STANDARD_NAME BENPORATH_SOX2_TARGETS SYSTEMATIC_NAME M3835 COLLECTION C2:CGP MSIGDB_URL https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/BENPORATH_SOX2_TARGETS NAMESPACE Human_NCBI_Gene_ID DESCRIPTION_BRIEF Set 'Sox2 targets': genes upregulated and identified by ChIP on chip as SOX2 [GeneID=6657] transcription factor targets in human embryonic stem cells. DESCRIPTION_FULL Cancer cells possess traits reminiscent of those ascribed to normal stem cells. It is unclear, however, whether these phenotypic similarities reflect the activity of common molecular pathways. Here, we analyze the enrichment patterns of gene sets associated with embryonic stem (ES) cell identity in the expression profiles of various human tumor types. We find that histologically poorly differentiated tumors show preferential overexpression of genes normally enriched in ES cells, combined with preferential repression of Polycomb-regulated genes. Moreover, activation targets of Nanog, Oct4, Sox2 and c-Myc are more frequently overexpressed in poorly differentiated tumors than in well-differentiated tumors. In breast cancers, this ES-like signature is associated with high-grade estrogen receptor (ER)-negative tumors, often of the basal-like subtype, and with poor clinical outcome. The ES signature is also present in poorly differentiated glioblastomas and bladder carcinomas. We identify a subset of ES cell-associated transcription regulators that are highly expressed in poorly differentiated tumors. Our results reveal a previously unknown link between genes associated with ES cell identity and the histopathological traits of tumors and support the possibility that these genes contribute to stem cell-like phenotypes shown by many tumors. PMID 18443585 GEOID AUTHORS Ben-Porath I,Thomson MW,Carey VJ,Ge R,Bell GW,Regev A,Weinberg RA CONTRIBUTOR Jessica Robertson CONTRIBUTOR_ORG MSigDB Team EXACT_SOURCE Table 1S: Sox2 targets FILTERED_BY_SIMILARITY EXTERNAL_NAMES_FOR_SIMILAR_TERMS EXTERNAL_DETAILS_URL SOURCE_MEMBERS 1000,10003,10005,1001,10061,10072,10075,10082,10121,10146,10147,1021,10212,10240,103,10346,10363,10431,10493,10521,10529,10541,10565,10622,10626,10630,10637,10640,10643,10672,1070,1072,10724,10741,10806,10826,10874,10912,10916,10933,10943,10978,10982,11004,11030,11065,11083,11100,1112,11137,11153,11163,11211,11237,112399,112464,11266,11335,11339,114876,114908,115825,116372,120,1201,122830,123,124491,124790,124997,125476,126299,126328,1303,1315,132949,134430,1374,140680,143279,143570,143684,144348,144608,144699,1454,1462,147699,148327,148645,1490,1491,149951,153572,154810,157,157506,157574,157695,158427,160,161742,162427,163859,1655,1785,1798,1