STANDARD_NAME CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_DN SYSTEMATIC_NAME M9192 COLLECTION C2:CGP MSIGDB_URL https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_DN NAMESPACE AFFY_HG_U133 DESCRIPTION_BRIEF Genes down-regulated in luminal-like breast cancer cell lines compared to the mesenchymal-like ones. DESCRIPTION_FULL A better molecular characterization of breast cell lines (BCL) may help discover new markers to apply to tumour samples. We performed gene and protein expression profiling of 31 BCL using whole-genome DNA microarrays and immunohistochemistry (IHC) on 'cell microarrays' (CMA), respectively. Global hierarchical clustering discriminated two groups of BCL: group I corresponded to luminal cell lines, group II to basal and mesenchymal cell lines. Correlations with centroids calculated from a published 'intrinsic 500-gene set' assigned 15 cell lines as luminal, eight as basal and four as mesenchymal. A set of 1.233 genes was differentially expressed between basal and luminal samples. Mesenchymal and basal subtypes were rather similar and discriminated by only 227 genes. The expression of 10 proteins (CAV1, CD44, EGFR, MET, ETS1, GATA3, luminal cytokeratin CK19, basal cytokeratin CK5/6, CD10, and ERM protein moesin) encoded by luminal vs basal discriminator genes confirmed the subtype classification and the validity of the identified markers. Our BCL basal/luminal signature correctly re-classified the published series of tumour samples that originally served to identify the molecular subtypes, suggesting that the identified markers should be useful for tumour classification and might represent promising targets for disease management. PMID 16288205 GEOID AUTHORS Charafe-Jauffret E,Ginestier C,Monville F,Finetti P,Adélaïde J,Cervera N,Fekairi S,Xerri L,Jacquemier J,Birnbaum D,Bertucci F CONTRIBUTOR Arthur Liberzon CONTRIBUTOR_ORG MSigDB Team EXACT_SOURCE Table 3S FILTERED_BY_SIMILARITY EXTERNAL_NAMES_FOR_SIMILAR_TERMS EXTERNAL_DETAILS_URL SOURCE_MEMBERS 1552277_a_at,1552309_a_at,1552619_a_at,1552658_a_at,1553101_a_at,1553613_s_at,1553994_at,1553995_a_at,1554082_a_at,1554168_a_at,1554390_s_at,1554696_s_at,1555355_a_at,1555480_a_at,1555579_s_at,1555630_a_at,1555705_a_at,1555841_at,1555889_a_at,1557051_s_at,1557905_s_at,1557938_s_at,1558015_s_at,200039_s_at,200600_at,200665_s_at,200671_s_at,200672_x_at,200713_s_at,200727_s_at,200728_at,200729_s_at,200770_s_at,200771_at,200782_at,200813_s_at,200824_at,200931_s_at,200958_s_at,200974_at,201012_at,201028_s_at,201029_s_at,201030_x_at,201037_at,201064_s_at,201069_at,201136_at,201162_at,201163_s_at,201185_at,201199_s_at,201272_at,201278_at,201279_s_at,201280_s_at,201426_s_at,201438_at,201505_at,201506_at,201530_x_at,201540_at,201564_s_at,201585_s_at,201590_x_at,201594