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{{f5samples
 
{{f5samples
 +
|DRA_sample_Accession=CAGE@SAMD00005944
 +
|accession_numbers=CAGE;DRX008032;DRR008904;DRZ000329;DRZ001714;DRZ011679;DRZ013064
 
|ancestors_in_anatomy_facet=
 
|ancestors_in_anatomy_facet=
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0002371,CL:0000542,CL:0000219,CL:0000945,CL:0000738,CL:0002087,CL:0002242,CL:0000255
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0002371,CL:0000542,CL:0000219,CL:0000945,CL:0000738,CL:0002087,CL:0002242,CL:0000255
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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=chr11:111249993..111250006,-!p1@POU2AF1!2.84!698.20!POU2AF1;;chr6:391743..391759,+!p1@IRF4!2.78!602.35!IRF4;;chr16:85932760..85932775,+!p1@IRF8!2.35!223.44!IRF8;;chr2:68592406..68592424,+!p1@PLEK!2.26!181.12!PLEK;;chr1:25291475..25291511,-!p2@RUNX3!2.03!106.75!RUNX3;;chr19:50922187..50922204,+!p1@SPIB!1.97!92.32!SPIB;;chr19:36204309..36204335,+!p1@ZBTB32!1.96!89.76!ZBTB32;;chr19:19281060..19281078,-!p2@MEF2BNB-MEF2B,p2@MEF2B!1.90!77.58!MEF2B;;chr17:38020392..38020477,-!p1@IKZF3!1.87!73.73!IKZF3;;chr1:25256756..25256774,-!p1@RUNX3!1.69!87.19!RUNX3;;chr14:75988771..75988826,+!p1@BATF!1.67!60.59!BATF;;chr2:231090433..231090469,+!p1@SP140!1.66!44.88!SP140;;chr2:231090471..231090504,+!p2@SP140!1.65!43.92!SP140;;chr14:75988831..75988847,+!p2@BATF!1.59!37.51!BATF;;chr7:128577972..128578047,+!p1@IRF5!1.55!53.21!IRF5;;chr11:615570..615721,-!p2@IRF7!1.49!57.70!IRF7;;chr4:185395590..185395627,-!p3@IRF2!1.48!36.22!IRF2;;chr2:68592394..68592405,+!p2@PLEK!1.48!29.17!PLEK;;chr8:135577829..135577861,-!p6@ZFAT!1.47!28.21!ZFAT;;chr5:133450365..133450444,+!p1@TCF7!1.38!101.62!TCF7;;chr3:189349162..189349207,+!p2@TP63!1.38!22.76!TP63;;chr11:47400078..47400106,-!p1@SPI1!1.36!22.12!SPI1;;chr5:88178983..88179012,-!p1@MEF2C!1.35!162.21!MEF2C;;chr1:38512457..38512474,-!p1@POU3F1!1.33!22.12!POU3F1;;chr5:88120151..88120177,-!p6@MEF2C!1.32!19.88!MEF2C;;chr17:40440359..40440386,+!p4@STAT5A!1.31!19.23!STAT5A;;chr10:104155480..104155534,+!p2@NFKB2!1.26!109.31!NFKB2;;chr8:72756063..72756125,-!p1@MSC!1.23!32.06!MSC;;chr19:42636586..42636607,-!p1@POU2F2!1.22!42.64!POU2F2;;chr8:72756667..72756736,-!p2@MSC!1.22!24.36!MSC;;chr5:142780237..142780261,-!p7@NR3C1!1.22!15.71!NR3C1;;chr8:72756637..72756664,-!p3@MSC!1.21!17.31!MSC;;chr9:37034469..37034474,-!p1@PAX5!1.21!15.39!PAX5;;chr6:29648890..29648944,-!p1@ZFP57!1.18!14.11!ZFP57;;chr2:68615031..68615055,+!p3@PLEK!1.14!12.82!PLEK;;chr8:135614084..135614119,-!p4@ZFAT!1.12!12.18!ZFAT;;chr19:50432453..50432468,+!p1@ATF5!1.10!644.98!ATF5;;chr3:101546827..101546847,+!p2@NFKBIZ!1.10!16.35!NFKBIZ;;chr1:25291620..25291635,-!p4@RUNX3!1.09!11.22!RUNX3;;chr20:50159198..50159299,-!p1@NFATC2!1.08!16.03!NFATC2;;chr2:60778035..60778060,-!p4@BCL11A!1.08!13.14!BCL