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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005424
|DRA_sample_Accession=CAGE@SAMD00005424
|accession_numbers=CAGE;DRX007950;DRR008822;DRZ000247;DRZ001632
|accession_numbers=CAGE;DRX007950;DRR008822;DRZ000247;DRZ001632;DRZ011597;DRZ012982
|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%253aNo36.CNhs13074.10857-111G2.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/mesothelioma%2520cell%2520line%253aNo36.CNhs13074.10857-111G2.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/mesothelioma%2520cell%2520line%253aNo36.CNhs13074.10857-111G2.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/mesothelioma%2520cell%2520line%253aNo36.CNhs13074.10857-111G2.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/mesothelioma%2520cell%2520line%253aNo36.CNhs13074.10857-111G2.hg38.nobarcode.ctss.bed.gz
|id=FF:10857-111G2
|id=FF:10857-111G2
|is_a=EFO:0002091;;FF:0000210;;FF:0102424
|is_a=EFO:0002091;;FF:0000210;;FF:0102424
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|library_id=CNhs13074
|library_id=CNhs13074
|library_id_phase_based=2:CNhs13074
|library_id_phase_based=2:CNhs13074
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10857
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10857
|name=mesothelioma cell line:No36
|name=mesothelioma cell line:No36
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
|profile_rnaseq=
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|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=ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.41124518203;bHLH_family:1.17359555866;E2F1..5:1.12261672852;TP53:1.11089997679;ELK1,4_GABP{A,B1}:1.06983922591;NRF1:0.963425720593;ADNP_IRX_SIX_ZHX:0.957752380811;POU1F1:0.922325851028;IKZF1:0.853141394137;TEAD1:0.849570002378;HOXA9_MEIS1:0.801273248859;EVI1:0.70766206112;PPARG:0.702591784552;FOXL1:0.693141798396;ESRRA:0.684982304129;NFY{A,B,C}:0.659483034019;HES1:0.631689263662;SREBF1,2:0.625134565786;STAT5{A,B}:0.615359330211;ZNF143:0.608368136069;AIRE:0.595463659171;MYB:0.593990638214;NR5A1,2:0.580129485456;ALX4:0.547977088986;GFI1:0.546825087927;LHX3,4:0.54106198438;TLX1..3_NFIC{dimer}:0.499687921042;NKX2-1,4:0.430964430307;NFE2L2:0.430414439488;TEF:0.42188902276;NR3C1:0.421842266381;RBPJ:0.410268420318;NR6A1:0.406041363131;HOX{A5,B5}:0.369533290178;PAX1,9:0.352597696205;RXR{A,B,G}:0.330168926648;NKX6-1,2:0.327759030965;NFE2:0.324926910959;ZBTB16:0.317067498421;YY1:0.3022593442;UFEwm:0.294752909494;TFDP1:0.267166929182;NR1H4:0.255054442546;NKX2-3_NKX2-5:0.233693029775;GCM1,2:0.218422282805;OCT4_SOX2{dimer}:0.156721023404;FOXQ1:0.154077967222;NKX3-1:0.14196592854;SRF:0.136561964568;HNF4A_NR2F1,2:0.100580242084;LMO2:0.0796792660698;MYOD1:0.0679051991199;IKZF2:0.0497695867459;PAX8:0.0458788796962;NKX3-2:0.0419061825971;MYBL2:0.0352128707174;PBX1:0.0317643371733;PRRX1,2:0.0239242398501;EN1,2:0.0129254946158;NFE2L1:0.0101084167268;CDX1,2,4:0.00751080966292;ARID5B:0.00143661579569;FOS_FOS{B,L1}_JUN{B,D}:-0.00656102472246;ONECUT1,2:-0.0114077926115;GTF2A1,2:-0.0134934498626;LEF1_TCF7_TCF7L1,2:-0.0282763520391