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{{f5samples
{{f5samples
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|DRA_sample_Accession=CAGE@SAMD00005173
|accession_numbers=CAGE;DRX008690;DRR009562;DRZ000987;DRZ002372
|accession_numbers=CAGE;DRX008690;DRR009562;DRZ000987;DRZ002372;DRZ012337;DRZ013722
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|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|fonse_treatment_closure=
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|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/occipital%2520cortex%2520-%2520adult%252c%2520donor10196.CNhs13798.10172-103C1.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/occipital%2520cortex%2520-%2520adult%252c%2520donor10196.CNhs13798.10172-103C1.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/occipital%2520cortex%2520-%2520adult%252c%2520donor10196.CNhs13798.10172-103C1.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/occipital%2520cortex%2520-%2520adult%252c%2520donor10196.CNhs13798.10172-103C1.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/occipital%2520cortex%2520-%2520adult%252c%2520donor10196.CNhs13798.10172-103C1.hg38.nobarcode.ctss.bed.gz
|id=FF:10172-103C1
|id=FF:10172-103C1
|is_a=EFO:0002091;;FF:0010163
|is_a=EFO:0002091;;FF:0010163
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|library_id=CNhs13798
|library_id=CNhs13798
|library_id_phase_based=2:CNhs13798
|library_id_phase_based=2:CNhs13798
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10172
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10172
|name=occipital cortex - adult, donor10196
|name=occipital cortex - adult, donor10196
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
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Line 91: Line 101:
|top_motifs=REST:3.77653850855;AHR_ARNT_ARNT2:3.75332144315;CUX2:3.71551026658;HOXA9_MEIS1:3.5186323938;MYFfamily:3.42285317772;NHLH1,2:3.33656701003;FOXM1:3.31749185884;PRDM1:3.23319140685;DBP:3.23085745141;ATF2:3.11147983255;PRRX1,2:3.06571500298;MTE{core}:3.0112181312;ZFP161:2.79723044406;NANOG:2.77345263337;MTF1:2.69747548001;PAX6:2.67279559414;NKX3-2:2.6302814921;RREB1:2.52017653735;SOX5:2.47197505874;GFI1B:2.45085224173;OCT4_SOX2{dimer}:2.40469586027;FOXQ1:2.38996244945;NFIX:2.38571906757;LMO2:2.37454741225;MED-1{core}:2.36220557208;NKX6-1,2:2.30032824568;ZBTB6:2.29891730556;MZF1:2.29191933386;GTF2I:2.23000331809;ALX1:2.21926476368;SOX2:2.16250634914;ESRRA:2.14890752194;POU6F1:2.14471139623;RFX1:2.12049049722;JUN:2.11815411654;BREu{core}:2.11312607137;ARID5B:2.10720193141;TGIF1:2.09597331282;EGR1..3:1.95839400081;PAX4:1.94517149795;SMAD1..7,9:1.89639407733;HIC1:1.86424485931;KLF4:1.81390827953;PAX5:1.77864814474;FOX{F1,F2,J1}:1.72243580975;NRF1:1.71816599419;XBP1:1.69807938459;GATA4:1.68623222786;LEF1_TCF7_TCF7L1,2:1.68386043794;SOX17:1.64467319264;NFIL3:1.64467295654;FOXP3:1.62666785879;NKX2-3_NKX2-5:1.57780465456;HOX{A4,D4}:1.53063055817;POU5F1:1.51237789353;TFAP2B:1.49459227109;HMGA1,2:1.41796945856;RFX2..5_RFXANK_RFXAP:1.27984056652;ZNF384:1.27462673445;HBP1_HMGB_SSRP1_UBTF:1.22495431397;IKZF2:1.19418209433;FOXN1:1.19252002846;PATZ1:1.19070257648;POU3F1..4