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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005481
|DRA_sample_Accession=CAGE@SAMD00005481
|accession_numbers=CAGE;DRX008375;DRR009247;DRZ000672;DRZ002057
|accession_numbers=CAGE;DRX008375;DRR009247;DRZ000672;DRZ002057;DRZ012022;DRZ013407
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000393,CL:0000211,CL:0000404,CL:0000255
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000393,CL:0000211,CL:0000404,CL:0000255
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|def=
|def=
|expression_enrichment_score=chr17:37764128..37764258,-!p1@NEUROD2!2.58!375.82!NEUROD2;;chr14:29235961..29236008,+!p1@FOXG1!2.44!272.20!FOXG1;;chr2:105470562..105470582,+!p@chr2:105470562..105470582,+!2.41!257.51!POU3F3;;chr2:5832508..5832524,+!p1@SOX11!2.39!243.59!SOX11;;chr7:31380292..31380351,-!p1@NEUROD6!2.35!222.71!NEUROD6;;chr3:181429704..181429722,+!p1@SOX2!2.08!119.09!SOX2;;chr14:29236269..29236285,+!p3@FOXG1!2.06!113.67!FOXG1;;chr4:81118647..81118666,+!p1@PRDM8!2.04!143.06!PRDM8;;chr1:244214577..244214593,+!p1@ZNF238!2.03!105.94!ZNF238;;chrX:25034067..25034088,-!p1@ARX!2.03!105.17!ARX;;chr2:5832493..5832507,+!p2@SOX11!2.01!101.30!SOX11;;chr1:151032922..151032951,+!p2@MLLT11!1.98!153.88!MLLT11;;chr20:20348740..20348757,+!p1@INSM1!1.98!95.11!INSM1;;chr2:105470536..105470556,+!p@chr2:105470536..105470556,+!1.96!91.25!POU3F3;;chr14:29234581..29234601,+!p2@FOXG1!1.76!56.45!FOXG1;;chr2:16080659..16080685,+!p1@MYCN!1.74!54.13!MYCN;;chr1:151032860..151032918,+!p1@MLLT11!1.70!555.99!MLLT11;;chr8:65492756..65492768,+!p2@BHLHE22!1.70!49.49!BHLHE22;;chr4:113437332..113437337,-!p1@NEUROG2!1.66!44.85!NEUROG2;;chr2:162272785..162272836,+!p1@TBR1!1.63!41.76!TBR1;;chr6:19837592..19837621,+!p1@ID4!1.62!238.17!ID4;;chr2:239148671..239148686,-!p1@HES6!1.61!140.74!HES6;;chr19:13134772..13134822,+!p2@NFIX!1.60!55.68!NFIX;;chr4:57547454..57547469,-!p1@HOPX!1.59!37.89!HOPX;;chr12:103351444..103351461,+!p1@ASCL1!1.58!37.12!ASCL1;;chr9:126773880..126773895,+!p2@LHX2!1.58!37.12!LHX2;;chr7:100065686..100065701,-!p2@TSC22D4!1.56!35.57!TSC22D4;;chr3:181429741..181429767,+!p2@SOX2!1.54!34.02!SOX2;;chr3:27764190..27764208,-!p2@EOMES!1.54!34.02!EOMES;;chr14:29237009..29237049,+!p4@FOXG1!1.54!34.02!FOXG1;;chr16:51185172..51185197,-!p1@SALL1!1.53!33.25!SALL1;;chr19:38720294..38720348,-!p1@DPF1!1.52!39.44!DPF1;;chr6:21594252..21594285,+!p11@SOX4!1.52!35.57!SOX4;;chr12:111471526..111471541,+!p1@CUX2!1.52!32.48!CUX2;;chr9:126774018..126774055,+!p1@LHX2!1.52!32.48!LHX2;;chr2:60780607..60780624,-!p2@BCL11A!1.51!94.34!BCL11A;;chr2:172967621..172967637,-!p1@DLX2!1.49!78.10!DLX2;;chr6:21594206..21594221,+!p15@SOX4!1.48!29.38!SOX4;;chr14:29236301..29236317,+!p5@FOXG1!1.44!26.29!FOXG1;;chr9:20621927..20621996,-!p3@MLLT3!1.42!41.76!MLLT3;;chr2:200322229..200322251,-!p3@SATB2!1.42!25.52!SATB2;;chr2:182545234..182545252,-!p1@NEUROD1!1.41!24.75!NEUROD1;;chr19:47523058..47523114,+!p1@NPAS1!1.41!24.75!NPAS1;;chr7:96654133..96