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{{f5samples
 
{{f5samples
|DRA_sample_Accession=CAGE@DRS007720
+
|DRA_sample_Accession=CAGE@SAMD00005820
|accession_numbers=CAGE;DRX007825;DRR008697;DRZ000122;DRZ001507
+
|accession_numbers=CAGE;DRX007825;DRR008697;DRZ000122;DRZ001507;DRZ011472;DRZ012857
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002048,UBERON:0002100,UBERON:0000483,UBERON:0004821,UBERON:0004903,UBERON:0000479,UBERON:0000058,UBERON:0000064,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0003914,UBERON:0007499,UBERON:0004802,UBERON:0000025,UBERON:0005911,UBERON:0000477,UBERON:0000467,UBERON:0000060,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0000490,UBERON:0006914,UBERON:0009569,UBERON:0005178,UBERON:0000487,UBERON:0000072,UBERON:0005177,UBERON:0004807,UBERON:0000117,UBERON:0000171,UBERON:0000115,UBERON:0000464,UBERON:0003215,UBERON:0005181,UBERON:0010317,UBERON:0009856,UBERON:0010368,UBERON:0009911,UBERON:0002299,UBERON:0007196,UBERON:0000065,UBERON:0001558,UBERON:0000170,UBERON:0001004,UBERON:0002224,UBERON:0000915,UBERON:0006524,UBERON:0008874,UBERON:0002169,UBERON:0004894,UBERON:0002173,UBERON:0002186
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002048,UBERON:0002100,UBERON:0000483,UBERON:0004821,UBERON:0004903,UBERON:0000479,UBERON:0000058,UBERON:0000064,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0003914,UBERON:0007499,UBERON:0004802,UBERON:0000025,UBERON:0005911,UBERON:0000477,UBERON:0000467,UBERON:0000060,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0000490,UBERON:0006914,UBERON:0009569,UBERON:0005178,UBERON:0000487,UBERON:0000072,UBERON:0005177,UBERON:0004807,UBERON:0000117,UBERON:0000171,UBERON:0000115,UBERON:0000464,UBERON:0003215,UBERON:0005181,UBERON:0010317,UBERON:0009856,UBERON:0010368,UBERON:0009911,UBERON:0002299,UBERON:0007196,UBERON:0000065,UBERON:0001558,UBERON:0000170,UBERON:0001004,UBERON:0002224,UBERON:0000915,UBERON:0006524,UBERON:0008874,UBERON:0002169,UBERON:0004894,UBERON:0002173,UBERON:0002186
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002202,CL:0000082,CL:0000255,CL:0002076,CL:0002632,CL:0002368,CL:0000322
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002202,CL:0000082,CL:0000255,CL:0002076,CL:0002632,CL:0002368,CL:0000322
Line 9: Line 9:
 
|created_by=
 
|created_by=
 
|creation_date=
 
|creation_date=
|data_phase=1
+
|data_phase=2
|datafreeze_phase=1
+
|datafreeze_phase=2
 
