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{{f5samples
 
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000118,UBERON:0000119,UBERON:0000170,UBERON:0000171,UBERON:0000310,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001443,UBERON:0001555,UBERON:0002048,UBERON:0002050,UBERON:0002224,UBERON:0002532,UBERON:0003104,UBERON:0003258,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005153,UBERON:0005178,UBERON:0005181,UBERON:0005423,UBERON:0005482,UBERON:0005597,UBERON:0005911,UBERON:0007026,UBERON:0008947,UBERON:0009142
+
|DRA_sample_Accession=CAGE@SAMD00004946
 +
|accession_numbers=CAGE;DRX009031;DRR009905;DRZ001330;DRZ002713;DRZ012680;DRZ014063
 +
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002048,UBERON:0000310,UBERON:0002100,UBERON:0000479,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0005178,UBERON:0005177,UBERON:0000117,UBERON:0000171,UBERON:0000464,UBERON:0005181,UBERON:0010317,UBERON:0000065,UBERON:0000170,UBERON:0001004,UBERON:0001443,UBERON:0002224,UBERON:0000915
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_disease_facet=
 
|ancestors_in_disease_facet=
 +
|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000999,FF:0000292,FF:0000004,FF:0000295,FF:0011319
 
|comment=
 
|comment=
 
|created_by=
 
|created_by=
 
|creation_date=
 
|creation_date=
 +
|data_phase=2
 +
|datafreeze_phase=2
 
|def=
 
|def=
 +
|expression_enrichment_score=chr8:123608252..123608268,+!p1@Foxf1a!1.54!49.08!Foxf1a;;chr2:180069370..180069409,-!p1@Gata5!1.52!37.71!Gata5;;chr11:85699862..85699920,+!p1@Tbx4!1.50!30.70!Tbx4;;chr10:22539932..22539956,-!p1@Tcf21!1.44!68.79!Tcf21;;chr10:119913278..119913298,-!p2@Hmga2!1.39!51.92!Hmga2;;chr9:24578720..24578735,-!p1@Tbx20!1.38!23.12!Tbx20;;chr6:52154386..52154407,-!p2@Hoxa5!1.34!26.53!Hoxa5;;chr10:119913546..119913583,-!p3@Hmga2!1.32!41.12!Hmga2;;chr6:52154414..52154462,-!p1@Hoxa5!1.30!25.96!Hoxa5;;chr12:3891810..3891829,+!p2@Dnmt3a!1.27!27.48!Dnmt3a;;chr10:119913310..119913366,-!p1@Hmga2!1.25!127.15!Hmga2;;chr11:18918434..18918489,-!p3@Meis1!1.23!25.20!Meis1;;chr14:63864056..63864102,-!p1@Gata4!1.22!26.91!Gata4;;chr12:34642510..34642530,+!p1@Twist1!1.17!43.96!Twist1;;chr11:96160426..96160443,+!p2@Hoxb6!1.17!13.64!Hoxb6;;chr8:59799772..59799789,+!p1@Hand2!1.16!38.09!Hand2;;chr6:14851440..14851497,+!p2@Foxp2!1.14!31.27!Foxp2;;chr10:119914001..119914078,-!p4@Hmga2!1.10!15.73!Hmga2;;chr11:18918406..18918431,-!p6@Meis1!1.08!14.97!Meis1;;chr11:85646303..85646329,+!p1@Tbx2!1.03!65.75!Tbx2;;chr11:85646263..85646278,+!p2@Tbx2!1.03!25.39!Tbx2;;chr10:126778916..126778974,-!p1@Gli1!1.01!21.03!Gli1;;chr11:96180045..96180059,+!p1@Hoxb4!1.01!13.07!Hoxb4;;chr12:58646974..58647003,-!p1@Foxa1!1.01!12.51!Foxa1;;chr11:96164821..96164865,+!p1@Hoxb5!1.00!9.10!Hoxb5;;chr17:26978409..26978442,-!p1@Nkx2-5!1.00!9.10!Nkx2-5;;chr13:31717548..31717596,+!p1@Foxf2!0.98!17.24!Foxf2;;chr11:96164905..96164919,+!p2@Hoxb5!0.97!8.34!Hoxb5;;chr12:28027561..28027591,-!p1@Sox11!0.96!54.95!Sox11;;chr13:72766250..72766273,+!p1@Irx2!0.96!12.70!Irx2;;chr13:99124189..99124205,+!p1@Foxd1!0.96!12.70!Foxd1;;chr10:12810631..12810649,+!p1@Plagl1!0.95!214.88!Plagl1;;chr9:71743854..71743909,-!p1@Tcf12!0.95!64.62!Tcf12;;chr13:72101161..72101177,-!p2@Irx1!0.95!11.18!Irx1;;chr12:57636220..57636236,-!p