654150,-!p1@DLX5!1.41!24.75!DLX5;;chr8:80679993..80680011,-!p1@HEY1!1.39!34.02!HEY1;;chr5:92919100..92919135,+!p3@NR2F1!1.37!27.07!NR2F1;;chr2:105470614..105470625,+!p@chr2:105470614..105470625,+!1.36!21.65!POU3F3;;chr2:162272889..162272915,+!p2@TBR1!1.36!21.65!TBR1;;chrX:84498989..84499003,+!p1@ZNF711!1.35!29.38!ZNF711;;chr20:55204351..55204377,+!p1@TFAP2C!1.32!25.52!TFAP2C;;chr1:50889103..50889145,-!p1@DMRTA2!1.32!20.11!DMRTA2;;chr2:2334997..2335053,-!p1@MYT1L!1.32!20.11!MYT1L;;chr6:99282475..99282501,+!p1@POU3F2!1.32!20.11!POU3F2;;chr14:29236169..29236216,+!p6@FOXG1!1.32!20.11!FOXG1;;chr11:63684602..63684664,-!p1@RCOR2!1.30!37.12!RCOR2;;chr2:200322723..200322739,-!p6@SATB2!1.29!18.56!SATB2;;chr15:37392094..37392116,-!p6@MEIS2!1.27!21.65!MEIS2;;chr2:63277948..63277974,+!p1@OTX1!1.27!17.79!OTX1;;chr6:99282438..99282457,+!p2@POU3F2!1.27!17.79!POU3F2;;chrX:82763292..82763317,+!p1@POU3F4!1.27!17.79!POU3F4;;chr1:41827095..41827155,+!p1@FOXO6!1.26!23.20!FOXO6;;chr12:24102576..24102623,-!p2@SOX5!1.26!17.01!SOX5;;chr8:65492915..65492932,+!p1@BHLHE22!1.26!17.01!BHLHE22;;chr6:21593973..21593988,+!p1@SOX4!1.24!579.97!SOX4;;chr1:2461692..2461710,-!p1@HES5!1.24!16.24!HES5;;chr11:31832862..31832884,-!p2@PAX6!1.24!16.24!PAX6;;chr2:175199675..175199688,+!p1@SP9!1.22!15.47!SP9;;chr2:200322654..200322707,-!p2@SATB2!1.20!21.65!SATB2;;chr2:172949484..172949522,+!p1@DLX1!1.20!14.69!DLX1;;chr5:124081979..124082021,-!p7@ZNF608!1.20!14.69!ZNF608;;chrY:21906594..21906622,-!p1@KDM5D!1.20!14.69!KDM5D;;chr1:151032957..151032968,+!p7@MLLT11!1.20!14.69!MLLT11;;chr5:92918919..92918942,+!p1@NR2F1!1.19!64.18!NR2F1;;chr13:72441315..72441454,-!p1@DACH1!1.17!27.84!DACH1;;chr2:162272716..162272753,+!p3@TBR1!1.17!13.92!TBR1;;chr6:99282592..99282616,+!p3@POU3F2!1.17!13.92!POU3F2;;chr9:14314131..14314147,-!p2@NFIB!1.15!73.46!NFIB;;chr2:60780753..60780800,-!p1@BCL11A!1.15!64.18!BCL11A;;chrX:84499081..84499115,+!p2@ZNF711!1.15!19.33!ZNF711;;chr11:31832807..31832823,-!p4@PAX6!1.15!13.15!PAX6;;chr19:13135582..13135600,+!p3@NFIX!1.15!13.15!NFIX;;chr15:37392724..37392757,-!p1@MEIS2!1.13!57.22!MEIS2;;chr14:73360799..73360817,-!p1@DPF3!1.13!43.30!DPF3;;chr9:126774058..126774081,+!p3@LHX2!1.13!12.37!LHX2;;chr19:58545454..58545498,+!p1@ZSCAN1!1.13!12.37!ZSCAN1;;chr1:244214611..244214624,+!p4@ZNF238!1.13!12.37!ZNF238;;chr2:105470599..105470610,+!p@chr2:105470599..105470610,+!1.13!12.37!POU3F3;;chr2:172950227..172950249,+!p2@DLX1!1.13!12.37!DLX1;;chr7:31380440..31380451,-!p4@NEUROD6!1.13!12.37!NEUROD6;;chr15:57511609..57511651,+!p2@TCF12!1.11!20.11!TCF12;;chr5:92918956..929189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|fantom_cat=http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000133;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000221;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000540;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0002319;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0001016
|ffid_belonging_in_development=CL:0000133,CL:0000031,CL:0000221