|def=
 
|def=
 
|expression_enrichment_score=chr17:46682321..46682362,-!p1@HOXB6!2.13!132.98!HOXB6;;chr17:46692457..46692484,-!p2@HOXB8!1.90!77.85!HOXB8;;chr3:25470156..25470227,+!p2@RARB!1.84!67.62!RARB;;chr17:46622205..46622218,-!p3@HOXB2!1.80!72.17!HOXB2;;chr17:46675558..46675577,-!p2@HOXB6!1.79!61.37!HOXB6;;chr17:46703687..46703740,-!p1@HOXB9!1.60!38.64!HOXB9;;chr5:92918919..92918942,+!p1@NR2F1!1.56!152.58!NR2F1;;chr17:46622229..46622257,-!p6@HOXB2!1.56!41.48!HOXB2;;chr12:66218598..66218645,+!p2@HMGA2!1.49!132.12!HMGA2;;chr12:54410664..54410684,+!p1@HOXC4,p1@HOXC5,p1@HOXC6!1.44!26.42!HOXC5;;chr3:12330560..12330579,+!p1@PPARG!1.43!29.55!PPARG;;chrX:2418949..2419024,-!p1@DHRSX,p1@ZBED1!1.43!25.86!ZBED1;;chr11:31832658..31832681,-!p1@PAX6!1.41!24.44!PAX6;;chr17:46622175..46622186,-!p12@HOXB2!1.41!24.44!HOXB2;;chr17:46690839..46690884,-!p1@HOXB8!1.40!23.87!HOXB8;;chr17:46621101..46621143,-!p7@HOXB2!1.39!31.25!HOXB2;;chr5:137804484..137804498,+!p2@EGR1!1.35!82.97!EGR1;;chr15:96874145..96874166,+!p7@NR2F2!1.35!40.35!NR2F2;;chr12:66218255..66218304,+!p3@HMGA2!1.34!55.41!HMGA2;;chr20:50179368..50179392,-!p2@NFATC2!1.34!26.99!NFATC2;;chr7:27153454..27153469,-!p2@HOXA3!1.34!20.74!HOXA3;;chr5:72744445..72744466,-!p2@FOXD1!1.33!33.53!FOXD1;;chr2:19558373..19558392,-!p1@OSR1!1.31!52.28!OSR1;;chr17:46692318..46692362,-!p5@HOXB8!1.31!19.61!HOXB8;;chr7:27205106..27205134,-!p2@HOXA9!1.31!19.32!HOXA9;;chr17:46622070..46622109,-!p1@HOXB2!1.30!41.77!HOXB2;;chr15:96869114..96869160,+!p11@NR2F2!1.30!25.57!NR2F2;;chr5:72744594..72744609,-!p1@FOXD1!1.29!83.82!FOXD1;;chr17:46622114..46622138,-!p4@HOXB2!1.29!27.85!HOXB2;;chr17:46621146..46621180,-!p10@HOXB2!1.26!17.05!HOXB2;;chr17:46692287..46692317,-!p7@HOXB8!1.26!17.05!HOXB8;;chr6:45390025..45390076,+!p2@RUNX2!1.24!38.93!RUNX2;;chr5:138609489..138609542,+!p8@MATR3!1.21!15.06!MATR3;;chr6:45390300..45390335,+!p4@RUNX2!1.19!22.45!RUNX2;;chr5:92919100..92919135,+!p3@NR2F1!1.18!17.05!NR2F1;;chr17:46692624..46692659,-!p3@HOXB8!1.18!14.21!HOXB8;;chr15:96874012..96874042,+!p2@NR2F2!1.17!123.60!NR2F2;;chr19:21950332..21950356,-!p2@ZNF100!1.17!29.55!ZNF100;;chr15:96869255..96869291,+!p6@NR2F2!1.16!24.15!NR2F2;;chr7:42276787..42276815,-!p1@GLI3!1.15!34.95!GLI3;;chr6:45390077..45390105,+!p9@RUNX2!1.14!16.48!RUNX2;;chr3:128206762..128206781,-!p2@GATA2!1.13!77.00!GATA2;;chr17:46667594..46667619,-!p1@HOXB3!1.13!12.50!HOXB3;;chr11:31832610..31832639,-!p5@PAX6!1.13!12.50!PAX6;;chr5:137804405..137804444,+!p3@EGR1!1.12!14.78!EGR1;;chr2:171571931..171571959,+!p3@SP5!1.12!12.22!SP5;;chr5:92