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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005071
|DRA_sample_Accession=CAGE@SAMD00005071
|accession_numbers=CAGE;DRX008605;DRR009477;DRZ000902;DRZ002287
|accession_numbers=CAGE;DRX008605;DRR009477;DRZ000902;DRZ002287;DRZ012252;DRZ013637
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|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
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|fonse_treatment_closure=
|fonse_treatment_closure=
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|has_quality=
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|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%2520rep2.CNhs13839.13437-144E8.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%2520rep2.CNhs13839.13437-144E8.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%2520rep2.CNhs13839.13437-144E8.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%2520rep2.CNhs13839.13437-144E8.hg38.nobarcode.ctss.bed.gz
|id=FF:13437-144E8
|id=FF:13437-144E8
|is_a=FF:0000210;;FF:0200003
|is_a=FF:0000210;;FF:0200003
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|library_id=CNhs13839
|library_id=CNhs13839
|library_id_phase_based=2:CNhs13839
|library_id_phase_based=2:CNhs13839
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;13437
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;13437
|name=iPS differentiation to neuron, control donor C32-CRL1502
|name=iPS differentiation to neuron, control donor C32-CRL1502
|namespace=
|namespace=
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|profile_rnaseq=
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Line 93: Line 103:
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|top_motifs=OCT4_SOX2{dimer}:3.70658150831;POU2F1..3:2.40284466901;SOX{8,9,10}:2.06234533895;NFY{A,B,C}:1.99987753593;E2F1..5:1.78589498924;FOXM1:1.72383992213;SNAI1..3:1.65323259242;PBX1:1.59256171083;GFI1:1.53279507576;ALX1:1.4846364112;ARID5B:1.47290431877;YY1:1.38416982139;UFEwm:1.35983986516;CDX1,2,4:1.35639401915;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.33266149788;CDC5L:1.32204860513;ZNF384:1.29508066191;ZNF143:1.25276510097;TOPORS:1.24003768598;FOX{I1,J2}:1.23112549942;LMO2:1.19897139974;FOXD3:1.19264078594;KLF4:1.15879702296;ONECUT1,2:1.15565809765;PATZ1:1.11671632992;SP1:1.0929515358;ZEB1:1.08568205478;PAX8:1.06780111019;CUX2:1.05602572053;RORA:1.04779911904;SOX2:1.04753192555;IKZF2:1.0087678056;MYOD1:0.968243633943;AIRE:0.952168581182;XCPE1{core}:0.900105501251;ZBTB16:0.899616422095;EVI1:0.891377919269;RBPJ:0.876020398473;NRF1:0.841202069577;ZIC1..3:0.801266600931;ATF4:0.754403049101;PITX1..3:0.725699064044;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.707311790232;HIF1A:0.689404325379;ELK1,4_GABP{A,B1}:0.66430536129;SOX17:0.652426704722;bHLH_family:0.632506277046;MZF1:0.625544003862;NKX2-2,8:0.600593073722;ALX4:0.566678599879;TBP:0.562611672425;GATA4:0.547334948551;T:0.543681340944;FOXQ1:0.492168115803;EBF1:0.479103286036;HOX{A4,D4}:0.450739329695;TFDP1:0.442746829043;POU3F1..4:0.428136552579;NKX6-1,2:0.386821925959;FOXP1:0.380158692176;ZBTB6:0.328066135036;PAX1,9:0.325979567217;TBX4,5:0.324704123