|ffid_belonging_in_development=CL:0000133,CL:0000031,CL:0000221
|fonse_cell_line=
|fonse_cell_line=
Line 41: Line 42:
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Neurons%252c%2520donor1.CNhs12338.11494-119E9.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Neurons%252c%2520donor1.CNhs12338.11494-119E9.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Neurons%252c%2520donor1.CNhs12338.11494-119E9.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Neurons%252c%2520donor1.CNhs12338.11494-119E9.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Neurons%252c%2520donor1.CNhs12338.11494-119E9.hg38.nobarcode.ctss.bed.gz
|id=FF:11494-119E9
|id=FF:11494-119E9
|is_a=EFO:0002091;;FF:0000348
|is_a=EFO:0002091;;FF:0000348
Line 46: Line 52:
|library_id=CNhs12338
|library_id=CNhs12338
|library_id_phase_based=2:CNhs12338
|library_id_phase_based=2:CNhs12338
|name="Neurons, donor1"
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11494
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11494
|name=Neurons, donor1
|namespace=
|namespace=
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage="CNhs12338,LSID913,release011,COMPLETED"
|profile_hcage=CNhs12338,LSID913,release011,COMPLETED
|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq=",,,"
|profile_srnaseq=,,,
|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 90: Line 101:
|top_motifs=SOX2:3.34815793636;NKX2-3_NKX2-5:2.74436713956;PRRX1,2:2.31190426673;TFDP1:2.29631260574;FOXM1:2.23379154006;IKZF2:2.18135033216;ZNF384:2.16019909792;LHX3,4:2.1411839302;POU6F1:2.05731205503;JUN:2.056103411;SOX{8,9,10}:2.04534767518;POU5F1:2.01832687505;T:1.92177332646;MZF1:1.88240860146;EGR1..3:1.86422737271;OCT4_SOX2{dimer}:1.84249393873;NKX6-1,2:1.82787163384;PAX8:1.77095291482;ADNP_IRX_SIX_ZHX:1.74845751373;MED-1{core}:1.74749048064;CDX1,2,4:1.71360223574;ONECUT1,2:1.70813130661;LEF1_TCF7_TCF7L1,2:1.70077257386;SOX17:1.63187064063;GFI1:1.51001213993;BREu{core}:1.48829484203;FOXD3:1.47979092474;VSX1,2:1.47491394275;RREB1:1.44867802192;CDC5L:1.41888887165;NR1H4:1.41477614278;MTE{core}:1.40258061595;YY1:1.39417895506;CUX2:1.39324541835;RFX1:1.36034332207;EVI1:1.34913725997;PBX1:1.33809720622;NHLH1,2:1.32779435796;NRF1:1.32496688367;NANOG:1.28462486737;PRDM1:1.28024244521;ALX1:1.26577884682;FOXP3:1.254573701;SMAD1..7,9:1.18977340907;GATA4:1.18523390789;ZFP161:1.18461528915;PAX4:1.16052355923;ZIC1..3:1.12787301236;ATF2:1.1191000575;NFY{A,B,C}:1.11754759167;ZBTB6:1.11412194545;STAT1,3:1.10528985759;RBPJ:1.08362830683;GZF1:1.04913438759;PATZ1:1.04638441481;GCM1,2:1.0366867867;ELK1,4_GABP{A,B1}:0.991236237824;GTF2I:0.984170295394;AHR_ARNT_ARNT2:0.980361649672;POU1F1:0.968876264788;PAX5:0.956714210302;POU2F1..3:0.950343438929;FOXP1:0.934666237823;POU3F1..4:0.918788830847;ATF4:0.908821215278;MAZ:0.889622576082;REST:0.880980476749;ZNF143:0.862230345634;FOXQ1:0.862067974471;CREB1:0.771712090163;GFI1B:0.734382356078;FOXL1:0.728532658625;KLF4:0.710569278114