918894..92918912,+!p2@NR2F1!1.11!38.93!NR2F1;;chr8:67525443..67525459,-!p2@MYBL1!1.11!17.62!MYBL1;;chr5:72743793..72743855,-!p4@FOXD1!1.11!13.92!FOXD1;;chr7:156803329..156803362,-!p1@MNX1!1.11!11.93!MNX1;;chr17:46688334..46688385,-!p1@HOXB7!1.10!16.76!HOXB7;;chr3:193853927..193853944,+!p1@HES1!1.09!363.69!HES1;;chr7:26191809..26191890,+!p1@NFE2L3!1.09!55.69!NFE2L3;;chr6:45390269..45390298,+!p5@RUNX2!1.09!19.04!RUNX2;;chr17:41623692..41623715,-!p1@ETV4!1.08!46.88!ETV4;;chr17:46655704..46655718,-!p2@HOXB4!1.06!15.63!HOXB4;;chr7:27192185..27192209,-!p1@HOXA3!1.06!10.51!HOXA3;;chr15:96874244..96874259,+!p5@NR2F2!1.05!24.72!NR2F2;;chr13:100634031..100634045,+!p1@ZIC2!1.05!10.23!ZIC2;;chr12:66218836..66218888,+!p1@HMGA2!1.04!94.62!HMGA2;;chr3:12329358..12329393,+!p3@PPARG!1.04!25.00!PPARG;;chr9:124991204..124991246,-!p1@LHX6!1.04!9.94!LHX6;;chr7:27183291..27183324,-!p1@HOXA5!1.04!9.94!HOXA5;;chr5:137801160..137801176,+!p1@EGR1!1.03!971.18!EGR1;;chr5:134369905..134369972,-!p1@PITX1!1.03!15.06!PITX1;;chr7:27205136..27205164,-!p1@HOXA9!1.03!9.66!HOXA9;;chr17:46675619..46675642,-!p5@HOXB6!1.03!9.66!HOXB6;;chr15:96869165..96869183,+!p20@NR2F2!1.02!9.38!NR2F2;;chr7:27196267..27196311,-!p1@HOXA7!1.02!9.38!HOXA7;;chr19:45971246..45971265,+!p1@FOSB!1.01!173.32!FOSB;;chr7:64023410..64023428,-!p2@ZNF680!1.01!14.78!ZNF680;;chr12:66218443..66218461,+!p8@HMGA2!1.01!11.93!HMGA2;;chr6:35310395..35310410,+!p2@PPARD!1.00!35.80!PPARD;;chr20:2673383..2673441,+!p1@EBF4!1.00!14.49!EBF4;;chr7:27183263..27183284,-!p2@HOXA5!1.00!9.09!HOXA5;;chr11:65667884..65667895,-!p2@FOSL1!0.99!34.95!FOSL1;;chr5:150284532..150284549,-!p1@ZNF300!0.99!18.47!ZNF300;;chr20:55204351..55204377,+!p1@TFAP2C!0.99!11.37!TFAP2C;;chr3:141087339..141087387,+!p2@ZBTB38!0.98!90.36!ZBTB38;;chr15:96874063..96874074,+!p10@NR2F2!0.98!15.91!NR2F2;;chr17:46675420..46675465,-!p3@HOXB6!0.98!9.94!HOXB6;;chr17:46692603..46692621,-!p6@HOXB8!0.98!8.52!HOXB8;;chr17:46703826..46703845,-!p3@HOXB9!0.98!8.52!HOXB9;;chr12:66218183..66218209,+!p4@HMGA2!0.97!16.48!HMGA2;;chr5:174151553..174151610,+!p1@MSX2!0.97!14.21!MSX2;;chr12:66218378..66218401,+!p6@HMGA2!0.97!13.07!HMGA2;;chr15:96874216..96874236,+!p13@NR2F2!0.97!13.07!NR2F2;;chr13:100634130..100634143,+!p3@ZIC2!0.97!8.24!ZIC2;;chr5:43067636..43067674,+!p6@ZNF131!0.96!11.08!ZNF131;;chr5:92919375..92919438,+!p6@NR2F1!0.96!8.81!NR2F1;;chr11:65667846..65667868,-!p1@FOSL1!0.95!215.66!FOSL1;;chr12:3068544..3068597,+!p1@TEAD4!0.95!48.59!TEAD4;;chr5:137804357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Line 41: Line 41:
 