11A;;chr9:2015335..2015370,+!p1@SMARCA2!1.07!132.39!SMARCA2;;chr11:615942..615957,-!p1@IRF7!1.07!102.58!IRF7;;chr9:2015306..2015323,+!p3@SMARCA2!1.05!26.93!SMARCA2;;chr5:158526917..158526932,-!p1@EBF1!1.05!25.65!EBF1;;chr18:52989031..52989079,-!p2@TCF4!1.04!23.72!TCF4;;chr19:19729477..19729542,-!p1@PBX4!1.04!21.80!PBX4;;chr12:54785074..54785122,-!p2@ZNF385A!1.04!15.39!ZNF385A;;chr2:60780607..60780624,-!p2@BCL11A!1.03!30.45!BCL11A;;chr17:45810594..45810608,+!p1@TBX21!1.03!9.62!TBX21;;chr6:41700616..41700664,-!p8@TFEB!1.03!9.62!TFEB;;chr19:45579725..45579743,-!p1@ZNF296!1.02!43.92!ZNF296;;chr1:151319654..151319698,-!p2@RFX5!1.00!19.88!RFX5;;chr10:64576105..64576133,-!p1@EGR2!1.00!18.59!EGR2;;chr4:113437332..113437337,-!p1@NEUROG2!1.00!8.98!NEUROG2;;chr5:142780189..142780223,-!p6@NR3C1!1.00!8.98!NR3C1;;chr19:36391434..36391450,-!p1@NFKBID!0.99!17.63!NFKBID;;chr8:72756267..72756296,-!p4@MSC!0.99!13.14!MSC;;chr10:104154246..104154347,+!p3@NFKB2!0.98!53.53!NFKB2;;chr16:85936412..85936431,+!p2@IRF8!0.98!8.66!IRF8;;chr2:68615063..68615089,+!p4@PLEK!0.98!8.66!PLEK;;chr6:44233252..44233296,-!p1@NFKBIE!0.97!83.99!NFKBIE;;chr6:41673552..41673571,-!p10@TFEB!0.97!8.33!TFEB;;chr3:141103634..141103665,+!p18@ZBTB38!0.97!8.33!ZBTB38;;chr2:97202480..97202499,+!p1@ARID5A!0.94!80.14!ARID5A;;chr2:214015111..214015179,-!p1@IKZF2!0.94!14.11!IKZF2;;chr6:157098579..157098634,+!p4@ARID1B!0.93!17.63!ARID1B;;chr6:144385698..144385742,-!p2@PLAGL1!0.93!9.30!PLAGL1;;chr9:117150254..117150271,-!p1@AKNA!0.92!20.52!AKNA;;chr20:56195474..56195506,-!p1@ZBP1!0.92!7.37!ZBP1;;chr6:34204973..34204990,+!p4@HMGA1!0.91!99.38!HMGA1;;chr8:135614120..135614149,-!p5@ZFAT!0.91!7.05!ZFAT;;chr19:42627037..42627084,-!p3@POU2F2!0.91!7.05!POU2F2;;chr15:74833584..74833626,+!p1@ARID3B!0.90!16.67!ARID3B;;chr2:214013461..214013517,-!p6@IKZF2!0.89!6.73!IKZF2;;chr2:214015343..214015366,-!p3@IKZF2!0.89!6.73!IKZF2;;chr6:41701557..41701578,-!p3@TFEB!0.89!6.73!TFEB;;chr2:191878874..191878938,-!p1@STAT1!0.88!372.18!STAT1;;chr2:231084659..231084721,-!p1@SP110!0.87!157.08!SP110;;chr2:45168834..45168847,+!p2@SIX3!0.87!6.41!SIX3;;chr1:158979686..158979745,+!p1@IFI16!0.86!218.95!IFI16;;chr5:88179017..88179046,-!p2@MEF2C!0.86!26.29!MEF2C;;chr14:35873947..35873965,-!p1@NFKBIA!0.85!410.33!NFKBIA;;chr5:321810..321877,+!p1@AHRR!0.85!20.20!AHRR;;chr2:148778973..148779035,+!p3@MBD5!0.85!16.67!MBD5;;chr15:76629123..76629151,+!p1@ISL2!0.85!6.73!ISL2;;chr6:166581333..166581349,-!p2@T!0.85!6.09!T;;chr5:124084466..124084484,-!p6@ZNF608!0.83!5.77!ZNF608;;chr17:37934365..37934387,-!p2@IKZF3!0.83!5.77!IKZF3;;chr14:75988851..75988862,+!p3@BATF!0.81!5.45!BATF;;chr5:142779999..142780026,-!p20@NR3C1!0.81!5.45!NR3C1;;chr8:86099884..86099918,+!p4@E2F5!0.81!5.45!E2F5;;chr8:72756023..72756055,-!p6@MSC!0.80!6.73!MSC;;c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Line 38: Line 41:
 