_s_at,201615_x_at,201616_s_at,201617_x_at,201642_at,201666_at,201667_at,201718_s_at,201719_s_at,201727_s_at,201739_at,201752_s_at,201809_s_at,201858_s_at,201859_at,201860_s_at,201865_x_at,201866_s_at,201983_s_at,201984_s_at,201995_at,202037_s_at,202052_s_at,202094_at,202133_at,202213_s_at,202214_s_at,202237_at,202238_s_at,202240_at,202305_s_at,202351_at,202369_s_at,202388_at,202391_at,202468_s_at,202506_at,202551_s_at,202552_s_at,202555_s_at,202589_at,202625_at,202626_s_at,202627_s_at,202628_s_at,202643_s_at,202644_s_at,202664_at,202685_s_at,202686_s_at,202690_s_at,202693_s_at,202759_s_at,202760_s_at,202765_s_at,202766_s_at,202779_s_at,202794_at,202845_s_at,202870_s_at,202882_x_at,202900_s_at,202910_s_at,202931_x_at,202974_at,202990_at,202997_s_at,202998_s_at,203044_at,203047_at,203065_s_at,203069_at,203085_s_at,203196_at,203212_s_at,203234_at,203300_x_at,203320_at,203323_at,203324_s_at,203325_s_at,203329_at,203348_s_at,203349_s_at,203390_s_at,203499_at,203510_at,203554_x_at,203570_at,203625_x_at,203632_s_at,203637_s_at,203695_s_at,203705_s_at,203725_at,203729_at,203810_at,203819_s_at,203820_s_at,203851_at,203879_at,203881_s_at,203921_at,203939_at,204011_at,204036_at,204037_at,204114_at,204115_at,204159_at,204162_at,204194_at,204235_s_at,204236_at,204237_at,204268_at,204279_at,204337_at,204359_at,204396_s_at,204420_at,204489_s_at,204490_s_at,204529_s_at,204556_s_at,204646_at,204735_at,204748_at,204781_s_at,204823_at,204948_s_at,204955_at,205006_s_at,205100_at,205120_s_at,205207_at,205339_at,205401_at,205433_at,205463_s_at,205479_s_at,205525_at,205573_s_at,205579_at,205729_at,205798_at,205891_at,205992_s_at,206157_at,206332_s_at,206377_at,206382_s_at,206412_at,206432_at,206550_s_at,206571_s_at,206580_s_at,206805_at,206924_at,207030_s_at,207057_at,207172_s_at,207173_x_at,207719_x_at,207808_s_at,207876_s_at,208025_s_at,208093_s_at,208178_x_at,208309_s_at,208636_at,208637_x_at,208747_s_at,208782_at,208789_at,208790_s_at,208816_x_at,208827_at,208931_s_at,208944_at,208965_s_at,208966_x_at,209011_at,209012_at,209013_x_at,209086_x_at,209087_x_at,209090_s_at,209156_s_at,209160_at,209191_at,209193_at,209297_at,209298_s_at,209356_x_at,209406_at,209505_at,209537_at,209576_at,209598_at,209651_at,209755_at,209774_x_at,209789_at,209834_at,209835_x_at,209897_s_at,209909_s_at,210018_x_at,210097_s_at,210135_s_at,210138_at,210139_s_at,210201_x_at,210220_at,210257_x_at,210298_x_at,210299_s_at,210427_x_at,210470_x_at,210510_s_at,210511_s_at,210517_s_at,210605_s_at,210664_s_at,210754_s_at,210757_x_at,210869_s_at,210875_s_at,210916_s_at,210933_s_at,210968_s_at,210986_s_at,210987_x_at,211031_s_at,211042_x_at,211126_s_at,211139_s_at,211160_x_at,211340_s_at,211343_s_at,211366_x_at,211599_x_at,211651_s_at,211668_s_at,211671_s_at,211675_s_at,211787_s_at,211953_s_at