|fonse_treatment_closure=
 
|fonse_treatment_closure=
 
|has_quality=
 
|has_quality=
 +
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/alveolar%2520cell%2520carcinoma%2520cell%2520line%253aSW%25201573.CNhs11838.10708-109H6.hg19.nobarcode.bam
 +
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/alveolar%2520cell%2520carcinoma%2520cell%2520line%253aSW%25201573.CNhs11838.10708-109H6.hg19.ctss.bed.gz
 +
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/alveolar%2520cell%2520carcinoma%2520cell%2520line%253aSW%25201573.CNhs11838.10708-109H6.hg19.nobarcode.rdna.fa.gz
 +
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/alveolar%2520cell%2520carcinoma%2520cell%2520line%253aSW%25201573.CNhs11838.10708-109H6.hg38.nobarcode.bam
 +
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/alveolar%2520cell%2520carcinoma%2520cell%2520line%253aSW%25201573.CNhs11838.10708-109H6.hg38.nobarcode.ctss.bed.gz
 
|id=FF:10708-109H6
 
|id=FF:10708-109H6
 
|is_a=EFO:0002091;;FF:0000210;;FF:0102060;;FF:0104802
 
|is_a=EFO:0002091;;FF:0000210;;FF:0102060;;FF:0104802
 
|is_obsolete=
 
|is_obsolete=
 
|library_id=CNhs11838
 
|library_id=CNhs11838
|library_id_phase_based=1:CNhs11838
+
|library_id_phase_based=2:CNhs11838
 +
|microRNAs=
 +
|microRNAs_nn=
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|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10708
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10708
 
|name=alveolar cell carcinoma cell line:SW 1573
 
|name=alveolar cell carcinoma cell line:SW 1573
 
|namespace=FANTOM5
 
|namespace=FANTOM5
Line 51: Line 60:
 
|profile_cagescan=,,,
 
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|profile_hcage=CNhs11838,LSID829,release010,COMPLETED
 
|profile_hcage=CNhs11838,LSID829,release010,COMPLETED
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|profile_rnaseq=
 
|profile_srnaseq=,,,
 
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|refex=http://refex.dbcls.jp/genelist.php?lang
 
