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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008218
|DRA_sample_Accession=CAGE@SAMD00005171
|accession_numbers=CAGE;DRX008326;DRR009198;DRZ000623;DRZ002008
|accession_numbers=CAGE;DRX008326;DRR009198;DRZ000623;DRZ002008;DRZ011973;DRZ013358
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000075,UBERON:0004765,UBERON:0001708,UBERON:0011159,UBERON:0002204,UBERON:0001434,UBERON:0008895,UBERON:0011137,UBERON:0010323
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000075,UBERON:0004765,UBERON:0001708,UBERON:0011159,UBERON:0002204,UBERON:0001434,UBERON:0008895,UBERON:0011137,UBERON:0010323
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002159,CL:0000255,CL:0002077,CL:0002166
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002159,CL:0000255,CL:0002077,CL:0002166
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|created_by=
|created_by=
|creation_date=
|creation_date=
|datafreeze_phase=1
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|expression_enrichment_score=chr11:34642612..34642646,+!p1@EHF!2.17!146.03!EHF;;chr17:7493405..7493419,-!p1@SOX15!2.12!130.72!SOX15;;chr1:209979467..209979494,-!p1@IRF6!2.11!143.19!IRF6;;chr3:111314186..111314204,-!p1@ZBED2!1.96!91.02!ZBED2;;chr1:209979411..209979433,-!p2@IRF6!1.86!71.17!IRF6;;chr8:10588010..10588030,-!p1@SOX7!1.83!66.49!SOX7;;chr3:189507432..189507459,+!p1@TP63!1.79!60.54!TP63;;chr1:6479968..6479986,-!p1@HES2!1.75!55.43!HES2;;chr6:10415276..10415341,-!p2@TFAP2A!1.64!51.32!TFAP2A;;chr15:83953397..83953425,-!p1@BNC1!1.62!46.64!BNC1;;chr15:101069113..101069169,-!p1@CERS3!1.52!32.18!CERS3;;chr12:54785054..54785072,-!p4@ZNF385A!1.46!31.19!ZNF385A;;chr3:111314230..111314241,-!p2@ZBED2!1.42!25.38!ZBED2;;chr6:10412600..10412637,-!p1@TFAP2A!1.36!36.15!TFAP2A;;chr6:10415484..10415508,-!p3@TFAP2A!1.30!19.14!TFAP2A;;chr12:54785074..54785122,-!p2@ZNF385A!1.29!28.36!ZNF385A;;chr17:7492684..7492778,-!p2@SOX15!1.24!34.59!SOX15;;chr5:134369905..134369972,-!p1@PITX1!1.21!23.25!PITX1;;chr4:111544219..111544240,-!p1@PITX2!1.15!13.19!PITX2;;chr11:34642656..34642667,+!p2@EHF!1.13!12.48!EHF;;chr8:49833948..49833973,-!p2@SNAI2!1.12!77.13!SNAI2;;chr9:100615499..100615519,+!p1@FOXE1!1.11!11.91!FOXE1;;chr1:158979792..158979814,+!p2@IFI16!1.03!94.71!IFI16;;chr5:134369879..134369898,-!p2@PITX1!1.02!9.50!PITX1;;chr12:66218598..66218645,+!p2@HMGA2!1.01!43.81!HMGA2;;chr21:36421535..36421610,-!p2@RUNX1!1.00!32.47!RUNX1;;chr3:141121847..141121868,+!p5@ZBTB38!0.99!13.61!ZBTB38;;chr19:42636586..42636607,-!p1@POU2F2!0.97!23.39!POU2F2;;chr2:46524897..46524911,+!p2@EPAS1!0.96!23.11!EPAS1;;chr8:49833978..49833996,-!p1@SNAI2!0.93!159.07!SNAI2;;chr12:27485762..27485776,+!p3@ARNTL2!0.93!20.70!ARNTL2;;chr19:45908292..45908374,-!p1@PPP1R13L!0.92!67.48!PPP1R13L;;chr5:72744594..72744609,-!p1@FOXD1!0.92!34.45!FOXD1;;chr15:83953373..83953386,-!p2@BNC1!0.92!7.23!BNC1;;chr22:19748231..19748317,+!p1@TBX1!0.92!7.23!TBX1;;chr16:67881588..67881612,-!p2@CENPT!0.90!9.64!CENPT;;chr1:158979872..158979898,+!p3@IFI16!0.89!21.83!IFI16;;chrY:21906594..21906622,-!p1@KDM5D!0.88!6.52!KDM5D;;chr2:231084639..231084654,-!p2@SP110!0.86!10.77!SP110;;chr7:96654133..96654150,-!p1@DLX5!0.86!6.24!DLX5;;chr8:102504651..102504683,+!p1@GRHL2!0.86!6.24!GRHL2;;chr5:2751762..2751784,-!p1@IRX2!0.85!6.10!IRX2;;chr1:209979375..209979386,-!p4@IRF6!0.85!6.10!IRF6;;chr11:65686802..65686818,+!p6@DRAP1!0.84!10.77!DRAP1;;chrY:2803415..2803468,+!p1@ZFY!0.82!5.67!ZFY;;chr12:66218255..66218304,+!p3@HMGA2!0.81!15.74!HMGA2;;chr3:189507460..189507471,+!p3@TP63!0.81!5.39!TP63;;chr12:66218836..66218888,+!p1@HMGA2!0.80!53.31!HMGA2;;chr1:158979851..158979865,+!p5@IFI16!0.80!12.33!IFI16;;chr17:80797886..80797906,-!p1@ZNF750!0.80!5.25!ZNF750;;chr6:28321909..28321965,-!p3@ZNF323!0.80!5.25!ZNF323;;chr6:28321971..28321995,-!p1@ZNF323!0.79!5.10!ZNF323;;chr3:32023232..32023273,+!p1@ZNF860!0.78!7.51!ZNF860;;chr1:37940170..37940190,+!p1@ZC3H12A!0.76!64.22!ZC3H12A;;chr4:111558135..111558198,-!p2@PITX2!0.76!4.82!PITX2;;chr8:128747661..128747703,+!p6@MYC!0.75!6.52!MYC;;chr20:55204351..55204377,+!p1@TFAP2C!0.73!5.67!TFAP2C;;chr12:27485823..27485868,+!p2@ARNTL2!0.71!18.57!ARNTL2;;chr2:122042770..122042785,-!p1@TFCP2L1!0.71!4.11!TFCP2L1;;chr1:151032860..151032918,+!p1@MLLT11!0.70!54.16!MLLT11;;chr12:66218183..66218209,+!p4@HMGA2!0.70!8.22!HMGA2;;chr6:10412576..10412599,-!p5@TFAP2A!0.70!3.97!TFAP2A;;chr12:27485785..27485816,+!p1@ARNTL2!0.69!30.91!ARNTL2;;chr8:128748308..128748324,+!p2@MYC!0.68!122.21!MYC;;chr8:128747757..128747800,+!p7@MYC!0.68!5.39!MYC;;chr5:3595977..3595999,+!p1@IRX1!0.68!3.83!IRX1;;chr1:24645832..24645853,+!p1@GRHL3!0.68!3.83!GRHL3;;chr16:86612320..86612394,+!p1@FOXL1!0.68!3.83!FOXL1;;chr6:126240380..126240430,+!p2@NCOA7!0.67!10.49!NCOA7;;chr17:41622765..41622821,-!p2@ETV4!0.67!5.95!ETV4;;chr3:18480217..18480239,-!p3@SATB1!0.67!3.69!SATB1;;chr17:70117153..70117174,+!p1@SOX9!0.66!42.39!SOX9;;chr4:299227..299272,-!p1@ZNF732!0.66!3.54!ZNF732;;chr1:151032782..151032801,+!p4@MLLT11!0.64!7.37!MLLT11;;chr5:72744445..72744466,-!p2@FOXD1!0.64!6.10!FOXD1;;chr6:106546808..106546833,+!p3@PRDM1!0.64!4.40!PRDM1;;chr3:141121820..141121838,+!p9@ZBTB38!0.64!3.40!ZBTB38;;chr3:37217736..37217753,-!p2@LRRFIP2!0.63!15.74!LRRFIP2;;chr19:53496768..53496799,-!p1@ZNF702P!0.63!5.53!ZNF702P;;chr12:66218212..66218244,+!p5@HMGA2!0.63!5.10!HMGA2;;chr6:126240356..126240379,+!p7@NCOA7!0.63!4.11!NCOA7;;chr17:3571863..3571881,-!p1@TAX1BP3!0.62!268.10!TAX1BP3;;chr2:208030647..208030689,-!p1@KLF7!0.62!31.19!KLF7;;chr11:65686732..65686756,+!p2@DRAP1!0.62!15.74!DRAP1;;chrX:56258844..56258882,+!