|fonse_treatment_closure=
 
|fonse_treatment_closure=
 
|has_quality=
 
|has_quality=
 +
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|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/xeroderma%2520pigentosum%2520b%2520cell%2520line%253aXPL%252017.CNhs11813.10563-108A5.hg19.ctss.bed.gz
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|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/xeroderma%2520pigentosum%2520b%2520cell%2520line%253aXPL%252017.CNhs11813.10563-108A5.hg19.nobarcode.rdna.fa.gz
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|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/xeroderma%2520pigentosum%2520b%2520cell%2520line%253aXPL%252017.CNhs11813.10563-108A5.hg38.nobarcode.bam
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|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/xeroderma%2520pigentosum%2520b%2520cell%2520line%253aXPL%252017.CNhs11813.10563-108A5.hg38.nobarcode.ctss.bed.gz
 
|id=FF:10563-108A5
 
|id=FF:10563-108A5
 
|is_a=DOID:0050427;;EFO:0002091;;FF:0000210;;FF:0101522
 
|is_a=DOID:0050427;;EFO:0002091;;FF:0000210;;FF:0101522
 
|is_obsolete=
 
|is_obsolete=
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|library_id=CNhs11813
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|library_id_phase_based=2:CNhs11813
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|microRNAs=
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|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10563
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|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10563
 
|name=xeroderma pigentosum b cell line:XPL 17
 
|name=xeroderma pigentosum b cell line:XPL 17
 
|namespace=FANTOM5
 
|namespace=FANTOM5
Line 46: Line 60:
 
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Line 85: Line 100:
 