;TEF:0.710300687944;E2F1..5:0.708992217488;ARID5B:0.69413888463;PAX6:0.68272764793;TBP:0.680959875586;TFAP2B:0.673531422256;PDX1:0.66817872936;ZBTB16:0.643490357724;TGIF1:0.638620849594;MYFfamily:0.554912738224;LMO2:0.532400182218;PPARG:0.530660131721;GTF2A1,2:0.503654293354;UFEwm:0.457165154391;PAX3,7:0.44605294861;HOXA9_MEIS1:0.434427222994;HOX{A4,D4}:0.402721192679;HMGA1,2:0.388236212497;HBP1_HMGB_SSRP1_UBTF:0.378313351531;NKX2-1,4:0.36529109359;BPTF:0.318787815219;NR3C1:0.293745178622;PAX1,9:0.291222128815;HAND1,2:0.290658305426;NR6A1:0.258366021347;NKX3-1:0.253531646603;MYB:0.210654223078;DBP:0.20726522984;NFIX:0.205003929243;HIC1:0.203397683274;ATF5_CREB3:0.184387366697;FOXN1:0.179851137602;NKX2-2,8:0.169491762642;STAT5{A,B}:0.141337363878;MAFB:0.108419359559;SOX5:0.0885884732857;RFX2..5_RFXANK_RFXAP:0.0844859711764;XCPE1{core}:0.0643319353471;TLX2:0.0490450627382;SRF:0.0476711409014;SPZ1:0.0276221696913;AIRE:-0.00577573711547;NFE2L1:-0.00840517662742;ZNF423:-0.0211255474208;MTF1:-0.042322185566;ATF6:-0.0509952377282;STAT2,4,6:-0.0739278597739;MEF2{A,B,C,D}:-0.0756674352272;HOX{A5,B5}:-0.0782208651706;TOPORS:-0.101261758615;CRX:-0.120117367605;HNF1A:-0.12574358508;TLX1..3_NFIC{dimer}:-0.176463180076;FOS_FOS{B,L1}_JUN{B,D}:-0.208352887311;HSF1,2:-0.208597647933;NKX3-2:-0.23147606718;HNF4A_NR2F1,2:-0.268896579777;NFIL3:-0.284525692687;PITX1..3:-0.296165379486;ESRRA:-0.308331236101;AR:-0.318498739131;PAX2:-0.356062973862;BACH2:-0.404732748509;TAL1_TCF{3,4,12}:-0.414091088074;FOX{F1,F2,J1}:-0.420755976843;NFE2L2:-0.423775363158;NFATC1..3:-0.424047944528;GATA6:-0.445298571196;EBF1:-0.457862139276;FOSL2:-0.468882850176;NFE2:-0.488054635807;MYOD1:-0.490409985319;RUNX1..3:-0.508607308238;EP300:-0.512963500618;RORA:-0.51406974908;NFKB1_REL_RELA:-0.517814311111;TP53:-0.533491208462;XBP1:-0.536913496107;SNAI1..3:-0.542541912174;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.568313707745;EN1,2:-0.590985736878;CEBPA,B_DDIT3:-0.593190001357;SPI1:-0.616233904435;DMAP1_NCOR{1,2}_SMARC:-0.638729290599;TEAD1:-0.667276225134;MYBL2:-0.687620742316;NANOG{mouse}:-0.697194736494;SREBF1,2:-0.70519977172;SP1:-0.710017898517;SPIB:-0.721871997231;FOX{D1,D2}:-0.730360355766;NR5A1,2:-0.748809774748;IRF7:-0.779719458512;HES1:-0.852401994766;ZEB1:-0.859917178882;HMX1:-0.887819493088;bHLH_family:-0.9150432536;IRF1,2:-0.933268843096;HLF:-0.962493472877;TFCP2:-1.0177672818;FOXA2:-1.02306925074;HOX{A6,A7,B6,B7}:-1.02930688148;FOX{I1,J2}:-1.0514028415;ELF1,2,4:-1.11821736258;ESR1:-1.16761021101;ZNF238:-1.17082921476;ETS1,2:-1.21311887842;GLI1..3:-1.22580203996;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.24049554016;TFAP2{A,C}:-1.27679290557;ALX4:-1.31596032432;FOXO1,3,4:-1.42608965998;TFAP4:-1.45564968707;ZNF148:-1.49839447864;RXRA_VDR{dimer}:-1.59202907042;RXR{A,B,G}:-1.63014397007;TBX4,5:-1.69866712143;IKZF1:-1.74352159547;HIF1A:-1.80993416983