3@Nkx2-1!0.95!7.96!Nkx2-1;;chr12:3891753..3891801,+!p4@Dnmt3a!0.94!12.89!Dnmt3a;;chr12:9581262..9581282,+!p1@Osr1!0.92!91.15!Osr1;;chr11:101755669..101755686,-!p1@Meox1!0.92!13.45!Meox1;;chr16:14705961..14705978,+!p2@Snai2!0.90!34.11!Snai2;;chr12:57636240..57636256,-!p4@Nkx2-1!0.89!6.82!Nkx2-1;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.88!11.56!Hoxb2;;chr2:147871627..147871641,-!p1@Foxa2!0.88!6.63!Foxa2;;chr7:52471143..52471186,+!p1@Tead2!0.85!69.16!Tead2;;chr16:14705925..14705951,+!p1@Snai2!0.85!45.10!Snai2;;chr2:104966766..104966786,+!p1@Wt1!0.85!9.85!Wt1;;chr5:120285144..120285160,+!p1@Tbx5!0.85!6.06!Tbx5;;chr17:48061584..48061601,-!p2@Foxp4!0.84!40.74!Foxp4;;chr1:170361730..170361769,-!p7@Pbx1!0.84!14.02!Pbx1;;chr13:72766279..72766296,+!p2@Irx2!0.84!9.10!Irx2;;chr11:96180069..96180089,+!p3@Hoxb4!0.84!5.87!Hoxb4;;chr1:136186574..136186592,+!p1@Myog!0.84!5.87!Myog;;chr1:170361695..170361722,-!p12@Pbx1!0.82!7.39!Pbx1;;chr2:167363692..167363710,+!p1@Snai1!0.81!72.01!Snai1;;chr11:85703483..85703508,+!p2@Tbx4!0.81!5.50!Tbx4;;chr13:15555670..15555771,+!p2@Gli3!0.80!14.40!Gli3;;chr1:170361678..170361689,-!p13@Pbx1!0.79!6.44!Pbx1;;chr6:14851403..14851422,+!p8@Foxp2!0.79!5.12!Foxp2;;chr18:11052642..11052659,+!p1@Gata6!0.77!27.10!Gata6;;chr15:102865088..102865107,+!p1@Hoxc4!0.77!6.63!Hoxc4;;chr11:96160360..96160397,+!p3@Hoxb6!0.77!4.93!Hoxb6;;chr7:17647736..17647772,-!p1@Hif3a!0.76!18.19!Hif3a;;chr8:90483433..90483457,-!p2@Zfp423!0.76!6.63!Zfp423;;chr11:96213434..96213452,+!p@chr11:96213434..96213452,+!0.76!6.44!Hoxb2;;chr9:106356211..106356242,+!p1@Pcbp4!0.74!97.40!Pcbp4;;chr12:12948633..12948651,-!p1@Mycn!0.74!47.75!Mycn;;chr7:6649134..6649167,-!p1@Zim1!0.74!26.72!Zim1;;chr14:17407549..17407575,-!p3@Rarb!0.74!7.20!Rarb;;chr9:87625971..87625992,-!p2@Tbx18!0.74!4.55!Tbx18;;chr3:66785857..66785873,-!p1@Shox2!0.74!4.55!Shox2;;chrX:45245679..45245702,-!p1@Smarca1!0.73!21.41!Smarca1;;chr11:85646341..85646352,+!p3@Tbx2!0.73!9.29!Tbx2;;chr8:123640063..123640077,+!p1@Foxc2!0.73!8.34!Foxc2;;chr13:72101178..72101203,-!p1@Irx1!0.73!7.20!Irx1;;chr3:130813736..130813752,+!p3@Lef1!0.73!6.44!Lef1;;chr15:40486883..40486903,+!p4@Zfpm2!0.73!6.06!Zfpm2;;chr6:14851250..14851277,+!p4@Foxp2!0.73!5.87!Foxp2;;chr7:108966820..108966835,+!p1@Phox2a!0.73!4.36!Phox2a;;chr7:53631837..53631850,+!p1@Myod1!0.73!4.36!Myod1;;chr11:23978291..23978323,+!p7@Bcl11a!0.73!4.36!Bcl11a;;chr10:119913266..119913277,-!p6@Hmga2!0.73!4.36!Hmga2;;chr14:22807083..22807104,-!p1@Zfp503!0.72!83.94!Zfp503;;chr15:102865131..102865151,+!p2@Hoxc4!0.72!4.93!Hoxc4;;chr6:52158644..52158677,-!p2@Hoxa6!0.71!4.17!Hoxa6;;chr2:104966874..104966907,+!p2@Wt1!0.71!4.17!Wt1;;chr14:22807107..22807119,-!p2@Zfp503!0.70!19.71!Zfp503;;chr10:119913792..119913820,-!p5@Hmga2!0.70!7.39!Hmga2;;chr2:30700788..30700824,+!p2@Prrx2!0.70!6.44!Prrx2;;chr8:87425854..87425891,+!p1@Klf1!0.70!3.98!Klf1;;chr17:37139472..37139514,+!p1@Zfp57!0.69!30.13!Zfp57;;chr17:35031460..35031518,+!p1@Zbtb12!0.69!22.36!Zbtb12;;chr11:74981654..74981658,-!p1@Hic1!0.69!17.24!Hic1;;chr14:17407878..17407926,-!p1@Rarb!0.69!9.47!Rarb;;chr14:56443806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 +
|ffid_belonging_in_development=UBERON:0001041,UBERON:0008947,UBERON:0002532,UBERON:0006595,UBERON:0010316,FF:0000294
 