,211954_s_at,211964_at,211966_at,211980_at,211981_at,211995_x_at,212012_at,212014_x_at,212063_at,212071_s_at,212077_at,212091_s_at,212097_at,212188_at,212190_at,212192_at,212197_x_at,212233_at,212234_at,212237_at,212238_at,212245_at,212263_at,212265_at,212294_at,212298_at,212320_at,212350_at,212414_s_at,212423_at,212470_at,212488_at,212489_at,212506_at,212561_at,212607_at,212609_s_at,212646_at,212653_s_at,212667_at,212672_at,212702_s_at,212746_s_at,212764_at,212771_at,212792_at,212795_at,212818_s_at,212822_at,212940_at,212992_at,213010_at,213069_at,213093_at,213139_at,213154_s_at,213238_at,213258_at,213260_at,213262_at,213302_at,213325_at,213338_at,213358_at,213428_s_at,213429_at,213434_at,213503_x_at,213524_s_at,213564_x_at,213689_x_at,213698_at,213802_at,213803_at,213807_x_at,213865_at,214104_at,214247_s_at,214390_s_at,214439_x_at,214452_at,214505_s_at,214577_at,214771_x_at,215000_s_at,215116_s_at,215198_s_at,215509_s_at,215707_s_at,215913_s_at,215997_s_at,216044_x_at,216268_s_at,216493_s_at,217762_s_at,217763_s_at,217764_s_at,217788_s_at,217879_at,217890_s_at,217943_s_at,217975_at,217989_at,217996_at,217997_at,217998_at,217999_s_at,218084_x_at,218181_s_at,218236_s_at,218273_s_at,218284_at,218418_s_at,218651_s_at,218656_s_at,218662_s_at,218717_s_at,218718_at,218726_at,218847_at,218854_at,218898_at,218950_at,218980_at,219201_s_at,219279_at,219427_at,219441_s_at,219654_at,219825_at,219926_at,219935_at,219973_at,219974_x_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GENE_SYMBOLS MSANTD3,NEXN,ANLN,NAV3,ALKBH5,FOXC1,NT5E,NT5E,NOL9,SH3KBP1,ACTR2,TYMS,ETS1,FBLIM1,PTPRM,RAB34,CMTM3,MSANTD3,CRTAP,HOTAIRM1,CD44,CAVIN1,ACTR2,PSMB2,MSN,SPARC,SPTBN1,SPTBN1,MAPRE1,ACTR2,ACTR2,ACTR2,LAMC1,LAMC1,ANXA5,PAFAH1B1,GSTP1,VCL,SDCBP,ACTA2,ANXA1,CD99,CD99,LDHB,PFKP,PABPC4,MMP2,PLP2,IGFBP7,IGFBP7,HTRA1,PSMD1,AKR1B1,DAB2,DAB2,DAB2,VIM,COL6A3,LAMB1,TGFBI,EIF4A1,FHL1,FSCN1,SFPQ,ANXA2,PPP4R1,CALD1,CALD1,CALD1,IFNGR2,TIMP1,GJA1,EPB41L2,EPB41L2,ELAVL1,SGK1,ADD3,ENG,SRGN,SRGN,PLAT,NR3C1,NR3C1,EGFR,EGFR,EXT1,SFRP1,RAI14,BIRC5,WWTR1,CUL4B,CUL4B,NNMT,NNMT,PLK1,FEZ2,ITGAV,TRAM2,RGS2,BASP1,CTNNAL1,ITPRID2,CRIM1,CRIM1,MYLK,TYMS,LYN,LYN,SERPINE1,SERPINE1,TNFAIP3,TNFAIP3,WIPF1,AXL,AXL,SNRPD1,STK17A,PALM2AKAP2,PALM2AKAP2,FBN1,FBN1,UBE2S,INPP1,RALBP1,CDC20,NOL7,NUP88,ADGRE5,BIN1,MPP1,PYGL,LOXL2,LOXL2,CHSY1,STK10,CAV1,SV2A,TGFB1,ABCC4,MTMR2,UPP1,AP1S2,SH2B3,CAV2,CAV2,COL5A1,PTPRM,ETV5,ETV5,KIF3C,EPHA2,MET,PTTG1,LOXL1,SKP2,GPRC5B,MID1,GSDME,FZD7,GADD45A,EMP3,DNAJB4,IGF2BP3,IGF2BP3,IGFBP6,PIK3CD,DMD,CHST2,NT5E,SPRY2,LPAR1,LPAR1,NID2,GNG11,CDKN2C,NDC80,BACH1,GULP1,FLI1,GULP1,S100A2,PSMB9,RGS4,FLRT2,GRK5,FOSL1,CD44,CD44,TOX,DZIP1,DPYD,PDE4A,PTGS2,FAS,NAV3,FST,SRPX,NMT2,GFPT2,SGCB,IL6,STIL,AGPS,BCHE,PDGFA,PLAU,CALD1,SNX7,HRH1,OSMR,IL7R,ADORA2B,IL15,PTX3,IFI16,FOXF2,BDNF,FER,