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Line 90: Line 100:
 
|top_motifs=PAX8:1.64518456319;LEF1_TCF7_TCF7L1,2:1.50395121218;ONECUT1,2:1.47976439114;E2F1..5:1.42454786383;PBX1:1.29812982798;HOX{A6,A7,B6,B7}:1.25397283837;TEF:1.1984755917;PITX1..3:1.1258469987;HSF1,2:1.12214464496;MYB:1.10192495458;bHLH_family:1.08737398384;AIRE:0.972203768671;CDX1,2,4:0.932613993893;EVI1:0.918249752651;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.91650729676;TOPORS:0.900979470353;HOX{A5,B5}:0.869730139511;FOXP1:0.867086322403;ZNF384:0.865832494298;TFDP1:0.863407253794;LHX3,4:0.859667447009;PPARG:0.822369305253;PAX4:0.819642290409;RBPJ:0.805443615555;PDX1:0.802522964614;NFY{A,B,C}:0.698047009815;FOXD3:0.62925893622;CDC5L:0.629022305107;PRRX1,2:0.614726610072;GFI1:0.612135895693;NKX6-1,2:0.609577775235;NRF1:0.588544687193;NKX2-3_NKX2-5:0.587182676193;ADNP_IRX_SIX_ZHX:0.567854490298;FOXM1:0.545573741548;STAT5{A,B}:0.536139831227;POU2F1..3:0.529507273738;RXR{A,B,G}:0.528083735672;EGR1..3:0.491967048005;RFX1:0.48434473499;OCT4_SOX2{dimer}:0.48056404927;ZNF143:0.475255913671;HES1:0.473086513256;POU1F1:0.468725431278;IKZF2:0.435134471597;NR6A1:0.433448501064;ZIC1..3:0.406419877715;FOXQ1:0.372996880763;UFEwm:0.359815208987;TEAD1:0.352534114666;NKX3-1:0.347252339363;FOX{I1,J2}:0.34720384568;DBP:0.34216951937;BREu{core}:0.322796226609;FOS_FOS{B,L1}_JUN{B,D}:0.286329963051;FOX{D1,D2}:0.283530964616;EN1,2:0.282292141214;PAX5:0.270869347236;FOXO1,3,4:0.267529774617;ZFP161:0.240917810469;RFX2..5_RFXANK_RFXAP:0.228548371797;ZBTB16:0.202634492715;CRX:0.187225621296;MTF1:0.145454677033;LMO2:0.139598253708;TP53:0.13945273617;POU6F1:0.136391853185;GATA4:0.132746892241;HNF4A_NR2F1,2:0.117514571983;VSX1,2:0.102891389395;ALX4:0.0865714803369;FOX{F1,F2,J1}:0.0842655861445;POU5F1:0.0791209126054;DMAP1_NCOR{1,2}_SMARC:0.0735476797332;HNF1A:0.0661962505928;REST:0.0496434576816;BACH2:0.0315990525005;NFE2:0.0295746740419;ELK1,4_GABP{A,B1}:0.0253568867025;FOSL2:0.00803831804375;FOXA2:0.00479811733526;GZF1:-0.0171568109588;XCPE1{core}:-0.019991076206;SRF:-0.0261169123268;SOX{8,9,10}:-0.0287732204815;YY1:-0.05439781065;FOXP3:-0.0609810346057;ALX1:-0.0625067932885;FOXL1:-0.068532347525;TFAP2{A,C}:-0.07410429374;NKX2-1,4:-0.0748507677433;ARID5B:-0.0825128288989;SOX2:-0.0840713213661;TLX2:-0.105596557149;HIC1:-0.111021022293;HLF:-0.1291059065;TFAP2B:-0.138139084093;GTF2A1,2:-0.163088848437;IKZF1:-0.163531989158;MTE{core}:-0.179205481835;BPTF:-0.186508004084;MYBL2:-0.187331505945;SP1:-0.209886026724;NFE2L2:-0.218867495165;STAT2,4,6:-0.226527741124;CEBPA,B_DDIT3:-0.230567930558;ZBTB6:-0.233590814998;ATF5_CREB3:-0.238331025025;GCM1,2:-0.240974844237;KLF4:-0.261322819137;ZEB1:-0.264217009611;TAL1_TCF{3,4,12}:-0.266886944464;GTF2I:-0.268817528773;AR:-0.271629550941;NR3C1:-0.277484471299;HBP1_HMGB_SSRP1_UBTF:-0.288320578883;MYOD1:-0.289839202745;RUNX1..3:-0.296585578159;MZF1:-0.297462917932;ESR1:-0.307066438633;TLX1..3_NFIC{dimer}:-0.309284223927;TBX4,5:-0.316412358983;AHR_ARNT_ARNT2:-0.327932233191;CUX2:-0.33085666699;SPIB:-0.33114184585;HOXA9_MEIS1:-0.337762478344;PAX3,7:-0.339475907583;NFE2L1:-0.341875035142;ATF4:-0.345689588672;HOX{A4,D4}:-0.348261623112;MED-1{core}:-0.351040573148;RREB1:-0.36721247928;NFKB1_REL_RELA:-0.415633222324;SNAI1..3:-0.422768501611;NR5A1,2:-0.440520635629;GFI1B:-0.456513206127;PRDM1:-0.462213800379;IRF7:-0.507731582814;RORA:-0.507763039437;NR1H4:-0.513349860518;POU3F1..4:-0.520491555678;NHLH1,2:-0.531815242609;ELF1,2,4:-0.534761359144;SOX17:-0.540805690977;NFIL3:-0.552732034737;PAX2:-0.568600720625;XBP1:-0.571036592034;SOX5:-0.575205160379;GATA6:-0.578175483545;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.582410054184;EP300:-0.584350578793;ATF2:-0.597589014466;NFATC1..3:-0.603953371349;NKX3-2:-0.622730975865;MEF2{A,B,C,D}:-0.655468858059;STAT1,3:-0.675497351786;GLI1..3:-0.682620740796;ETS1,2:-0.687724053376;SPI1:-0.734910546624;EBF1:-0.742438365655;JUN:-0.757177184838;PATZ1:-0.758889629984;TFAP4:-0.770585951253;MAZ:-0.771084993123;RXRA_VDR{dimer}:-0.815101973906;NFIX:-0.81642575775;NKX2-2,8:-0.819151729031;T:-0.820451155132;TBP:-0.828009073625;NANOG{mouse}:-0.828803284095;IRF1,2:-0.860226045094;TFCP2:-0.89214343469;CREB1:-0.895032231;PAX1,9:-0.926793191532;TGIF1:-0.9277195692;MAFB:-0.931201679091;NANOG:-0.933118317913;HAND1,2:-0.958533338458;MYFfamily:-0.962072478502;ZNF423:-1.06149052181;FOXN1:-1.09186724299;HMGA1,2:-1.10409866433;ZNF238:-1.17141466109;SREBF1,2:-1.24141715121;ESRRA:-1.26466460241;ATF6:-1.42097328935;SMAD1..7,9:-1.44725523851;HIF1A:-1.51181959697;ZNF148:-1.53537634206;SPZ1:-1.55330825742;PAX6:-1.7141582357;HMX1:-2.50280428201
 
