Pathway 22/59 Reactome 0.999999893590849 0.999999893590849 4550 4434.27272727273 4548 0.767678716637664 3674 0.127235771247816 -0.123411512871788 -1 3.52483880898295e-10 4548 4675 3674 4404 4636 4580 4186 4621 4683 4379 4391 4684 M1807 MATZUK_OVULATION http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_OVULATION.html Genes important for ovulation, based on mouse models with female fertility defects. 18989307 8/27 Jessica Robertson 0.739798910677351 0.775200736903861 4195 4382 4550 0.125960799623489 3708 0.422298132526705 0.383323180758841 1 0.0170701689953989 4192 4116 4484 4614 3997 4550 4668 3708 4584 4606 4683 4685 M3766 SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP.html Up-regulated genes whose expression correlated with histologic grade of invasive breast cancer tumors: comparison of grade 1 vs grade 3. 16478745 99/229 Arthur Liberzon 0.998444025612634 0.999999893590849 3435 4259.27272727273 4556 0.444444444444444 3102 0.929794553777467 0.967691004085395 1 1.39093533938404e-08 3432 4567 3102 3963 4678 4605 4431 4665 4556 4202 4651 4686 M1486 KAMMINGA_EZH2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KAMMINGA_EZH2_TARGETS.html Putative targets or partners of EZH2 [GeneID=2146] in hematopoietic stem cells. 16293602 22/56 Kevin Vogelsang 0.999999322486778 0.999999893590849 4665 4350.90909090909 4623 0.725100251072822 3187 0.221381339978689 -0.172903174946283 -1 1.94279628952116e-09 3806 4600 3187 3749 4684 4662 4666 4623 4663 4580 4640