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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004863
|DRA_sample_Accession=CAGE@SAMD00004863
|accession_numbers=CAGE;DRX007951;DRR008823;DRZ000248;DRZ001633
|accession_numbers=CAGE;DRX007951;DRR008823;DRZ000248;DRZ001633;DRZ011598;DRZ012983
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000076,CL:0000213,CL:0000215,CL:0000255,CL:0000077
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000076,CL:0000213,CL:0000215,CL:0000255,CL:0000077
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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/mesothelioma%2520cell%2520line%253aONE58.CNhs13075.10858-111G3.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/mesothelioma%2520cell%2520line%253aONE58.CNhs13075.10858-111G3.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/mesothelioma%2520cell%2520line%253aONE58.CNhs13075.10858-111G3.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/mesothelioma%2520cell%2520line%253aONE58.CNhs13075.10858-111G3.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/mesothelioma%2520cell%2520line%253aONE58.CNhs13075.10858-111G3.hg38.nobarcode.ctss.bed.gz
|id=FF:10858-111G3
|id=FF:10858-111G3
|is_a=EFO:0002091;;FF:0000210;;FF:0102424
|is_a=EFO:0002091;;FF:0000210;;FF:0102424
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|library_id=CNhs13075
|library_id=CNhs13075
|library_id_phase_based=2:CNhs13075
|library_id_phase_based=2:CNhs13075
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10858
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10858
|name=mesothelioma cell line:ONE58
|name=mesothelioma cell line:ONE58
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|refex=http://refex.dbcls.jp/genelist.php?lang=en&db=human&roku_valid=1&rk[]=&order_key=score
|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 91: Line 100:
|top_motifs=bHLH_family:1.85475422615;HES1:1.64533084009;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.30546315327;HIF1A:1.27079230235;TAL1_TCF{3,4,12}:1.09953141101;ZBTB16:0.969231203837;ATF6:0.760881135746;NR3C1:0.74801014131;AIRE:0.733678720997;IRF7:0.729275200711;EVI1:0.727203651251;NR6A1:0.645242010887;NKX3-1:0.624654814317;NFE2L1:0.623327603103;MYOD1:0.619933392978;PPARG:0.59835500254;ESRRA:0.573932042142;UFEwm:0.572129666932;FOXM1:0.569053322623;RXR{A,B,G}:0.565264090613;E2F1..5:0.556129153469;IRF1,2:0.526121757172;TFDP1:0.516367351124;ZBTB6:0.501703402242;NKX2-2,8:0.492000971777;NFE2:0.491754410177;ADNP_IRX_SIX_ZHX:0.479074513679;GZF1:0.474663931135;HOXA9_MEIS1:0.465007907845;TEAD1:0.463439182963;HNF4A_NR2F1,2:0.452537138423;SREBF1,2:0.443613562318;FOX{I1,J2}:0.43705426188;BACH2:0.43517353567;HSF1,2:0.430535866899;MYB:0.399439578875;NFE2L2:0.384773319219;PAX1,9:0.379630517957;POU1F1:0.368887281164;PDX1:0.361947637723;FOXQ1:0.356061627943;ELK1,4_GABP{A,B1}:0.340463611819;AHR_ARNT_ARNT2:0.269779483875;POU5F1:0.265501626013;YY1:0.261717690207;LHX3,4:0.249155646563;FOXD3:0.230968199129;GFI1B:0.223370314073;RXRA_VDR{dimer}:0.205039570248;NFY{A,B,C}:0.176016408562;NFIX:0.150442449529;IKZF1:0.14505686745;PRRX1,2:0.135152719045;HOX{A5,B5}:0.135031081796;ZNF384:0.113174026889;FOS_FOS{B,L1}_JUN{B,D}:0.111813624756;CEBPA,B_DDIT3:0.10647399479;PAX8:0.0905765223576;TBX4,5:0.0874355135443;HIC1:0.0687293297935;STAT2,4,6:0.0673274402466;MAFB:0.0567868986148;POU3F1..4:0.0530024214264;ONECUT1,2:0.0315819703971;NRF1:0.0282481187072;TFAP2B:0.0261797857049;LMO2:-0.0208409748024;PAX4:-0.0279146794657;PAX3,7:-0.0312166731855;TLX1..3_NFIC{dimer}:-0.031855074487;CDX1,2,4:-0.0460102678391;FOXN1:-0.0498641892173;PITX1..3:-0.0607452312702;HOX{A4,D4}:-0.0634365276614;HMX1:-0.063458023078;ALX4:-0.0716908647562;ARID5B:-0.080346717509;FOSL2:-0.0904192895586;HLF:-0.103687153699;ATF5_CREB3:-0.106211737466;RFX1:-0.110590555911;STAT5{A,B}:-0.114877496162;TOPORS:-0.119845405582;GFI1:-0.125140955521;TP53:-0.132480201028;NKX6-1,2:-0.138844931476;XCPE1{core}:-0.141937357533;REST:-0.148648806895;TBP:-0.164748868143;STAT1,3:-0.166041238761;OCT4_SOX2{dimer}:-0.168981124892;EN1,2:-0.171441527233;BREu{core}:-0.175002632244;GATA4:-0.187877731025;DMAP1_NCOR{1,2}_SMARC:-0.198719773295;PBX1:-0.202305089164;GTF2A1,2:-0.2039952371;NKX2-3_NKX2-5:-0.205694980337;ALX1:-0.208024349692;NKX3-2:-0.219171369662;TFCP2:-0.220484851961;FOXL1:-0.221322826789;HNF1A:-0.223592863881;NANOG:-0.237372621368;NFKB1_REL_RELA:-0.243831471938;FOXP3:-0.252943308226;SP1:-0.254254786906;KLF4:-0.254903010918;ELF1,2,4:-0.255621027843;ATF4:-0.256659510684;SNAI1..3:-0.27237296016;EP300:-0.272386147302;IKZF2:-0.287682676745;NKX2-1,4:-0.296052749213;CDC5L:-0.298280060676;ZNF143:-0.301348807496;NR1H4:-0.303186554342;PAX5:-0.306423180299;MYFfamily:-0.313581835935;GTF2I:-0.314762566747;NHLH1,2:-0.340361731788;T:-0.345183764024;LEF1_TCF7_TCF7L1,2:-0.35602596149;ESR1:-0.366575257926;MED-1{core}:-0.38004456587;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.381791378805;ETS1,2:-0.384861148631;SOX{8,9,10}:-0.39029579233;SMAD1..7,9:-0.406212577031;PAX2:-0.414964643144;ZIC1..3:-0.420396552193;PAX6:-0.421339609423;TEF:-0.433539953345;PRDM1:-0.441437298326;SPIB:-0.445977207626;MYBL2:-0.449218028813;CUX2:-0.47697438043;ZEB1:-0.482979073672;FOXO1,3,4:-0.486888437109;RREB1:-0.492225069028;POU6F1:-0.4935304081;EGR1..3:-0.501287588583;RFX2..5_RFXANK_RFXAP:-0.508268116161;FOXP1:-0.515401934388;SPI1:-0.515666621781;RORA:-0.548810791587;RUNX1..3:-0.551675849561;NFIL3:-0.552667517684;EBF1:-0.555825840247;SRF:-0.562865551089;RBPJ:-0.564424349456;HAND1,2:-0.572608955703;CREB1:-0.574504256073;FOX{D1,D2}:-0.576240332932;TFAP2{A,C}:-0.58193857566;SPZ1:-0.589475409885;HOX{A6,A7,B6,B7}:-0.595277824667;FOX{F1,F2,J1}:-0.598943511355;POU2F1..3:-0.616217282688;HMGA1,2:-0.627128940051;FOXA2:-0.630348835758;GLI1..3:-0.646804506055;MZF1:-0.669828344833;PATZ1:-0.673828375543;MEF2{A,B,C,D}:-0.678620118301;MTF1:-0.692923646759;ZNF423:-0.712448389696;HBP1_HMGB_SSRP1_UBTF:-0.716545351642;GATA6:-0.717783415336;SOX17:-0.720674354809;XBP1:-0.785267843574;DBP:-0.787521957036;SOX2:-0.78921770486;MAZ:-0.824746020248;ZNF148:-0.830397312056;NR5A1,2:-0.84402507529;ZNF238:-0.847447951086;NFATC1..3:-0.88072725166;ZFP161:-0.895444618672;MTE{core}:-0.90060255102;TGIF1:-0.926688880545;VSX1,2:-0.934370159826;TFAP4:-0.940415486392;JUN:-0.974553908349;SOX5:-1.00556112584;AR:-1.02243830832;ATF2:-1.02498476414;BPTF:-1.07728697298;CRX:-1.18210660471;GCM1,2:-1.205328513;TLX2:-1.41880721647;NANOG{mouse}:-1.42692102406
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10858-111G3;search_select_hide=table117:FF:10858-111G3
}}
}}