962;NR5A1,2:0.309931102353;MYB:0.298665807548;STAT5{A,B}:0.23888083293;FOXL1:0.217095815731;LEF1_TCF7_TCF7L1,2:0.206165331658;REST:0.204248712245;NKX3-1:0.196230693592;LHX3,4:0.191402209771;HAND1,2:0.173607864695;NANOG{mouse}:0.169035973752;CREB1:0.158499935079;HOX{A6,A7,B6,B7}:0.149734578168;TP53:0.142567629002;ZFP161:0.111641457283;GFI1B:0.0781185096679;VSX1,2:0.0742736511663;TEAD1:0.0620714659012;STAT1,3:0.0422845260575;MYFfamily:0.0325023802984;HNF4A_NR2F1,2:-0.0248758016425;NR6A1:-0.0379096862669;CRX:-0.0590905583696;NKX2-1,4:-0.0691133273453;NKX2-3_NKX2-5:-0.0746167888042;MAZ:-0.0807440919135;JUN:-0.0820377558768;POU5F1:-0.0866233115337;MTF1:-0.100943896691;ESRRA:-0.103745722878;FOXN1:-0.13717529705;MTE{core}:-0.145083227716;ESR1:-0.157285295722;FOXO1,3,4:-0.17660331188;PRDM1:-0.188817552564;BREu{core}:-0.191552003583;RFX1:-0.203115230187;XBP1:-0.213022813211;ATF5_CREB3:-0.221987551345;PAX4:-0.229226979266;HOX{A5,B5}:-0.253755320518;ZNF423:-0.2721368271;HNF1A:-0.280800381877;NFKB1_REL_RELA:-0.285386959171;HMGA1,2:-0.309884892854;HIC1:-0.348464409476;NFE2L1:-0.35305909892;ATF2:-0.386890378214;SPZ1:-0.411043529282;POU6F1:-0.413446670064;PAX5:-0.415088226974;RREB1:-0.431000528737;HMX1:-0.434905084624;NANOG:-0.43879475892;RFX2..5_RFXANK_RFXAP:-0.450942555427;RXR{A,B,G}:-0.454910821287;GTF2I:-0.464195037989;EN1,2:-0.470695763889;DMAP1_NCOR{1,2}_SMARC:-0.479729276744;NHLH1,2:-0.491096420133;MED-1{core}:-0.500293048528;PAX2:-0.505887397697;FOX{F1,F2,J1}:-0.511942165268;GATA6:-0.532038414248;SPI1:-0.557107887375;GCM1,2:-0.578655750814;BACH2:-0.589227056506;NR1H4:-0.616248675398;TFAP2B:-0.637603746777;TLX2:-0.641154084538;TFAP2{A,C}:-0.650893754566;SPIB:-0.658113417652;MYBL2:-0.675505930101;HSF1,2:-0.680375860914;NKX3-2:-0.700635524831;PAX3,7:-0.704432550107;MEF2{A,B,C,D}:-0.718623533844;NFE2L2:-0.725636856395;FOXP3:-0.731926856766;TEF:-0.741173129354;SREBF1,2:-0.746075555123;POU1F1:-0.748640116887;FOX{D1,D2}:-0.76265336939;NFE2:-0.776321737317;IKZF1:-0.788190778061;RXRA_VDR{dimer}:-0.79088293364;FOS_FOS{B,L1}_JUN{B,D}:-0.790952733821;AR:-0.804857013803;SRF:-0.811127423068;TFAP4:-0.813960044076;NFIX:-0.815996817801;RUNX1..3:-0.824571949938;DBP:-0.8689696891;AHR_ARNT_ARNT2:-0.87449467787;BPTF:-0.941507479988;EGR1..3:-0.945106985665;FOSL2:-0.949802977137;TFCP2:-0.986854101208;ELF1,2,4:-0.999594887032;SOX5:-1.00953206339;GTF2A1,2:-1.04450184588;HLF:-1.04629021875;NR3C1:-1.06146785394;ZNF238:-1.09202414544;HBP1_HMGB_SSRP1_UBTF:-1.15603514203;IRF1,2:-1.16096486331;ETS1,2:-1.16523939015;ZNF148:-1.19487948226;HES1:-1.26299888721;IRF7:-1.30533456968;GZF1:-1.3166059819;GLI1..3:-1.32018069655;NFIL3:-1.3962124098;PRRX1,2:-1.44512676417;FOXA2:-1.47995114662;CEBPA,B_DDIT3:-1.48256359873;STAT2,4,6:-1.50616615697;TAL1_TCF{3,4,12}:-1.59297997819;NFATC1..3:-1.63635070782;ADNP_IRX_SIX_ZHX:-1.65324471722;EP300:-1.74620134881;PAX6:-1.79713437317;TLX1..3_NFIC{dimer}:-1.79919658934;ATF6:-1.82040749598;SMAD1..7,9:-1.84038436317;PDX1:-1.84254183767;TGIF1:-1.95443901996;MAFB:-2.08345472166;HOXA9_MEIS1:-2.09904656777;PPARG:-2.14476663193
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:13437-144E8;search_select_hide=table117:FF:13437-144E8
}}
}}