|top_motifs=SOX2:3.34815793636;NKX2-3_NKX2-5:2.74436713956;PRRX1,2:2.31190426673;TFDP1:2.29631260574;FOXM1:2.23379154006;IKZF2:2.18135033216;ZNF384:2.16019909792;LHX3,4:2.1411839302;POU6F1:2.05731205503;JUN:2.056103411;SOX{8,9,10}:2.04534767518;POU5F1:2.01832687505;T:1.92177332646;MZF1:1.88240860146;EGR1..3:1.86422737271;OCT4_SOX2{dimer}:1.84249393873;NKX6-1,2:1.82787163384;PAX8:1.77095291482;ADNP_IRX_SIX_ZHX:1.74845751373;MED-1{core}:1.74749048064;CDX1,2,4:1.71360223574;ONECUT1,2:1.70813130661;LEF1_TCF7_TCF7L1,2:1.70077257386;SOX17:1.63187064063;GFI1:1.51001213993;BREu{core}:1.48829484203;FOXD3:1.47979092474;VSX1,2:1.47491394275;RREB1:1.44867802192;CDC5L:1.41888887165;NR1H4:1.41477614278;MTE{core}:1.40258061595;YY1:1.39417895506;CUX2:1.39324541835;RFX1:1.36034332207;EVI1:1.34913725997;PBX1:1.33809720622;NHLH1,2:1.32779435796;NRF1:1.32496688367;NANOG:1.28462486737;PRDM1:1.28024244521;ALX1:1.26577884682;FOXP3:1.254573701;SMAD1..7,9:1.18977340907;GATA4:1.18523390789;ZFP161:1.18461528915;PAX4:1.16052355923;ZIC1..3:1.12787301236;ATF2:1.1191000575;NFY{A,B,C}:1.11754759167;ZBTB6:1.11412194545;STAT1,3:1.10528985759;RBPJ:1.08362830683;GZF1:1.04913438759;PATZ1:1.04638441481;GCM1,2:1.0366867867;ELK1,4_GABP{A,B1}:0.991236237824;GTF2I:0.984170295394;AHR_ARNT_ARNT2:0.980361649672;POU1F1:0.968876264788;PAX5:0.956714210302;POU2F1..3:0.950343438929;FOXP1:0.934666237823;POU3F1..4:0.918788830847;ATF4:0.908821215278;MAZ:0.889622576082;REST:0.880980476749;ZNF143:0.862230345634;FOXQ1:0.862067974471;CREB1:0.771712090163;GFI1B:0.734382356078;FOXL1:0.728532658625;KLF4:0.710569278114;TEF:0.710300687944;E2F1..5:0.708992217488;ARID5B:0.69413888463;PAX6:0.68272764793;TBP:0.680959875586;TFAP2B:0.673531422256;PDX1:0.66817872936;ZBTB16:0.643490357724;TGIF1:0.638620849594;MYFfamily:0.554912738224;LMO2:0.532400182218;PPARG:0.530660131721;GTF2A1,2:0.503654293354;UFEwm:0.457165154391;PAX3,7:0.44605294861;HOXA9_MEIS1:0.434427222994;HOX{A4,D4}:0.402721192679;HMGA1,2:0.388236212497;HBP1_HMGB_SSRP1_UBTF:0.378313351531;NKX2-1,4:0.36529109359;BPTF:0.318787815219;NR3C1:0.293745178622;PAX1,9:0.291222128815;HAND1,2:0.290658305426;NR6A1:0.258366021347;NKX3-1:0.253531646603;MYB:0.210654223078;DBP:0.20726522984;NFIX:0.205003929243;HIC1:0.203397683274;ATF5_CREB3:0.184387366697;FOXN1:0.179851137602;NKX2-2,8:0.169491762642;STAT5{A,B}:0.141337363878;MAFB:0.108419359559;SOX5:0.0885884732857;RFX2..5_RFXANK_RFXAP:0.0844859711764;XCPE1{core}:0.0643319353471;TLX2:0.0490450627382;SRF:0.0476711409014;SPZ1:0.0276221696913;AIRE:-0.00577573711547;NFE2L1:-0.00840517662742;ZNF423:-0.0211255474208;MTF1:-0.042322185566;ATF6:-0.0509952377282;STAT2,4,6:-0.0739278597739;MEF2{A,B,C,D}:-0.0756674352272;HOX{A5,B5}:-0.0782208651706;TOPORS:-0.101261758615;CRX:-0.120117367605;HNF1A:-0.12574358508;TLX1..3_NFIC{dimer}:-0.176463180076;FOS_FOS{B,L1}_JUN{B,D}:-0.208352887311;HSF1,2:-0.208597647933;NKX3-2:-0.23147606718;HNF4A_NR2F1,2:-0.268896579777;NFIL3:-0.284525692687;PITX1..3:-0.296165379486;ESRRA:-0.308331236101;AR:-0.318498739131;PAX2:-0.356062973862;BACH2:-0.404732748509;TAL1_TCF{3,4,12}:-0.414091088074;FOX{F1,F2,J1}:-0.420755976843;NFE2L2:-0.423775363158;NFATC1..3:-0.424047944528;GATA6:-0.445298571196;EBF1:-0.457862139276;FOSL2:-0.468882850176;NFE2:-0.488054635807;MYOD1:-0.490409985319;RUNX1..3:-0.508607308238;EP300:-0.512963500618;RORA:-0.51406974908;NFKB1_REL_RELA:-0.517814311111;TP53:-0.533491208462;XBP1:-0.536913496107;SNAI1..3:-0.542541912174;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.568313707745;EN1,2:-0.590985736878;CEBPA,B_DDIT3:-0.593190001357;SPI1:-0.616233904435;DMAP1_NCOR{1,2}_SMARC:-0.638729290599;TEAD1:-0.667276225134;MYBL2:-0.687620742316;NANOG{mouse}:-0.697194736494;SREBF1,2:-0.70519977172;SP1:-0.710017898517;SPIB:-0.721871997231;FOX{D1,D2}:-0.730360355766;NR5A1,2:-0.748809774748;IRF7:-0.779719458512;HES1:-0.852401994766;ZEB1:-0.859917178882;HMX1:-0.887819493088;bHLH_family:-0.9150432536;IRF1,2:-0.933268843096;HLF:-0.962493472877;TFCP2:-1.0177672818;FOXA2:-1.02306925074;HOX{A6,A7,B6,B7}:-1.02930688148;FOX{I1,J2}:-1.0514028415;ELF1,2,4:-1.11821736258;ESR1:-1.16761021101;ZNF238:-1.17082921476;ETS1,2:-1.21311887842;GLI1..3:-1.22580203996;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.24049554016;TFAP2{A,C}:-1.27679290557;ALX4:-1.31596032432;FOXO1,3,4:-1.42608965998;TFAP4:-1.45564968707;ZNF148:-1.49839447864;RXRA_VDR{dimer}:-1.59202907042;RXR{A,B,G}:-1.63014397007;TBX4,5:-1.69866712143;IKZF1:-1.74352159547;HIF1A:-1.80993416983
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11494-119E9;search_select_hide=table117:FF:11494-119E9
}}
}}

Latest revision as of 18:04, 4 June 2020

Name:Neurons, donor1
Species:Human (Homo sapiens)
Library ID:CNhs12338
Sample type:primary cells
Genomic View: UCSC
RefEX:Specific genes
FANTOM CAT:1, 2, 3, 4, 5
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuebrain
dev stageNA
sexNA
ageNA
cell typeneuron
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC1525
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005481
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12338 CAGE DRX008375 DRR009247
Accession ID Hg19

Library idBAMCTSS
CNhs12338 DRZ000672 DRZ002057
Accession ID Hg38

Library idBAMCTSS
CNhs12338 DRZ012022 DRZ013407
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0.406
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C83-choriocarcinoma-pancreatic-placenta-chorionic-HES3GFP-testicular-amniotic0
C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12338

Jaspar motifP-value
MA0002.22.15388e-5
MA0003.10.134
MA0004.10.442
MA0006.10.377
MA0007.10.206
MA0009.10.163
MA0014.10.517
MA0017.10.00107
MA0018.20.00336
MA0019.10.377
MA0024.10.00198
MA0025.10.125
MA0027.10.517
MA0028.10.646
MA0029.10.611
MA0030.10.252
MA0031.10.0216
MA0035.20.0753
MA0038.10.00157
MA0039.20.0617
MA0040.10.214
MA0041.10.493
MA0042.10.59
MA0043.10.103
MA0046.10.0237
MA0047.20.0139
MA0048.10.954
MA0050.18.00699e-8
MA0051.10.00146
MA0052.10.244
MA0055.10.59
MA0057.10.302
MA0058.10.257
MA0059.10.229
MA0060.11.64252e-7
MA0061.10.0214
MA0062.20.666