p1@KLF8!0.62!4.68!KLF8;;chr3:18486354..18486377,-!p2@SATB1!0.62!4.11!SATB1;;chr13:73633131..73633149,+!p1@KLF5!0.61!39.56!KLF5;;chr7:28725740..28725778,+!p1@CREB5!0.60!31.76!CREB5;;chr12:48298765..48298783,-!p2@VDR!0.60!6.95!VDR;;chr16:54320101..54320125,-!p4@IRX3!0.60!4.54!IRX3;;chr5:72743793..72743855,-!p4@FOXD1!0.60!3.69!FOXD1;;chr16:67881647..67881663,-!p3@CENPT!0.60!2.98!CENPT;;chr17:41622731..41622764,-!p5@ETV4!0.60!2.98!ETV4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|fantom_cat=http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000066;;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:0002077;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0002159;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0002166;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0000075;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0003350;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0008814;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0010323;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0011137
|ffid_belonging_in_development=CL:0000221
|ffid_belonging_in_development=CL:0000221
|fonse_cell_line=
|fonse_cell_line=
Line 40: 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/Mallassez-derived%2520cells%252c%2520donor3.CNhs13551.11930-125I4.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Mallassez-derived%2520cells%252c%2520donor3.CNhs13551.11930-125I4.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Mallassez-derived%2520cells%252c%2520donor3.CNhs13551.11930-125I4.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Mallassez-derived%2520cells%252c%2520donor3.CNhs13551.11930-125I4.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Mallassez-derived%2520cells%252c%2520donor3.CNhs13551.11930-125I4.hg38.nobarcode.ctss.bed.gz
|id=FF:11930-125I4
|id=FF:11930-125I4
|is_a=EFO:0002091;;FF:0000087
|is_a=EFO:0002091;;FF:0000087
|is_obsolete=
|is_obsolete=
|library_id=CNhs13551
|library_id=CNhs13551
|library_id_phase_based=2:CNhs13551
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11930
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11930
|name=Mallassez-derived cells, donor3
|name=Mallassez-derived cells, donor3
|namespace=
|namespace=
Line 51: Line 63:
|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq=
|profile_srnaseq=
|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 88: Line 101:
|top_motifs=TP53:2.44026533975;TBX4,5:1.85872842141;TEF:1.44256695294;SNAI1..3:1.43341712795;ZEB1:1.427377201;ADNP_IRX_SIX_ZHX:1.26494775298;NKX3-2:1.22284172049;VSX1,2:1.18850955778;TEAD1:1.08442284013;NKX2-3_NKX2-5:1.07362316528;ELK1,4_GABP{A,B1}:0.931775696211;TBP:0.888921974862;NFIL3:0.856148212969;NANOG:0.85494274163;ONECUT1,2:0.782673102481;PPARG:0.774815466784;POU1F1:0.763918642004;MYOD1:0.744569274975;PAX4:0.743420472233;ALX1:0.730330342002;IRF7:0.669702856112;HSF1,2:0.668193312536;NFIX:0.630233157048;NKX2-2,8:0.629484637191;POU3F1..4:0.622159544972;FOS_FOS{B,L1}_JUN{B,D}:0.605094934049;XCPE1{core}:0.590099514743;BACH2:0.542853622822;TFCP2:0.518943019087;ZNF148:0.467031453;SOX17:0.430590017117;GFI1B:0.425766510723;HAND1,2:0.403280294415;ZNF238:0.387251768684;FOXM1:0.386711660146;FOSL2:0.368157339118;LMO2:0.36107015832;SP1:0.358262368491;NR1H4:0.357242358411;ZIC1..3:0.320354123815;NRF1:0.295738719753;ARID5B:0.277776978234;TLX2:0.251570489438;HIF1A:0.220097545636;ZNF143:0.215155661752;IKZF1:0.211404443321;PDX1:0.209911981061;GCM1,2:0.181248363249;MTF1:0.159039680739;RBPJ:0.15327277482;FOXN1:0.144836151272;KLF4:0.142809848423;GLI1..3:0.13600552642;POU6F1:0.0730049537197;TLX1..3_NFIC{dimer}:0.0681347926945;HLF:0.0680063999992;ELF1,2,4:0.0678905720823;SOX2:0.0633991376734;HES1:0.0509549938482;ALX4:0.0450974752031;MAZ:0.0441474999394;PAX5:0.0408593003353;NKX2-1,4:0.0406744019473;CDC5L:0.0376988113108;NKX3-1:0.0351185071604;NFE2:0.0226031306511;NFKB1_REL_RELA:0.0221228764937;LEF1_TCF7_TCF7L1,2:0.0198305573984;GZF1:0.0142454766737;CEBPA,B_DDIT3:0.0132739866491;NFE2L1:0.00962520460139;PAX1,9:0.00914400427241;SPZ1:-0.00110885616761;MAFB:-0.01102750816;HMX1:-0.0150363106595;STAT5{A,B}:-0.0221021229372;HMGA1,2:-0.028799681353;EVI1:-0.0335170505939;FOXO1,3,4:-0.0454213280001;GFI1:-0.0482145017234;HOX{A4,D4}:-0.0540774169386;YY1:-0.0568774470273;TFAP2{A,C}:-0.0570621791798;JUN:-0.0626528439006;UFEwm:-0.0693464304815;SOX{8,9,10}:-0.0712427750042;E2F1..5:-0.0858920317782;NFATC1..3:-0.106805650457;SMAD1..7,9:-0.127732274672;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.128208823458;ZBTB6:-0.128953603794;OCT4_SOX2{dimer}:-0.129693757733;HNF1A:-0.137107249409;IRF1,2:-0.137387573041;REST:-0.164129292369;HOX{A5,B5}:-0.16833412011;PAX2:-0.187061426918;CRX:-0.188550748325;LHX3,4:-0.21148590894;bHLH_family:-0.212999890933;NFY{A,B,C}:-0.222455381728;ATF4:-0.223014000387;NHLH1,2:-0.232367032646;SRF:-0.232866735881;FOXA2:-0.237173456935;EN1,2:-0.244398611449;MYBL2:-0.25497416809;ETS1,2:-0.25894190383;PITX1..3:-0.275421020522;PAX6:-0.276503722148;T:-0.279299477673;NR5A1,2:-0.280927474081;EBF1:-0.285937219487;ATF5_CREB3:-0.291436275684;RFX2..5_RFXANK_RFXAP:-0.303067496257;MYB:-0.309127831895;STAT1,3:-0.338464846598;RUNX1..3:-0.344628183838;NR6A1:-0.35722991236;PAX8:-0.364499315743;SPI1:-0.390812465578;TFDP1:-0.394424563083;GATA6:-0.399561078772;POU2F1..3:-0.399670794218;MTE{core}:-0.402593499116;ATF2:-0.409696910917;SPIB:-0.409778096864;PRRX1,2:-0.412753271991;GTF2I:-0.415077393629;EP300:-0.424491885497;AHR_ARNT_ARNT2:-0.436409845565;FOXQ1:-0.438358655979;TFAP4:-0.460464439772;MYFfamily:-0.464652096543;HNF4A_NR2F1,2:-0.476896349311;AR:-0.481338922535;GTF2A1,