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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005507
|DRA_sample_Accession=CAGE@SAMD00005507
|accession_numbers=CAGE;DRX008087;DRR008959;DRZ000384;DRZ001769
|accession_numbers=CAGE;DRX008087;DRR008959;DRZ000384;DRZ001769;DRZ011734;DRZ013119
|ancestors_in_anatomy_facet=UBERON:0002384,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_anatomy_facet=UBERON:0002384,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000325,CL:0000255,CL:0000136
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000325,CL:0000255,CL:0000136
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|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.LQhCAGE/mature%2520adipocyte%252c%2520donor3.CNhs12560.12233-129G1.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.LQhCAGE/mature%2520adipocyte%252c%2520donor3.CNhs12560.12233-129G1.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.LQhCAGE/mature%2520adipocyte%252c%2520donor3.CNhs12560.12233-129G1.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.LQhCAGE/mature%2520adipocyte%252c%2520donor3.CNhs12560.12233-129G1.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.LQhCAGE/mature%2520adipocyte%252c%2520donor3.CNhs12560.12233-129G1.hg38.nobarcode.ctss.bed.gz
|id=FF:12233-129G1
|id=FF:12233-129G1
|is_a=EFO:0002091;;FF:0000266
|is_a=EFO:0002091;;FF:0000266
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|library_id=CNhs12560
|library_id=CNhs12560
|library_id_phase_based=2:CNhs12560
|library_id_phase_based=2:CNhs12560
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;12233
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;12233
|name=mature adipocyte, donor3
|name=mature adipocyte, donor3
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
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|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 92: Line 101:
|top_motifs=STAT2,4,6:3.2585286379;AR:2.88351654454;RXR{A,B,G}_{NR1H2,PPAR}dimers:2.74350460994;ATF6:2.57311440402;ESRRA:2.44726669697;HBP1_HMGB_SSRP1_UBTF:2.40113841093;PDX1:2.26318420558;NFATC1..3:2.23665925019;RORA:2.23467480431;XBP1:2.20864274118;NFIL3:2.13094120909;STAT1,3:2.07639441405;FOXO1,3,4:1.88642901912;FOX{D1,D2}:1.8737798122;TFCP2:1.83956214024;ATF2:1.62037519435;NFE2L1:1.59708087817;TGIF1:1.58100939713;ZNF238:1.57302286227;GCM1,2:1.53821561658;IKZF1:1.48563195108;EP300:1.45102628016;DBP:1.43365743342;NFIX:1.42646837362;FOXL1:1.36047742776;SP1:1.35871330386;HNF4A_NR2F1,2:1.34887260461;SOX5:1.33788012605;TLX1..3_NFIC{dimer}:1.33697356397;MTF1:1.33214133625;ARID5B:1.28388502181;TBP:1.26659330975;HOXA9_MEIS1:1.2238205379;IKZF2:1.2172611897;MAZ:1.19891800149;MYBL2:1.13751752316;FOXN1:1.10703128457;TFAP2{A,C}:1.09941587526;MEF2{A,B,C,D}:1.09342807938;CEBPA,B_DDIT3:1.09255056922;PRRX1,2:1.0904745912;HLF:1.0875362069;FOXA2:1.08263269414;HMX1:1.07616488666;GZF1:1.05280145254;MAFB:1.05101990467;NR3C1:1.04409717102;SRF:1.03410665918;FOXP3:1.03076617222;TEAD1:0.999911559244;NFE2:0.997830267217;HIC1:0.977682191208;bHLH_family:0.964371086544;EBF1:0.865387501956;PAX6:0.860724019988;EGR1..3:0.843943586615;SPZ1:0.831646600337;MED-1{core}:0.824630161994;JUN:0.811668567836;TFAP2B:0.804804821717;NR1H4:0.796901828099;NFKB1_