|fonse_cell_line=
 
|fonse_cell_line=
 
|fonse_cell_line_closure=
 
|fonse_cell_line_closure=
Line 35: Line 42:
 
|has_quality=
 
|has_quality=
 
|id=FF:354-16G2
 
|id=FF:354-16G2
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011319
+
|is_a=EFO:0002091;;FF:0011319
 +
|is_obsolete=
 +
|library_id=CNhs10522
 +
|library_id_phase_based=2:CNhs10522
 +
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;354
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;354
 +
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520embryo%2520E12.CNhs10522.354-16G2.mm10.nobarcode.bam
 +
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520embryo%2520E12.CNhs10522.354-16G2.mm10.nobarcode.ctss.bed.gz
 +
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/lung%252c%2520embryo%2520E12.CNhs10522.354-16G2.mm9.nobarcode.bam
 +
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/lung%252c%2520embryo%2520E12.CNhs10522.354-16G2.mm9.ctss.bed.gz
 +
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/lung%252c%2520embryo%2520E12.CNhs10522.354-16G2.mm9.nobarcode.rdna.fa.gz
 
|name=lung, embryo E12
 
|name=lung, embryo E12
 
|namespace=FANTOM5
 
|namespace=FANTOM5
Line 41: Line 60:
 
|profile_cagescan=,,,
 
|profile_cagescan=,,,
 
|profile_hcage=CNhs10522,LSID649,release008,COMPLETED
 
|profile_hcage=CNhs10522,LSID649,release008,COMPLETED
|profile_rnaseq=,,,
+
|profile_rnaseq=
 
|profile_srnaseq=,,,
 
|profile_srnaseq=,,,
 +
|repeat_enrich_byfamily=-0.0480161679978621,0,0,0,0,0,-0.175836219120618,0,0,0,0,0.0552196162884936,0,0,0,0,0,0,-0.0523344941975395,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.418863935638996,0,0,0,0,0,-0.171642070125137,0.0197304458223997,-0.178099132349739,0.0588774684979744,0.0968231963864864,0,0,0,0,0,0,0,0,0,0,0.0753613107413788,0,0.223462342755979,0.0753613107413788,0,0,0,-0.0428469550828748,0,0,0,0,0,-0.0200278201667805,0.0191433925766993,0.131376847548337,0.00108794637383595,0,0,0,0,0.0753613107413788,0,0.00067952821583006,-0.118143945456838,-0.163679750110377,-0.00347028409852859,0,0,0,0,0,0,-0.0326378624110613,-0.0255797093871855,0.0440532576404373,0,0,0,0,0
 
|rna_box=16
 
|rna_box=16
 
|rna_catalog_number=
 
|rna_catalog_number=
Line 56: Line 76:
 
|rna_weight_ug=
 
|rna_weight_ug=
 
|sample_age=
 
|sample_age=
 +
|sample_category=developmental
 
|sample_cell_catalog=
 
|sample_cell_catalog=
 
|sample_cell_line=
 
|sample_cell_line=
Line 75: Line 96:
 
