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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008217
|DRA_sample_Accession=CAGE@SAMD00005551
|accession_numbers=CAGE;DRX008325;DRR009197;DRZ000622;DRZ002007;DRZ011972;DRZ013357
|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=chr1:209979467..209979494,-!p1@IRF6!2.19!171.34!IRF6;;chr17:7493405..7493419,-!p1@SOX15!2.06!112.88!SOX15;;chr3:111314186..111314204,-!p1@ZBED2!2.05!111.71!ZBED2;;chr11:34642612..34642646,+!p1@EHF!1.97!93.40!EHF;;chr1:209979411..209979433,-!p2@IRF6!1.84!68.54!IRF6;;chr1:6479968..6479986,-!p1@HES2!1.79!60.81!HES2;;chr3:189507432..189507459,+!p1@TP63!1.74!54.09!TP63;;chr6:10415276..10415341,-!p2@TFAP2A!1.64!52.24!TFAP2A;;chr6:10412600..10412637,-!p1@TFAP2A!1.51!51.74!TFAP2A;;chr15:83953397..83953425,-!p1@BNC1!1.50!34.94!BNC1;;chr4:111544219..111544240,-!p1@PITX2!1.50!30.74!PITX2;;chr11:34645791..34645836,+!p3@EHF!1.48!29.40!EHF;;chr15:101069113..101069169,-!p1@CERS3!1.46!28.05!CERS3;;chr12:54785054..54785072,-!p4@ZNF385A!1.42!28.72!ZNF385A;;chr3:111314230..111314241,-!p2@ZBED2!1.42!25.20!ZBED2;;chr5:134369905..134369972,-!p1@PITX1!1.39!35.44!PITX1;;chrX:2418949..2419024,-!p1@DHRSX,p1@ZBED1!1.31!19.49!ZBED1;;chr12:54785074..54785122,-!p2@ZNF385A!1.30!28.72!ZNF385A;;chr21:36421535..36421610,-!p2@RUNX1!1.27!62.32!RUNX1;;chr17:7492684..7492778,-!p2@SOX15!1.19!30.74!SOX15;;chr6:10415484..10415508,-!p3@TFAP2A!1.15!13.10!TFAP2A;;chr8:49833948..49833973,-!p2@SNAI2!1.14!80.46!SNAI2;;chr8:10588010..10588030,-!p1@SOX7!1.09!11.42!SOX7;;chr5:134369879..134369898,-!p2@PITX1!1.07!10.75!PITX1;;chr12:66218598..66218645,+!p2@HMGA2!1.04!46.87!HMGA2;;chr4:111558135..111558198,-!p2@PITX2!1.04!10.08!PITX2;;chr20:39317868..39317884,-!p1@MAFB!1.03!115.74!MAFB;;chr8:49833978..49833996,-!p1@SNAI2!1.02!196.54!SNAI2;;chr12:66218836..66218888,+!p1@HMGA2!1.02!89.37!HMGA2;;chr11:34642656..34642667,+!p2@EHF!1.02!9.57!EHF;;chr9:100615499..100615519,+!p1@FOXE1!1.02!9.41!FOXE1;;chr19:45908292..45908374,-!p1@PPP1R13L!1.01!82.82!PPP1R13L;;chr14:74256787..74256858,-!p6@C14orf43!0.97!8.23!C14orf43;;chr16:67881588..67881612,-!p2@CENPT!0.96!11.25!CENPT;;chr19:53496768..53496799,-!p1@ZNF702P!0.93!11.76!ZNF702P;;chr5:72744594..72744609,-!p1@FOXD1!0.91!34.27!FOXD1;;chr1:158979792..158979814,+!p2@IFI16!0.90!69.21!IFI16;;chr8:102504651..102504683,+!p1@GRHL2!0.88!6.55!GRHL2;;chr2:231084639..231084654,-!p2@SP110!0.87!10.92!SP110;;chr5:2751762..2751784,-!p1@IRX2!0.87!6.38!IRX2;;chr19:42636586..42636607,-!p1@POU2F2!0.85!17.64!POU2F2;;chr20:55204351..55204377,+!p1@TFAP2C!0.82!7.22!TFAP2C;;chr12:27485762..27485776,+!p3@ARNTL2!0.81!15.62!ARNTL2;;chr1:209979375..209979386,-!p4@IRF6!0.80!5.38!IRF6;;chr5:3595977..3595999,+!p1@IRX1!0.79!5.21!IRX1;;chr2:122042770..122042785,-!p1@TFCP2L1!0.79!5.21!TFCP2L1;;chr16:54320646..54320672,-!p2@IRX3!0.78!7.90!IRX3;;chr17:3571863