2:-0.482217946746;FOX{F1,F2,J1}:-0.486230866416;RFX1:-0.494830718706;HOX{A6,A7,B6,B7}:-0.499480881936;FOXL1:-0.537695977475;NR3C1:-0.548443970865;NFE2L2:-0.551688507641;PRDM1:-0.557166420521;FOX{I1,J2}:-0.567703361714;FOXP3:-0.568889706874;CDX1,2,4:-0.577308709212;CUX2:-0.581909887975;CREB1:-0.592696512059;ZBTB16:-0.609361009176;DBP:-0.610259910728;MEF2{A,B,C,D}:-0.625511794085;HOXA9_MEIS1:-0.638404668852;MED-1{core}:-0.645351974562;TOPORS:-0.655303900585;ZNF423:-0.665135792542;ZFP161:-0.665458482978;RXR{A,B,G}:-0.673432646162;ZNF384:-0.681870238912;STAT2,4,6:-0.695513796676;POU5F1:-0.73816703281;NKX6-1,2:-0.787181331768;HIC1:-0.787841094127;TAL1_TCF{3,4,12}:-0.834695106263;PBX1:-0.877947906874;RREB1:-0.88704865113;MZF1:-0.908916261883;ATF6:-0.912636249011;TFAP2B:-0.913569410323;SREBF1,2:-0.937788574825;GATA4:-0.949265697507;TGIF1:-0.956238182212;FOX{D1,D2}:-0.96553079287;RORA:-0.966300981884;BPTF:-1.01562094221;AIRE:-1.02325633789;ESRRA:-1.03098982849;PAX3,7:-1.03192353753;DMAP1_NCOR{1,2}_SMARC:-1.03363373894;NANOG{mouse}:-1.04249275303;RXRA_VDR{dimer}:-1.12141898709;HBP1_HMGB_SSRP1_UBTF:-1.15562701282;EGR1..3:-1.17063464438;SOX5:-1.1882751349;FOXP1:-1.18883633455;PATZ1:-1.26178542477;ESR1:-1.29973423698;XBP1:-1.31059357344;FOXD3:-1.33914546843;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.42651801706;IKZF2:-1.48568867179;BREu{core}:-1.60191646019
|top_motifs=TP53:2.44026533975;TBX4,5:1.85872842141;TEF:1.44256695294;SNAI1..3:1.43341712795;ZEB1:1.427377201;ADNP_IRX_SIX_ZHX:1.26494775298;NKX3-2:1.22284172049;VSX1,2:1.18850955778;TEAD1:1.08442284013;NKX2-3_NKX2-5:1.07362316528;ELK1,4_GABP{A,B1}:0.931775696211;TBP:0.888921974862;NFIL3:0.856148212969;NANOG:0.85494274163;ONECUT1,2:0.782673102481;PPARG:0.774815466784;POU1F1:0.763918642004;MYOD1:0.744569274975;PAX4:0.743420472233;ALX1:0.730330342002;IRF7:0.669702856112;HSF1,2:0.668193312536;NFIX:0.630233157048;NKX2-2,8:0.629484637191;POU3F1..4:0.622159544972;FOS_FOS{B,L1}_JUN{B,D}:0.605094934049;XCPE1{core}:0.590099514743;BACH2:0.542853622822;TFCP2:0.518943019087;ZNF148:0.467031453;SOX17:0.430590017117;GFI1B:0.425766510723;HAND1,2:0.403280294415;ZNF238:0.387251768684;FOXM1:0.386711660146;FOSL2:0.368157339118;LMO2:0.36107015832;SP1:0.358262368491;NR1H4:0.357242358411;ZIC1..3:0.320354123815;NRF1:0.295738719753;ARID5B:0.277776978234;TLX2:0.251570489438;HIF1A:0.220097545636;ZNF143:0.215155661752;IKZF1:0.211404443321;PDX1:0.209911981061;GCM1,2:0.181248363249;MTF1:0.159039680739;RBPJ:0.15327277482;FOXN1:0.144836151272;KLF4:0.142809848423;GLI1..3:0.13600552642;POU6F1:0.0730049537197;TLX1..3_NFIC{dimer}:0.0681347926945;HLF:0.0680063999992;ELF1,2,4:0.0678905720823;SOX2:0.0633991376734;HES1:0.0509549938482;ALX4:0.0450974752031;MAZ:0.0441474999394;PAX5:0.0408593003353;NKX2-1,4:0.0406744019473;CDC5L:0.0376988