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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005806
|DRA_sample_Accession=CAGE@SAMD00005806
|accession_numbers=CAGE;DRX008088;DRR008960;DRZ000385;DRZ001770
|accession_numbers=CAGE;DRX008088;DRR008960;DRZ000385;DRZ001770;DRZ011735;DRZ013120
|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%2520donor4.CNhs12562.12234-129G2.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.LQhCAGE/mature%2520adipocyte%252c%2520donor4.CNhs12562.12234-129G2.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.LQhCAGE/mature%2520adipocyte%252c%2520donor4.CNhs12562.12234-129G2.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.LQhCAGE/mature%2520adipocyte%252c%2520donor4.CNhs12562.12234-129G2.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.LQhCAGE/mature%2520adipocyte%252c%2520donor4.CNhs12562.12234-129G2.hg38.nobarcode.ctss.bed.gz
|id=FF:12234-129G2
|id=FF:12234-129G2
|is_a=EFO:0002091;;FF:0000266
|is_a=EFO:0002091;;FF:0000266
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|library_id=CNhs12562
|library_id=CNhs12562
|library_id_phase_based=2:CNhs12562
|library_id_phase_based=2:CNhs12562
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;12234
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;12234
|name=mature adipocyte, donor4
|name=mature adipocyte, donor4
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
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Line 92: Line 101:
|top_motifs=RXR{A,B,G}_{NR1H2,PPAR}dimers:3.1691786956;STAT2,4,6:3.0890586847;AR:2.59974175261;FOXO1,3,4:2.59089270292;RORA:2.48551891734;HBP1_HMGB_SSRP1_UBTF:2.45304893483;PDX1:2.3738891648;ESRRA:2.34716771604;NFIL3:2.263220011;FOX{D1,D2}:2.18171064659;XBP1:2.06488513424;NFATC1..3:1.92986219568;TGIF1:1.70497683659;IKZF1:1.704841217;ATF6:1.65053348793;STAT1,3:1.64974825853;GCM1,2:1.54801658237;SPZ1:1.47541516713;DBP:1.43974165512;TFCP2:1.42753332185;EP300:1.39099334792;HNF4A_NR2F1,2:1.34509793263;MTF1:1.31473178263;SOX5:1.29907560771;ATF2:1.28056192402;ARID5B:1.27475869871;HMX1:1.20479355627;MAZ:1.18584060258;NFIX:1.17898093246;FOXA2:1.17495499929;ZNF238:1.14605554252;TLX1..3_NFIC{dimer}:1.10403893829;bHLH_family:1.080576698;MEF2{A,B,C,D}:1.08040383379;SRF:1.04194031453;NR3C1:1.03903879466;FOXL1:1.034938839;MYBL2:1.03326629;PAX6:1.01575681999;HSF1,2:1.01212977872;SP1:0.99377725063;NFE2L1:0.959660443818;TBP:0.946323274119;MED-1{core}:0.942524500581;NR1H4:0.93348840259;PRRX1,2:0.933065525063;RXR{A,B,G}:0.924071460513;FOXN1:0.913112000058;TFAP2{A,C}:0.898419976095;CEBPA,B_DDIT3:0.856761384807;JUN:0.813794105345;HLF:0.796071745444;EBF1:0.785686438699;EN1,2:0.782940777959;TEAD1:0.744860819876;NANOG{mouse}:0.735413248182;TFAP2B:0.726113390187;FOXD3:0.719520913855;ATF4:0.719376759839;NHLH1,2:0.718292436032;NR6A1:0.707181292307;EGR1..3:0.705984888881;NFE2:0.699942826691;NANOG:0.696203633431;GFI1B:0.694946449616;RFX2..5_RFXANK_RFXAP:0.690189427185;CDC5L:0.677406467578;FOXP3:0.662786763078;HOXA9_MEIS1:0.658207503257;HOX{A5,B5}:0.644285318224