FF:13433-144E4: Difference between revisions
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{{f5samples | {{f5samples | ||
|DRA_sample_Accession=CAGE@SAMD00005143 | |DRA_sample_Accession=CAGE@SAMD00005143 | ||
|accession_numbers=CAGE;DRX008604;DRR009476;DRZ000901;DRZ002286 | |accession_numbers=CAGE;DRX008604;DRR009476;DRZ000901;DRZ002286;DRZ012251;DRZ013636 | ||
|ancestors_in_anatomy_facet= | |ancestors_in_anatomy_facet= | ||
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000393,CL:0000211,CL:0000404,CL:0000255 | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000393,CL:0000211,CL:0000404,CL:0000255 | ||
| Line 42: | Line 42: | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |has_quality= | ||
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/iPS%2520differentiation%2520to%2520neuron%252c%2520control%2520donor%2520C32-CRL1502%252c%2520day00%252c%2520rep1.CNhs13826.13433-144E4.hg19.nobarcode.bam | |||
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/iPS%2520differentiation%2520to%2520neuron%252c%2520control%2520donor%2520C32-CRL1502%252c%2520day00%252c%2520rep1.CNhs13826.13433-144E4.hg19.ctss.bed.gz | |||
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/iPS%2520differentiation%2520to%2520neuron%252c%2520control%2520donor%2520C32-CRL1502%252c%2520day00%252c%2520rep1.CNhs13826.13433-144E4.hg19.nobarcode.rdna.fa.gz | |||
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/iPS%2520differentiation%2520to%2520neuron%252c%2520control%2520donor%2520C32-CRL1502%252c%2520day00%252c%2520rep1.CNhs13826.13433-144E4.hg38.nobarcode.bam | |||
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/iPS%2520differentiation%2520to%2520neuron%252c%2520control%2520donor%2520C32-CRL1502%252c%2520day00%252c%2520rep1.CNhs13826.13433-144E4.hg38.nobarcode.ctss.bed.gz | |||
|id=FF:13433-144E4 | |id=FF:13433-144E4 | ||
|is_a=FF:0000210;;FF:0200003 | |is_a=FF:0000210;;FF:0200003 | ||
| Line 47: | Line 52: | ||
|library_id=CNhs13826 | |library_id=CNhs13826 | ||
|library_id_phase_based=2:CNhs13826 | |library_id_phase_based=2:CNhs13826 | ||
|microRNAs= | |||
|microRNAs_nn= | |||
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;13433 | |||
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;13433 | |||
|name=iPS differentiation to neuron, control donor C32-CRL1502 | |name=iPS differentiation to neuron, control donor C32-CRL1502 | ||
|namespace= | |namespace= | ||
| Line 54: | Line 63: | ||
|profile_rnaseq= | |profile_rnaseq= | ||
|profile_srnaseq= | |profile_srnaseq= | ||
|refex=http://refex.dbcls.jp/genelist.php?lang | |||
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| Line 93: | Line 103: | ||
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| |top_motifs=OCT4_SOX2{dimer}:3.87930755594;POU2F1..3:2.39694370186;NFY{A,B,C}:2.17002785368;SOX{8,9,10}:2.11767876123;SP1:1.86918129714;E2F1..5:1.74280008079;SNAI1..3:1.60651072238;PBX1:1.51634665538;PATZ1:1.50248889854;GFI1:1.45428649877;XCPE1{core}:1.44250235086;CUX2:1.41474929797;PITX1..3:1.38744497457;ZNF143:1.32465197972;SOX2:1.30615619903;TOPORS:1.26453984692;CDX1,2,4:1.22137635205;ZEB1:1.14278292871;LMO2:1.1312998109;AIRE:1.06578463794;CDC5L:1.05291432144;YY1:0.991826677634;MYOD1:0.983889677744;TFDP1:0.967278534147;RORA:0.93146291617;ARID5B:0.930595317043;ONECUT1,2:0.929010444728;FOXP1:0.911640881503;bHLH_family:0.874822977198;MZF1:0.850917310849;NRF1:0.782207909822;POU3F1..4:0.776322182775;ZIC1..3:0.755957934343;RBPJ:0.738782137884;ALX1:0.720409159802;PAX8:0.714873780768;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.685380223452;NKX6-1,2:0.683058270934;HOX{A4,D4}:0.679237758352;SOX17:0.674521067015;ATF4:0.666461967885;POU5F1:0.655470563218;EVI1:0.637128104218;STAT1,3:0.623355434064;EBF1:0.620285071494;T:0.61371320748;ELK1,4_GABP{A,B1}:0.605322508886;IKZF2:0.602510325461;FOXM1:0.575390539045;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.516437658185;ZNF384:0.514642216301;KLF4:0.457014346409;FOXD3:0.443481903386;ZFP161:0.406568035219;UFEwm:0.401761677306;FOXQ1:0.393243819713;TBP:0.373051810573;NKX2-3_NKX2-5:0.358748390018;REST:0.332032954139;GFI1B:0.316145533456;LEF1_TCF7_TCF7L1,2:0.307030683325;MAZ:0.306391241648;FOX{I1,J2}:0.279147406083;NR5A1,2:0.271736587509;TP53:0.211977564653;MYFfamily:0.194927418804;HIC1:0.188984761389;ZBTB16:0.186312550535;BREu{core}:0.180342692142;MYB:0.160892903512;VSX1,2:0.142017908336;HIF1A:0.119576652086;STAT5{A,B}:0.118896583988;NKX2-2,8:0.0994733936617;NANOG:0.0955566347256;MTF1:0.0768610424206;HAND1,2:0.0738980866405;TEAD1:0.0731823290725;FOXL1:0.0590096657772;MTE{core}:0.0146844272745;CREB1:0.0112416401605;PAX5:-0.000441052182195;PAX1,9:-0.0024766949146;TFAP2B:-0.010583164721;JUN:-0.0335748192758;CRX:-0.057738371499;ZBTB6:-0.0718233098043;ESRRA:-0.0958134919684;LHX3,4:-0.142730421517;GATA4:-0.143415058642;HNF4A_NR2F1,2:-0.144866699633;ATF2:-0.151095265628;ZNF423:-0.154219591042;NKX3-1:-0.154284216732;NANOG{mouse}:-0.156872318258;ATF5_CREB3:-0.163205192132;PAX4:-0.166209497453;HOX{A6,A7,B6,B7}:-0.166222492106;HOX{A5,B5}:-0.203629541305;EN1,2:-0.220579014093;NHLH1,2:-0.221830440656;HNF1A:-0.267233388383;PRDM1:-0.277499834447;NFKB1_REL_RELA:-0.278554404462;FOXN1:-0.281284055904;RFX1:-0.302517226575;RREB1:-0.304906982456;NKX2-1,4:-0.305518745991;MED-1{core}:-0.310824828412;GTF2I:-0.323493852505;TBX4,5:-0.330617058512;MYBL2:-0.342154815616;NR6A1:-0.34835560207;IKZF1:-0.385584942229;TFAP2{A,C}:-0.388521300736;PAX2:-0.390592896102;SREBF1,2:-0.390980304161;XBP1:-0.404543796243;EGR1..3:-0.410184178999;GCM1,2:-0.432152508783;DBP:-0.437106827284;ALX4:-0.441468119883;FOXO1,3,4:-0.448746353839;GATA6:-0.466590834881;PAX3,7:-0.493342749208;HMGA1,2:-0.531894762744;PPARG:-0.532198080947;FOX{F1,F2,J1}:-0.532492657993;POU1F1:-0.546045922641;POU6F1:-0.551894896835;FOX{D1,D2}:-0.57716877346;DMAP1_NCOR{1,2}_SMARC:-0.595281693789;MEF2{A,B,C,D}:-0.598135158762;NR1H4:-0.599312787604;FOXP3:-0.606531071853;GTF2A1,2:-0.606761865655;RXR{A,B,G}:-0.610252923607;BACH2:-0.619654398153;TFAP4:-0.655833346977;SPIB:-0.65783110914;RFX2..5_RFXANK_RFXAP:-0.670511567235;NFE2L2:-0.691537847699;ESR1:-0.700463861195;NFE2:-0.711407905357;SPI1:-0.726283971555;NFE2L1:-0.732431582112;FOS_FOS{B,L1}_JUN{B,D}:-0.744488411109;RUNX1..3:-0.754899962398;HSF1,2:-0.76020277939;ADNP_IRX_SIX_ZHX:-0.782305856292;SPZ1:-0.808856557975;FOSL2:-0.823088470119;SOX5:-0.839134181701;SRF:-0.840685793279;AR:-0.882242580975;PRRX1,2:-0.887515903768;AHR_ARNT_ARNT2:-0.887737175505;ELF1,2,4:-0.904039404482;ZNF238:-0.915542804476;HMX1:-0.936281508717;TEF:-0.938172201436;NKX3-2:-0.957260538829;HLF:-1.0104382978;TFCP2:-1.05554645276;ZNF148:-1.09756731282;RXRA_VDR{dimer}:-1.10432851016;FOXA2:-1.12558669658;CEBPA,B_DDIT3:-1.12742072026;ETS1,2:-1.14599926135;HBP1_HMGB_SSRP1_UBTF:-1.17650897198;IRF1,2:-1.19851795507;TLX2:-1.25893226022;NR3C1:-1.26078249022;PAX6:-1.27665249932;BPTF:-1.34605954682;NFIX:-1.36611212924;NFATC1..3:-1.37966369812;HES1:-1.40249569701;HOXA9_MEIS1:-1.41602575449;NFIL3:-1.430953776;IRF7:-1.43755331084;GZF1:-1.51064166147;EP300:-1.57326233493;STAT2,4,6:-1.59135384983;GLI1..3:-1.61548059701;TAL1_TCF{3,4,12}:-1.65076914677;TLX1..3_NFIC{dimer}:-1.66220884388;TGIF1:-1.66860215255;ATF6:-1.67321833894;MAFB:-1.90229604737;PDX1:-1.97771510505;SMAD1..7,9:-2.24592239245 | ||
|xref= | |xref= | ||
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:13433-144E4;search_select_hide=table117:FF:13433-144E4 | |||
}} | }} | ||
Latest revision as of 18:59, 4 June 2020
| Name: | iPS differentiation to neuron, control donor C32-CRL1502 |
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| Species: | Human (Homo sapiens) |
| Library ID: | CNhs13826 |
| Sample type: | time courses |
| Genomic View: | UCSC |
| RefEX: | Specific genes |
| CAGEd-oPOSSUM: | link |
| ZENBU report : | link |
| ExpandAdditional information |
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| ExpandCAGE Accession numbers |
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| ExpandDownload raw sequence, BAM & CTSS |
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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
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: CNhs13826
| MA0099.2 |  | 1.02e-12 |
| MA0142.1 |  | 1.04e-12 |
| MA0060.1 |  | 1.12e-13 |
| MA0103.1 |  | 1.14e-1 |
| MA0125.1 |  | 1.27e-1 |
| Jaspar motif | Logo | p-value |
|---|
Showing 1 to 5 of 113 entries
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: CNhs13826
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: CNhs13826
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)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
FF: FANTOM5
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0200005 (iPS differentiation to neuron sample)
0200003 (iPS differentiation to neuron, control 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:0000133 (neurectodermal cell)
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)