113108;NKX3-1:0.0351185071604;NFE2:0.0226031306511;NFKB1_REL_RELA:0.0221228764937;LEF1_TCF7_TCF7L1,2:0.0198305573984;GZF1:0.0142454766737;CEBPA,B_DDIT3:0.0132739866491;NFE2L1:0.00962520460139;PAX1,9:0.00914400427241;SPZ1:-0.00110885616761;MAFB:-0.01102750816;HMX1:-0.0150363106595;STAT5{A,B}:-0.0221021229372;HMGA1,2:-0.028799681353;EVI1:-0.0335170505939;FOXO1,3,4:-0.0454213280001;GFI1:-0.0482145017234;HOX{A4,D4}:-0.0540774169386;YY1:-0.0568774470273;TFAP2{A,C}:-0.0570621791798;JUN:-0.0626528439006;UFEwm:-0.0693464304815;SOX{8,9,10}:-0.0712427750042;E2F1..5:-0.0858920317782;NFATC1..3:-0.106805650457;SMAD1..7,9:-0.127732274672;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.128208823458;ZBTB6:-0.128953603794;OCT4_SOX2{dimer}:-0.129693757733;HNF1A:-0.137107249409;IRF1,2:-0.137387573041;REST:-0.164129292369;HOX{A5,B5}:-0.16833412011;PAX2:-0.187061426918;CRX:-0.188550748325;LHX3,4:-0.21148590894;bHLH_family:-0.212999890933;NFY{A,B,C}:-0.222455381728;ATF4:-0.223014000387;NHLH1,2:-0.232367032646;SRF:-0.232866735881;FOXA2:-0.237173456935;EN1,2:-0.244398611449;MYBL2:-0.25497416809;ETS1,2:-0.25894190383;PITX1..3:-0.275421020522;PAX6:-0.276503722148;T:-0.279299477673;NR5A1,2:-0.280927474081;EBF1:-0.285937219487;ATF5_CREB3:-0.291436275684;RFX2..5_RFXANK_RFXAP:-0.303067496257;MYB:-0.309127831895;STAT1,3:-0.338464846598;RUNX1..3:-0.344628183838;NR6A1:-0.35722991236;PAX8:-0.364499315743;SPI1:-0.390812465578;TFDP1:-0.394424563083;GATA6:-0.399561078772;POU2F1..3:-0.399670794218;MTE{core}:-0.402593499116;ATF2:-0.409696910917;SPIB:-0.409778096864;PRRX1,2:-0.412753271991;GTF2I:-0.415077393629;EP300:-0.424491885497;AHR_ARNT_ARNT2:-0.436409845565;FOXQ1:-0.438358655979;TFAP4:-0.460464439772;MYFfamily:-0.464652096543;HNF4A_NR2F1,2:-0.476896349311;AR:-0.481338922535;GTF2A1,2:-0.482217946746;FOX{F1,F2,J1}:-0.486230866416;RFX1:-0.494830718706;HOX{A6,A7,B6,B7}:-0.499480881936;FOXL1:-0.537695977475;NR3C1:-0.548443970865;NFE2L2:-0.551688507641;PRDM1:-0.557166420521;FOX{I1,J2}:-0.567703361714;FOXP3:-0.568889706874;CDX1,2,4:-0.577308709212;CUX2:-0.581909887975;CREB1:-0.592696512059;ZBTB16:-0.609361009176;DBP:-0.610259910728;MEF2{A,B,C,D}:-0.625511794085;HOXA9_MEIS1:-0.638404668852;MED-1{core}:-0.645351974562;TOPORS:-0.655303900585;ZNF423:-0.665135792542;ZFP161:-0.665458482978;RXR{A,B,G}:-0.673432646162;ZNF384:-0.681870238912;STAT2,4,6:-0.695513796676;POU5F1:-0.73816703281;NKX6-1,2:-0.787181331768;HIC1:-0.787841094127;TAL1_TCF{3,4,12}:-0.834695106263;PBX1:-0.877947906874;RREB1:-0.88704865113;MZF1:-0.908916261883;ATF6:-0.912636249011;TFAP2B:-0.913569410323;SREBF1,2:-0.937788574825;GATA4:-0.949265697507;TGIF1:-0.956238182212;FOX{D1,D2}:-0.96553079287;RORA:-0.966300981884;BPTF:-1.01562094221;AIRE:-1.02325633789;ESRRA:-1.03098982849;PAX3,7:-1.03192353753;DMAP1_NCOR{1,2}_SMARC:-1.03363373894;NANOG{mouse}:-1.04249275303;RXRA_VDR{dimer}:-1.12141898709;HBP1_HMGB_SSRP1_UBTF:-1.15562701282;EGR1..3:-1.17063464438;SOX5:-1.1882751349;FOXP1:-1.18883633455;PATZ1:-1.26178542477;ESR1:-1.29973423698;XBP1:-1.31059357344;FOXD3:-1.33914546843;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.42651801706;IKZF2:-1.48568867179;BREu{core}:-1.60191646019
