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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005101
|DRA_sample_Accession=CAGE@SAMD00005101
|accession_numbers=CAGE;DRX007943;DRR008815;DRZ000240;DRZ001625
|accession_numbers=CAGE;DRX007943;DRR008815;DRZ000240;DRZ001625;DRZ011590;DRZ012975
|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%253aMero-83.CNhs13070.10854-111F8.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/mesothelioma%2520cell%2520line%253aMero-83.CNhs13070.10854-111F8.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/mesothelioma%2520cell%2520line%253aMero-83.CNhs13070.10854-111F8.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/mesothelioma%2520cell%2520line%253aMero-83.CNhs13070.10854-111F8.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/mesothelioma%2520cell%2520line%253aMero-83.CNhs13070.10854-111F8.hg38.nobarcode.ctss.bed.gz
|id=FF:10854-111F8
|id=FF:10854-111F8
|is_a=EFO:0002091;;FF:0000210;;FF:0102424
|is_a=EFO:0002091;;FF:0000210;;FF:0102424
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|library_id=CNhs13070
|library_id=CNhs13070
|library_id_phase_based=2:CNhs13070
|library_id_phase_based=2:CNhs13070
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10854
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10854
|name=mesothelioma cell line:Mero-83
|name=mesothelioma cell line:Mero-83
|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:
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10854-111F8;search_select_hide=table117:FF:10854-111F8
}}
}}

Latest revision as of 15:10, 3 June 2020

Name:mesothelioma cell line:Mero-83
Species:Human (Homo sapiens)
Library ID:CNhs13070
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 lineMero-83
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  SAMD00005101
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13070 CAGE DRX007943 DRR008815
Accession ID Hg19

Library idBAMCTSS
CNhs13070 DRZ000240 DRZ001625
Accession ID Hg38

Library idBAMCTSS
CNhs13070 DRZ011590 DRZ012975
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
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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: CNhs13070

Jaspar motifP-value
MA0002.22.05832e-4
MA0003.10.0344
MA0004.10.728
MA0006.10.691
MA0007.10.309
MA0009.10.143
MA0014.10.0457
MA0017.10.063
MA0018.21.58566e-5
MA0019.10.728
MA0024.10.369
MA0025.10.771
MA0027.10.181
MA0028.10.00592
MA0029.10.48
MA0030.10.0761
MA0031.10.0432
MA0035.20.409
MA0038.10.115
MA0039.20.00688
MA0040.10.868
MA0041.10.877
MA0042.10.641
MA0043.13.72998e-5
MA0046.10.00575
MA0047.20.188
MA0048.16.17529e-4
MA0050.15.36797e-4
MA0051.10.696
MA0052.18.63181e-5
MA0055.10.0286
MA0057.10.914
MA0058.10.57
MA0059.10.0628
MA0060.10.24
MA0061.10.0101
MA0062.20.349
MA0065.20.235
MA0066.10.439
MA0067.10.00171
MA0068.10.0218
MA0069.10.655
MA0070.10.507
MA0071.10.956
MA0072.10.0856
MA0073.10.806
MA0074.10.891
MA0076.10.0204
MA0077.10.985
MA0078.10.11
MA0079.20.00806
MA0080.25.1406e-12
MA0081.10.0544
MA0083.10.0994
MA0084.10.237
MA0087.10.0468
MA0088.10.0934
MA0090.10.0024
MA0091.10.116
MA0092.10.836
MA0093.10.429
MA0099.20.0624
MA0100.10.14
MA0101.10.00601
MA0102.20.00283
MA0103.10.918
MA0104.20.106
MA0105.10.0453
MA0106.10.00386
MA0107.16.08837e-4
MA0108.20.0448
MA0111.10.4
MA0112.20.55
MA0113.10.218
MA0114.10.519
MA0115.10.57
MA0116.10.0291
MA0117.10.297
MA0119.10.552
MA0122.10.555
MA0124.10.0985
MA0125.10.553
MA0131.10.318
MA0135.10.412
MA0136.13.92682e-8
MA0137.20.057
MA0138.20.00278
MA0139.10.236
MA0140.10.401
MA0141.10.238
MA0142.10.06
MA0143.10.408
MA0144.10.0862
MA0145.10.128
MA0146.10.065
MA0147.10.02
MA0148.10.0304
MA0149.10.494
MA0150.10.0723
MA0152.10.7
MA0153.10.218
MA0154.10.0332
MA0155.10.362
MA0156.10.00388
MA0157.10.0165
MA0159.10.255
MA0160.10.13
MA0162.10.666
MA0163.10.207
MA0164.10.147
MA0258.10.295
MA0259.10.144



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: CNhs13070

Novel motifP-value
10.899
100.872
1000.093
1010.377
1020.748
1030.0866
1040.458
1050.00803
1060.0013
1070.104
1080.743
1090.455
110.392
1100.945
1110.776
1120.428
1130.0149
1140.609
1150.744
1160.904
1170.754
1180.0984
1190.648
120.1
1200.0463
1210.327
1220.5
1230.181
1240.0226
1250.929
1260.139
1270.677
1281.29755e-4
1290.255
130.95
1300.996
1310.531
1320.334
1331
1340.332
1350.0174
1360.308
1370.324
1380.469
1390.709
140.218
1400.997
1410.142
1420.164
1430.609
1440.656
1450.732
1460.493
1470.624
1480.145
1490.903
150.853
1500.712
1510.593
1520.0669
1530.652
1540.885
1550.15
1560.462
1570.719
1580.0418
1590.597
160.836
1600.94
1610.391
1620.198
1630.994
1640.0134
1650.573
1660.477
1670.188
1680.707
1690.254
170.894
180.756
190.506
20.294
200.304
210.00852
220.0702
230.281
240.177
250.538
260.427
270.741
280.977
290.411
30.827
300.46
310.914
320.365
330.893
340.143
350.968
360.67
370.861
380.894
390.659
40.684
400.764
410.0446
420.549
430.0682
440.796
450.242
460.872
470.943
480.663
490.0927
50.688
500.861
510.802
520.0345
530.375
540.725
550.786
560.81
570.296
580.275
590.133
60.968
600.0241
610.815
620.736
630.772
640.266
650.473
660.11
670.984
680.878
690.335
70.315
700.904
710.265
720.155
730.266
740.993
750.551
760.466
770.47
780.601
790.571
80.59
800.0664
810.729
820.752
830.642
840.105
850.0432
860.493
870.925
880.728
890.911
90.117
900.126
910.49
920.00888
930.692
940.65
950.659
960.854
970.63
980.62
990.14



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: CNhs13070


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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