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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005203
|DRA_sample_Accession=CAGE@SAMD00005203
|accession_numbers=CAGE;DRX008016;DRR008888;DRZ000313;DRZ001698
|accession_numbers=CAGE;DRX008016;DRR008888;DRZ000313;DRZ001698;DRZ011663;DRZ013048
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000076,CL:0000255
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000076,CL:0000255
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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.cell_line.hCAGE/squamous%2520cell%2520carcinoma%2520cell%2520line%253aT3M-5.CNhs11739.10616-108G4.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/squamous%2520cell%2520carcinoma%2520cell%2520line%253aT3M-5.CNhs11739.10616-108G4.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/squamous%2520cell%2520carcinoma%2520cell%2520line%253aT3M-5.CNhs11739.10616-108G4.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/squamous%2520cell%2520carcinoma%2520cell%2520line%253aT3M-5.CNhs11739.10616-108G4.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/squamous%2520cell%2520carcinoma%2520cell%2520line%253aT3M-5.CNhs11739.10616-108G4.hg38.nobarcode.ctss.bed.gz
|id=FF:10616-108G4
|id=FF:10616-108G4
|is_a=EFO:0002091;;FF:0000210;;FF:0102024
|is_a=EFO:0002091;;FF:0000210;;FF:0102024
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|library_id=CNhs11739
|library_id=CNhs11739
|library_id_phase_based=2:CNhs11739
|library_id_phase_based=2:CNhs11739
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10616
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10616
|name=squamous cell carcinoma cell line:T3M-5
|name=squamous cell carcinoma cell line:T3M-5
|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 89: Line 99:
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|top_motifs=ELK1,4_GABP{A,B1}:2.20699747775;TP53:1.64690689655;POU1F1:1.51214667929;ZEB1:1.3937975203;POU2F1..3:1.3313972956;bHLH_family:1.16923940776;VSX1,2:1.03627752038;SNAI1..3:1.00694729207;ONECUT1,2:1.0068024684;TBX4,5:0.98830854121;BACH2:0.906408023434;ARID5B:0.890436894487;TEF:0.867396002379;TLX2:0.852685414825;FOSL2:0.834576024737;FOXQ1:0.815283922985;GLI1..3:0.796792583696;FOS_FOS{B,L1}_JUN{B,D}:0.775603246037;MYOD1:0.754732347822;PPARG:0.741005526116;ELF1,2,4:0.650800929978;POU6F1:0.593314014355;FOXD3:0.547828380745;ADNP_IRX_SIX_ZHX:0.523979442044;POU3F1..4:0.516440455831;HLF:0.467374322651;NFE2:0.465831631254;SOX17:0.462351674904;IKZF1:0.444294961848;ZBTB6:0.437364186017;TEAD1:0.428411357327;NKX2-1,4:0.417154116209;FOXM1:0.401205275667;HOXA9_MEIS1:0.399076222244;TBP:0.362016135754;HOX{A6,A7,B6,B7}:0.347953635309;PITX1..3:0.345542291976;LEF1_TCF7_TCF7L1,2:0.342138612558;FOXN1:0.319522074682;RBPJ:0.306087779687;HOX{A4,D4}:0.258786365974;OCT4_SOX2{dimer}:0.204972078323;NANOG:0.197451266859;NKX3-1:0.196268199665;NKX3-2:0.193916633732;PAX2:0.191059645706;ZBTB16:0.165239440408;ALX1:0.162223496661;LMO2:0.127023136019;GFI1:0.106085404479;PDX1:0.104736224694;TFDP1:0.0890169554498;NFIX:0.0865751720597;STAT5{A,B}:0.0860859160913;ATF4:0.0751152990267;PAX1,9:0.070735850862;ZNF143:0.0677370820329;ATF5_CREB3:0.0568815228559;FOX{F1,F2,J1}:0.0554853737149;HES1:0.0477668763483;IRF7:0.0390697745766;PRDM1:0.0349445