|sample_tissue=lung
 
|sample_tissue=lung
 
|top_motifs=GFI1:1.58708585954;NFY{A,B,C}:1.53879051282;E2F1..5:1.3954008139;ZNF143:1.37766404425;GZF1:1.32411018308;NANOG{mouse}:1.15629758521;SRF:1.06992537896;NRF1:1.02951229728;TFDP1:1.01414599438;SOX2:0.983333726912;HOX{A5,B5}:0.95206364268;SOX{8,9,10}:0.944183543061;LEF1_TCF7_TCF7L1,2:0.922231000106;SOX17:0.921962853929;ZNF384:0.913094509947;RXR{A,B,G}:0.90187251623;HIF1A:0.895746220749;PATZ1:0.865786058797;YY1:0.865410082959;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.859361127699;EN1,2:0.810208716502;MAZ:0.805297795419;PBX1:0.804327557787;ZNF238:0.802380130659;HBP1_HMGB_SSRP1_UBTF:0.798833944598;HSF1,2:0.781028262706;ELK1,4_GABP{A,B1}:0.769246865805;NANOG:0.762445499153;IKZF1:0.721459994844;TOPORS:0.707201295421;MZF1:0.703893451801;GATA4:0.699472156114;TEAD1:0.686510487979;RREB1:0.685741154474;SOX5:0.654584859378;GATA6:0.646839809801;BREu{core}:0.63456692982;MYBL2:0.596864174936;PAX1,9:0.587279492539;bHLH_family:0.580416498407;ZIC1..3:0.574389858154;STAT5{A,B}:0.56864501985;PAX6:0.543755179448;HOXA9_MEIS1:0.529311781058;HMX1:0.524107959184;DBP:0.502681381111;EP300:0.483728614283;XCPE1{core}:0.480254079895;STAT1,3:0.478298101438;ALX1:0.430062233184;GFI1B:0.409974850327;NKX3-1:0.391301508962;POU3F1..4:0.381046861777;MEF2{A,B,C,D}:0.376617176098;CDX1,2,4:0.364704243687;GTF2I:0.358970167791;HIC1:0.325915860296;HMGA1,2:0.309210345147;NKX2-3_NKX2-5:0.303402212806;PRRX1,2:0.299918535146;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.296493969187;ADNP_IRX_SIX_ZHX:0.294407804528;FOXL1:0.283785629843;HES1:0.282894121209;TFCP2:0.275217771124;GCM1,2:0.273476160094;HAND1,2:0.257816197245;ZFP161:0.236775021369;PAX8:0.231117945315;FOXD3:0.228940441269;TBX4,5:0.222553615929;ELF1,2,4:0.222236496208;T:0.206995212555;MYB:0.196321265511;POU2F1..3:0.186006501772;CDC5L:0.171431115168;TFAP2B:0.168683699824;MTE{core}:0.147953849496;TBP:0.147003642895;GTF2A1,2:0.125842801317;PAX5:0.108685101593;KLF4:0.0968367669884;EGR1..3:0.0791534773765;NR3C1:0.0671928692791;TFAP2{A,C}:0.0642162510335;TLX1..3_NFIC{dimer}:0.0608122511795;HOX{A4,D4}:0.0600801234184;AHR_ARNT_ARNT2:0.0597601978203;MED-1{core}:0.0528796543482;VSX1,2:0.046586947207;ZBTB16:0.0302839433856;MTF1:0.026578537741;NFE2L1:0.0151527