HAS2,NUP155,MAP4K4,EFEMP2,SEMA3A,IL11,CSRP2,SLC16A7,CDH11,CDH11,CEP170,PROS1,FLNC,HMGA2,NDEL1,TRIO,MALT1,ACTN1,ACTN1,C1S,FSTL1,CAVIN1,CAVIN1,ANXA2P2,PSMB6,ILF3,TGFBR2,IFI16,IFI16,TRIO,TRIO,TRIO,MCAM,MCAM,SH3GLB1,COL6A2,AKR1C3,TUBB6,PIM1,ITSN1,ITSN1,EFEMP2,BAG2,NR2F1,EXTL2,GNAI1,PNMA2,TGFB1I1,NMNAT2,CXCL2,CORO2B,CHST3,CD44,SLIT2,TGFB2,MALT1,NOL7,SHOX2,RGS20,PMP22,BIN1,FZD2,CUL4B,FHL1,FHL1,ANXA2,NONO,NRP1,INHBA,AKAP12,MFGE8,TFPI,LYN,DAB2,MCAM,ZEB1,CD44,FSCN1,RTN4,TPM1,TPM1,CLIP2,SKP2,CSRP2,NAB1,ACTN1,MCAM,COL13A1,CASP1,MET,LAMB1,PLAU,NR3C1,MDFIC,EIF4A1,IPO5,IPO5,COL4A2,COL4A2,COL4A1,COL4A1,ACTG1,PXDN,CD44,CD44,SPTBN1,CALD1,COL6A1,CAV1,KCTD12,SERPINE2,KCTD12,MPRIP,MAP1B,ASXL1,ASXL1,ASXL1,MCFD2,QKI,QKI,GNG12,NRP1,TUBB,TBC1D1,SEPTIN6,ZCCHC24,SPAG9,COL5A1,COL5A1,PICALM,DENND5A,AKT3,AKT3,RFTN1,EHBP1,SPARC,ATM,BICD2,CEP170,ZEB1,FAM171A1,DPY19L1,WASHC4,ASB1,HEG1,COL6A1,AHNAK2,CAVIN3,HEG1,PRKCA,SNAI2,BICD2,ATP10D,TFPI,FOXC1,SACS,PFAS,NECTIN3,TMEM158,MTCL1,COL6A1,BICC1,STX2,ANXA2,G0S2,LDHB,DIPK1A,TMEM35B,PRSS12,KPNB1,MET,DCBLD2,GPR161,DKK3,BCAT1,BIN1,BCAT1,FHL1,MAP1B,MPRIP,FEZ2,DNM1,CALD1,BUB1,PRNP,GULP1,CUL4B,DIPK1A,JAG1,IGF2BP3,RAB31,RAB31,RAB31,GALNT2,CDC27,PARVA,MAP7D1,TCEAL9,HSD17B11,NAP1L1,NAP1L1,NAP1L1,NAP1L1,FXYD5,MAP4K4,PRKD3,PDP1,SMAD3,KANK2,LARP6,LHFPL6,NCAPG,P3H2,PDGFC,HJURP,IGF2BP2,DSE,TLCD3A,ARAP3,FHOD3,TWSG1,DOCK10,FAT4,LRRK1,HACD1,CYP26B1,POPDC3,ADAMTS5,ARSJ,ECHDC1,PRR16,AIDA,ARHGEF40,TGFB2,P3H1,ITM2C,LBH,WNT5B,ASAP1,GLS,TRAF3,SPDL1,ELK3,WLS,KIF18B,SPATS2L,CORO1C,SLC25A37,PDP1,CAVIN2,PDGFC,ZDHHC2,ZDHHC2,GNG12,AK5,DHX33,TMEM245,TMEM245,GLS,SH3KBP1,ECHDC1,ECHDC1,ANKH,ANKH,ANKH,MARVELD1,STRADB,ELP5,CCDC82,HYCC1,ZIC2,LTBP2,BMAL2,FXYD5,CFL2,EMILIN2,TIMP2,C17orf49,CFL2,ANTXR1,RAB34,CMTM3,ARHGAP21,NAV1,NAV1,NAV1,ASAP1,ASAP1,MYLK,ETS1,CDK6,CDK6,CDK6,TTL,DCBLD2,PPP1R18,PAPPA,PAPPA,PAPPA,TEAD1,GNG2,EGFR,CCDC88A,POGLUT3,CPNE2,FBLIM1,EDIL3,BCAT1,KIRREL1,ZYG11B,MIR100HG,TWSG1,AAK1,ANTXR2,ITPRIP,GLIPR2,B3GNT5,CTSC,CTSC,PHLDB2,MSRB3,MSRB3,LIX1L,LUZP1,NAP1L1,SLC35B4,TAP2,UBE2G1,CMTM7,RNF145,MAP1B,NEXN,SGCB,GLIPR1,FMNL2,IL7R,DHX33,SPTBN1,BCAT1,CENPV,CENPV,OSMR,RAB8B,ARHGAP23,PALM2AKAP2,CCDC50,FAM20C,ITGA1,CNRIP1,CLMP,FST,RFLNB,RFLNB,ADAMTS12,PTPRG,CRTAP,INHBA,HYCC1,FAM200B,IKBIP,MXRA7,TNFRSF10D,UBLCP1,FOXQ1,,AKAP12,NAV1,STAMBPL1,STAMBPL1,GPX8,GNAI1,SOCS3,KATNAL1,SMAD9,IGFBPL1,EVA1A,GPR176,TRNP1,CIBAR1,NAP1L5,LAYN,CLMP,TGFB2,PAPPA,GPX8,FOSL2,ALPK2,GID4,SOAT1,,PDE3A,ANTXR2,SERPINB1,TOX2,SGTB,WLS,WLS,NR2F1-AS1,,CD44,ANKRD28,KLHL29,TWIST2,GLIS3,CKAP2L,ERFE,CCBE1,PDE7B,,F2RL2,ST3GAL6,EXT1,AP1S2,HAS2,RNF182,BNC2,SH2D5,TRIO,IRAK2,ZC3H12C,ANKRD33B,,,RUNX2,,,ECHDC1,,VPS54,,EIF5A2,GXYLT2,CIBAR1,MAML2,HRCT1,DEPDC1,APCDD1L,,CDH11,PDE3A,LARP6,,,FZD2,RBMS3,UBASH3B,UBASH3B,EYA4,,BDNF,,ASXL1,ASXL1,INCENP,ITPRIP,,CHST3,MRC2,STK10,WRAP53,SYDE1,ARHGEF40 FOUNDER_NAMES