;MAFB:0.63898092305;PATZ1:0.630977863519;NKX3-2:0.627395550972;GZF1:0.626192950877;MTE{core}:0.622219643795;HOX{A4,D4}:0.606185690683;HIC1:0.555901007538;TEF:0.526090614187;ATF5_CREB3:0.492079092698;IKZF2:0.48325923608;GTF2I:0.469784475586;NFKB1_REL_RELA:0.460780743289;STAT5{A,B}:0.401248746669;LHX3,4:0.401058776317;BREu{core}:0.399775621633;FOXQ1:0.390584681495;MYFfamily:0.387400499916;NKX2-1,4:0.360596082416;TLX2:0.359678338234;FOS_FOS{B,L1}_JUN{B,D}:0.354500470636;GTF2A1,2:0.30403207925;SREBF1,2:0.289776016717;MZF1:0.285034544658;CREB1:0.266246663322;BPTF:0.265591456933;FOX{I1,J2}:0.257370399399;ADNP_IRX_SIX_ZHX:0.247362625386;FOSL2:0.214367520481;NKX2-2,8:0.212685666329;ZNF384:0.191340925081;HNF1A:0.170150669399;FOX{F1,F2,J1}:0.133254432916;IRF7:0.125101208586;BACH2:0.114563262051;PAX2:0.0931505886942;TBX4,5:0.0917319678305;ZNF423:0.0735577707864;POU6F1:0.0601975356948;RFX1:0.0348538471706;SOX17:0.0244851503787;TFAP4:0.00580080520028;NR5A1,2:0.00030034290855;PAX5:-0.00019307199413;FOXP1:-0.0158513556795;DMAP1_NCOR{1,2}_SMARC:-0.0408043694614;ZFP161:-0.0587450262821;NKX6-1,2:-0.0730793006568;ZIC1..3:-0.0949620352568;NFY{A,B,C}:-0.101024672153;RBPJ:-0.115163974935;GATA6:-0.130765554847;NKX2-3_NKX2-5:-0.139367484017;ETS1,2:-0.141610633721;PAX8:-0.142257520189;PBX1:-0.160768824625;HIF1A:-0.165665263977;IRF1,2:-0.17911136735;ZNF148:-0.196655217017;GATA4:-0.210744553876;HAND1,2:-0.218653475585;SMAD1..7,9:-0.224277773117;ELF1,2,4:-0.238458785866;TP53:-0.252270820578;AHR_ARNT_ARNT2:-0.27361563547;REST:-0.286837701964;NRF1:-0.329647995229;ZNF143:-0.34462288702;SPIB:-0.350859023498;SOX2:-0.363761487984;YY1:-0.369716838841;CUX2:-0.384562977231;SPI1:-0.410195694141;ZBTB6:-0.420765381617;NFE2L2:-0.420882019291;VSX1,2:-0.422175467662;TAL1_TCF{3,4,12}:-0.449736696817;GFI1:-0.472145568566;RXRA_VDR{dimer}:-0.477819033322;RUNX1..3:-0.487570797919;GLI1..3:-0.501794785846;HES1:-0.509314443954;KLF4:-0.52783224253;PRDM1:-0.534092484794;CRX:-0.558783224413;PPARG:-0.572414294161;XCPE1{core}:-0.598651892836;PAX1,9:-0.605528052065;LEF1_TCF7_TCF7L1,2:-0.606335028517;RREB1:-0.622016225378;ESR1:-0.656714801705;OCT4_SOX2{dimer}:-0.658820185265;PAX3,7:-0.682420685948;MYB:-0.690672664544;E2F1..5:-0.733822048939;ALX1:-0.751965984414;SOX{8,9,10}:-0.773258360219;T:-0.796965602045;PAX4:-0.798460278965;ELK1,4_GABP{A,B1}:-0.834451550028;HOX{A6,A7,B6,B7}:-0.834586309032;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.83465679316;HMGA1,2:-0.878479228906;PITX1..3:-0.881914520228;UFEwm:-0.898342551095;POU2F1..3:-0.975808394403;ZEB1:-0.985863012495;LMO2:-1.00927937345;SNAI1..3:-1.01672455345;ALX4:-1.02037137421;EVI1:-1.06882500962;TFDP1:-1.07349378897;ZBTB16:-1.07811065624;POU5F1:-1.32683186265;POU1F1:-1.35391596606;FOXM1:-1.36381973182;CDX1,2,4:-1.37271965638;POU3F1..4:-1.50190380335;ONECUT1,2:-1.64042249134;AIRE:-1.67069182697;NKX3-1:-1.7137140742;TOPORS:-1.86117208994;MYOD1:-1.97677633283
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:12234-129G2;search_select_hide=table117:FF:12234-129G2
}}
}}