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11930-125I4;search_select_hide=table117:FF:11930-125I4
}}
}}

Latest revision as of 18:29, 4 June 2020

Name:Mallassez-derived cells, donor3
Species:Human (Homo sapiens)
Library ID:CNhs13551
Sample type:primary cells
Genomic View: UCSC
RefEX:Specific genes
FANTOM CAT:1, 2, 3, 4, 5, 6, 7, 8, 9, 10
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexmale
age18
cell typeepithelial cell rests of Malassez
cell lineNA
companyNA
collaborationMitsuhiro Ohshima (Nihon University School of Dentistry)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberMZH7
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005171
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13551 CAGE DRX008326 DRR009198
Accession ID Hg19

Library idBAMCTSS
CNhs13551 DRZ000623 DRZ002008
Accession ID Hg38

Library idBAMCTSS
CNhs13551 DRZ011973 DRZ013358
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
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
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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: CNhs13551

Jaspar motifP-value
MA0002.20.676
MA0003.10.717
MA0004.10.022
MA0006.10.0459
MA0007.10.476
MA0009.10.0304
MA0014.10.103
MA0017.10.482
MA0018.20.0157
MA0019.10.327
MA0024.10.0624
MA0025.10.937
MA0027.10.456
MA0028.12.18441e-4
MA0029.10.997
MA0030.10.194
MA0031.10.0769
MA0035.20.218
MA0038.10.525
MA0039.25.84388e-4
MA0040.10.336
MA0041.10.377
MA0042.10.932
MA0043.10.347
MA0046.10.537
MA0047.20.89
MA0048.10.596
MA0050.10.787
MA0051.10.387
MA0052.10.0464
MA0055.10.0269
MA0057.10.0736
MA0058.10.00463
MA0059.10.977
MA0060.10.153
MA0061.10.53
MA0062.28.72169e-4
MA0065.20.106
MA0066.10.141
MA0067.10.0104
MA0068.11.69328e-5
MA0069.10.559
MA0070.10.235
MA0071.10.0527
MA0072.10.152
MA0073.10.441
MA0074.10.362
MA0076.10.00704
MA0077.10.103
MA0078.10.81
MA0079.20.57
MA0080.20.0107
MA0081.10.553
MA0083.10.176
MA0084.10.0405
MA0087.10.917
MA0088.10.253
MA0090.13.66148e-5
MA0091.10.186
MA0092.10.553
MA0093.10.0154
MA0099.23.03293e-11
MA0100.10.302
MA0101.10.185
MA0102.20.487
MA0103.11.25701e-6
MA0104.20.247
MA0105.10.173
MA0106.16.80846e-13
MA0107.10.31
MA0108.20.695
MA0111.10.878
MA0112.20.135
MA0113.10.271
MA0114.10.26
MA0115.10.911
MA0116.10.161
MA0117.10.993
MA0119.10.362
MA0122.10.853
MA0124.10.958
MA0125.10.0266
MA0131.10.861
MA0135.10.996
MA0136.10.584
MA0137.20.614
MA0138.20.406
MA0139.10.343
MA0140.10.577