|top_motifs=POU2F1..3:1.84405278157;POU5F1:1.81338605971;HOXA9_MEIS1:1.69490393331;IRF1,2:1.66853966197;NFKB1_REL_RELA:1.64568209132;IRF7:1.49174859233;CDX1,2,4:1.396137302;PAX6:1.3674984499;NKX6-1,2:1.31520232922;ELF1,2,4:1.25621888659;PDX1:1.25609591506;LMO2:1.03928661283;SPI1:1.00384743864;DMAP1_NCOR{1,2}_SMARC:0.922599822436;PAX3,7:0.915171404905;NFY{A,B,C}:0.905419924473;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.869675026459;YY1:0.847676410982;MYOD1:0.818401934582;ELK1,4_GABP{A,B1}:0.734564739611;RUNX1..3:0.712873968016;POU1F1:0.693420214504;ZEB1:0.664444872595;NANOG{mouse}:0.631727153408;ESR1:0.603062432118;EVI1:0.578600285251;TOPORS:0.526356250211;AIRE:0.526031346951;CRX:0.519857470512;MYB:0.519390382182;ZBTB16:0.518927933678;NR5A1,2:0.485774006726;TP53:0.464370930394;SPIB:0.453115311295;E2F1..5:0.434737161401;FOXP3:0.421862835845;ETS1,2:0.420112056083;OCT4_SOX2{dimer}:0.418539544006;FOXA2:0.402941073046;TFAP4:0.389963367915;CUX2:0.371522911193;FOXP1:0.370921357311;IKZF2:0.367336979938;FOXN1:0.366378462013;ESRRA:0.351794164851;SNAI1..3:0.345821779849;PBX1:0.340326100733;PITX1..3:0.318631134046;RBPJ:0.312066692329;HIF1A:0.310216966981;TLX2:0.304404857522;GATA6:0.273377375363;PRDM1:0.265847128237;PRRX1,2:0.2286801522;VSX1,2:0.155817371924;HOX{A6,A7,B6,B7}:0.148961500039;ATF5_CREB3:0.121552428111;TGIF1:0.117863924052;FOX{F1,F2,J1}:0.114675507216;PAX8:0.106505455577;NRF1:0.0546340960603;RFX2..5_RFXANK_RFXAP:0.0401879840259;STAT1,3:0.0257078289343;ZNF384:0.0245734625029;ZNF143:0.00643232718189;NR6A1:0.00623990843835;GCM1,2:0.000221505089799;STAT5{A,B}:-0.000527920110485;PAX2:-0.0116144955476;DBP:-0.0220703731726;bHLH_family:-0.0340346400029;NKX2-1,4:-0.0378433791852;SOX5:-0.0419584531216;HNF4A_NR2F1,2:-0.0431598478597;ALX4:-0.0490902009985;SOX{8,9,10}:-0.0872023218044;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.091325953909;NKX3-2:-0.0969667483792;EBF1:-0.096990091787;ONECUT1,2:-0.112070343378;RORA:-0.11273903149;AHR_ARNT_ARNT2:-0.116994453072;HES1:-0.117565678879;CDC5L:-0.123738005123;MEF2{A,B,C,D}:-0.145907386845;GATA4:-0.177762236595;GFI1:-0.219720740356;HMGA1,2:-0.247120786204;GFI1B:-0.253338606795;BPTF:-0.25834237521;SMAD1..7,9:-0.263092516821;HOX{A5,B5}:-0.269695367488;ARID5B:-0.289327965498;NFE2:-0.306649999442;BREu{core}:-0.307309349011;FOXQ1:-0.341418771322;HNF1A:-0.34464292399;NFIX:-0.378893268832;SRF:-0.397836214949;STAT2,4,6:-0.431571386834;FOSL2:-0.435240767507;NKX2-3_NKX2-5:-0.443119677804;NKX2-2,8:-0.463269375597;PAX4:-0.470556604857;ATF4:-0.47531203582;CEBPA,B_DDIT3:-0.501571051517;FOS_FOS{B,L1}_JUN{B,D}:-0.515431998452;SOX17:-0.518585127136;SREBF1,2:-0.519657119611;NANOG:-0.536346952982;HOX{A4,D4}:-0.537497406618;UFEwm:-0.543753201379;MAFB:-0.55669554187;CREB1:-0.574771805684;POU3F1..4:-0.609297712871;LEF1_TCF7_TCF7L1,2:-0.617251811832;BACH2:-0.620774415419;EN1,2:-0.666190504481;HAND1,2:-0.671016873617;ZIC1..3:-0.672196951409;LHX3,4:-0.705310678723;HSF1,2:-0.710991646096;RREB1:-0.724188809771;RXR{A,B,G}:-0.727350784437;IKZF1:-0.73600496878;FOXD3:-0.739364442045;HBP1_HMGB_SSRP1_UBTF:-0.746527408333;ZNF238:-0.75161526636;TBP:-0.763624137414;TAL1_TCF{3,4,12}:-0.767560132539;NKX3-1:-0.775730249656;FOXO1,3,4:-0.79422251626;NFE2L2:-0.796916650937;HLF:-0.802668030025;T:-0.813306019036;NHLH1,2:-0.818573898174;EP300:-0.831580501083;ADNP_IRX_SIX_ZHX:-0.838606630329;KLF4:-0.847578886393;TFDP1:-0.855189552609;GLI1..3:-0.856446478595;ZFP161:-0.859562256359;MYBL2:-0.860526235717;MZF1:-0.861280707988;TEF:-0.862711946842;REST:-0.869600864787;RFX1:-0.890412549523;NR1H4:-0.911886868349;ATF2:-0.914746178673;MYFfamily:-0.922939017824;GTF2A1,2:-0.92758647809;TBX4,5:-0.933082279874;ZNF148:-0.942172500695;NFIL3:-0.954579261299;AR:-0.965244837759;HMX1:-0.985210045944;POU6F1:-1.00788946451;JUN:-1.01242899729;PPARG:-1.02419804293;SPZ1:-1.02622928228;NFATC1..3:-1.02901374912;EGR1..3:-1.06174205093;GZF1:-1.0648973933;PATZ1:-1.06691103826;ATF6:-1.07777321811;MTF1:-1.09493802335;TFCP2:-1.10749698128;ZBTB6:-1.13209998313;SOX2:-1.13227660837;GTF2I:-1.17260248214;TLX1..3_NFIC{dimer}:-1.18296307074;MED-1{core}:-1.19332684771;NFE2L1:-1.20422663855;FOXM1:-1.22009463038;MTE{core}:-1.22528359868;HIC1:-1.29387712163;FOX{D1,D2}:-1.30620070007;NR3C1:-1.30997932904;ZNF423:-1.3104457902;XCPE1{core}:-1.32959422091;RXRA_VDR{dimer}:-1.36548643447;FOX{I1,J2}:-1.3686059889;PAX5:-1.39251584296;TFAP2{A,C}:-1.4076474374;MAZ:-1.4192400812;TEAD1:-1.42017081085;SP1:-1.44802754231;PAX1,9:-1.46267993258;XBP1:-1.46676535656;FOXL1:-1.4793682023;TFAP2B:-1.53228810734;ALX1:-1.9917025735
 