;ZNF423:-0.0347655526932;HOX{A6,A7,B6,B7}:-0.0354845536951;ZNF384:-0.0371810005249;POU3F1..4:-0.0392751687406;BACH2:-0.0559156291688;PAX2:-0.0571880553041;FOSL2:-0.0736205383836;PITX1..3:-0.076529621826;TOPORS:-0.0881549363785;CRX:-0.0992061921165;FOXA2:-0.103627517331;ZNF148:-0.118681570447;MEF2{A,B,C,D}:-0.122279588755;NKX2-2,8:-0.15033179405;ZIC1..3:-0.161898079303;TFCP2:-0.176293280136;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.178774620069;PAX5:-0.181401140846;SOX{8,9,10}:-0.185128679796;NFKB1_REL_RELA:-0.190478905719;HNF1A:-0.202158452594;HIC1:-0.21370086035;T:-0.215952662902;TBX4,5:-0.229318148979;HOX{A4,D4}:-0.230983677925;VSX1,2:-0.233782005962;RFX1:-0.268988447356;SNAI1..3:-0.269191025505;ELF1,2,4:-0.269209942455;CREB1:-0.272710354913;GFI1B:-0.275963895591;GATA4:-0.278011449628;IRF7:-0.281673268153;SOX17:-0.28211649543;GTF2I:-0.283472680185;ATF4:-0.288985223983;CEBPA,B_DDIT3:-0.293056021873;PAX4:-0.29697085213;STAT2,4,6:-0.304022023613;GATA6:-0.310236320765;MAFB:-0.312116793946;FOXD3:-0.317653917499;IRF1,2:-0.319625406304;POU5F1:-0.32410333889;SMAD1..7,9:-0.332044083956;HLF:-0.336053937824;ZEB1:-0.337364221069;POU2F1..3:-0.341356201016;REST:-0.349602458259;ATF5_CREB3:-0.356601116031;FOX{F1,F2,J1}:-0.363683951579;TFAP2B:-0.379495539573;BREu{core}:-0.388625717927;PDX1:-0.409997031541;FOXP1:-0.414185697487;POU6F1:-0.442056007305;GLI1..3:-0.449812253172;XCPE1{core}:-0.451050021488;TBP:-0.480570602547;MAZ:-0.49462668823;NFATC1..3:-0.495790010021;CUX2:-0.497551986024;ESR1:-0.512891760272;STAT1,3:-0.532683700921;FOXP3:-0.537700623094;AHR_ARNT_ARNT2:-0.537794355966;FOX{I1,J2}:-0.539862678823;KLF4:-0.543580676266;RXRA_VDR{dimer}:-0.547301572418;ZFP161:-0.554001003556;FOXM1:-0.559559074968;EP300:-0.572900220166;SOX2:-0.573274898632;HMGA1,2:-0.588575783811;NHLH1,2:-0.622880011591;CDC5L:-0.631373953794;RUNX1..3:-0.63371639162;NANOG{mouse}:-0.633781429988;SPI1:-0.634370496324;EBF1:-0.635972391477;TFAP2{A,C}:-0.641354821543;SPIB:-0.64674193986;SPZ1:-0.660757375027;ATF2:-0.66505767942;HSF1,2:-0.671660248552;RFX2..5_RFXANK_RFXAP:-0.676008087186;GZF1:-0.680631415703;HIF1A:-0.683931092441;RREB1:-0.708269952968;MTF1:-0.709967474905;SP1:-0.714979375865;FOXN1:-0.720426696508;NANOG:-0.723048654269;PAX6:-0.725397350992;EGR1..3:-0.726950422961;PATZ1:-0.755102265891;MTE{core}:-0.76070888621;HAND1,2:-0.760981992039;PRDM1:-0.761841917242;TGIF1:-0.769624988694;TAL1_TCF{3,4,12}:-0.780399293956;RORA:-0.78702569727;AR:-0.790103016303;ALX1:-0.790488638286;DMAP1_NCOR{1,2}_SMARC:-0.795509005542;ETS1,2:-0.795697090095;SOX5:-0.817573425367;ZBTB6:-0.876953693976;HMX1:-0.891530690648;MYFfamily:-0.894183927759;FOXO1,3,4:-0.904830001258;JUN:-0.905246176482;TFAP4:-0.92907016829;FOX{D1,D2}:-0.96310020261;TLX2:-0.965325419243;DBP:-0.974696282616;XBP1:-0.976206940761;NFIX:-0.976589085817;BPTF:-1.07118064029;HBP1_HMGB_SSRP1_UBTF:-1.08061316436;MED-1{core}:-1.08962118486;PAX3,7:-1.09519293104;NFIL3:-1.11144402503;ATF6:-1.12348342297;MZF1:-1.17783130567;ZNF238:-1.24746207305
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10857-111G2;search_select_hide=table117:FF:10857-111G2
}}
}}