..3571881,-!p1@TAX1BP3!0.74!356.46!TAX1BP3;;chr2:46524897..46524911,+!p2@EPAS1!0.74!13.77!EPAS1;;chr16:54320101..54320125,-!p4@IRX3!0.74!6.72!IRX3;;chrX:56258844..56258882,+!p1@KLF8!0.73!6.22!KLF8;;chr22:19748231..19748317,+!p1@TBX1!0.73!4.37!TBX1;;chr3:69811858..69811881,+!p5@MITF!0.73!4.37!MITF;;chr11:34643638..34643667,+!p8@EHF!0.73!4.37!EHF;;chr12:48298765..48298783,-!p2@VDR!0.72!9.57!VDR;;chr6:28321909..28321965,-!p3@ZNF323!0.72!4.20!ZNF323;;chr15:83953373..83953386,-!p2@BNC1!0.72!4.20!BNC1;;chr16:31076332..31076388,-!p3@ZNF668!0.72!4.20!ZNF668;;chr3:32023232..32023273,+!p1@ZNF860!0.71!6.22!ZNF860;;chr13:73633131..73633149,+!p1@KLF5!0.70!48.71!KLF5;;chr12:66218255..66218304,+!p3@HMGA2!0.70!11.76!HMGA2;;chr3:141121847..141121868,+!p5@ZBTB38!0.70!6.38!ZBTB38;;chr2:231084820..231084836,-!p5@SP110!0.70!4.70!SP110;;chr2:63277948..63277974,+!p1@OTX1!0.70!4.03!OTX1;;chr1:209979449..209979460,-!p3@IRF6!0.70!4.03!IRF6;;chr16:67881647..67881663,-!p3@CENPT!0.70!4.03!CENPT;;chr16:54320617..54320643,-!p3@IRX3!0.69!5.21!IRX3;;chr6:10412576..10412599,-!p5@TFAP2A!0.69!3.86!TFAP2A;;chr13:41593425..41593480,-!p1@ELF1!0.68!27.55!ELF1;;chr1:151032782..151032801,+!p4@MLLT11!0.68!8.23!MLLT11;;chr3:170076314..170076334,+!p2@SKIL!0.66!4.87!SKIL;;chr12:66218904..66218913,+!p11@HMGA2!0.66!3.53!HMGA2;;chr1:37940170..37940190,+!p1@ZC3H12A!0.65!49.89!ZC3H12A;;chr6:10412392..10412409,-!p4@TFAP2A!0.65!4.03!TFAP2A;;chr1:203764633..203764674,+!p2@ZC3H11A!0.64!5.88!ZC3H11A;;chr19:57792157..57792170,+!p6@ZNF460!0.64!5.21!ZNF460;;chr6:106546808..106546833,+!p3@PRDM1!0.64!4.37!PRDM1;;chr6:10415263..10415274,-!p8@TFAP2A!0.64!3.36!TFAP2A;;chr1:151032860..151032918,+!p1@MLLT11!0.63!46.20!MLLT11;;chr17:70117153..70117174,+!p1@SOX9!0.63!39.64!SOX9;;chr7:28725740..28725778,+!p1@CREB5!0.63!34.10!CREB5;;chr16:54320675..54320715,-!p1@IRX3!0.62!7.73!IRX3;;chr12:66218183..66218209,+!p4@HMGA2!0.62!6.72!HMGA2;;chr12:66218003..66218018,+!p9@HMGA2!0.62!4.03!HMGA2;;chr11:31832658..31832681,-!p1@PAX6!0.62!3.19!PAX6;;chr6:28321971..28321995,-!p1@ZNF323!0.62!3.19!ZNF323;;chr6:41701557..41701578,-!p3@TFEB!0.62!3.19!TFEB;;chr4:188916918..188916942,+!p1@ZFP42!0.62!3.19!ZFP42;;chr12:72056800..72056834,+!p1@THAP2!0.61!4.37!THAP2;;chr2:231084659..231084721,-!p1@SP110!0.60!83.66!SP110;;chr2:208030647..208030689,-!p1@KLF7!0.60!30.24!KLF7;;chr19:20278012..20278034,+!p1@ZNF486!0.60!30.07!ZNF486;;chr12:27485785..27485816,+!p1@ARNTL2!0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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 39: 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%2520donor2.CNhs13550.11929-125I3.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Mallassez-derived%2520cells%252c%2520donor2.CNhs13550.11929-125I3.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Mallassez-derived%2520cells%252c%2520donor2.CNhs13550.11929-125I3.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%2520donor2.CNhs13550.11929-125I3.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Mallassez-derived%2520cells%252c%2520donor2.CNhs13550.11929-125I3.hg38.nobarcode.ctss.bed.gz