|top_motifs=POU2F1..3:1.84405278157;POU5F1:1.81338605971;HOXA9_MEIS1:1.69490393331;IRF1,2:1.66853966197;NFKB1_REL_RELA:1.64568209132;IRF7:1.49174859233;CDX1,2,4:1.396137302;PAX6:1.3674984499;NKX6-1,2:1.31520232922;ELF1,2,4:1.25621888659;PDX1:1.25609591506;LMO2:1.03928661283;SPI1:1.00384743864;DMAP1_NCOR{1,2}_SMARC:0.922599822436;PAX3,7:0.915171404905;NFY{A,B,C}:0.905419924473;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.869675026459;YY1:0.847676410982;MYOD1:0.818401934582;ELK1,4_GABP{A,B1}:0.734564739611;RUNX1..3:0.712873968016;POU1F1:0.693420214504;ZEB1:0.664444872595;NANOG{mouse}:0.631727153408;ESR1:0.603062432118;EVI1:0.578600285251;TOPORS:0.526356250211;AIRE:0.526031346951;CRX:0.519857470512;MYB:0.519390382182;ZBTB16:0.518927933678;NR5A1,2:0.485774006726;TP53:0.464370930394;SPIB:0.453115311295;E2F1..5:0.434737161401;FOXP3:0.421862835845;ETS1,2:0.420112056083;OCT4_SOX2{dimer}:0.418539544006;FOXA2:0.402941073046;TFAP4:0.389963367915;CUX2:0.371522911193;FOXP1:0.370921357311;IKZF2:0.367336979938;FOXN1:0.366378462013;ESRRA:0.351794164851;SNAI1..3:0.345821779849;PBX1:0.340326100733;PITX1..3:0.318631134046;RBPJ:0.312066692329;HIF1A:0.310216966981;TLX2:0.304404857522;GATA6:0.273377375363;PRDM1:0.265847128237;PRRX1,2:0.2286801522;VSX1,2:0.155817371924;HOX{A6,A7,B6,B7}:0.148961500039;ATF5_CREB3:0.121552428111;TGIF1:0.117863924052;FOX{F1,F2,J1}:0.114675507216;PAX8:0.106505455577;NRF1:0.0546340960603;RFX2..5_RFXANK_RFXAP:0.0401879840259;STAT1,3:0.0257078289343;ZNF384:0.0245734625029;ZNF143:0.00643232718189;NR6A1:0.00623990843835;GCM1,2:0.000221505089799;STAT5{A,B}:-0.000527920110485;PAX2:-0.0116144955476;DBP:-0.0220703731726;bHLH_family:-0.0340346400029;NKX2-1,4:-0.0378433791852;SOX5:-0.0419584531216;HNF4A_NR2F1,2:-0.0431598478597;ALX4:-0.0490902009985;SOX{8,9,10}:-0.0872023218044;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.091325953909;NKX3-2:-0.0969667483792;EBF1:-0.096990091787;ONECUT1,2:-0.112070343378;RORA:-0.11273903149;AHR_ARNT_ARNT2:-0.116994453072;HES1:-0.117565678879;CDC5L:-0.123738005123;MEF2{A,B,C,D}:-0.145907386845;GATA4:-0.177762236595;GFI1:-0.219720740356;HMGA1,2:-0.247120786204;GFI1B:-0.253338606795;BPTF:-0.25834237521;SMAD1..7,9:-0.263092516821;HOX{A5,B5}:-0.269695367488;ARID5B:-0.289327965498;NFE2:-0.306649999