STANDARD_NAME GSE18281_CORTEX_VS_MEDULLA_THYMUS_DN SYSTEMATIC_NAME M7243 COLLECTION C7:IMMUNESIGDB MSIGDB_URL https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/GSE18281_CORTEX_VS_MEDULLA_THYMUS_DN NAMESPACE HUMAN_GENE_SYMBOL DESCRIPTION_BRIEF Genes down-regulated in thymus: whole cortex versus whole medulla. DESCRIPTION_FULL Interaction of hematopoietic progenitors with the thymic stromal microenvironment induces them to proliferate, adopt the T cell fate, and asymmetrically diverge into multiple T lineages. Progenitors at various developmental stages are stratified among different regions of the thymus, implying that the corresponding microenvironments differ from one another, and provide unique sets of signals to progenitors migrating between them. The nature of these differences remains undefined. Here we use novel physical and computational approaches to characterize these stromal subregions, distinguishing gene expression in microdissected tissues from that of their lymphoid constituents. Using this approach, we comprehensively map gene expression in functionally distinct stromal microenvironments, and identify clusters of genes that define each region. Quite unexpectedly, we find that the central cortex lacks distinctive features of its own, and instead appears to function by sequestering unique microenvironments found at the cortical extremities, and modulating the relative proximity of progenitors moving between them. PMID 20064453 GEOID GSE18281 AUTHORS Griffith AV,Fallahi M,Nakase H,Gosink M,Young B,Petrie HT CONTRIBUTOR Jernej Godec CONTRIBUTOR_ORG Dana-Farber Cancer Institute EXACT_SOURCE GSE18281_2556_200_DN FILTERED_BY_SIMILARITY EXTERNAL_NAMES_FOR_SIMILAR_TERMS EXTERNAL_DETAILS_URL SOURCE_MEMBERS ABHD4,AKAP7,AMICA1,ANKH,APLP1,ARHGAP26,ARHGAP9,ARHGEF6,ARIH2,ARL4C,ARL6IP4,ASAP2,ASL,BAP1,BCKDK,BCL3,BCL6,BCL7A,C12orf40,C14orf28,C17orf99,C19orf54,C19orf61,C1orf38,C3orf27,C3orf35,C5,C6orf70,C7orf55,C9orf11,CABLES1,CAMKK1,CAPS2,CAV2,CCBP2,CCDC28A,CCDC42,CCDC63,CCL1,CDK14,CDO1,CEACAM21,CEACAM7,CENPK,CHPF2,CHTF8,CLCN5,COX7A1,CST7,CTSD,CXADR,CYP27A1,CYP2R1,DALRD3,DDB2,DHPS,DHRS9,DHX16,DISP1,DNAJB6,DOCK11,DUSP22,EHBP1,ENC1,EPS8L2,EXOC3,FAM160A1,FBN1,FES