|top_motifs=PAX8:1.64518456319;LEF1_TCF7_TCF7L1,2:1.50395121218;ONECUT1,2:1.47976439114;E2F1..5:1.42454786383;PBX1:1.29812982798;HOX{A6,A7,B6,B7}:1.25397283837;TEF:1.1984755917;PITX1..3:1.1258469987;HSF1,2:1.12214464496;MYB:1.10192495458;bHLH_family:1.08737398384;AIRE:0.972203768671;CDX1,2,4:0.932613993893;EVI1:0.918249752651;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.91650729676;TOPORS:0.900979470353;HOX{A5,B5}:0.869730139511;FOXP1:0.867086322403;ZNF384:0.865832494298;TFDP1:0.863407253794;LHX3,4:0.859667447009;PPARG:0.822369305253;PAX4:0.819642290409;RBPJ:0.805443615555;PDX1:0.802522964614;NFY{A,B,C}:0.698047009815;FOXD3:0.62925893622;CDC5L:0.629022305107;PRRX1,2:0.614726610072;GFI1:0.612135895693;NKX6-1,2:0.609577775235;NRF1:0.588544687193;NKX2-3_NKX2-5:0.587182676193;ADNP_IRX_SIX_ZHX:0.567854490298;FOXM1:0.545573741548;STAT5{A,B}:0.536139831227;POU2F1..3:0.529507273738;RXR{A,B,G}:0.528083735672;EGR1..3:0.491967048005;RFX1:0.48434473499;OCT4_SOX2{dimer}:0.48056404927;ZNF143:0.475255913671;HES1:0.473086513256;POU1F1:0.468725431278;IKZF2:0.435134471597;NR6A1:0.433448501064;ZIC1..3:0.406419877715;FOXQ1:0.372996880763;UFEwm:0.359815208987;TEAD1:0.352534114666;NKX3-1:0.347252339363;FOX{I1,J2}:0.34720384568;DBP:0.34216951937;BREu{core}:0.322796226609;FOS_FOS{B,L1}_JUN{B,D}:0.286329963051;FOX{D1,D2}:0.283530964616;EN1,2:0.282292141214;PAX5:0.270869347236;FOXO1,3,4:0.267529774617;ZFP161:0.240917810469;RFX2..5_RFXANK_RFXAP:0.228548371797;ZBTB16:0.202634492715;CRX:0.187225621296;MTF1:0.145454677033;LMO2:0.139598253708;TP53:0.13945273617;POU6F1:0.136391853185;GATA4:0.132746892241;HNF4A_NR2F1,2:0.117514571983;VSX1,2:0.102891389395;ALX4:0.0865714803369;FOX{F1,F2,J1}:0.0842655861445;POU5F1:0.0791209126054;DMAP1_NCOR{1,2}_SMARC:0.0735476797332;HNF1A:0.0661962505928;REST:0.0496434576816;BACH2:0.0315990525005;NFE2:0.0295746740419;ELK1,4_GABP{A,B1}:0.0253568867025;FOSL2:0.00803831804375;FOXA2:0.00479811733526;GZF1:-0.0171568109588;XCPE1{core}:-0.019991076206;SRF:-0.0261169123268;SOX{8,9,10}:-0.0287732204815;YY1:-0.05439781065;FOXP3:-0.0609810346057;ALX1:-0.0625067932885;FOXL1:-0.068532347525;TFAP2{A,C}:-0.07410429374;NKX2-1,4:-0.0748507677433;ARID5B:-0.0825128288989;SOX2:-0.0840713213661;TLX2:-0.105596557149;HIC1:-0.111021022293;HLF:-0.1291059065;TFAP2B:-0.138139084093;GTF2A1,2:-0.163088848437;IKZF1:-0.163531989158;MTE{core}:-0.179205481835;BPTF:-0.186508004084;MYBL2:-0.187331505945;SP1:-0.209886026724;NFE2L2:-0.218867495165;STAT2,4,6:-0.226527741124;CEBPA,B_DDIT3:-0.230567930558;ZBTB6:-0.233590814998;ATF5_CREB3:-0.238331025025;GCM1,2:-0.240974844237;KLF4:-0.261322819137;ZEB1:-0.264217009611;TAL1_TCF{3,4,12}:-0.266886944464;GTF2I:-0.268817528773;AR:-0.271629550941;NR3C1:-0.277484471299;HBP1_HMGB_SSRP1_UBTF:-0.288320578883;MYOD1:-0.289839202745;RUNX1..3:-0.296585578159;MZF1:-0.297462917932;ESR1:-0.307066438633;TLX1..3_NFIC{dimer}:-0.309284223927;TBX4,5:-0.316412358983;AHR_ARNT_ARNT2:-0.327932233191;CUX2:-0.33085666699;SPIB:-0.33114184585;HOXA9_MEIS1:-0.337762478344;PAX3,7:-0.339475907583;NFE2L1:-0.341875035142;ATF4:-0.345689588672;HOX{A4,D4}:-0.348261623112;MED-1{core}:-0.351040573148;RREB1:-0.36721247928;NFKB1_REL_RELA:-0.415633222324;SNAI1..3:-0.422768501611;NR5A1,2:-0.440520635629;GFI1B:-0.456513206127;PRDM1:-0.462213800379;IRF7:-0.507731582814;RORA:-0.507763039437;NR1H4:-0.513349860518;POU3F1..4:-0.520491555678;NHLH1,2:-0.531815242609;ELF1,2,4:-0.534761359144;SOX17:-0.540805690977;NFIL3:-0.552732034737;PAX2:-0.568600720625;XBP1:-0.571036592034;SOX5:-0.575205160379;GATA6:-0.578175483545;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.582410054184;EP300:-0.584350578793;ATF2:-0.597589014466;NFATC1..3:-0.603953371349;NKX3-2:-0.622730975865;MEF2{A,B,C,D}:-0.655468858059;STAT1,3:-0.675497351786;GLI1..3:-0.682620740796;ETS1,2:-0.687724053376;SPI1:-0.734910546624;EBF1:-0.742438365655;JUN:-0.757177184838;PATZ1:-0.758889629984;TFAP4:-0.770585951253;MAZ:-0.771084993123;RXRA_VDR{dimer}:-0.815101973906;NFIX:-0.81642575775;NKX2-2,8:-0.819151729031;T:-0.820451155132;TBP:-0.828009073625;NANOG{mouse}:-0.828803284095;IRF1,2:-0.860226045094;TFCP2:-0.89214343469;CREB1:-0.895032231;PAX1,9:-0.926793191532;TGIF1:-0.9277195692;MAFB:-0.931201679091;NANOG:-0.933118317913;HAND1,2:-0.958533338458;MYFfamily:-0.962072478502;ZNF423:-1.06149052181;FOXN1:-1.09186724299;HMGA1,2:-1.10409866433;ZNF238:-1.17141466109;SREBF1,2:-1.24141715121;ESRRA:-1.26466460241;ATF6:-1.42097328935;SMAD1..7,9:-1.44725523851;HIF1A:-1.51181959697;ZNF148:-1.53537634206;SPZ1:-1.55330825742;PAX6:-1.7141582357;HMX1:-2.50280428201
 