|id=FF:11929-125I3
|id=FF:11929-125I3
|is_a=EFO:0002091;;FF:0000087
|is_a=EFO:0002091;;FF:0000087
|is_obsolete=
|is_obsolete=
|library_ids=CNhs13550
|library_id=CNhs13550
|library_id_phase_based=2:CNhs13550
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11929
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11929
|name=Mallassez-derived cells, donor2
|name=Mallassez-derived cells, donor2
|namespace=
|namespace=
Line 50: Line 63:
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|profile_srnaseq=
|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 87: Line 101:
|top_motifs=TP53:2.80914205801;TBX4,5:2.37828263609;NKX3-2:1.83977568216;TEF:1.8056156966;PAX4:1.42474871389;TEAD1:1.32950532179;PPARG:1.29162178043;ZEB1:1.2079460969;EVI1:1.07788914972;HAND1,2:1.05352844808;SNAI1..3:1.0096940471;ADNP_IRX_SIX_ZHX:1.00730469318;HSF1,2:0.962065096701;NKX2-3_NKX2-5:0.931692381447;NFIX:0.849710768293;TFCP2:0.822556814095;PDX1:0.774959749839;IRF7:0.774540799456;VSX1,2:0.771852435736;HMGA1,2:0.733550085535;ZNF238:0.725084959372;POU3F1..4:0.684043015349;ELK1,4_GABP{A,B1}:0.680527996792;GLI1..3:0.640868577972;FOS_FOS{B,L1}_JUN{B,D}:0.61768667376;FOXN1:0.616506003746;XCPE1{core}:0.590848457105;NR1H4:0.58984081989;NFIL3:0.577800749342;MYOD1:0.570085259105;ZIC1..3:0.564993204052;BACH2:0.554093807044;NANOG:0.54980933477;TLX2:0.543102784506;SP1:0.507536308056;MAZ:0.499318854079;POU1F1:0.497480964413;FOSL2:0.492830266617;ZNF148:0.489631395452;NKX2-2,8:0.474969404948;SOX17:0.47239568965;NKX2-1,4:0.458957378796;UFEwm:0.412289055086;SOX2:0.406238164946;ARID5B:0.402095492683;ONECUT1,2:0.369912029918;KLF4:0.361996900084;SPZ1:0.328589469817;NR3C1:0.320892864771;NKX3-1:0.319304855734;MAFB:0.296351163464;TLX1..3_NFIC{dimer}:0.278495867591;GCM1,2:0.212367680963;SMAD1..7,9:0.206526735337;TBP:0.193048732547;IKZF1:0.191001806378;HOX{A4,D4}:0.178566129575;GFI1B:0.170292605899;LMO2:0.151620043594;ZNF143:0.150467187327;NRF1:0.0831109435566;MYBL2:0.0767720392189;HLF:0.0632680901138;MTF1:0.0487603792357;NFATC1..3:0.0433770504579;TFAP2{A,C}:0.0395966442323;IRF1,2:0.0351926634326;HIF1A:0.0309940614223;LHX3,4:0.012367015289;HMX1:0.00965678572197;GFI1:0.00793873099197;LEF1_TCF7_TCF7L1,2:0.00662569791811;NFE2:-0.00536701622073;STAT1,3:-0.0121255209373;RBPJ:-0.0404028792318;FOXA2:-0.0462090782455;ZBTB6:-0.0599814969446;NFKB1_REL_RELA:-0.0606801066544;ALX1:-0.0767933944241;GTF2A1,2:-0.0791661261148;MTE{core}:-0.0841257166108;POU6F1:-0.0881998866156;OCT4_SOX2{dimer}:-0.102161020932;GZF1:-0.10224680257;PAX1,9:-0.103691722798;RUNX1..3:-0.149448317782;HOX{A5,B5}:-0.151080558409;NFE2L1:-0.166393562