371928;IKZF2:0.0134569222049;RFX1:0.0090523396207;TFAP4:-0.00223295595267;CUX2:-0.00684283221217;NKX2-1,4:-0.00819944917643;JUN:-0.00861521032686;SP1:-0.0137259469393;TGIF1:-0.0409592689127;UFEwm:-0.0619224960064;PDX1:-0.0702694970384;ATF2:-0.0781798700904;NHLH1,2:-0.0783516828702;SPIB:-0.0875307119425;RUNX1..3:-0.105532347286;NFATC1..3:-0.116720038562;ONECUT1,2:-0.151558752777;RFX2..5_RFXANK_RFXAP:-0.171015915898;PITX1..3:-0.184664370864;ZBTB6:-0.189925074569;CREB1:-0.191602948321;CRX:-0.193314656081;ETS1,2:-0.212790661064;ESR1:-0.214008028968;ZNF423:-0.220541092507;NFIL3:-0.233081225815;PAX4:-0.239433370165;RORA:-0.242886130896;HNF1A:-0.25078689796;DMAP1_NCOR{1,2}_SMARC:-0.258897998956;SPI1:-0.264091055442;FOX{F1,F2,J1}:-0.265293334862;POU5F1:-0.276141438472;ZNF148:-0.277999279156;LHX3,4:-0.280062918843;PRDM1:-0.289594915677;FOXP3:-0.297573217824;NR6A1:-0.315193897154;ALX4:-0.316483813226;FOXQ1:-0.31904284289;FOXM1:-0.321502303322;OCT4_SOX2{dimer}:-0.323594495311;NKX3-2:-0.325968496718;RBPJ:-0.326570525508;ATF4:-0.334419967886;GLI1..3:-0.336359360566;FOXA2:-0.342940912238;REST:-0.352275479596;NKX6-1,2:-0.36462629915;POU6F1:-0.370910719235;FOSL2:-0.396940227908;FOX{I1,J2}:-0.405163930154;TP53:-0.413882936035;TEF:-0.417024252302;PAX2:-0.418832222717;HLF:-0.453193573522;SMAD1..7,9:-0.458602321811;TLX2:-0.469876792351;NFKB1_REL_RELA:-0.482637008191;ATF5_CREB3:-0.488043596444;HNF4A_NR2F1,2:-0.494534027665;TAL1_TCF{3,4,12}:-0.519861875337;EBF1:-0.524814983935;FOXP1:-0.536208119134;MYFfamily:-0.5412296681;BACH2:-0.543161704712;NFIX:-0.567721300396;MAFB:-0.58506505436;EVI1:-0.586245897975;PPARG:-0.59500947476;FOXN1:-0.632345917083;ATF6:-0.637742584122;SNAI1..3:-0.642958352847;FOX{D1,D2}:-0.65538665282;ESRRA:-0.661217451126;ZEB1:-0.683548298589;NKX2-2,8:-0.690666747151;ARID5B:-0.718171886056;NFE2:-0.727996221316;BPTF:-0.74678931383;NR5A1,2:-0.79676507098;FOS_FOS{B,L1}_JUN{B,D}:-0.798547630429;SPZ1:-0.803243686604;SREBF1,2:-0.844828623151;FOXO1,3,4:-0.865582424468;RXRA_VDR{dimer}:-0.86932620054;IRF7:-0.882498249724;NR1H4:-0.898749094841;AIRE:-0.940771062079;NFE2L2:-0.976968830297;AR:-1.00304768098;LMO2:-1.0099194966;MYOD1:-1.06397427381;IRF1,2:-1.08564452978;CEBPA,B_DDIT3:-1.1176660914;POU1F1:-1.20277206219;STAT2,4,6:-1.30756984146
 