|xref=
 
|xref=
 +
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10708-109H6;search_select_hide=table117:FF:10708-109H6
 
}}
 
}}

Latest revision as of 05:34, 3 June 2020

Name:alveolar cell carcinoma cell line:SW 1573
Species:Human (Homo sapiens)
Library ID:CNhs11838
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuelung
dev stageNA
sexfemale
age44
cell typepneumocyte
cell lineSW 1573
companyATCC
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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  SAMD00005820
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11838 CAGE DRX007825 DRR008697
Accession ID Hg19

Library idBAMCTSS
CNhs11838 DRZ000122 DRZ001507
Accession ID Hg38

Library idBAMCTSS
CNhs11838 DRZ011472 DRZ012857
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-penis0.255
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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: CNhs11838

Jaspar motif P-value
MA0002.2 0.0201
MA0003.1 0.0189
MA0004.1 0.655
MA0006.1 0.666
MA0007.1 0.368
MA0009.1 0.421
MA0014.1 0.486
MA0017.1 0.409
MA0018.2 0.186
MA0019.1 0.337
MA0024.1 2.35471e-6
MA0025.1 0.772
MA0027.1 0.807
MA0028.1 0.0706
MA0029.1 0.633
MA0030.1 0.197
MA0031.1 0.734
MA0035.2 0.473
MA0038.1 0.288
MA0039.2 0.905
MA0040.1 0.436
MA0041.1 0.361
MA0042.1 0.582
MA0043.1 0.0141
MA0046.1 0.0912
MA0047.2 0.918
MA0048.1 0.00642
MA0050.1 1.75509e-7
MA0051.1 1.07786e-5
MA0052.1 0.0351
MA0055.1 0.00354
MA0057.1 0.736
MA0058.1 0.826
MA0059.1 0.214
MA0060.1 0.00237
MA0061.1 0.0083
MA0062.2 0.32
MA0065.2 0.268
MA0066.1 0.356
MA0067.1 0.342
MA0068.1 0.604
MA0069.1 0.343
MA0070.1 0.681
MA0071.1 0.932
MA0072.1 0.0873
MA0073.1 0.592
MA0074.1 0.882
MA0076.1 0.669
MA0077.1 0.242
MA0078.1 0.201
MA0079.2 0.161
MA0080.2 9.12134e-11
MA0081.1 0.0332
MA0083.1 0.583
MA0084.1 0.451
MA0087.1 0.457
MA0088.1 0.198
MA0090.1 0.228
MA0091.1 0.093
MA0092.1 0.431
MA0093.1 0.594
MA0099.2 0.0317
MA0100.1 0.0076
MA0101.1 0.0413
MA0102.2 0.00174
MA0103.1 0.759
MA0104.2 0.102
MA0105.1 0.0211
MA0106.1 0.683
MA0107.1 0.00408
MA0108.2 1.64882e-4
MA0111.1 0.461
MA0112.2 0.177
MA0113.1 0.255
MA0114.1 0.602
MA0115.1 0.535
MA0116.1 0.0557
MA0117.1 0.634
MA0119.1 0.622
MA0122.1 0.186
MA0124.1 0.361
MA0125.1 0.997
MA0131.1 0.22
MA0135.1 0.312
MA0136.1 1.082e-8
MA0137.2 0.0391
MA0138.2 0.208
MA0139.1 0.326
MA0140.1 0.898
MA0141.1 0.776
MA0142.1 0.618
MA0143.1 0.383
MA0144.1 0.00641
MA0145.1 0.173
MA0146.1 0.379
MA0147.1 0.112
MA0148.1 0.768
MA0149.1 0.165
MA0150.1 0.214
MA0152.1 0.299
MA0153.1 0.433
MA0154.1 0.0222
MA0155.1 0.014
MA0156.1 8.38264e-7
MA0157.1 0.376
MA0159.1 0.529
MA0160.1 0.309
MA0162.1 0.155
MA0163.1 0.178
MA0164.1 0.569
MA0258.1 0.31
MA0259.1 0.271