808,1809,1837,1848,1856,1871,1938,1960,197131,1982,1993,2029,203068,2041,205860,2064,214,2176,2188,2193,22,220108,221443,2247,2260,2263,22823,22859,22943,22983,22985,22994,2308,23086,23107,23133,23154,23157,23174,23189,23201,23212,23213,23279,23291,23327,23328,23341,23363,23392,23396,23401,23412,23446,23463,23468,23474,23528,23594,23645,23648,23657,23678,23708,23731,249,2512,2521,2535,25776,25782,25788,25804,25805,25820,25841,25862,259230,25932,25940,25943,25957,26000,26030,26088,26128,26133,26153,26520,26521,26959,2697,27000,27063,27086,27134,27161,27173,27258,27327,27339,27345,27430,2770,2790,283209,283464,283991,284307,284325,28512,2870,2895,28956,28971,28973,28985,29028,29088,29089,29105,29106,2931,2932,29761,29796,29896,29922,3014,3021,3037,3066,3070,3087,3162,3178,3181,3183,3190,3191,328,3326,3371,339448,3397,3421,3428,342926,348235,3485,3491,351,3550,359,3608,3609,3624,3720,3728,376267,377,378,3781,379,3791,3832,3839,387254,389792,3910,392,3927,3983,399909,4013,4017,4036,4076,4077,4088,4123,4292,4296,4336,439,4534,4649,467,468,4686,4695,4711,4714,4817,4820,4851,4860,4919,4947,4998,50,501,5018,5052,5058,50808,50813,5082,5093,51,51016,51060,51088,51107,51109,51144,51147,51155,51203,51232,5125,51268,5127,5128,51320,51366,51388,515,51501,51569,51574,51585,51594,51649,5168,51684,51700,51720,51729,51742,51755,51773,51808,5218,5265,5303,5308,53827,53916,5393,54107,54206,54332,54407,5451,54520,5460,54620,54629,54700,54802,54859,54882,54891,549,54904,5495,54958,54962,54989,54993,55011,55012,55017,5504,55072,55122,5514,55147,55157,5518,55183,55188,5519,55196,55211,5523,55237,5527,55284,55341,55422,5546,55527,55620,55644,55662,55677,55696,55702,55718,5573,55737,55739,55745,55758,55762,55766,55771,55810,55818,55837,55847,55892,55906,5621,5635,5652,5664,5689,56893,56898,56907,56915,56916,56944,56949,56984,56992,5701,57099,57111,57129,57212,57335,57456,57466,57489,57492,57532,57556,57561,57610,57633,5764,57685,5771,57719,5774,58506,58516,586,5868,5886,5921,5924,593,59343,595,5978,5989,6001,60436,60485,607,6129,6133,6138,6156,6173,6176,6189,6222,6231,6235,6253,6272,6293,6299,6303,6309,6337,6374,63899,6392,63925,63978,64077,6418,6421,6422,6423,64284,6429,64318,6432,6449,6457,64598,64710,6483,64963,6498,650,65083,65117,6520,65260,655,6596,65977,65997,66000,6617,6619,6626,6634,6638,6642,6657,6668,6748,677,6774,6781,6782,6813,688,6883,6886,6888,6895,6908,6934,694,6942,6992,6997,701,7044,7058,7064,7072,7073,7079,7088,7089,7090,7127,7153,7170,7184,7283,7296,7316,7323,7342,7353,7368,7408,7431,7545,7546,7547,760,762,7699,773,7764,7786,781,7874,79002,79005,79016,79073,79075,79084,79142,79158,79414,79596,79609,79618,79630,79647,79706,79718,79