317;NHLH1,2:-0.169665478797;JUN:-0.179443026808;RXR{A,B,G}:-0.182157098784;SRF:-0.182677973616;HNF1A:-0.182901363719;REST:-0.188998367319;EBF1:-0.191892571617;PAX2:-0.200766692417;MYFfamily:-0.205825795033;EP300:-0.217303050066;AIRE:-0.222916736785;NFY{A,B,C}:-0.225603880368;CEBPA,B_DDIT3:-0.236601857068;ELF1,2,4:-0.238179792827;FOXO1,3,4:-0.265618698829;FOXP3:-0.278523305933;YY1:-0.280569623918;EN1,2:-0.282341975805;RXRA_VDR{dimer}:-0.29063432527;ATF5_CREB3:-0.297855364751;ALX4:-0.307930867341;AR:-0.327027826859;GTF2I:-0.334680496278;PAX5:-0.346334594414;ETS1,2:-0.347400149546;SPI1:-0.353687831599;FOXM1:-0.355360832816;ZFP161:-0.372358246491;ATF6:-0.380758415745;SPIB:-0.388748993198;RFX1:-0.389367554348;CDC5L:-0.391395988842;SOX{8,9,10}:-0.393017979835;PRDM1:-0.399362477065;FOX{I1,J2}:-0.413860727888;bHLH_family:-0.419662416574;ZNF384:-0.425052574122;ATF4:-0.428449311397;GATA6:-0.430990432789;TAL1_TCF{3,4,12}:-0.444325025186;NFE2L2:-0.458788482738;NR6A1:-0.475052191855;MED-1{core}:-0.493115749526;STAT5{A,B}:-0.534844581828;TFDP1:-0.546664201709;ATF2:-0.54973663009;RFX2..5_RFXANK_RFXAP:-0.564611727485;SREBF1,2:-0.566457217796;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.579517148813;TFAP2B:-0.581077451243;MYB:-0.593459465672;CDX1,2,4:-0.600061799407;E2F1..5:-0.601144111604;HES1:-0.60243618655;NANOG{mouse}:-0.613038751154;PITX1..3:-0.625234094834;CRX:-0.626570959838;FOX{F1,F2,J1}:-0.630400618716;T:-0.642750093683;BPTF:-0.645015547673;PAX8:-0.651268749566;DBP:-0.653761234484;HNF4A_NR2F1,2:-0.65501186595;MEF2{A,B,C,D}:-0.66865284772;HOX{A6,A7,B6,B7}:-0.669812604809;HIC1:-0.67036758808;PRRX1,2:-0.678756579127;CUX2:-0.683395903917;MZF1:-0.685550370467;TGIF1:-0.685564841147;TOPORS:-0.695497558855;GATA4:-0.699164115858;TFAP4:-0.709772026407;ZBTB16:-0.720096450582;FOXL1:-0.765471945303;FOX{D1,D2}:-0.780902778132;CREB1:-0.795558033029;NR5A1,2:-0.810735708063;ZNF423:-0.835302069919;HOXA9_MEIS1:-0.855197887328;AHR_ARNT_ARNT2:-0.921401745221;RREB1:-0.932233602466;NKX6-1,2:-0.957427067188;ESR1:-0.969674772952;EGR1..3:-1.00529612903;STAT2,4,6:-1.03315898787;POU5F1:-1.04912495156;DMAP1_NCOR{1,2}_SMARC:-1.0609928452;FOXQ1:-1.13269105643;HBP1_HMGB_SSRP1_UBTF:-1.14894890924;POU2F1..3:-1.18473518621;PAX6:-1.1870195198;SOX5:-1.20169424821;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.28192428365;XBP1:-1.30802327431;PATZ1:-1.33134049433;FOXP1:-1.35341928318;PBX1:-1.35427625133;RORA:-1.35882596649;PAX3,7:-1.41695041239;ESRRA:-1.45805746596;BREu{core}:-1.58436443353;IKZF2:-1.6215430053;FOXD3:-1.76408328813