442;BREu{core}:-0.307309349011;FOXQ1:-0.341418771322;HNF1A:-0.34464292399;NFIX:-0.378893268832;SRF:-0.397836214949;STAT2,4,6:-0.431571386834;FOSL2:-0.435240767507;NKX2-3_NKX2-5:-0.443119677804;NKX2-2,8:-0.463269375597;PAX4:-0.470556604857;ATF4:-0.47531203582;CEBPA,B_DDIT3:-0.501571051517;FOS_FOS{B,L1}_JUN{B,D}:-0.515431998452;SOX17:-0.518585127136;SREBF1,2:-0.519657119611;NANOG:-0.536346952982;HOX{A4,D4}:-0.537497406618;UFEwm:-0.543753201379;MAFB:-0.55669554187;CREB1:-0.574771805684;POU3F1..4:-0.609297712871;LEF1_TCF7_TCF7L1,2:-0.617251811832;BACH2:-0.620774415419;EN1,2:-0.666190504481;HAND1,2:-0.671016873617;ZIC1..3:-0.672196951409;LHX3,4:-0.705310678723;HSF1,2:-0.710991646096;RREB1:-0.724188809771;RXR{A,B,G}:-0.727350784437;IKZF1:-0.73600496878;FOXD3:-0.739364442045;HBP1_HMGB_SSRP1_UBTF:-0.746527408333;ZNF238:-0.75161526636;TBP:-0.763624137414;TAL1_TCF{3,4,12}:-0.767560132539;NKX3-1:-0.775730249656;FOXO1,3,4:-0.79422251626;NFE2L2:-0.796916650937;HLF:-0.802668030025;T:-0.813306019036;NHLH1,2:-0.818573898174;EP300:-0.831580501083;ADNP_IRX_SIX_ZHX:-0.838606630329;KLF4:-0.847578886393;TFDP1:-0.855189552609;GLI1..3:-0.856446478595;ZFP161:-0.859562256359;MYBL2:-0.860526235717;MZF1:-0.861280707988;TEF:-0.862711946842;REST:-0.869600864787;RFX1:-0.890412549523;NR1H4:-0.911886868349;ATF2:-0.914746178673;MYFfamily:-0.922939017824;GTF2A1,2:-0.92758647809;TBX4,5:-0.933082279874;ZNF148:-0.942172500695;NFIL3:-0.954579261299;AR:-0.965244837759;HMX1:-0.985210045944;POU6F1:-1.00788946451;JUN:-1.01242899729;PPARG:-1.02419804293;SPZ1:-1.02622928228;NFATC1..3:-1.02901374912;EGR1..3:-1.06174205093;GZF1:-1.0648973933;PATZ1:-1.06691103826;ATF6:-1.07777321811;MTF1:-1.09493802335;TFCP2:-1.10749698128;ZBTB6:-1.13209998313;SOX2:-1.13227660837;GTF2I:-1.17260248214;TLX1..3_NFIC{dimer}:-1.18296307074;MED-1{core}:-1.19332684771;NFE2L1:-1.20422663855;FOXM1:-1.22009463038;MTE{core}:-1.22528359868;HIC1:-1.29387712163;FOX{D1,D2}:-1.30620070007;NR3C1:-1.30997932904;ZNF423:-1.3104457902;XCPE1{core}:-1.32959422091;RXRA_VDR{dimer}:-1.36548643447;FOX{I1,J2}:-1.3686059889;PAX5:-1.39251584296;TFAP2{A,C}:-1.4076474374;MAZ:-1.4192400812;TEAD1:-1.42017081085;SP1:-1.44802754231;PAX1,9:-1.46267993258;XBP1:-1.46676535656;FOXL1:-1.4793682023;TFAP2B:-1.53228810734;ALX1:-1.9917025735
 