MA0141.10.132
MA0142.10.639
MA0143.10.458
MA0144.10.856
MA0145.10.0376
MA0146.10.541
MA0147.10.56
MA0148.10.563
MA0149.10.0243
MA0150.10.747
MA0152.10.501
MA0153.10.956
MA0154.10.215
MA0155.10.426
MA0156.10.214
MA0157.10.0641
MA0159.10.888
MA0160.10.386
MA0162.10.0646
MA0163.10.219
MA0164.10.956
MA0258.10.468
MA0259.10.45



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: CNhs13551

Novel motifP-value
10.794
100.766
1000.682
1010.139
1020.261
1030.0825
1040.839
1050.509
1060.923
1070.743
1080.899
1090.00205
110.365
1100.163
1110.232
1120.345
1130.121
1140.0841
1150.714
1160.648
1170.161
1180.543
1190.841
120.844
1200.0405
1210.231
1220.29
1230.114
1240.054
1250.497
1260.102
1270.0709
1280.678
1290.11
130.00351
1300.924
1310.808
1320.639
1330.00111
1340.373
1350.702
1360.00894
1370.09
1380.423
1390.19
140.928
1400.79
1410.346
1420.721
1430.798
1440.256
1450.643
1460.153
1470.548
1480.709
1490.965
150.915
1500.323
1510.64
1520.0211
1530.628
1540.764
1550.625
1560.601
1570.104
1580.0975
1590.605
160.0203
1600.723
1610.239
1620.698
1630.937
1640.871
1650.443
1660.635
1670.692
1680.12
1690.0929
170.391
180.485
190.884
20.229
200.895
210.956
220.914
230.915
240.00309
250.531
260.886
270.501
280.459
290.491
30.605
300.0753
310.864
320.0525
330.0551
340.79
350.0966
360.732
370.0617
380.67
390.318
40.649
400.0153
410.465
420.385
430.983
440.561
450.0873
460.959
470.129
480.0846
490.335
50.703
500.429
510.919
520.372
530.313
540.915
550.299
560.272
570.542
580.669
590.544
60.388
600.305
610.795
620.918
630.207
640.935
650.808
660.398
670.777
680.343
690.676
70.147
700.448
710.271
720.627
730.00447
740.0791
750.247
760.787
770.0491
780.00228
790.576
80.43
800.666
810.173
820.555
830.97
840.508
850.792
860.985
870.00149
880.715
890.0291
90.7
900.49
910.751
920.753
930.083
940.851
950.0245
960.876
970.655
980.904
990.388



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: CNhs13551


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)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002159 (general ecto-epithelial cell)
0000255 (eukaryotic cell)
0002077 (ecto-epithelial cell)
0002166 (epithelial cell of Malassez)

UBERON: Anatomy
0000468 (multi-cellular organism)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000075 (subdivision of skeletal system)
0004765 (skeletal element)
0001708 (jaw skeleton)
0011159 (primary subdivision of cranial skeletal system)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0008895 (splanchnocranium)
0011137 (axial skeletal system)
0010323 (cranial skeletal system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000087 (human Malassez derived epithelial cell sample)

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:0000221 (ectodermal cell)

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