Latest revision as of 18:35, 4 June 2020

Name:mature adipocyte, donor4
Species:Human (Homo sapiens)
Library ID:CNhs12562
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
age28
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  SAMD00005806
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12562 CAGE DRX008088 DRR008960
Accession ID Hg19

Library idBAMCTSS
CNhs12562 DRZ000385 DRZ001770
Accession ID Hg38

Library idBAMCTSS
CNhs12562 DRZ011735 DRZ013120
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-0.147
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-0.393
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs12562

Jaspar motifP-value
MA0002.20.0778
MA0003.10.997
MA0004.10.659
MA0006.10.917
MA0007.10.761
MA0009.10.233
MA0014.10.873
MA0017.10.0832
MA0018.20.0442
MA0019.10.244
MA0024.10.121
MA0025.12.19101e-4
MA0027.10.713
MA0028.10.00162
MA0029.10.925
MA0030.10.00102
MA0031.12.46061e-5
MA0035.20.881
MA0038.10.259
MA0039.20.364
MA0040.10.08
MA0041.10.0254
MA0042.10.0445
MA0043.15.9108e-5
MA0046.10.786
MA0047.20.00284
MA0048.10.761
MA0050.10.196
MA0051.10.789
MA0052.11.03653e-5
MA0055.10.355
MA0057.10.153
MA0058.10.902
MA0059.10.0752
MA0060.10.939
MA0061.10.6
MA0062.25.85054e-6
MA0065.20.0256
MA0066.10.0493
MA0067.10.0606
MA0068.11.17707e-5
MA0069.10.451
MA0070.10.286
MA0071.10.982
MA0072.10.0651
MA0073.10.688
MA0074.10.589
MA0076.10.0101
MA0077.10.0438
MA0078.10.0779
MA0079.20.112
MA0080.20.0123
MA0081.10.235
MA0083.10.0494
MA0084.10.855
MA0087.10.916
MA0088.10.229
MA0090.10.0696
MA0091.10.454
MA0092.10.857
MA0093.10.662
MA0099.20.103
MA0100.10.34
MA0101.10.0011
MA0102.20.02
MA0103.14.03641e-6
MA0104.20.183
MA0105.10.0204
MA0106.10.0702
MA0107.11.78923e-4
MA0108.21.2624e-7
MA0111.10.213
MA0112.20.022
MA0113.10.067
MA0114.14.38775e-4
MA0115.10.493
MA0116.11.31075e-4
MA0117.10.972
MA0119.10.859
MA0122.10.249
MA0124.10.331
MA0125.10.513
MA0131.10.364
MA0135.10.352
MA0136.10.00963
MA0137.21.73365e-11
MA0138.20.866
MA0139.10.0426
MA0140.10.76
MA0141.10.563
MA0142.10.162
MA0143.10.552
MA0144.16.31709e-5
MA0145.10.708
MA0146.10.579
MA0147.10.0855
MA0148.10.013
MA0149.10.728
MA0150.10.525
MA0152.10.0645
MA0153.10.0589
MA0154.10.283
MA0155.10.567
MA0156.10.00463
MA0157.13.23102e-4
MA0159.10.589
MA0160.10.233
MA0162.10.355
MA0163.11.6534e-8
MA0164.10.904
MA0258.10.00799
MA0259.10.173



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: CNhs12562

Novel motifP-value
10.128
100.407
1000.853
1010.566
1020.0875
1030.395
1040.997
1050.83
1060.926
1070.711
1080.452
1090.093
110.0828
1100.0707
1110.0561
1120.446
1130.571
1140.0247
1150.595
1160.0946
1170.0162
1180.328
1190.639
120.378
1200.0678
1210.721
1220.926
1230.0183
1240.463
1250.11
1260.978
1270.129
1280.798
1290.748
130.928
1300.308
1310.29
1320.566
1330.431
1340.602
1350.757
1360.354
1370.769
1380.0899
1390.668
140.918
1400.004
1410.366
1420.944
1430.03
1440.648
1450.113
1460.313
1470.573
1480.0837
1490.518
150.326
1500.726
1510.319
1520.858
1530.0491
1540.249
1550.215
1560.38
1570.567
1580.394
1590.188
160.176
1600.379
1610.301
1620.701
1630.733
1640.323
1650.359
1660.839
1670.962
1680.852
1690.157
170.309
180.0802
190.994
20.666
200.891
210.326
220.681
230.508
240.858
250.96
260.0625
270.211
280.963
290.171
30.149
300.485
310.601
322.18799e-4
330.729
340.87
350.241
360.789
370.474
380.386
390.0884
40.139
400.35
410.928
420.474
430.416
440.00641
450.484
460.0463
470.0797
480.0595
490.101
50.158
500.796
510.568
520.285
530.796
540.796
550.0861
560.244
570.341
580.738
590.107
60.952
600.442
610.0895
620.587
630.56
640.0664
650.6
660.608
670.439
680.842
690.00288
70.337
700.0287
710.0453
720.76
730.347
740.787
750.12
760.337
770.254
780.853
790.0724
80.242
800.181
810.319
820.741
830.013
840.809
850.608
860.761
870.267
880.851
890.142
90.585
900.943
910.377
920.86
930.669
940.143
950.108
960.884
970.348
980.323
990.354



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: CNhs12562


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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