|top_motifs=TP53:2.80914205801;TBX4,5:2.37828263609;NKX3-2:1.83977568216;TEF:1.8056156966;PAX4:1.42474871389;TEAD1:1.32950532179;PPARG:1.29162178043;ZEB1:1.2079460969;EVI1:1.07788914972;HAND1,2:1.05352844808;SNAI1..3:1.0096940471;ADNP_IRX_SIX_ZHX:1.00730469318;HSF1,2:0.962065096701;NKX2-3_NKX2-5:0.931692381447;NFIX:0.849710768293;TFCP2:0.822556814095;PDX1:0.774959749839;IRF7:0.774540799456;VSX1,2:0.771852435736;HMGA1,2:0.733550085535;ZNF238:0.725084959372;POU3F1..4:0.684043015349;ELK1,4_GABP{A,B1}:0.680527996792;GLI1..3:0.640868577972;FOS_FOS{B,L1}_JUN{B,D}:0.61768667376;FOXN1:0.616506003746;XCPE1{core}:0.590848457105;NR1H4:0.58984081989;NFIL3:0.577800749342;MYOD1:0.570085259105;ZIC1..3:0.564993204052;BACH2:0.554093807044;NANOG:0.54980933477;TLX2:0.543102784506;SP1:0.507536308056;MAZ:0.499318854079;POU1F1:0.497480964413;FOSL2:0.492830266617;ZNF148:0.489631395452;NKX2-2,8:0.474969404948;SOX17:0.47239568965;NKX2-1,4:0.458957378796;UFEwm:0.412289055086;SOX2:0.406238164946;ARID5B:0.402095492683;ONECUT1,2:0.369912029918;KLF4:0.361996900084;SPZ1:0.328589469817;NR3C1:0.320892864771;NKX3-1:0.319304855734;MAFB:0.296351163464;TLX1..3_NFIC{dimer}:0.278495867591;GCM1,2:0.212367680963;SMAD1..7,9:0.206526735337;TBP:0.193048732547;IKZF1:0.191001806378;HOX{A4,D4}:0.178566129575;GFI1B:0.170292605899;LMO2:0.151620043594;ZNF143:0.150467187327;NRF1:0.0831109435566;MYBL2:0.0767720392189;HLF:0.0632680901138;MTF1:0.0487603792357;NFATC1..3:0.0433770504579;TFAP2{A,C}:0.0395966442323;IRF1,2:0.0351926634326;HIF1A:0.0309940614223;LHX3,4:0.012367015289;HMX1:0.00965678572197;GFI1:0.00793873099197;LEF1_TCF7_TCF7L1,2:0.00662569791811;NFE2:-0.00536701622073;STAT1,3:-0.0121255209373;RBPJ:-0.0404028792318;FOXA2:-0.0462090782455;ZBTB6:-0.0599814969446;NFKB1_REL_RELA:-0.0606801066544;ALX1:-0.0767933944241;GTF2A1,2:-0.0791661261148;MTE{core}:-0.0841257166108;POU6F1:-0.0881998866156;OCT4_SOX2{dimer}:-0.102161020932;GZF1:-0.10224680257;PAX1,9:-0.103691722798;RUNX1..3:-0.149448317782;HOX{A5,B5}:-0.151080558409;NFE2L1:-0.166393562317;NHLH1,2:-0.169665478797;JUN:-0.179443026808;RXR{A,B,G}:-0.182157098784;SRF:-0.182677973616;HNF1A:-0.182901363719;REST:-0.188998367319;EBF1:-0.191892571617;PAX2:-0.200766692417;MYFfamily:-0.205825795033;EP300:-0.217303050066;AIRE:-0.222916736785;NFY{A,B,C}:-0.225603880368;CEBPA,B_DDIT3:-0.236601857068;ELF1,2,4:-0.238179792827;FOXO1,3,4:-0.265618698829;FOXP3:-0.278523305933;YY1:-0.280569623918;EN1,2:-0.282341975805;RXRA_VDR{dimer}:-0.29063432527;ATF5_CREB3:-0.297855364751;ALX4:-0.307930867341;AR:-0.327027826859;GTF2I:-0.334680496278;PAX5:-0.346334594414;ETS1,2:-0.347400149546;SPI1:-0.353687831599;FOXM1:-0.355360832816;ZFP161:-0.372358246491;ATF6:-0.380758415745;SPIB:-0.388748993198;RFX1:-0.389367554348;CDC5L:-0.391395988842;SOX{8,9,10}:-0.393017979835;PRDM1:-0.399362477065;FOX{I1,J2}:-0.413860727888;bHLH_family:-0.419662416574;ZNF384:-0.425052574122;ATF4:-0.428449311397;GATA6:-0.430990432789;TAL1_TCF{3,4,12}:-0.444325025186;NFE2L2:-0.458788482738;NR6A1:-0.475052191855;MED-1{core}:-0.493115749526;STAT5{A,B}:-0.534844581828;TFDP1:-0.546664201709;ATF2:-0.54973663009;RFX2..5_RFXANK_RFXAP:-0.564611727485;SREBF1,2:-0.566457217796;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.579517148813;TFAP2B:-0.581077451243;MYB:-0.593459465672;CDX1,2,4:-0.600061799407;E2F1..5:-0.601144111604;HES1:-0.60243618655;NANOG{mouse}:-0.613038751154;PITX1..3:-0.625234094834;CRX:-0.626570959838;FOX{F1,F2,J1}:-0.630400618716;T:-0.642750093683;BPTF:-0.645015547673;PAX8:-0.651268749566;DBP:-0.653761234484;HNF4A_NR2F1,2:-0.65501186595;MEF2{A,B,C,D}:-0.66865284772;HOX{A6,A7,B6,B7}:-0.669812604809;HIC1:-0.67036758808;PRRX1,2:-0.678756579127;CUX2:-0.683395903917;MZF1:-0.685550370467;TGIF1:-0.685564841147;TOPORS:-0.695497558855;GATA4:-0.699164115858;TFAP4:-0.709772026407;ZBTB16:-0.720096450582;FOXL1:-0.765471945303;FOX{D1,D2}:-0.780902778132;CREB1:-0.795558033029;NR5A1,2:-0.810735708063;ZNF423:-0.835302069919;HOXA9_MEIS1:-0.855197887328;AHR_ARNT_ARNT2:-0.921401745221;RREB1:-0.932233602466;NKX6-1,2:-0.957427067188;ESR1:-0.969674772952;EGR1..3:-1.00529612903;STAT2,4,6:-1.03315898787;POU5F1:-1.04912495156;DMAP1_NCOR{1,2}_SMARC:-1.0609928452;FOXQ1:-1.13269105643;HBP1_HMGB_SSRP1_UBTF:-1.14894890924;POU2F1..3:-1.18473518621;PAX6:-1.1870195198;SOX5:-1.20169424821;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.28192428365;XBP1:-1.30802327431;PATZ1:-1.33134049433;FOXP1:-1.35341928318;PBX1:-1.35427625133;RORA:-1.35882596649;PAX3,7:-1.41695041239;ESRRA:-1.45805746596;BREu{core}:-1.58436443353;IKZF2:-1.6215430053;FOXD3:-1.76408328813
|xref=
|xref=
}} {{DRAAccessionNumbers
|DRA_sample_Accession=CAGE@DRS008217
|accession_numbers=DRX008325;DRR009197;DRZ000622;DRZ002007;CAGE
|library_id=CNhs13550
}}
}}

Revision as of 21:31, 10 August 2017

Name:Mallassez-derived cells, donor2
Species:Human (Homo sapiens)
Library ID:CNhs13550
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
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexfemale
age29
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 numberMZe6
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005551
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13550 CAGE DRX008325 DRR009197
Accession ID Hg19

Library idBAMCTSS
CNhs13550 DRZ000622 DRZ002007
Accession ID Hg38

Library idBAMCTSS
CNhs13550 DRZ011972 DRZ013357
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
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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: CNhs13550

Jaspar motifP-value
MA0002.20.46
MA0003.10.905
MA0004.10.0162
MA0006.10.0048
MA0007.10.477
MA0009.10.203
MA0014.10.0898
MA0017.10.759
MA0018.20.00472
MA0019.10.024
MA0024.12.31427e-5
MA0025.10.556
MA0027.10.497
MA0028.10.0981
MA0029.10.339
MA0030.10.173
MA0031.10.123
MA0035.20.204
MA0038.10.271
MA0039.20.0022
MA0040.10.402
MA0041.10.401
MA0042.10.985
MA0043.10.0337
MA0046.10.403
MA0047.20.936
MA0048.10.696
MA0050.10.792
MA0051.10.428
MA0052.10.00146
MA0055.10.206
MA0057.10.0571