|top_motifs=GFI1:1.58708585954;NFY{A,B,C}:1.53879051282;E2F1..5:1.3954008139;ZNF143:1.37766404425;GZF1:1.32411018308;NANOG{mouse}:1.15629758521;SRF:1.06992537896;NRF1:1.02951229728;TFDP1:1.01414599438;SOX2:0.983333726912;HOX{A5,B5}:0.95206364268;SOX{8,9,10}:0.944183543061;LEF1_TCF7_TCF7L1,2:0.922231000106;SOX17:0.921962853929;ZNF384:0.913094509947;RXR{A,B,G}:0.90187251623;HIF1A:0.895746220749;PATZ1:0.865786058797;YY1:0.865410082959;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.859361127699;EN1,2:0.810208716502;MAZ:0.805297795419;PBX1:0.804327557787;ZNF238:0.802380130659;HBP1_HMGB_SSRP1_UBTF:0.798833944598;HSF1,2:0.781028262706;ELK1,4_GABP{A,B1}:0.769246865805;NANOG:0.762445499153;IKZF1:0.721459994844;TOPORS:0.707201295421;MZF1:0.703893451801;GATA4:0.699472156114;TEAD1:0.686510487979;RREB1:0.685741154474;SOX5:0.654584859378;GATA6:0.646839809801;BREu{core}:0.63456692982;MYBL2:0.596864174936;PAX1,9:0.587279492539;bHLH_family:0.580416498407;ZIC1..3:0.574389858154;STAT5{A,B}:0.56864501985;PAX6:0.543755179448;HOXA9_MEIS1:0.529311781058;HMX1:0.524107959184;DBP:0.502681381111;EP300:0.483728614283;XCPE1{core}:0.480254079895;STAT1,3:0.478298101438;ALX1:0.430062233184;GFI1B:0.409974850327;NKX3-1:0.391301508962;POU3F1..4:0.381046861777;MEF2{A,B,C,D}:0.376617176098;CDX1,2,4:0.364704243687;GTF2I:0.358970167791;HIC1:0.325915860296;HMGA1,2:0.309210345147;NKX2-3_NKX2-5:0.303402212806;PRRX1,2:0.299918535146;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.296493969187;ADNP_IRX_SIX_ZHX:0.294407804528;FOXL1:0.283785629843;HES1:0.282894121209;TFCP2:0.275217771124;GCM1,2:0.273476160094;HAND1,2:0.257816197245;ZFP161:0.236775021369;PAX8:0.231117945315;FOXD3:0.228940441269;TBX4,5:0.222553615929;ELF1,2,4:0.222236496208;T:0.206995212555;MYB:0.196321265511;POU2F1..3:0.186006501772;CDC5L:0.171431115168;TFAP2B:0.168683699824;MTE{core}:0.147953849496;TBP:0.147003642895;GTF2A1,2:0.125842801317;PAX5:0.108685101593;KLF4:0.0968367669884;EGR1..3:0.0791534773765;NR3C1:0.0671928692791;TFAP2{A,C}:0.0642162510335;TLX1..3_NFIC{dimer}:0.0608122511795;HOX{A4,D4}:0.0600801234184;AHR_ARNT_ARNT2:0.0597601978203;MED-1{core}:0.0528796543482;VSX1,2:0.046586947207;ZBTB16:0.0302839433856;MTF1:0.026578537741;NFE2L1:0.0151527371928;IKZF2:0.0134569222049;RFX1:0.0090523396207;TFAP4:-0.00223295595267;CUX2:-0.00684283221217;NKX2-1,4:-0.00819944917643;JUN:-0.00861521032686;SP1:-0.0137259469393;TGIF1:-0.0409592689127;UFEwm:-0.0619224960064;PDX1:-0.0702694970384;ATF2:-0.0781798700904;NHLH1,2:-0.0783516828702;SPIB:-0.0875307119425;RUNX1..3:-0.105532347286;NFATC1..3:-0.116720038562;ONECUT1,2:-0.151558752777;RFX2..5_RFXANK_RFXAP:-0.171015915898;PITX1..3:-0.184664370864;ZBTB6:-0.189925074569;CREB1:-0.191602948321;CRX:-0.193314656081;ETS1,2:-0.212790661064;ESR1:-0.214008028968;ZNF423:-0.220541092507;NFIL3:-0.233081225815;PAX4:-0.239433370165;RORA:-0.242886130896;HNF1A:-0.25078689796;DMAP1_NCOR{1,2}_SMARC:-0.258897998956;SPI1:-0.264091055442;FOX{F1,F2,J1}:-0.265293334862;POU5F1:-0.276141438472;ZNF148:-0.277999279156;LHX3,4:-0.280062918843;PRDM1:-0.289594915677;FOXP3:-0.297573217824;NR6A1:-0.315193897154;ALX4:-0.316483813226;FOXQ1:-0.31904284289;FOXM1:-0.321502303322;OCT4_SOX2{dimer}:-0.323594495311;NKX3-2:-0.325968496718;RBPJ:-0.326570525508;ATF4:-0.334419967886;GLI1..3:-0.336359360566;FOXA2:-0.342940912238;REST:-0.352275479596;NKX6-1,2:-0.36462629915;POU6F1:-0.370910719235;FOSL2:-0.396940227908;FOX{I1,J2}:-0.405163930154;TP53:-0.413882936035;TEF:-0.417024252302;PAX2:-0.418832222717;HLF:-0.453193573522;SMAD1..7,9:-0.458602321811;TLX2:-0.469876792351;NFKB1_REL_RELA:-0.482637008191;ATF5_CREB3:-0.488043596444;HNF4A_NR2F1,2:-0.494534027665;TAL1_TCF{3,4,12}:-0.519861875337;EBF1:-0.524814983935;FOXP1:-0.536208119134;MYFfamily:-0.5412296681;BACH2:-0.543161704712;NFIX:-0.567721300396;MAFB:-0.58506505436;EVI1:-0.586245897975;PPARG:-0.59500947476;FOXN1:-0.632345917083;ATF6:-0.637742584122;SNAI1..3:-0.642958352847;FOX{D1,D2}:-0.65538665282;ESRRA:-0.661217451126;ZEB1:-0.683548298589;NKX2-2,8:-0.690666747151;ARID5B:-0.718171886056;NFE2:-0.727996221316;BPTF:-0.74678931383;NR5A1,2:-0.79676507098;FOS_FOS{B,L1}_JUN{B,D}:-0.798547630429;SPZ1:-0.803243686604;SREBF1,2:-0.844828623151;FOXO1,3,4:-0.865582424468;RXRA_VDR{dimer}:-0.86932620054;IRF7:-0.882498249724;NR1H4:-0.898749094841;AIRE:-0.940771062079;NFE2L2:-0.976968830297;AR:-1.00304768098;LMO2:-1.0099194966;MYOD1:-1.06397427381;IRF1,2:-1.08564452978;CEBPA,B_DDIT3:-1.1176660914;POU1F1:-1.20277206219;STAT2,4,6:-1.30756984146
 +
|xref=
 