:1.18664926015;GZF1:1.0985664897;TFDP1:0.978809049547;SOX{8,9,10}:0.961557299133;CREB1:0.937001226047;PDX1:0.926459736525;ZEB1:0.920903814141;BPTF:0.871087645766;LHX3,4:0.856108443728;CDC5L:0.819392007185;FOXD3:0.79112015476;MYOD1:0.772399849263;MAZ:0.768255989952;ZNF238:0.712994027833;ONECUT1,2:0.692472474235;YY1:0.686505142501;ZNF143:0.661916649965;RORA:0.659786976487;GTF2A1,2:0.649934528969;MEF2{A,B,C,D}:0.64787990553;EBF1:0.621445126298;RBPJ:0.616311784845;TLX2:0.582002645209;MAFB:0.496028412806;ATF5_CREB3:0.491636329865;ZNF423:0.467079950719;ZIC1..3:0.440347255444;CRX:0.429666773112;STAT2,4,6:0.427721579952;PBX1:0.412193006568;PAX8:0.408163984839;ATF4:0.403209529947;STAT1,3:0.402557687223;SREBF1,2:0.390464327269;TEF:0.366947222962;SPZ1:0.332693714931;AR:0.313850879893;GFI1:0.305387959975;NANOG{mouse}:0.295070088155;T:0.25963338934;POU1F1:0.256380312314;GCM1,2:0.239997234661;HMX1:0.237193362351;EP300:0.230199241832;NKX3-1:0.224218314148;HAND1,2:0.202407385782;UFEwm:0.167497102355;VSX1,2:0.107437779987;ZBTB16:0.0880654341799;FOX{D1,D2}:0.0864295144527;IRF7:0.0573244738917;PAX3,7:0.0187624573202;TFAP2{A,C}:0.00283410996215;CEBPA,B_DDIT3:-0.0163855905934;TOPORS:-0.0378768094689;FOXP1:-0.0575111367718;GATA6:-0.0625372797349;PAX1,9:-0.0934338124049;NR3C1:-0.150901730718;NFATC1..3:-0.180164598605;SNAI1..3:-0.188436199894;PAX2:-0.25807988529;NFE2L2:-0.26822933843;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.270779996829;NFE2:-0.281767427498;bHLH_family:-0.306281519791;NFY{A,B,C}:-0.319744200851;TBX4,5:-0.342259241894;TLX1..3_NFIC{dimer}:-0.361436683929;STAT5{A,B}:-0.363177592594;FOX{I1,J2}:-0.377513805209;NFE2L1:-0.385625529814;FOXL1:-0.419137318916;SPI1:-0.469577295769;DMAP1_NCOR{1,2}_SMARC:-0.487055216607;EVI1:-0.497680087218;FOXA2:-0.508774573827;HNF1A:-0.524380361025;SP1:-0.527489813281;ADNP_IRX_SIX_ZHX:-0.611373209833;NR5A1,2:-0.653446087408;MYBL2:-0.671470844169;IRF1,2:-0.688026368578;ATF6:-0.698286710893;IKZF1:-0.733133279141;NKX2-1,4:-0.736204986217;FOSL2:-0.746130932517;SPIB:-0.780221704335;BACH2:-0.797453100166;ESR1:-0.798771073652;HSF1,2:-0.819678704605;AIRE:-0.826511393571;FOXO1,3,4:-0.832072483453;FOS_FOS{B,L1}_JUN{B,D}:-0.864902067006;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.882006218053;TAL1_TCF{3,4,12}:-0.890583019023;TEAD1:-0.953018697331;ETS1,2:-0.968203033994;TFAP4:-0.992608226732;HNF4A_NR2F1,2:-1.03116394957;HOX{A6,A7,B6,B7}:-1.04085220369;NFKB1_REL_RELA:-1.06619024925;HLF:-1.07774741933;HIF1A:-1.10324053312;CDX1,2,4:-1.10514034898;MYB:-1.14917421106;E2F1..5:-1.15121652205;PITX1..3:-1.18061254755;RUNX1..3:-1.2080732344;NKX2-2,8:-1.25775848023;ELK1,4_GABP{A,B1}:-1.30199482659;ALX4:-1.32925057142;GLI1..3:-1.35801606589;TP53:-1.38438364424;POU2F1..3:-1.39400892079;RXR{A,B,G}:-1.41017928817;NR1H4:-1.42067455005;RXRA_VDR{dimer}:-1.48187178295;SRF:-1.51597861206;TBP:-1.56921514892;ELF1,2,4:-1.60202135551;HOX{A5,B5}:-1.63535614218;HES1:-1.75986006462;ZNF148:-1.77977881711;XCPE1{core}:-1.92924850681;TFCP2:-1.97723245041;PPARG:-2.15795496345;EN1,2:-2.62747695611;NR6A1:-3.06681653925
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10172-103C1;search_select_hide=table117:FF:10172-103C1
}}
}}