|xref=
 
|xref=
 +
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10563-108A5;search_select_hide=table117:FF:10563-108A5
 
}}
 
}}

Latest revision as of 05:29, 3 June 2020

Name:xeroderma pigentosum b cell line:XPL 17
Species:Human (Homo sapiens)
Library ID:CNhs11813
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexunknown
ageNA
cell typeb cell
cell lineXPL 17
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005944
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11813 CAGE DRX008032 DRR008904
Accession ID Hg19

Library idBAMCTSS
CNhs11813 DRZ000329 DRZ001714
Accession ID Hg38

Library idBAMCTSS
CNhs11813 DRZ011679 DRZ013064
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.
Analyst:NA

link to dataset.
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
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.327
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
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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 sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data



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


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs11813

Jaspar motif P-value
MA0002.2 5.9492e-4
MA0003.1 0.578
MA0004.1 0.122
MA0006.1 0.634
MA0007.1 0.492
MA0009.1 0.603
MA0014.1 0.999
MA0017.1 0.0859
MA0018.2 0.0175
MA0019.1 0.361
MA0024.1 0.235
MA0025.1 0.061
MA0027.1 0.496
MA0028.1 0.00727
MA0029.1 0.551
MA0030.1 0.0377
MA0031.1 0.0299
MA0035.2 0.859
MA0038.1 0.918
MA0039.2 0.89
MA0040.1 0.199
MA0041.1 0.141
MA0042.1 0.373
MA0043.1 0.00452
MA0046.1 0.167
MA0047.2 0.307
MA0048.1 0.851
MA0050.1 1.53921e-21
MA0051.1 6.1582e-16
MA0052.1 0.75
MA0055.1 0.115
MA0057.1 0.987
MA0058.1 0.118
MA0059.1 0.00987
MA0060.1 0.07
MA0061.1 5.62198e-9
MA0062.2 1.24885e-6
MA0065.2 0.0109
MA0066.1 0.242
MA0067.1 0.672
MA0068.1 0.0878
MA0069.1 0.423
MA0070.1 0.302
MA0071.1 0.695
MA0072.1 0.844
MA0073.1 0.451
MA0074.1 0.716
MA0076.1 0.00329
MA0077.1 0.336
MA0078.1 0.25
MA0079.2 0.426
MA0080.2 8.88022e-8
MA0081.1 0.0387
MA0083.1 0.324
MA0084.1 0.291
MA0087.1 0.162
MA0088.1 0.0309
MA0090.1 2.78236e-5
MA0091.1 0.962
MA0092.1 0.921
MA0093.1 0.154
MA0099.2 0.0651
MA0100.1 0.684
MA0101.1 5.18614e-10
MA0102.2 0.116
MA0103.1 0.00793
MA0104.2 0.0233
MA0105.1 7.74521e-12
MA0106.1 0.0225
MA0107.1 2.64165e-11
MA0108.2 6.19976e-6
MA0111.1 0.433
MA0112.2 0.0215
MA0113.1 0.973
MA0114.1 0.0353
MA0115.1 0.717
MA0116.1 9.85995e-5
MA0117.1 0.645
MA0119.1 0.504
MA0122.1 0.815
MA0124.1 0.424
MA0125.1 0.487
MA0131.1 0.655
MA0135.1 0.277
MA0136.1 4.44063e-9
MA0137.2 0.744
MA0138.2 0.488
MA0139.1 0.222
MA0140.1 0.805
MA0141.1 0.064
MA0142.1 0.186
MA0143.1 0.755
MA0144.1 0.671
MA0145.1 0.841
MA0146.1 0.174
MA0147.1 0.0118
MA0148.1 0.141
MA0149.1 0.271
MA0150.1 0.56
MA0152.1 0.111
MA0153.1 0.00143
MA0154.1 1.82544e-4
MA0155.1 0.919
MA0156.1 2.45376e-6
MA0157.1 0.0555
MA0159.1 0.0845
MA0160.1 0.0717
MA0162.1 0.412
MA0163.1 8.57005e-14
MA0164.1 0.958
MA0258.1 0.0209
MA0259.1 0.18



FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs11813

Novel motif P-value
1 0.0172
10 0.0348
100 0.547
101 0.21
102 0.45
103 0.276
104 0.968
105 0.945
106 0.152
107 0.435
108 0.742
109 0.0159
11 0.0583
110 0.121
111 0.00596
112 0.0722
113 0.465
114 0.131
115 0.431
116 0.321
117 0.0209
118 0.0771
119 0.0387
12 0.892
120 0.446
121 0.47
122 0.284
123 0.00382
124 0.226
125 0.0268
126 0.119
127 0.182
128 0.437
129 0.415
13 0.209
130 0.913
131 0.995
132 0.957
133 0.627
134 0.932
135 0.901
136 0.553
137 0.284
138 0.555
139 0.0624
14 0.587
140 0.197
141 0.192
142 0.845
143 0.0502
144 0.873
145 0.335
146 0.586
147 0.247
148 0.105
149 0.743
15 0.0858
150 0.754
151 0.876
152 0.986
153 0.789
154 0.762
155 0.105
156 0.695
157 0.527
158 0.395
159 0.338
16 0.537
160 0.117
161 0.0175
162 0.967
163 0.649
164 0.16
165 0.851
166 0.453
167 0.305
168 0.586
169 0.0887
17 0.391
18 0.338
19 0.782
2 0.945
20 0.554
21 0.13
22 0.702
23 0.927
24 0.165
25 0.208
26 0.0611
27 0.443
28 0.502
29 0.0147
3 0.0557
30 0.461
31 0.67
32 0.868
33 0.364
34 0.837
35 0.0915
36 0.0164
37 0.165
38 0.124
39 0.727
4 0.457
40 0.141
41 0.635
42 0.0638
43 0.199
44 0.0132
45 0.689
46 0.116
47 0.0232
48 0.0701
49 0.133
5 0.779
50 0.833
51 0.603
52 0.993
53 0.341
54 0.909
55 0.733
56 0.6
57 0.209
58 0.0702
59 0.13
6 0.748
60 0.386
61 0.0728
62 0.0776
63 0.322
64 0.146
65 0.253
66 0.704
67 0.353
68 0.258
69 0.924
7 0.195
70 0.172
71 0.0372
72 0.228
73 0.429
74 0.852
75 0.0229
76 0.438
77 0.576
78 0.186
79 0.87
8 0.139
80 0.541
81 0.241
82 0.352
83 0.927
84 0.174
85 0.664
86 0.215
87 0.112
88 0.625
89 0.414
9 0.968
90 0.0479
91 0.784
92 0.289
93 0.907
94 0.177
95 0.0364
96 0.433
97 0.223
98 0.168
99 0.703



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs11813


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000945 (lymphocyte of B lineage)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
630 (genetic disease)
0050177 (monogenic disease)
0050427 (xeroderma pigmentosum)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0101522 (B-lymphocyte cell line sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

CL:0000134 (mesenchymal cell)
CL:0000051 (common lymphoid progenitor)