Latest revision as of 16:24, 3 June 2020

Name:mesothelioma cell line:No36
Species:Human (Homo sapiens)
Library ID:CNhs13074
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 lineNo36
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  SAMD00005424
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13074 CAGE DRX007950 DRR008822
Accession ID Hg19

Library idBAMCTSS
CNhs13074 DRZ000247 DRZ001632
Accession ID Hg38

Library idBAMCTSS
CNhs13074 DRZ011597 DRZ012982
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-penis0.285
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-lymphoma0.501
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs13074

Jaspar motifP-value
MA0002.20.365
MA0003.10.272
MA0004.10.0022
MA0006.10.945
MA0007.10.292
MA0009.10.595
MA0014.10.497
MA0017.10.981
MA0018.20.00768
MA0019.10.911
MA0024.17.07753e-5
MA0025.10.693
MA0027.10.0724
MA0028.14.76176e-6
MA0029.10.187
MA0030.10.0717
MA0031.10.00277
MA0035.20.0653
MA0038.10.193
MA0039.20.0593
MA0040.10.404
MA0041.10.858
MA0042.10.178
MA0043.10.00853
MA0046.10.451
MA0047.20.308
MA0048.10.0585
MA0050.10.395
MA0051.10.398
MA0052.10.117
MA0055.14.42051e-5
MA0057.10.785
MA0058.16.55581e-5
MA0059.10.005
MA0060.12.47092e-6
MA0061.10.273
MA0062.26.01663e-4
MA0065.20.0272
MA0066.10.38
MA0067.10.811
MA0068.10.00485
MA0069.10.0887
MA0070.10.901
MA0071.10.172
MA0072.10.478
MA0073.10.954
MA0074.10.536
MA0076.13.91529e-5
MA0077.10.539
MA0078.10.785
MA0079.20.0535
MA0080.24.31208e-13
MA0081.10.183
MA0083.10.726
MA0084.10.835
MA0087.10.487
MA0088.12.7764e-4
MA0090.11.90369e-4
MA0091.10.206
MA0092.10.648
MA0093.11.78112e-4
MA0099.20.0832
MA0100.10.438
MA0101.10.999
MA0102.20.0236
MA0103.10.354
MA0104.20.00602
MA0105.10.674
MA0106.10.012
MA0107.10.357
MA0108.20.0593
MA0111.10.988
MA0112.20.00365
MA0113.10.579
MA0114.10.0681
MA0115.10.131
MA0116.10.364
MA0117.10.811
MA0119.10.135
MA0122.10.513
MA0124.10.384
MA0125.10.703
MA0131.10.657
MA0135.10.14
MA0136.18.09848e-8
MA0137.20.0281
MA0138.20.799
MA0139.10.399
MA0140.10.143
MA0141.10.0301
MA0142.10.199
MA0143.10.0956
MA0144.10.154
MA0145.10.773
MA0146.10.0606
MA0147.10.0061
MA0148.10.381
MA0149.10.0122
MA0150.14.64661e-4
MA0152.10.862
MA0153.10.859
MA0154.10.59
MA0155.10.469
MA0156.10.00197
MA0157.10.00397
MA0159.10.0878
MA0160.10.186
MA0162.10.0532
MA0163.10.193
MA0164.10.447
MA0258.10.0133
MA0259.10.121



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: CNhs13074

Novel motifP-value
10.0121
100.123
1000.00395
1010.857
1020.344
1030.134
1040.738
1050.428
1060.00646
1070.361
1080.843
1090.019
110.577
1100.174
1110.261
1120.941
1130.11
1140.778
1150.99
1160.538
1170.254
1180.0359
1190.185
120.874
1200.298
1210.833
1220.69
1230.328
1240.547
1250.803
1260.27
1270.868
1280.00394
1290.712
132.41803e-4
1300.636
1310.403
1320.368
1330.272
1340.636
1350.307
1360.00633
1370.111
1380.776
1390.978
140.463
1400.627
1410.497
1420.512
1430.224
1440.374
1450.114
1460.676
1470.477
1480.379
1490.955
150.21
1500.833
1510.808
1520.988
1530.61
1540.166
1550.711
1560.144
1570.384
1580.571
1590.805
160.781
1600.428
1610.189
1620.544
1630.753
1640.0318
1650.575
1660.48
1670.406
1680.132
1690.0102
170.707
180.391
190.75
20.252
200.327
210.181
220.546
230.0386
240.279
250.779
260.772
270.938
280.868
290.0361
30.744
300.281
310.886
320.524
330.226
340.586
350.596
360.046
370.0915
380.805
390.66
40.826
409.88734e-4
410.376
420.56
430.965
440.211
450.583
460.408
470.0797
480.183
490.899
50.64
500.571
510.813
520.102
530.651
540.797
550.119
560.704
570.0242
580.302
590.596
60.651
600.0989
610.0982
620.55
630.546
640.534
650.452
660.0172
670.678
680.284
690.37
70.266
700.528
710.0183
720.392
730.175
740.978
750.0089
760.827
770.566
780.00239
790.814
80.0994
800.196
810.379
820.103
830.74
840.316
850.647
860.787
870.00467
880.555
890.552
90.323
900.657
910.353
920.0265
930.722
940.292
950.0816
960.798
970.624
980.211
990.498



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: CNhs13074


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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