901041;SPZ1:0.0341057989097;NFKB1_REL_RELA:0.0108199514261;GZF1:0.00172625731213;CRX:-0.00327923785429;AIRE:-0.00526347873271;AR:-0.00709413732587;CEBPA,B_DDIT3:-0.0155953317827;TFAP2{A,C}:-0.0164717589512;CDC5L:-0.039870736456;GTF2A1,2:-0.0659185948281;FOXA2:-0.0760936636707;ZNF148:-0.0823514925837;T:-0.0847885670641;CREB1:-0.0877646710835;NFIL3:-0.103804373331;ATF2:-0.116718830473;GATA6:-0.130188155028;AHR_ARNT_ARNT2:-0.139828582475;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.140462926885;SMAD1..7,9:-0.141078706786;PAX8:-0.143820581616;EN1,2:-0.144020863817;PAX4:-0.147931007804;TLX1..3_NFIC{dimer}:-0.159190221946;ATF6:-0.165240031047;REST:-0.168339711222;ETS1,2:-0.173761113614;GFI1B:-0.177450972997;MTF1:-0.180030587416;TFCP2:-0.180432096119;YY1:-0.227184053207;XCPE1{core}:-0.270059076654;FOXP1:-0.273640878882;NR1H4:-0.274500790996;UFEwm:-0.276183910742;CDX1,2,4:-0.277727261441;RFX2..5_RFXANK_RFXAP:-0.283073895326;SPI1:-0.287070677963;NFY{A,B,C}:-0.287575742421;HNF1A:-0.288850682003;DMAP1_NCOR{1,2}_SMARC:-0.302768302244;FOX{D1,D2}:-0.306312936222;FOX{I1,J2}:-0.330916788912;HIC1:-0.334404059626;NR6A1:-0.336077199773;NHLH1,2:-0.343797343235;ZFP161:-0.348303270891;MYBL2:-0.357858522228;MED-1{core}:-0.368096449745;RFX1:-0.375797884352;ZIC1..3:-0.381599444697;PRRX1,2:-0.389014732211;SP1:-0.393380866504;TOPORS:-0.40034252857;MEF2{A,B,C,D}:-0.402513421254;E2F1..5:-0.40898966897;SPIB:-0.424408344657;HOX{A5,B5}:-0.432115969847;SOX{8,9,10}:-0.434014419407;IRF1,2:-0.435253618494;KLF4:-0.454950261388;EP300:-0.471029584882;NFE2L2:-0.475849714813;XBP1:-0.488116551441;MYB:-0.49328612538;JUN:-0.506663730196;NRF1:-0.5104834559;SRF:-0.511349755147;LHX3,4:-0.524349675333;EGR1..3:-0.537542864007;NKX2-2,8:-0.539616288777;NKX2-3_NKX2-5:-0.54084244149;MTE{core}:-0.548816687959;TFAP2B:-0.584919409379;PAX6:-0.601846431291;ZNF423:-0.602879224337;TFAP4:-0.621902720699;SOX2:-0.622273928688;BPTF:-0.623050907503;HNF4A_NR2F1,2:-0.627649150688;GTF2I:-0.645545986713;PBX1:-0.647241173534;EVI1:-0.657698210348;CUX2:-0.661619275701;RORA:-0.663096765488;ESR1:-0.67211617827;BREu{core}:-0.680342647361;PAX5:-0.691741315441;FOXL1:-0.694615499685;HBP1_HMGB_SSRP1_UBTF:-0.698234781805;POU5F1:-0.700780254215;HAND1,2:-0.70849225329;HIF1A:-0.715262522038;MAFB:-0.718086421628;STAT2,4,6:-0.736022693726;FOXO1,3,4:-0.778720975387;RXR{A,B,G}:-0.780287298299;PAX3,7:-0.783224689557;MYFfamily:-0.785537609176;TAL1_TCF{3,4,12}:-0.788858735175;DBP:-0.826869825777;RUNX1..3:-0.831945183179;GCM1,2:-0.843929309452;NFATC1..3:-0.855842162468;SREBF1,2:-0.865961148587;MAZ:-0.907761457793;HMGA1,2:-0.935177156742;NR3C1:-0.943628756756;ZNF384:-0.975768954968;IKZF2:-0.984229707559;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.991059119653;NKX6-1,2:-1.009375593;NR5A1,2:-1.03510866895;TGIF1:-1.04520899516;ALX4:-1.08902631381;PATZ1:-1.12125727086;STAT1,3:-1.13003903238;EBF1:-1.19016849318;HSF1,2:-1.19414273825;RREB1:-1.22831493838;SOX5:-1.27099482947;ZNF238:-1.28042972054;NFE2L1:-1.3151860105;GATA4:-1.32146343781;RXRA_VDR{dimer}:-1.39731661232;NANOG{mouse}:-1.46759813414;HMX1:-1.5174585526;MZF1:-1.52139571826;ESRRA:-1.65567376086;FOXP3:-1.81382814498
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10616-108G4;search_select_hide=table117:FF:10616-108G4
}}
}}