Latest revision as of 16:24, 3 June 2020

Name:mesothelioma cell line:ONE58
Species:Human (Homo sapiens)
Library ID:CNhs13075
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuemesothelium
dev stageNA
sexmale
ageunknown
cell typemesothelial cell
cell lineONE58
companyECACC
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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  SAMD00004863
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13075 CAGE DRX007951 DRR008823
Accession ID Hg19

Library idBAMCTSS
CNhs13075 DRZ000248 DRZ001633
Accession ID Hg38

Library idBAMCTSS
CNhs13075 DRZ011598 DRZ012983
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-penis0.151
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-lymphoma0.268
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs13075

Jaspar motifP-value
MA0002.20.178
MA0003.10.74
MA0004.15.15008e-6
MA0006.10.76
MA0007.10.794
MA0009.10.529
MA0014.10.736
MA0017.10.678
MA0018.20.00364
MA0019.10.674
MA0024.10.208
MA0025.10.128
MA0027.10.495
MA0028.10.0677
MA0029.10.954
MA0030.10.203
MA0031.10.0623
MA0035.20.729
MA0038.10.819
MA0039.20.0926
MA0040.10.947
MA0041.10.171
MA0042.10.406
MA0043.10.00313
MA0046.10.143
MA0047.20.503
MA0048.10.313
MA0050.12.16605e-8
MA0051.14.9194e-8
MA0052.10.0216
MA0055.10.0928
MA0057.10.13
MA0058.12.64064e-6
MA0059.16.53223e-8
MA0060.10.459
MA0061.10.276
MA0062.20.0852
MA0065.20.0189
MA0066.10.262
MA0067.10.969
MA0068.12.40584e-5
MA0069.10.719
MA0070.10.412
MA0071.10.0998
MA0072.10.194
MA0073.10.878
MA0074.10.708
MA0076.10.408
MA0077.10.513
MA0078.10.553
MA0079.20.0265
MA0080.25.67124e-6
MA0081.10.28
MA0083.10.0607
MA0084.10.709
MA0087.10.523
MA0088.10.684
MA0090.10.0384
MA0091.10.927
MA0092.10.379
MA0093.12.54179e-6
MA0099.23.25215e-10
MA0100.10.346
MA0101.10.105
MA0102.20.077
MA0103.10.826
MA0104.23.02731e-5
MA0105.10.206
MA0106.10.982
MA0107.10.0847
MA0108.20.0308
MA0111.10.613
MA0112.20.376
MA0113.10.0502
MA0114.10.0439
MA0115.10.00651
MA0116.10.109
MA0117.10.982
MA0119.10.61
MA0122.10.199
MA0124.10.35
MA0125.10.848
MA0131.10.803
MA0135.10.00882
MA0136.10.00827
MA0137.20.478
MA0138.20.317
MA0139.10.838
MA0140.10.595
MA0141.10.222
MA0142.10.76
MA0143.10.529
MA0144.10.614
MA0145.10.468
MA0146.10.0235
MA0147.11.95628e-6
MA0148.10.897
MA0149.10.00754
MA0150.13.06867e-6
MA0152.10.274
MA0153.10.42
MA0154.10.0937
MA0155.10.545
MA0156.10.726
MA0157.10.79
MA0159.10.0545
MA0160.10.383
MA0162.10.0963
MA0163.10.556
MA0164.10.286
MA0258.10.529
MA0259.10.0105



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: CNhs13075

Novel motifP-value
10.38
100.179
1000.0064
1010.745
1020.781
1030.444
1040.698
1050.00799
1060.388
1070.41
1080.982
1090.0485
110.738
1100.459
1110.133
1120.756
1130.0992
1140.0846
1150.0532
1160.19
1170.286
1180.0145
1190.936
120.0954
1200.104
1210.507
1220.723
1230.729
1240.484
1250.412
1260.342
1270.235
1280.00877
1290.637
130.00908
1300.636
1310.902
1320.583
1330.495
1340.0302
1350.0528
1360.0888
1370.992
1380.905
1390.185
140.23
1400.822
1410.761
1420.334
1430.322
1440.769
1450.0371
1460.25
1470.344
1480.168
1490.8
150.0309
1500.316
1510.601
1520.0645
1530.133
1540.324
1550.6
1560.547
1570.519
1580.46
1590.653
160.975
1600.797
1610.261
1620.779
1630.158
1640.208
1650.719
1660.898
1670.446
1680.0531
1690.0202
170.686
180.11
190.554
20.575
200.495
210.117
220.376
230.53
240.449
250.993
260.734
270.248
280.199
290.0136
30.617
300.429
310.525
320.293
330.0508
340.105
350.774
360.372
370.0202
380.872
390.917
40.136
400.048
410.157
420.762
430.348
440.0955
450.507
460.928
470.0831
480.278
490.406
50.481
500.776
510.388
520.41
530.302
540.393
550.381
560.421
570.325
580.313
590.132
60.756
600.837
610.0675
620.557
630.813
640.831
650.937
660.0392
670.666
680.896
690.731
70.969
700.663
710.00602
720.981
730.0123
740.352
750.532
760.446
770.562
780.862
790.865
80.0384
800.00991
810.41
820.846
830.748
840.0182
850.218
860.461
870.00831
880.971
890.374
90.0775
900.0617
910.576
920.821
930.154
940.443
950.048
960.903
970.887
980.584
990.335



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: CNhs13075


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)
0000213 (lining cell)
0000215 (barrier cell)
0000255 (eukaryotic cell)
0000077 (mesothelial cell)

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0102424 (mesothelioma 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
CL:0000222 (mesodermal cell)

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