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: CNhs11838

Novel motif P-value
1 0.702
10 0.943
100 0.168
101 0.529
102 0.754
103 0.779
104 0.505
105 0.832
106 0.00262
107 0.258
108 0.546
109 0.491
11 0.796
110 0.82
111 0.258
112 0.331
113 0.682
114 0.628
115 0.849
116 0.967
117 0.982
118 0.519
119 0.344
12 0.952
120 0.0584
121 0.787
122 0.589
123 0.148
124 0.195
125 0.223
126 0.25
127 0.708
128 0.0288
129 0.998
13 0.719
130 0.917
131 0.29
132 0.322
133 0.19
134 0.968
135 0.0139
136 0.0808
137 0.174
138 0.539
139 0.629
14 0.799
140 0.663
141 0.801
142 0.56
143 0.606
144 0.949
145 0.617
146 0.131
147 0.229
148 0.886
149 0.0649
15 0.352
150 0.973
151 0.811
152 0.342
153 0.106
154 0.51
155 0.664
156 0.491
157 0.624
158 0.407
159 0.307
16 0.858
160 0.916
161 0.274
162 0.858
163 0.115
164 0.331
165 0.995
166 0.454
167 0.0391
168 0.0713
169 0.932
17 0.88
18 0.256
19 0.691
2 0.432
20 0.0646
21 0.06
22 0.261
23 0.0603
24 0.515
25 0.733
26 0.148
27 0.28
28 0.682
29 0.609
3 0.662
30 0.222
31 0.207
32 0.0168
33 0.642
34 0.14
35 0.909
36 0.949
37 0.291
38 0.471
39 0.807
4 0.325
40 0.269
41 0.277
42 0.397
43 0.223
44 0.107
45 0.0153
46 0.821
47 0.619
48 0.717
49 0.363
5 0.0516
50 0.932
51 0.798
52 0.0285
53 0.844
54 0.92
55 0.903
56 0.858
57 0.13
58 0.226
59 0.432
6 0.221
60 0.0442
61 0.914
62 0.396
63 0.944
64 0.724
65 0.113
66 0.16
67 0.828
68 0.902
69 0.643
7 0.725
70 0.248
71 0.934
72 0.0027
73 0.478
74 0.409
75 0.663
76 0.915
77 0.119
78 0.437
79 0.2
8 0.172
80 0.525
81 0.605
82 0.352
83 0.805
84 0.152
85 0.0555
86 0.414
87 0.955
88 0.599
89 0.0595
9 0.217
90 0.267
91 0.034
92 0.249
93 0.362
94 0.245
95 0.873
96 0.984
97 0.447
98 0.755
99 0.24



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: CNhs11838


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)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002202 (epithelial cell of tracheobronchial tree)
0000082 (epithelial cell of lung)
0000255 (eukaryotic cell)
0002076 (endo-epithelial cell)
0002632 (epithelial cell of lower respiratory tract)
0002368 (respiratory epithelial cell)
0000322 (pneumocyte)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
0050615 (respiratory system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
1324 (lung cancer)
305 (carcinoma)
1325 (bronchus cancer)
3905 (lung carcinoma)
3908 (non-small cell lung carcinoma)
3910 (lung adenocarcinoma)
3904 (bronchogenic carcinoma)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002048 (lung)
0002100 (trunk)
0000483 (epithelium)
0004821 (pulmonary alveolus epithelium)
0004903 (bronchoalveolar duct junction)
0000479 (tissue)
0000058 (duct)
0000064 (organ part)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0003914 (epithelial tube)
0007499 (epithelial sac)
0004802 (respiratory tract epithelium)
0000025 (tube)
0005911 (endo-epithelium)
0000477 (anatomical cluster)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0006914 (squamous epithelium)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0000487 (simple squamous epithelium)
0000072 (segment of respiratory tract)
0005177 (trunk region element)
0004807 (respiratory system epithelium)
0000117 (respiratory tube)
0000171 (respiration organ)
0000115 (lung epithelium)
0000464 (anatomical space)
0003215 (alveolus)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0009856 (sac)
0010368 (pulmonary lobule)
0009911 (lobule)
0002299 (alveolus of lung)
0007196 (tracheobronchial tree)
0000065 (respiratory tract)
0001558 (lower respiratory tract)
0000170 (pair of lungs)
0001004 (respiratory system)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)
0006524 (alveolar system)
0008874 (pulmonary acinus)
0002169 (alveolar sac)
0004894 (alveolar wall)
0002173 (alveolar duct)
0002186 (bronchiole)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0100353 (lung cell line sample)
0102061 (bronchogenic carcinoma cell sample)
0101120 (epithelial cell line sample)
0100762 (lung cancer cell line sample)
0102058 (non-small cell lung cancer cell sample)
0102057 (lung adenocarcinoma cell sample)
0102060 (bronchioalveolar carcinoma cell sample)
0104802 (bronchioloalveolar carcinoma cell 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:0000223 (endodermal cell)
UBERON:0001041 (foregut)
UBERON:0008947 (respiratory primordium)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)