,FEZ1,FKBP9,FLJ34521,FLJ38109,FLJ90757,GANAB,GINS3,GPX7,HAGH,HEATR8,HEXB,HLX,IDS,IFNAR2,IGSF1,IL10RA,INPP5A,INTS8,IRS2,KBTBD10,KDSR,KIT,KLK14,LAGE3,LIAS,LMO2,LOC100130700,LOC100134361,LOC100288410,LOC100289019,LOC100289084,LOC100505483,LOC145783,LOC283567,LOC283663,LOC284100,LOC286238,LOC340340,LOC389641,LOC399875,LOC645984,LOC728175,LRRC20,LRRC56,LRWD1,LTB,LY86,MAGED1,MAPK14,MAST3,MBTPS1,MEN1,MICAL2,MICAL3,MIPEP,MMP13,MRPS6,MS4A14,MYLK,NAV2,NCAPD2,NCRNA00271,NDUFA11,NEK11,NF2,NFATC1,NFATC2,NISCH,NKX2-2,NUDT13,NYNRIN,OPN5,PDE4A,PECAM1,PGBD2,PIH1D1,PLAU,PLXNB2,PPP3CA,PRPF40B,PVR,PYCARD,QARS,RAB4B,RAB7B,RAC2,RAP2A,REEP4,RELB,REPS2,RIMS3,RUNDC2A,SERPINC1,SFRP4,SHB,SHOX,SLC39A9,SLCO3A1,SMUG1,SMYD4,SORL1,SSH1,STARD9,STK11,STX7,SURF1,SYTL1,TIFAB,TNF,TRAF3IP3,TRAPPC6A,TRIM39,TRIM45,TSHZ1,TTC15,UBXN6,UTF1,UTS2D,VASP,WWC3,XPR1,YPEL5,ZBED2,ZBTB46,ZCRB1,ZDHHC11,ZFP161,ZNF23,ZNF264,ZNF706,ZSWIM7 GENE_SYMBOLS ABHD4,AKAP7,JAML,ANKH,APLP1,ARHGAP26,ARHGAP9,ARHGEF6,ARIH2,ARL4C,ARL6IP4,ASAP2,ASL,BAP1,BCKDK,BCL3,BCL6,BCL7A,C12orf40,C14orf28,C17orf99,ACTMAP,SMG9,THEMIS2,LINC01565,APRG1,C5,ERMARD,FMC1,EQTN,CABLES1,CAMKK1,CAPS2,CAV2,ACKR2,CCDC28A,CCDC42,CCDC63,CCL1,CDK14,CDO1,CEACAM21,CEACAM7,CENPK,CHPF2,CHTF8,CLCN5,COX7A1,CST7,CTSD,CXADR,CYP27A1,CYP2R1,DALRD3,DDB2,DHPS,DHRS9,DHX16,DISP1,DNAJB6,DOCK11,DUSP22,EHBP1,ENC1,EPS8L2,EXOC3,FHIP1A,FBN1,FES,FEZ1,FKBP9,ZBTB44-DT,SAP30L-AS1,BAIAP2-DT,GANAB,GINS3,GPX7,HAGH,MROH7,HEXB,HLX,IDS,IFNAR2,IGSF1,IL10RA,INPP5A,INTS8,IRS2,KLHL41,KDSR,KIT,KLK14,LAGE3,LIAS,LMO2,TP53TG3HP,,,SLC25A25-AS1,,PRKAG2-AS1,TCF12-DT,SIPA1L1,LINC00926,YWHAEP7,LINC02843,LINC02577,TNFRSF10A-DT,NAV2-AS5,,LINC02363,LRRC20,LRRC56,LRWD1,LTB,LY86,MAGED1,MAPK14,MAST3,MBTPS1,MEN1,MICAL2,MICAL3,MIPEP,MMP13,MRPS6,MS4A14,MYLK,NAV2,NCAPD2,AHI1-DT,NDUFA11,NEK11,NF2,NFATC1,NFATC2,NISCH,NKX2-2,NUDT13,NYNRIN,OPN5,PDE4A,PECAM1,PGBD2,PIH1D1,PLAU,PLXNB2,PPP3CA,PRPF40B,PVR,PYCARD,EPRS1,RAB4B,RAB7B,RAC2,RAP2A,REEP4,RELB,REPS2,RIMS3,SNX29,SERPINC1,SFRP4,SHB,SHOX,SLC39A9,SLCO3A1,SMUG1,SMYD4,SORL1,SSH1,STARD9,STK11,STX7,SURF1,SYTL1,TIFAB,TNF,TRAF3IP3,TRAPPC6A,TRIM39,TRIM45,TSHZ1,TRAPPC12,UBXN6,UTF1,UTS2B,VASP,WWC3,XPR1,YPEL5,ZBED2,ZBTB46,ZCRB1,ZDHHC11,ZBTB14,ZNF23,ZNF264,ZNF706,ZSWIM7 FOUNDER_NAMES