}}
 
}}

Latest revision as of 13:25, 10 August 2017


Name:lung, embryo E12
Species:Mouse (Mus musculus)
Library ID:CNhs10522
Sample type:developmental
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuelung
dev stage12 days embryo
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00004946
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10522 CAGE DRX009031 DRR009905
Accession ID Mm9

Library idBAMCTSS
CNhs10522 DRZ001330 DRZ002713
Accession ID Mm10

Library idBAMCTSS
CNhs10522 DRZ012680 DRZ014063
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
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

CNhs10522

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0668
1002 0.194
1003 --0.119
1004 0
1005 --0.0389
1006 --0.0351
1007 0.118
1008 0
1009 --0.0045
101 0.141
1010 0
1011 0
1012 0
1013 --0.164
1014 0.339
1015 0.323
1016 0.26
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.14
1022 --0.12
1023 0
1024 --0.0298
1025 0.713
1026 0.0147
1027 0.107
1028 0
1029 --0.107
103 0
1030 0
1031 0.364
1032 --0.108
1033 1.40711e-4
1034 0
1035 0
1036 0.162
1037 0
1038 --0.0181
1039 --0.157
104 0
1040 --0.016
1041 0



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: CNhs10522

Jaspar motif P-value
MA0002.2 0.0146
MA0003.1 0.673
MA0004.1 0.57
MA0006.1 0.549
MA0007.1 0.193
MA0009.1 0.373
MA0014.1 0.632
MA0017.1 1.42932e-4
MA0018.2 0.329
MA0019.1 0.897
MA0024.1 2.18435e-6
MA0025.1 0.728
MA0027.1 0.0148
MA0028.1 0.0211
MA0029.1 0.948
MA0030.1 0.421
MA0031.1 0.114
MA0035.2 0.296
MA0038.1 0.00568
MA0039.2 0.439
MA0040.1 0.684
MA0041.1 0.353
MA0042.1 0.357
MA0043.1 0.00569
MA0046.1 7.03748e-6
MA0047.2 0.534
MA0048.1 0.261
MA0050.1 1.16588e-6
MA0051.1 5.34885e-5
MA0052.1 0.138
MA0055.1 0.00987
MA0057.1 0.236
MA0058.1 0.284
MA0059.1 0.49
MA0060.1 1.51678e-16
MA0061.1 0.0837
MA0062.2 0.0515
MA0065.2 3.21981e-4
MA0066.1 0.0238
MA0067.1 0.46
MA0068.1 0.203
MA0069.1 0.914
MA0070.1 0.437
MA0071.1 0.134
MA0072.1 0.0481
MA0073.1 0.893
MA0074.1 0.396
MA0076.1 0.0311
MA0077.1 0.0938
MA0078.1 0.57
MA0079.2 0.365
MA0080.2 1.12909e-6
MA0081.1 0.606
MA0083.1 7.41234e-5
MA0084.1 0.224
MA0087.1 0.878
MA0088.1 0.649
MA0090.1 0.302
MA0091.1 0.689
MA0092.1 0.639
MA0093.1 0.49
MA0099.2 3.52694e-4
MA0100.1 0.57
MA0101.1 0.57
MA0102.2 0.595
MA0103.1 3.3923e-4
MA0104.2 0.339
MA0105.1 0.00262
MA0106.1 0.163
MA0107.1 0.318
MA0108.2 7.10597e-4
MA0111.1 0.268
MA0112.2 1.96819e-6
MA0113.1 0.583
MA0114.1 4.08906e-4
MA0115.1 0.0562
MA0116.1 0.00872
MA0117.1 0.192
MA0119.1 0.071
MA0122.1 0.599
MA0124.1 0.799
MA0125.1 0.139
MA0131.1 0.16
MA0135.1 0.102
MA0136.1 0.202
MA0137.2 0.421
MA0138.2 0.00169
MA0139.1 0.0801
MA0140.1 0.31
MA0141.1 0.0156
MA0142.1 0.404
MA0143.1 0.229
MA0144.1 0.445
MA0145.1 0.0332
MA0146.1 0.608
MA0147.1 0.411
MA0148.1 0.0717
MA0149.1 0.0183
MA0150.1 0.00727
MA0152.1 0.991
MA0153.1 0.00346
MA0154.1 0.00287
MA0155.1 0.823
MA0156.1 0.982
MA0157.1 0.161
MA0159.1 0.0286
MA0160.1 0.051
MA0162.1 0.574
MA0163.1 0.0803
MA0164.1 0.665
MA0258.1 1.66496e-4
MA0259.1 0.488