MA0058.10.0025
MA0059.10.426
MA0060.10.164
MA0061.10.865
MA0062.20.292
MA0065.20.81
MA0066.10.286
MA0067.10.0166
MA0068.13.57043e-6
MA0069.10.209
MA0070.10.593
MA0071.10.0267
MA0072.10.319
MA0073.10.649
MA0074.10.325
MA0076.10.339
MA0077.10.0472
MA0078.10.781
MA0079.20.418
MA0080.29.87442e-4
MA0081.10.304
MA0083.10.414
MA0084.10.122
MA0087.10.839
MA0088.10.952
MA0090.11.45975e-7
MA0091.10.453
MA0092.10.199
MA0093.10.00907
MA0099.21.06479e-11
MA0100.10.454
MA0101.10.45
MA0102.20.18
MA0103.11.58236e-4
MA0104.20.00979
MA0105.10.479
MA0106.12.725e-13
MA0107.10.425
MA0108.20.00701
MA0111.10.878
MA0112.20.15
MA0113.10.51
MA0114.10.772
MA0115.10.143
MA0116.10.606
MA0117.10.645
MA0119.10.288
MA0122.10.794
MA0124.10.834
MA0125.10.0873
MA0131.10.833
MA0135.10.732
MA0136.10.151
MA0137.20.24
MA0138.20.603
MA0139.10.499
MA0140.10.602
MA0141.10.00958
MA0142.10.937
MA0143.10.554
MA0144.10.621
MA0145.10.0178
MA0146.10.539
MA0147.10.0517
MA0148.10.928
MA0149.10.112
MA0150.10.674
MA0152.10.815
MA0153.10.962
MA0154.10.27
MA0155.10.317
MA0156.10.647
MA0157.10.0927
MA0159.10.871
MA0160.10.332
MA0162.10.0357
MA0163.10.821
MA0164.10.814
MA0258.10.333
MA0259.10.0532



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: CNhs13550

Novel motifP-value
10.911
100.281
1000.351
1010.327
1020.704
1030.0162
1040.978
1050.518
1060.475
1070.241
1080.605
1090.031
110.765
1100.488
1110.269
1120.122
1130.261
1140.0518
1150.925
1160.727
1170.288
1180.724
1190.967
120.831
1200.0345
1210.302
1220.45
1230.0356
1240.0302
1250.965
1260.246
1270.131
1280.966
1290.229
130.0458
1300.676
1310.306
1320.851
1330.0864
1340.34
1350.693
1360.0609
1370.184
1380.552
1390.859
140.849
1400.547
1410.731
1420.87
1430.747
1440.561
1450.282
1460.15
1470.519
1480.367
1490.798
150.745
1500.129
1510.52
1520.0072
1530.726
1540.748
1550.851
1560.538
1570.287
1580.106
1590.819
160.075
1600.663
1610.956
1620.877
1630.873
1640.899
1650.239
1660.95
1670.321
1680.0934
1690.0957
170.466
180.253
190.989
20.223
200.796
210.583
220.703
230.211
240.0106
250.687
260.799
270.676
280.303
290.699
30.919
300.0434
310.943
320.763
330.074
340.401
350.0358
360.232
370.0893
380.706
390.391
40.42
400.0883
410.509
420.868
430.73
440.345
450.0457
460.979
470.469
480.187
490.307
50.863
500.634
510.94
520.136
530.228
540.62
550.133
560.333
570.593
580.968
590.517
60.524
600.255
610.266
620.891
630.345
640.78
650.88
660.441
670.675
680.357
690.384
70.519
700.134
710.496
720.845
730.00204
740.0941
750.439
760.852
770.0972
780.0132
790.613
80.841
800.978
810.205
820.803
830.308
840.113
850.704
860.772
870.00852
880.855
890.0318
90.725
900.258
910.751
920.592
930.152
940.883
950.121
960.866
970.393
980.415
990.207



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: CNhs13550


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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