Latest revision as of 12:24, 3 June 2020

Name:occipital cortex - adult, donor10196
Species:Human (Homo sapiens)
Library ID:CNhs13798
Sample type:tissues
Genomic View: UCSC
RefEX:Specific genes
FANTOM CAT:1, 2, 3, 4, 5, 6, 7
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueoccipital cortex
dev stageNA
sexfemale
age60
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationPeter Heutink
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  SAMD00005173
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13798 CAGE DRX008690 DRR009562
Accession ID Hg19

Library idBAMCTSS
CNhs13798 DRZ000987 DRZ002372
Accession ID Hg38

Library idBAMCTSS
CNhs13798 DRZ012337 DRZ013722
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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C81-trachea-salivary-throat-aorta-eye-submaxillary-parotid0
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: CNhs13798

Jaspar motifP-value
MA0002.20.114
MA0003.10.333
MA0004.10.329
MA0006.10.175
MA0007.10.254
MA0009.10.195
MA0014.10.601
MA0017.10.00304
MA0018.20.0509
MA0019.10.633
MA0024.10.686
MA0025.10.368
MA0027.10.805
MA0028.10.0379
MA0029.10.0636
MA0030.10.966
MA0031.10.729
MA0035.20.0423
MA0038.10.421
MA0039.20.0339
MA0040.10.939
MA0041.10.603
MA0042.10.798
MA0043.10.979
MA0046.10.0182
MA0047.20.0573
MA0048.10.0492
MA0050.12.6555e-4
MA0051.10.00437
MA0052.10.241
MA0055.12.56496e-4
MA0057.10.791
MA0058.10.28
MA0059.10.132
MA0060.10.899
MA0061.10.0116
MA0062.27.33473e-4
MA0065.20.00101
MA0066.10.0483
MA0067.10.751
MA0068.10.545
MA0069.10.282
MA0070.10.745
MA0071.10.00748
MA0072.10.439
MA0073.10.378
MA0074.10.171
MA0076.10.0795
MA0077.10.422
MA0078.10.791
MA0079.20.786
MA0080.21.67408e-8
MA0081.10.0362
MA0083.10.0149
MA0084.10.321
MA0087.10.661
MA0088.10.191
MA0090.10.36
MA0091.10.554
MA0092.10.348
MA0093.10.347
MA0099.21.16525e-16
MA0100.10.606
MA0101.10.00201
MA0102.20.0486
MA0103.10.374
MA0104.20.676
MA0105.10.0158
MA0106.10.0402
MA0107.10.00618
MA0108.20.207
MA0111.10.726
MA0112.20.00302
MA0113.10.373
MA0114.10.00162
MA0115.10.227
MA0116.10.0288
MA0117.10.942
MA0119.10.0866
MA0122.10.587
MA0124.10.841
MA0125.10.548
MA0131.10.647
MA0135.10.0251
MA0136.17.0423e-12
MA0137.20.696
MA0138.20.0555
MA0139.10.517
MA0140.10.0305
MA0141.10.0142
MA0142.10.445
MA0143.10.474
MA0144.10.728
MA0145.10.168
MA0146.10.0018
MA0147.10.535
MA0148.10.178
MA0149.10.055
MA0150.18.30165e-4
MA0152.10.502
MA0153.10.0562
MA0154.10.0824
MA0155.10.454
MA0156.18.22215e-9
MA0157.10.546
MA0159.10.0186
MA0160.10.0151
MA0162.10.159
MA0163.15.85521e-4
MA0164.10.8
MA0258.10.0134
MA0259.10.982



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: CNhs13798

Novel motifP-value
10.101
100.0705
1000.275
1010.284
1020.995
1030.424
1040.207
1050.102
1060.0223
1070.0402
1080.957
1090.00185
110.0139
1100.0549
1110.306
1120.621
1130.538
1140.373
1150.972
1160.0917
1170.00636
1180.11
1190.274
120.462
1200.319
1210.425
1220.857
1230.743
1240.0021
1250.275
1260.0343
1270.534
1280.14
1290.845
131.40386e-4
1300.169
1310.0143
1320.685
1330.0294
1340.714
1350.0555
1362.14956e-4
1370.751
1380.91
1390.319
140.712
1400.541
1410.863
1420.831
1430.197
1440.994
1450.0423
1460.32
1470.514
1480.565
1490.405
150.157
1500.116
1510.7
1520.0401
1530.876
1540.417
1550.493
1560.619
1570.351
1580.249
1590.0421
160.0675
1600.365
1610.214
1620.729
1630.903
1640.0138
1650.07
1660.864
1670.908
1680.48
1690.0169
170.112
180.312
190.218
20.966
200.0666
210.0522
220.149
230.473
240.0332
250.457
267.47965e-6
270.793
280.638
290.0123
30.0442
300.893
310.989
320.0249
330.0749
340.527
350.933
360.276
370.0358
380.375
390.129
40.736
400.0399
410.574
420.306
430.109
440.241
450.654
460.112
470.0829
480.0502
490.232
50.992
500.11
510.592
520.543
530.987
540.411
550.624
560.437
570.406
580.518
590.0674
60.796
600.0548
610.0485
620.314
630.113
640.33
650.299
660.214
670.497
680.167
690.433
70.0338
700.141
710.0121
720.425
730.015
740.907
750.0413
760.364
770.147
780.00496
790.306
80.0589
800.868
810.666
820.805
830.0215
840.392
850.356
860.22
878.2408e-5
880.773
890.861
90.362
900.253
910.588
920.934
930.472
940.305
950.00584
960.847
970.619
980.46
990.566



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: CNhs13798


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0000955 (brain)
0002021 (occipital lobe)
0000956 (cerebral cortex)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0001950 (neocortex)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0010163 (occipital cortex - adult donor)

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
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)

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