REL_RELA:0.729523789923;HSF1,2:0.717187242852;NKX3-2:0.71555108541;PATZ1:0.709598430345;ADNP_IRX_SIX_ZHX:0.704540060936;PAX5:0.679728047753;MYFfamily:0.669098481232;EN1,2:0.648033136807;ATF4:0.630334454954;HIF1A:0.621968389895;MTE{core}:0.61799916162;GTF2A1,2:0.613203525855;NHLH1,2:0.577422807623;NANOG:0.544914282317;IRF7:0.544605794307;RXR{A,B,G}:0.531134110591;RFX2..5_RFXANK_RFXAP:0.514589820706;GTF2I:0.496230980269;HOX{A5,B5}:0.495422694675;FOS_FOS{B,L1}_JUN{B,D}:0.490300934229;GFI1B:0.480314764987;SREBF1,2:0.443267139616;TLX2:0.381479373704;FOSL2:0.35728152607;CREB1:0.345675601333;ATF5_CREB3:0.321932309276;HOX{A4,D4}:0.293819701569;TFAP4:0.27856717959;NKX2-1,4:0.254215792993;DMAP1_NCOR{1,2}_SMARC:0.249719642479;BACH2:0.239699786965;FOXD3:0.2263222826;POU6F1:0.188821106369;CDC5L:0.177969623427;RBPJ:0.175620387812;HAND1,2:0.172103863581;MZF1:0.160948552475;BREu{core}:0.111634497715;NANOG{mouse}:0.110698968916;ZNF423:0.0999773304258;HNF1A:0.0821474457137;ZFP161:0.0813511446991;STAT5{A,B}:0.0645824971955;PAX2:0.0617508880757;PAX1,9:0.0231933020264;IRF1,2:0.0176146238061;FOX{F1,F2,J1}:0.00132016669149;ETS1,2:-0.00600957019373;LHX3,4:-0.00847419535164;ESR1:-0.048514275309;TBX4,5:-0.0540584288917;FOXP1:-0.0675079721375;SMAD1..7,9:-0.0830058353912;GATA4:-0.0858971309391;ZIC1..3:-0.0900343717821;SOX17:-0.101905650485;FOXQ1:-0.109265773408;NR6A1:-0.13274523916;PBX1:-0.142397330918;HMGA1,2:-0.163812275665;NFE2L2:-0.169381686621;NR5A1,2:-0.172099533266;TP53:-0.182758840976;GATA6:-0.190546223478;TEF:-0.20138785884;PAX8:-0.213754127823;FOX{I1,J2}:-0.226058061041;SPIB:-0.268957039268;NFY{A,B,C}:-0.284740997778;SPI1:-0.295124392524;ELF1,2,4:-0.317307419598;GLI1..3:-0.323234521776;NKX2-2,8:-0.329460744857;SOX2:-0.33195863964;ALX4:-0.351899039499;PRDM1:-0.382521813593;NKX2-3_NKX2-5:-0.387441149122;REST:-0.388411886914;RUNX1..3:-0.396696319948;ZNF148:-0.404809673941;ZNF143:-0.406417232698;ZNF384:-0.416291964692;RFX1:-0.416901613794;GFI1:-0.421118304436;BPTF:-0.433842391186;XCPE1{core}:-0.457426656001;KLF4:-0.528632211238;NKX6-1,2:-0.536407121454;NRF1:-0.56516797354;PAX3,7:-0.579922068034;ZBTB6:-0.61096486316;CUX2:-0.650284485583;RXRA_VDR{dimer}:-0.693618178084;PPARG:-0.694934436413;LEF1_TCF7_TCF7L1,2:-0.703752131237;OCT4_SOX2{dimer}:-0.728370853977;YY1:-0.751451236333;PAX4:-0.764075153343;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.765823067055;RREB1:-0.766318693374;AHR_ARNT_ARNT2:-0.784133085827;CRX:-0.792231730261;POU2F1..3:-0.859744669414;SOX{8,9,10}:-0.911400109704;PITX1..3:-0.917631894208;SNAI1..3:-0.920047156471;TAL1_TCF{3,4,12}:-0.921204387899;TFDP1:-0.937124685458;HOX{A6,A7,B6,B7}:-0.937283009387;UFEwm:-0.970006339302;ELK1,4_GABP{A,B1}:-0.986876962535;MYB:-1.00970162134;ZEB1:-1.0137128303;E2F1..5:-1.02268733736;LMO2:-1.04197530191;POU5F1:-1.08673520041;ALX1:-1.10148851789;CDX1,2,4:-1.11550665122;ONECUT1,2:-1.1708459876;HES1:-1.17349504452;T:-1.18420515806;POU3F1..4:-1.22070327946;AIRE:-1.26193200996;POU1F1:-1.31888341272;EVI1:-1.4304983882;VSX1,2:-1.59625487518;FOXM1:-1.74847189273;ZBTB16:-1.7838481828;MYOD1:-1.81235704396;TOPORS:-2.01483821396;NKX3-1:-2.2325325988
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:12233-129G1;search_select_hide=table117:FF:12233-129G1
}}
}}