MA0065.22.59684e-4
MA0066.10.133
MA0067.10.532
MA0068.10.615
MA0069.10.38
MA0070.10.0128
MA0071.10.0698
MA0072.10.589
MA0073.10.162
MA0074.10.169
MA0076.10.252
MA0077.10.0208
MA0078.10.151
MA0079.20.428
MA0080.27.80918e-13
MA0081.10.0591
MA0083.10.434
MA0084.10.134
MA0087.10.364
MA0088.10.263
MA0090.10.076
MA0091.10.716
MA0092.10.657
MA0093.10.475
MA0099.22.07519e-10
MA0100.10.375
MA0101.10.0139
MA0102.20.0308
MA0103.10.0558
MA0104.20.903
MA0105.10.0446
MA0106.10.184
MA0107.10.0115
MA0108.29.58465e-4
MA0111.10.603
MA0112.22.15012e-4
MA0113.10.085
MA0114.10.00671
MA0115.10.469
MA0116.10.0196
MA0117.10.66
MA0119.10.181
MA0122.10.311
MA0124.10.72
MA0125.10.0222
MA0131.10.52
MA0135.10.0906
MA0136.12.12459e-9
MA0137.20.383
MA0138.20.463
MA0139.10.299
MA0140.10.0076
MA0141.10.00979
MA0142.10.0334
MA0143.10.0905
MA0144.10.0244
MA0145.10.0754
MA0146.10.013
MA0147.10.759
MA0148.10.0332
MA0149.10.0169
MA0150.11.02179e-4
MA0152.10.14
MA0153.10.0528
MA0154.10.0714
MA0155.10.492
MA0156.17.44223e-6
MA0157.10.00418
MA0159.10.00155
MA0160.10.0083
MA0162.10.149
MA0163.17.37565e-4
MA0164.10.562
MA0258.10.0101
MA0259.10.845



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12338

Novel motifP-value
10.102
100.129
1000.776
1010.702
1020.71
1030.192
1040.19
1050.191
1060.0138
1070.11
1080.966
1090.00157
110.0261
1100.168
1110.427
1120.148
1130.772
1140.0316
1150.18
1160.785
1170.0384
1180.261
1190.267
120.655
1200.403
1210.245
1220.535
1230.524
1240.675
1250.406
1260.00955
1270.63
1280.1
1290.717
130.0206
1300.488
1310.477
1320.994
1330.618
1340.812
1350.781
1360.00676
1370.33
1380.327
1390.0958
140.676
1400.976
1410.547
1420.939
1430.0916
1440.967
1450.367
1460.386
1470.843
1480.0621
1490.136
150.12
1500.298
1510.408
1520.0376
1530.954
1540.815
1550.816
1560.945
1570.142
1580.301
1590.0431
160.054
1600.173
1610.109
1620.799
1630.264
1640.0263
1650.393
1660.658
1670.887
1680.192
1690.00927
170.0741
180.329
190.106
20.255
200.79
210.139
220.074
230.0407
240.133
250.744
260.0658
270.327
280.735
290.101
30.0527
300.559
310.768
320.00946
330.184
340.422
350.725
360.3
370.0467
380.276
390.142
40.382
400.0701
410.364
420.294
430.134
440.595
450.463
460.178
470.142
480.0763
490.211
50.258
500.367
510.516
520.328
530.477
540.349
550.183
560.378
570.533
580.171
590.0253
60.964
600.0533
610.0345
620.144
630.136
640.375
650.179
660.905
670.984
680.18
690.496
70.218
700.0236
710.018
720.175
730.024
740.896
750.0757
760.544
770.0596
780.0133
790.629
80.26
800.169
810.769
820.234
830.192
840.723
850.033
860.276
870.0252
880.479
890.432
90.278
900.81
910.819
920.108
930.557
940.279
950.0116
960.887
970.561
980.426
990.5



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs12338


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000348 (human neuron samples)

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
CL:0000133 (neurectodermal cell)
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)

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