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: CNhs10522

Novel motif P-value
1 0.0554
10 0.27
100 0.952
101 0.636
102 0.47
103 0.0642
104 0.859
105 0.673
106 0.017
107 0.144
108 0.978
109 0.208
11 0.141
110 0.284
111 0.0178
112 0.0316
113 0.535
114 0.00857
115 0.783
116 0.646
117 0.36
118 0.646
119 0.0267
12 0.568
120 0.449
121 0.991
122 0.907
123 0.138
124 0.263
125 0.491
126 0.585
127 0.67
128 0.0357
129 0.0402
13 0.692
130 0.171
131 0.89
132 0.376
133 0.259
134 0.587
135 0.469
136 0.547
137 0.413
138 0.859
139 0.0021
14 0.276
140 0.0153
141 0.186
142 0.397
143 0.533
144 0.771
145 0.716
146 0.568
147 0.427
148 0.0189
149 0.383
15 0.0963
150 0.539
151 0.129
152 0.167
153 0.171
154 0.24
155 0.627
156 3.11907e-5
157 0.725
158 0.335
159 0.0391
160 0.645
161 0.556
162 0.786
163 0.161
164 0.516
165 0.537
166 0.656
167 0.467
168 0.941
169 0.018
17 0.0579
18 0.331
19 0.203
2 0.695
20 0.769
21 0.813
22 0.357
23 0.0324
24 0.858
25 0.406
26 0.57
27 0.233
28 0.249
29 0.553
3 0.0972
30 0.853
31 0.323
32 0.148
33 0.815
34 0.968
35 0.133
36 0.374
37 0.119
38 0.517
39 0.775
4 0.649
40 0.776
41 0.927
42 0.294
43 0.116
44 0.177
45 0.596
46 0.229
47 0.177
48 0.216
49 0.0909
5 0.13
50 0.812
51 0.588
52 0.461
53 0.736
54 0.44
55 0.83
56 0.324
57 0.397
58 0.259
59 0.366
6 0.4
60 0.158
61 0.506
62 0.0603
63 0.152
64 0.469
65 0.146
66 0.276
67 0.713
68 0.279
69 0.56
7 0.379
70 9.4056e-4
71 0.339
72 0.465
73 0.218
74 0.446
75 0.0751
76 0.984
77 0.197
78 0.244
79 0.517
8 0.245
80 0.463
81 0.325
82 0.0593
83 0.896
84 0.645
85 0.0114
86 0.527
87 0.432
88 0.998
89 0.307
9 0.555
90 0.0389
91 0.216
92 0.0864
93 0.364
94 0.199
95 0.368
96 0.365
97 0.313
98 0.127
99 0.804



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: CNhs10522


FANTOM5 (FF) ontology


Direct parent terms

part_of relathionship
UBERON:0000310 breast

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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002048 (lung)
0000310 (breast)
0002100 (trunk)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0005177 (trunk region element)
0000117 (respiratory tube)
0000171 (respiration organ)
0000464 (anatomical space)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0000065 (respiratory tract)
0000170 (pair of lungs)
0001004 (respiratory system)
0001443 (chest)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000295 (mouse embryonic day 12 sample)
0011319 (mouse lung- embryo E12 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

UBERON:0001041 (foregut)
UBERON:0008947 (respiratory primordium)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)