Latest revision as of 18:59, 4 June 2020

Name:iPS differentiation to neuron, control donor C32-CRL1502
Species:Human (Homo sapiens)
Library ID:CNhs13839
Sample type:time courses
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexfemale
age12wk gestation
cell typefibroblast-derived iPS
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
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  SAMD00005071
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13839 CAGE DRX008605 DRR009477
Accession ID Hg19

Library idBAMCTSS
CNhs13839 DRZ000902 DRZ002287
Accession ID Hg38

Library idBAMCTSS
CNhs13839 DRZ012252 DRZ013637
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
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C82-Basophils-CD14-Eosinophils-Natural-Peripheral-immature-CD340
C83-choriocarcinoma-pancreatic-placenta-chorionic-HES3GFP-testicular-amniotic0
C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data



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

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13839

Jaspar motifP-value
MA0002.20.00355
MA0003.10.0516
MA0004.10.869
MA0006.10.411
MA0007.10.899
MA0009.10.572
MA0014.10.259
MA0017.10.105
MA0018.20.183
MA0019.10.944
MA0024.11.31685e-6
MA0025.10.984
MA0027.10.352
MA0028.10.0274
MA0029.10.701
MA0030.10.0941
MA0031.10.171
MA0035.20.873
MA0038.10.0172
MA0039.20.0317
MA0040.10.193
MA0041.10.039
MA0042.10.387
MA0043.10.688
MA0046.10.0828
MA0047.20.0521
MA0048.10.274
MA0050.11.24582e-5
MA0051.17.71939e-4
MA0052.10.0107
MA0055.10.143
MA0057.10.304
MA0058.10.917
MA0059.10.563
MA0060.17.68601e-12
MA0061.10.0406
MA0062.20.481
MA0065.20.411
MA0066.10.382
MA0067.10.167
MA0068.10.0267
MA0069.10.631
MA0070.10.507
MA0071.10.69
MA0072.10.866
MA0073.10.89
MA0074.10.746
MA0076.10.096
MA0077.10.0848
MA0078.10.933
MA0079.20.806
MA0080.23.69241e-11
MA0081.10.0809
MA0083.10.0193
MA0084.10.664
MA0087.10.356
MA0088.10.488
MA0090.10.819
MA0091.10.0546
MA0092.10.0827
MA0093.10.997
MA0099.23.99629e-17
MA0100.10.935
MA0101.10.07
MA0102.20.00181
MA0103.10.034
MA0104.20.598
MA0105.10.423
MA0106.10.768
MA0107.10.0355
MA0108.20.00357
MA0111.10.936
MA0112.25.97121e-4
MA0113.10.0146
MA0114.10.687
MA0115.10.666
MA0116.10.661
MA0117.10.418
MA0119.10.00165
MA0122.10.703
MA0124.10.0766
MA0125.10.099
MA0131.10.387
MA0135.10.861
MA0136.14.29728e-9
MA0137.20.0435
MA0138.20.672
MA0139.10.309
MA0140.10.256
MA0141.10.725
MA0142.12.39403e-14
MA0143.13.17892e-5
MA0144.10.0147
MA0145.10.316
MA0146.10.0842
MA0147.10.575
MA0148.10.0221
MA0149.10.16
MA0150.19.58151e-5
MA0152.10.75
MA0153.10.182
MA0154.10.211
MA0155.10.676
MA0156.15.13962e-6
MA0157.10.245
MA0159.10.235
MA0160.10.164
MA0162.10.384
MA0163.10.218
MA0164.10.883
MA0258.10.075
MA0259.10.611



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: CNhs13839

Novel motifP-value
10.32
100.516
1000.495
1010.788
1020.59
1030.11
1040.64
1050.0434
1060.0498
1070.29
1080.901
1090.472
110.353
1100.596
1110.0934
1120.568
1130.0503
1140.0931
1150.0343
1160.601
1170.865
1180.648
1190.278
120.887
1200.364
1210.448
1220.492
1230.58
1240.165
1250.481
1260.438
1270.394
1280.373
1290.469
130.652
1300.863
1310.735
1320.911
1330.0689
1340.345
1350.00605
1360.0506
1370.342
1380.126
1390.022
140.459
1400.241
1410.828
1420.352
1430.0103
1440.612
1450.571
1460.268
1470.687
1480.0997
1490.0976
150.102
1500.95
1510.0298
1520.365
1530.16
1540.531
1550.899
1560.5
1570.661
1580.101
1590.158
160.564
1600.498
1610.844
1620.227
1630.407
1640.668
1650.61
1660.867
1670.215
1680.516
1690.00216
170.225
180.177
190.25
20.414
200.907
210.973
220.0639
230.00708
240.949
250.696
260.908
270.42
280.965
290.97
30.263
300.688
310.86
320.268
330.812
340.421
350.414
360.924
370.411
380.309
390.942
40.45
400.542
410.0763
420.315
430.119
440.335
450.244
460.16
470.707
480.946
490.0718
50.0835
500.997
510.539
520.308
530.315
540.33
550.0277
560.573
570.53
580.105
590.418
60.7
600.0568
610.746
620.0568
630.184
640.693
650.0871
660.681
670.308
680.837
690.669
70.486
700.0274
710.206
720.417
730.208
740.857
750.451
760.619
770.335
780.637
790.49
80.294
800.0657
810.439
820.156
830.748
840.725
850.0632
860.795
870.0465
880.799
890.198
90.0806
900.547
910.166
920.0321
930.235
940.146
950.747
960.0662
970.514
980.293
990.639



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: CNhs13839


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)

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