Latest revision as of 18:35, 4 June 2020

Name:mature adipocyte, donor3
Species:Human (Homo sapiens)
Library ID:CNhs12560
Sample type:primary cells
Genomic View: UCSC
RefEX:Specific genes
FANTOM CAT:1
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueadipose tissue
dev stageNA
sexfemale
age64
cell typeadipocyte
cell lineNA
companyNA
collaborationPeter Arner (Karolinska Institutet)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005507
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12560 CAGE DRX008087 DRR008959
Accession ID Hg19

Library idBAMCTSS
CNhs12560 DRZ000384 DRZ001769
Accession ID Hg38

Library idBAMCTSS
CNhs12560 DRZ011734 DRZ013119
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
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-penis-0.122
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.42
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12560

Jaspar motifP-value
MA0002.20.172
MA0003.10.784
MA0004.10.851
MA0006.10.972
MA0007.10.279
MA0009.10.194
MA0014.10.667
MA0017.10.122
MA0018.20.0645
MA0019.10.17
MA0024.10.00537
MA0025.11.84862e-4
MA0027.10.463
MA0028.14.11359e-4
MA0029.10.923
MA0030.10.0107
MA0031.16.93696e-4
MA0035.20.734
MA0038.10.292
MA0039.20.264
MA0040.10.109
MA0041.10.00431
MA0042.10.0655
MA0043.13.43371e-5
MA0046.10.672
MA0047.20.0194
MA0048.10.784
MA0050.10.88
MA0051.10.237
MA0052.14.5795e-6
MA0055.10.247
MA0057.10.453
MA0058.10.899
MA0059.10.105
MA0060.10.495
MA0061.10.328
MA0062.21.9699e-6
MA0065.20.0944
MA0066.10.0109
MA0067.10.171
MA0068.12.11274e-6
MA0069.10.867
MA0070.10.299
MA0071.10.993
MA0072.10.129
MA0073.10.839
MA0074.10.449
MA0076.19.53883e-4
MA0077.10.177
MA0078.10.077
MA0079.20.0665
MA0080.20.133
MA0081.10.391
MA0083.10.101
MA0084.10.968
MA0087.10.831
MA0088.10.201
MA0090.10.00814
MA0091.10.279
MA0092.10.714
MA0093.10.864
MA0099.20.00308
MA0100.10.688
MA0101.17.38194e-6
MA0102.20.0136
MA0103.11.28113e-5
MA0104.20.121
MA0105.10.00784
MA0106.10.159
MA0107.13.25951e-7
MA0108.25.26481e-11
MA0111.10.154
MA0112.20.0312
MA0113.10.0304
MA0114.10.00117
MA0115.10.461
MA0116.14.9006e-4
MA0117.10.951
MA0119.10.972
MA0122.10.127
MA0124.10.587
MA0125.10.458
MA0131.10.882
MA0135.10.346
MA0136.10.0777
MA0137.22.11143e-12
MA0138.20.973
MA0139.10.0163
MA0140.10.632
MA0141.10.747
MA0142.10.115
MA0143.10.441
MA0144.12.47953e-6
MA0145.10.314
MA0146.10.535
MA0147.10.0431
MA0148.10.0465
MA0149.10.728
MA0150.10.0961
MA0152.10.101
MA0153.10.129
MA0154.10.494
MA0155.10.797
MA0156.10.0185
MA0157.10.00564
MA0159.10.461
MA0160.10.169
MA0162.10.481
MA0163.12.90417e-9
MA0164.10.91
MA0258.10.00964
MA0259.10.178



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: CNhs12560

Novel motifP-value
10.117
100.212
1000.748
1010.574
1020.16
1030.769
1040.987
1050.907
1060.595
1070.709
1080.428
1090.136
110.106
1100.0913
1110.0591
1120.461
1130.7
1140.0166
1150.738
1160.107
1170.00339
1180.26
1190.744
120.194
1200.14
1210.944
1220.363
1230.0202
1240.371
1250.142
1260.733
1270.161
1280.937
1290.59
130.652
1300.281
1310.385
1320.458
1330.172
1340.499
1350.649
1360.399
1370.765
1380.117
1390.823
140.851
1404.61278e-4
1410.416
1420.93
1430.0707
1440.546
1450.21
1460.326
1470.507
1480.421
1490.727
150.371
1500.65
1510.41
1520.474
1530.0391
1540.232
1550.171
1560.452
1570.519
1580.517
1590.207
160.166
1600.394
1610.313
1620.63
1630.986
1640.239
1650.429
1660.894
1670.576
1680.985
1690.408
170.54
180.202
190.776
20.892
200.844
210.212
220.696
230.349
240.615
250.739
260.0836
270.338
280.774
290.0302
30.18
300.49
310.809
322.81139e-4
330.942
340.766
350.17
360.305
370.447
380.663
390.0427
40.124
400.291
410.988
420.477
430.594
440.014
450.374
460.0449
470.0621
480.0599
490.116
50.218
500.822
510.594
520.272
530.805
540.849
550.176
560.274
570.211
580.67
590.325
60.506
600.502
610.13
620.414
630.626
640.0975
650.872
660.424
670.48
680.932
690.0018
70.554
700.0135
710.0683
720.47
730.749
740.613
750.0661
760.436
770.715
780.68
790.116
80.231
800.16
810.474
820.584
830.0256
840.734
850.92
860.534
870.38
880.581
890.427
90.403
900.968
910.853
920.733
930.475
940.214
950.159
960.598
970.308
980.33
990.494



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: CNhs12560


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)
0000003 (native cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000325 (stuff accumulating cell)
0000255 (eukaryotic cell)
0000136 (fat cell)

UBERON: Anatomy
0002384 (connective tissue)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000266 (human mature adipocyte 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:0000134 (mesenchymal cell)

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