735,79759,7976,79768,79805,79877,79923,79932,7994,79947,79960,79977,80010,80017,80119,80198,80204,8028,80344,805,811,8125,8140,8148,81563,81605,81608,81624,81857,81893,8195,830,8317,8318,8320,8321,8324,8337,83439,83443,83451,8349,83606,8364,84101,84159,84191,842,84271,84316,84335,84513,84545,8458,8463,84705,84717,8473,8476,84894,84902,84936,84950,84954,84962,85027,8503,8505,85364,85437,8546,8555,8611,8615,8665,8705,8729,8737,8805,8819,8820,8848,8864,89978,9043,90799,90809,91408,9147,9168,91768,9184,9188,91975,9215,9227,9240,9242,9249,92815,93210,9331,9337,93436,9350,94081,94104,9425,9440,9453,9550,95681,9584,9585,9603,9604,9638,9643,9656,9658,9692,9698,9725,9726,9734,9735,9747,9766,9774,9785,9788,9789,9824,983,9839,9843,9852,9887,9968 GENE_SYMBOLS CDH2,NAALAD2,ACOT8,CDH3,ABCF2,DPP3,HUWE1,GPC6,ACTR1A,G3BP1,SUGP2,CDK6,DDX39A,MRPS31,ADAR,TRIM22,HMG20A,TIMM23B,VAT1,DDX17,NEBL,ANP32B,ARFGEF1,POLR3G,TRIM16,PDPN,LEFTY1,EXOC5,IGF2BP3,GNA13,CETN3,CFL1,OGA,RBBP9,SDCCAG8,FAXDC2,NMU,GADD45G,MAGED2,MORF4L1,MSL3,CLP1,MAPRE2,KIF2C,RBPMS,UBE2C,DIDO1,HNRNPUL1,FOXN3,PWP1,FICD,NUDT4,FZD10,RNF24,EGLN3,CAVIN3,DUSP12,CBX3,OIP5,OSBPL1A,TMEM123,WDFY2,LYPD1,ADD3,CLN3,NAA30,PLIN2,TMEM170A,HEXIM2,WDR81,INO80C,ZNF428,NDUFA11,COL12A1,COPB1,AASDH,WDR36,CPT1A,C20orf96,HECTD2,XRRA1,FAM76B,ZNF664,C12orf60,FBXL14,CSNK1E,VCAN,PPM1N,CREB3L4,ICMT-DT,CCN2,CTH,COMMD7,IRX2,AMOTL1,GRK3,RDH10,FBXO16,TDRP,TSTD2,AP2A1,SPRED1,RETREG3,SDE2,DDX5,DNM2,DPAGT1,DPYSL2,DPYSL3,DTNA,DUSP6,DVL2,E2F3,EEF2,EGR3,UBR1,EIF4G2,ELAVL2,ENSA,TUBB,EPHA1,TRIML2,ERBB2,ALCAM,FANCC,FANCF,FARSA,ABCB7,FAM124A,OARD1,FGF2,FGFR1,FGFR2,MTF2,ADGRL1,DKK1,MAST1,ACIN1,CEP131,FOXO1,EXPH5,MRPS27,PHF8,NCDN,SEPTIN6,ZCCHC14,KANK1,FAM168A,RRS1,SULF1,NUP160,FBXW11,NEDD4L,SASH1,DNAJC16,OBSL1,ECPAS,PIP5K1C,FRAT2,COMMD3,SLC44A1,ICMT,CBX5,ETHE1,ZNF281,ORC6,PPP1R15A,SSBP3,SLC7A11,SGK3,GSPT2,TMEM245,ALPL,FTL,FUS,FZD2,CBY1,RAB3GAP2,RAD54B,LSM4,BAMBI,ARIH1,ABTB2,USP49,SGMS1,CLIC4,FAM98A,DNAAF9,PNISR,TBC1D10B,PLEKHG3,GGA1,KIFBP,TRPC4AP,KIF26A,TIMM9,TIMM8B,HBP1,GJA1,DNAJC2,ANKRD1,FOXP1,TJP3,AGO2,SLC39A1,LSM3,TNRC6A,PRPF19,KCNMB4,MAT2B,GNAI1,GNG10,PGM2L1,GXYLT1,UBALD2,ZIK1,ACTMAP,NKIRAS1,GRK6,GRID2,LAMTOR2,AAMDC,MRPS18B,MCTS1,ATAD2,MRPL15,UBE2T,CFAP20,SCG3,GSK3A,GSK3B,USP25,UQCR10,TRA2A,NME7,H2AX,H3-3B,HAS2,HDAC2,HELLS,HHEX,HMOX1,HNRNPA1,HNRNPA2B1,HNRNPC,HNRNPK,HNRNPL,APEX1,HSP90AB1,TNC,C1orf174,ID1,IDH3G,IFI16,ZNF677,SKA2,IGFBP2,CCN1,APP,IK,AQP2,ILF2,ILF3,INHBA,JARID2,JUP,RAB15,ARF3,ARF4,KCNN2,ARL4D,KDR,KIF11,KPNA3,SLC7A5P2,IER5L,LAMA4,ARHGAP1,LASP1,ABLIM1,PCNX3,VWA5A,LOXL2,LRP2,CAPRIN1,NBR1,SMAD3,MAN2C1,MLH1,MAP3K11,MOBP,GET3,MTM1,MYO9A,ATF3,ATF4,NCBP1,NDUFA2,NDUFB5,NDUFB8,NIT1,NKTR,NOTCH1,PNP,ROR1,OAZ2,ORC1,ACO2,ALDH7A1,OXA1L,PRDX1,PAK1,AK3,COPS7A,PDCL,PCBP1,ACOX1,EMC9,TXNDC12,KLHL5,APH1A,RDH11,HSD17B12,ING4,JPT1,NUSAP1,CRIM1,PCSK5,PIPOX,CDK16,CDK17,MEX3C,UBR5,NIP7,ATP5PB,HIKESHI,UFM1,LARP7,PCF11,NBAS,MRPS23,ENPP2,SUFU,CYB5R2,UIMC1,WBP11,ARID4B,CDK12,RSF1,PHAX,CDK14,SERPINA1,PIN4,PITX2,FXYD5,RAB4B,EXOSC9,POLE3,ERRFI1,GDAP1,SLC38A2,POU2F1,CCDC93,POU5F1,FBXL19,MINDY2,RRN3,TRIT1,ELP6,ANKHD1,INO80D,AUH,NSD3,PPM1B,TMEM160,TIPIN,ZNF770,ZSCAN2,PIH1D1,PPP2R3C,C14orf119,PPP1R2,RNF31,AKIRIN2,PPP1R10,RBM23,DARS2,PPP2R1A,RIF1,RIC8B,PPP2R1B,RESF1,DPPA4,PPP2R3A,VRTN,PPP2R5C,UBE2W,LSG1,ZNF331,PRCC,FEM1A,STAP2,OSGEP,HIF1AN,IWS1,RBM22,YJU2,POLR3E,PRKAR1A,VPS35,NAXD,AP5M1,RCOR3,ZNF701,H2AJ,PRR11,FOXJ2,KDM3A,EAPP,CISD1,MYNN,ZC4H2,PRNP,PRPSAP1,PRSS8,PSEN2,PSMB1,UBQLN4,BDH2,SPIRE1,EXOSC5,SMARCAD1,OLFML3,XAB2,PSMG2,KIF15,PSMC2,AVEN,RAB25,MRPL47,TP73-AS1,ZNF286A,KIAA1143,SCAF4,ODF2L,ARID1B,NUFIP2,SEMA6A,ARRDC3,RANBP10,LRRN1,PTN,CACHD1,PTPN2,ANO8,PTPN3,SCAF1,SINHCAF,BCAT1,RAB5A,RAD23A,RASA1,RASGRF2,BCKDHA,SENP2,CCND1,REST,RFX1,RGS10,TGIF2,SAV1,BCL9,RPL7,RPL9,RPL15,RPL30,RPL36A,RPLP1,RPS3A,RPS18,RPS26,RPS29,RTN2,SORT1,VPS52,SALL1,SAT1,SC5D,SCNN1A,CXCL5,NSUN3,SDHD,ZNF335,PRDM14,LHPP,SET,SFPQ,SFRP1,SFRP2,RAB17,SRSF4,NOC3L,SRSF7,SGTA,SH3GL3,MOSPD3,NUCKS1,ST3GAL2,MRPS11,SKIL,BMP2,NOL6,RSRC2,SLC3A2,COA7,BMP7,HLTF,PLEKHA3,RASL11B,TMEM108,SNAPC1,SNAPC3,SNRPA,SNRPD3,SNRPN,SNX1,SOX2,SP2,SSR4,ZFP36L1,STAT3,STC1,HSPA13,STXBP2,KLF5,TAF12,TAL1,TALDO1,TARBP2,TBP,TCF7L2,BTG1,TCF20,PPP1R11,TDGF1,BUB1B,LEFTY2,THBS2,THOP1,TIA1,TIAL1,TIMP4,TLE1,TLE2,TLE3,TNFAIP2,TOP2A,TPM3,HSP90B1,TUBG1,TXNRD1,UBC,UBE2D3,UBP1,UFD1,UGT8,VASP,VIM,ZIC1,ZIC2,ZIC3,CA2,CA4,ZNF140,CACNA1A,ZNF217,MAP3K12,CACNA2D1,USP7,TRIR,SCNM1,DDA1,TMEM109,DSCC1,WDR77,PHF23,GNPTAB,LRFN3,OBI1,VCPKMT,HMBOX1,C1orf54,AKIRIN1,PRKRIP1,TBL1XR1,TBC1D17,ZNF668,FZD3,KATNBL1,VASH2,DCAKD,NANOG,KIAA0319L,KAT6A,DHDDS,JADE1,GRHL2,RMI1,DGLUCY,PIF1,MUS81,FBXO11,MLLT10,DCAF11,CALM2,CALR,ANP32A,SLC7A5,TAF15,C1orf21,URM1,FIP1L1,DIAPH3,MED25,SLC7A5P1,MKKS,CAPZA2,CDC7,CDC45,EOMES,FZD1,FZD7,H2AC18,TCF7L1,SF3B5,ABHD11,H2BC21,GUCD1,H4C3,USP44,ARID5B,CIAO2A,CASP9,POLDIP3,NAA38,AKT1S1,PLPP5,MRPL43,TTF2,TEAD2,GTPBP3,HDGFL2,OGT,CDC42BPA,LINGO1,CEP89,ZFYVE19,PRPF38A,MPND,AJUBA,SMIM3,PIK3R3,PARG,ZCCHC3,ZCRB1,AP3B1,CDC14B,PLPP1,USO1,EIF3F,B3GALT4,GBF1,RIPK1,TRIM24,SAP30,HESX1,TSC22D1,PER2,DPH6,SPAG9,CEP95,PIP4P1,BTF3L4,NEMF,TMSB10,CABLES1,BUB3,DDX21,ZNF300,LARGE1,LRAT,PNMA1,MSC,DHRS3,H2AC25,PGAP3,B4GALT6,CNOT8,ARMC6,CER1,SFXN1,PAXBP1,CDYL,MED17,GGPS1,ATP6V1G1,CEP41,RBM39,KIF20B,NFE2L3,RNF14,FEZ1,MORF4L2,MDC1,ZNF516,PRORP,PUM1,TMEM63A,ZNF646,HDAC9,KNTC1,TCAF1,SUSD6,BCLAF1,DHX38,MTSS1,SPCS2,ARHGAP11A,CDK1,ZEB2,HEPH,EPM2AIP1,SMG7,MED12 FOUNDER_NAMES