STANDARD_NAME GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP SYSTEMATIC_NAME M7247 COLLECTION C7:IMMUNESIGDB MSIGDB_URL https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP NAMESPACE HUMAN_GENE_SYMBOL DESCRIPTION_BRIEF Genes up-regulated in medullary thymocytes versus thymus 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_2558_200_UP FILTERED_BY_SIMILARITY EXTERNAL_NAMES_FOR_SIMILAR_TERMS EXTERNAL_DETAILS_URL SOURCE_MEMBERS ACP6,AGPAT2,AKAP9,ALOX5AP,AMICA1,AP1G1,ARFGAP1,ARHGAP9,ARHGEF6,ARRDC2,ASF1B,ASH1L,ASL,ATP5G1,AVPR1B,BRD9,BSCL2,BTC,BTK,C14orf28,C16orf53,C17orf99,C19orf54,C19orf61,C2orf19,C3orf27,C6orf70,C9orf130,CCDC28A,CCKBR,CD79B,CEACAM1,CELF3,CENPK,CHN2,CHST2,CLCN5,CLN3,CNPY3,CSNK1D,CXCL1,CXCL2,CYP2R1,DDB2,DEF6,DGUOK,DHX30,DNAJB6,DPPA2,DSG3,DUS1L,EMB,ENG,ENHO,ENKUR,ETFB,EYA4,FAU,FBP1,FBXL7,FBXO18,FBXO25,FBXO42,FEZ1,FKBP1A,FXYD2,G0S2,GALR2,GGA1,GNG11,GPX4,H2AFX,HEMK1,HERC2,HGS,HIST1H1D,HLX,IFNAR2,IFT80,IL10RA,IL18R1,IL3RA,IL5RA,INTS8,IRAK2,JUNB,KIAA1147,KIAA1586,KLHDC8A,KRT35,LAGE3,LAIR1,LMO2,LOC100128840,LOC100129488,LOC100129858,LOC100216479,LOC100287081,LOC100505839,LOC283587,LOC283663,LOC283745,LOC284561,LOC401588,LPCAT2,LTB,MAGED1,MAMDC2,MAN2B2,MAP2K2,MBP,MEN1,MFHAS1,MICAL2,MMP9,MRPL52,MYCBP,MYH10,MZT2B,NAA10,NCR2,NEFH,NFATC1,NMT2,NQO2,NR4A2,NUDT1,OR7C1,PAQR7,PAXIP1,PBXIP1,PDE4A,PHF17,PI15,PIGK,PIH1D1,PKD1P1,PLEKHJ1,PLG,PLIN5,PLXDC2,POGLUT1,PRC1,PRDX6,PRSS54,PTTG3P,PYCARD,QARS,R3HCC1,RAB3D,RAB7B,RAPGEF1,RDH8,RELB,RHOF,RPL15,RPL31,RPS6KA1,RPTOR,SCAND2,SDCCAG3,SDR39U1,SERPINI1,SFXN1,SKA3,SLC22A25,SLC26A11,SLC35B3,SORT1,SPSB2,SSU72,ST3GAL1,ST6GALNAC2,STK11,STX7,SURF1,TAF3,TAOK1,TBCD,TEX10,TIAM1,TLN1,TNFRSF1B,TRAF3IP3,TRPT1,TTC15,TXN2,UBTD1,UTS2D,VWA5A,WDR72,WEE1,ZBTB10,ZBTB25,ZNF628,ZNF641,ZNF768,ZNF862,ZSCAN18,ZYG11A GENE_SYMBOLS ACP6,AGPAT2,AKAP9,ALOX5AP,JAML,AP1G1,ARFGAP1,ARHGAP9,ARHGEF6,ARRDC2,ASF1B,ASH1L,ASL,ATP5MC1,AVPR1B,BRD9,BSCL2,BTC,BTK,C14orf28,PAGR1,C17orf99,ACTMAP,SMG9,KLHL30-AS1,LINC01565,ERMARD,ERCC6L2-AS1,CCDC28A,CCKBR,CD79B,CEACAM1,CELF3,CENPK,CHN2,CHST2,CLCN5,CLN3,CNPY3,CSNK1D,CXCL1,CXCL2,CYP2R1,DDB2,DEF6,DGUOK,DHX30,DNAJB6,DPPA2,DSG3,DUS1L,EMB,ENG,ENHO,ENKUR,ETFB,EYA4,FAU,FBP1,FBXL7,FBH1,FBXO25,FBXO42,FEZ1,FKBP1A,FXYD2,G0S2,GALR2,GGA1,GNG11,GPX4,H2AX,HEMK1,HERC2,HGS,H1-3,HLX,IFNAR2,IFT80,IL10RA,IL18R1,IL3RA,IL5RA,INTS8,IRAK2,JUNB,DENND11,KIAA1586,KLHDC8A,KRT35,LAGE3,LAIR1,LMO2,,,SCOC-AS1,FAR2P2,,SH3PXD2A-AS1,HISLA,LINC00926,,LINC02806,ZNF674-AS1,LPCAT2,LTB,MAGED1,MAMDC2,MAN2B2,MAP2K2,MBP,MEN1,MFHAS1,MICAL2,MMP9,MRPL52,MYCBP,MYH10,MZT2B,NAA10,NCR2,NEFH,NFATC1,NMT2,NQO2,NR4A2,NUDT1,OR7C1,PAQR7,PAXIP1,PBXIP1,PDE4A,JADE1,PI15,PIGK,PIH1D1,PKD1P1,PLEKHJ1,PLG,PLIN5,PLXDC2,POGLUT1,PRC1,PRDX6,PRSS54,PTTG3P,PYCARD,EPRS1,R3HCC1,RAB3D,RAB7B,RAPGEF1,RDH8,RELB,RHOF,RPL15,RPL31,RPS6KA1,RPTOR,SCAND2P,ENTR1,SDR39U1,SERPINI1,SFXN1,SKA3,SLC22A25,SLC26A11,SLC35B3,SORT1,SPSB2,SSU72,ST3GAL1,ST6GALNAC2,STK11,STX7,SURF1,TAF3,TAOK1,TBCD,TEX10,TIAM1,TLN1,TNFRSF1B,TRAF3IP3,TRPT1,TRAPPC12,TXN2,UBTD1,UTS2B,VWA5A,WDR72,WEE1,ZBTB10,ZBTB25,ZNF628,ZNF641,ZNF768,ZNF862,ZSCAN18,ZYG11A FOUNDER_NAMES