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Revision as of 17:22, 27 November 2014


Name:mesothelioma cell line:ACC-MESO-4
Species:Human (Homo sapiens)
Library ID:CNhs11264
Sample type:cell lines
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuemesothelium
dev stageNA
sexmale
age59
cell typemesothelial cell
cell lineACC-MESO-4
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  SAMD00005932
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11264 CAGE DRX007937 DRR008809
Accession ID Hg19

Library idBAMCTSS
CNhs11264 DRZ000234 DRZ001619
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


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
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-lymphoma0.387
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
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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: CNhs11264

Jaspar motifP-value
MA0002.20.00834
MA0003.10.545
MA0004.10.771
MA0006.10.104
MA0007.10.113
MA0009.10.975
MA0014.10.472
MA0017.10.581
MA0018.20.625
MA0019.10.583
MA0024.15.00264e-4
MA0025.10.29
MA0027.10.536
MA0028.10.0844
MA0029.10.435
MA0030.10.32
MA0031.10.195
MA0035.27.76258e-4
MA0038.10.144
MA0039.20.957
MA0040.10.455
MA0041.10.336
MA0042.10.634
MA0043.10.674
MA0046.10.243
MA0047.20.0634
MA0048.10.0651
MA0050.13.34703e-7
MA0051.14.00778e-8
MA0052.10.0114
MA0055.10.0015
MA0057.10.614
MA0058.10.884
MA0059.10.661
MA0060.13.62764e-4
MA0061.10.926
MA0062.20.435
MA0065.20.729
MA0066.10.427
MA0067.10.556
MA0068.10.765
MA0069.10.62
MA0070.10.201
MA0071.10.589
MA0072.10.757
MA0073.10.827
MA0074.10.181
MA0076.10.18
MA0077.10.937
MA0078.10.419
MA0079.20.659
MA0080.22.59905e-8
MA0081.10.0197
MA0083.10.681
MA0084.10.552
MA0087.10.725
MA0088.10.217
MA0090.13.98869e-14
MA0091.10.102
MA0092.10.298
MA0093.10.92
MA0099.20.0316
MA0100.10.473
MA0101.10.177
MA0102.20.94
MA0103.10.00392
MA0104.20.202
MA0105.10.422
MA0106.10.0376
MA0107.10.159
MA0108.20.638
MA0111.10.814
MA0112.20.278
MA0113.10.94
MA0114.10.498
MA0115.10.896
MA0116.10.368
MA0117.10.804
MA0119.10.366
MA0122.10.636
MA0124.10.111
MA0125.10.557
MA0131.10.816
MA0135.10.00785
MA0136.18.76318e-6
MA0137.22.29314e-4
MA0138.20.0014
MA0139.10.738
MA0140.10.114
MA0141.10.0268
MA0142.10.0528
MA0143.10.012
MA0144.10.119
MA0145.10.397
MA0146.10.849
MA0147.10.269
MA0148.10.536
MA0149.10.994
MA0150.10.00851
MA0152.10.828
MA0153.10.44
MA0154.10.256
MA0155.10.435
MA0156.10.153
MA0157.10.155
MA0159.10.974
MA0160.10.301
MA0162.10.414
MA0163.10.0677
MA0164.10.36
MA0258.10.355
MA0259.10.0449



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: CNhs11264

Novel motifP-value
10.985
100.289
1000.364
1010.818
1020.498
1030.179
1040.878
1050.769
1060.73
1070.211
1080.864
1090.924
110.531
1100.18
1110.107
1120.263
1130.0809
1140.215
1150.741
1160.79
1170.991
1180.57
1190.761
120.583
1200.593
1210.566
1220.874
1230.139
1240.765
1250.154
1260.482
1270.404
1280.995
1290.543
130.0939
1300.368
1310.893
1320.544
1330.0107
1340.777
1350.00541
1360.112
1370.0249
1380.568
1390.00826
140.486
1400.0967
1410.504
1420.876
1430.0256
1440.714
1450.885
1460.746
1470.618
1480.964
1490.311
150.323
1500.0277
1510.594
1520.00732
1530.126
1540.762
1550.56
1560.521
1570.156
1580.251
1590.902
160.548
1600.806
1610.534
1620.773
1630.353
1640.47
1650.052
1660.454
1670.134
1680.0435
1690.257
170.956
180.268
190.0977
20.974
200.129
210.38
220.597
230.326
240.737
250.269
260.837
270.192
280.106
290.923
30.734
300.626
310.159
320.173
330.4
340.756
350.184
360.246
370.659
380.817
390.261
40.612
400.811
411.94563e-4
420.608
430.217
440.0258
450.459
460.266
470.973
480.928
490.25
50.153
500.792
510.722
520.419
530.579
540.934
550.5
560.605
570.25
580.0413
590.617
60.849
600.302
610.451
620.0455
630.941
640.928
650.211
660.021
670.727
680.433
690.792
70.495
700.9
710.484
720.896
730.19
740.592
750.522
760.882
770.0981
780.302
790.375
80.169
800.176
810.484
820.176
830.0585
840.355
850.282
860.643
870.0287
880.622
890.92
90.336
900.516
910.109
920.111
930.578
940.503
950.661
960.37
970.2
980.0705
990.497



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: CNhs11264


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)
0000151 (secretory cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000076 (squamous epithelial cell)
0000213 (lining cell)
0002078 (meso-epithelial cell)
0000150 (glandular epithelial cell)
0000163 (endocrine cell)
0000215 (barrier cell)
0000174 (steroid hormone secreting cell)
0000255 (eukaryotic cell)
0000077 (mesothelial cell)
0002097 (cortical cell of adrenal gland)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
305 (carcinoma)
170 (endocrine gland cancer)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002369 (adrenal gland)
0002100 (trunk)
0001851 (cortex)
0001235 (adrenal cortex)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0005172 (abdomen element)
0002530 (gland)
0006858 (adrenal/interrenal gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0000916 (abdomen)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0101120 (epithelial cell line sample)
0102219 (adrenocortical carcinoma cell)
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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