Latest revision as of 14:31, 3 June 2020

Name:squamous cell carcinoma cell line:T3M-5
Species:Human (Homo sapiens)
Library ID:CNhs11739
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuethyroid
dev stageNA
sexfemale
age71
cell typeunclassifiable
cell lineT3M-5
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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  SAMD00005203
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11739 CAGE DRX008016 DRR008888
Accession ID Hg19

Library idBAMCTSS
CNhs11739 DRZ000313 DRZ001698
Accession ID Hg38

Library idBAMCTSS
CNhs11739 DRZ011663 DRZ013048
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-penis0
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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: CNhs11739

Jaspar motifP-value
MA0002.20.571
MA0003.10.761
MA0004.10.321
MA0006.10.183
MA0007.10.394
MA0009.10.292
MA0014.10.0509
MA0017.10.667
MA0018.20.779
MA0019.10.406
MA0024.10.00591
MA0025.10.83
MA0027.10.899
MA0028.16.92274e-14
MA0029.10.167
MA0030.10.607
MA0031.10.702
MA0035.20.0511
MA0038.10.184
MA0039.20.0281
MA0040.10.59
MA0041.10.606
MA0042.10.551
MA0043.10.812
MA0046.10.128
MA0047.20.643
MA0048.10.477
MA0050.10.699
MA0051.10.289
MA0052.10.507
MA0055.10.00418
MA0057.10.18
MA0058.10.565
MA0059.10.0172
MA0060.10.153
MA0061.10.957
MA0062.25.73817e-19
MA0065.20.456
MA0066.10.795
MA0067.10.193
MA0068.10.464
MA0069.10.172
MA0070.10.481
MA0071.10.12
MA0072.10.984
MA0073.10.978
MA0074.10.535
MA0076.11.62074e-14
MA0077.10.3
MA0078.10.837
MA0079.20.792
MA0080.20.0253
MA0081.10.959
MA0083.10.702
MA0084.10.439
MA0087.10.0567
MA0088.10.0156
MA0090.10.01
MA0091.10.0716
MA0092.10.538
MA0093.10.246
MA0099.22.91381e-30
MA0100.10.284
MA0101.10.472
MA0102.20.528
MA0103.15.33524e-7
MA0104.20.179
MA0105.10.378
MA0106.15.07306e-10
MA0107.10.819
MA0108.20.153
MA0111.10.502
MA0112.20.45
MA0113.10.2
MA0114.10.847
MA0115.10.824
MA0116.10.059
MA0117.10.425
MA0119.10.183
MA0122.10.982
MA0124.10.212
MA0125.10.194
MA0131.10.878
MA0135.10.754
MA0136.10.00778
MA0137.20.242
MA0138.20.0427
MA0139.10.0406
MA0140.10.193
MA0141.10.325
MA0142.10.522
MA0143.10.799
MA0144.10.68
MA0145.10.0319
MA0146.10.371
MA0147.10.052
MA0148.10.086
MA0149.10.0671
MA0150.10.0156
MA0152.10.282
MA0153.10.84
MA0154.10.479
MA0155.10.186
MA0156.13.0494e-6
MA0157.10.66
MA0159.10.0105
MA0160.10.534
MA0162.10.766
MA0163.10.042
MA0164.10.57
MA0258.10.355
MA0259.10.513



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: CNhs11739

Novel motifP-value
10.287
100.326
1000.925
1010.27
1020.492
1030.166
1040.558
1050.826
1060.0178
1070.00122
1080.247
1090.0085
110.599
1100.116
1110.481
1120.563
1130.0833
1140.456
1150.905
1160.246
1170.056
1180.957
1190.538
120.742
1200.281
1210.581
1220.61
1230.839
1240.089
1250.827
1260.233
1270.658
1280.418
1290.0628
130.0554
1300.956
1310.831
1320.782
1330.758
1340.0437
1350.0323
1360.0316
1370.455
1380.117
1390.448
140.999
1400.227
1410.774
1420.628
1430.764
1440.543
1450.271
1460.795
1470.558
1480.714
1490.961
150.435
1500.588
1510.301
1520.128
1530.898
1540.642
1550.767
1560.433
1570.856
1580.685
1590.482
160.0296
1600.696
1610.308
1620.455
1630.538
1640.604
1650.284
1660.142
1670.36
1680.801
1690.0475
170.119
180.157
190.982
20.851
200.257
210.903
220.815
230.502
240.197
250.786
260.206
270.71
280.0801
290.421
30.179
300.392
310.854
320.224
330.0212
340.128
350.397
360.0362
370.224
380.181
390.698
40.538
400.196
410.153
420.154
430.694
440.896
450.378
460.0907
470.265
480.24
490.71
50.349
500.416
510.905
520.874
530.452
540.445
550.0245
560.444
570.0319
580.886
590.848
60.95
600.257
610.607
620.815
630.126
640.948
650.358
660.00476
670.396
680.124
690.951
70.933
700.019
710.136
720.736
730.0294
740.817
750.0322
760.278
770.592
780.0283
790.107
80.279
800.611
810.7
820.647
830.485
840.604
850.969
860.277
870.00335
880.915
890.332
90.366
900.253
910.234
920.49
930.403
940.765
950.251
960.293
970.221
980.967
990.652



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: CNhs11739


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)
0000066 (epithelial cell)
0000076 (squamous epithelial cell)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
305 (carcinoma)
1749 (squamous cell carcinoma)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0102024 (squamous cell carcinoma cell line sample)
0101120 (epithelial cell line 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
NA

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