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Revision as of 18:29, 27 November 2014


Name:mesothelioma cell line:Mero-48a
Species:Human (Homo sapiens)
Library ID:CNhs13068
Sample type:cell lines
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuemesothelium
dev stageNA
sexmale
ageunknown
cell typemesothelial cell
cell lineMero-48a
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  SAMD00005350
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13068 CAGE DRX007941 DRR008813
Accession ID Hg19

Library idBAMCTSS
CNhs13068 DRZ000238 DRZ001623
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-penis0.301
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-lymphoma0.16
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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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: CNhs13068

Jaspar motifP-value
MA0002.20.00829
MA0003.10.935
MA0004.10.662
MA0006.10.201
MA0007.10.0875
MA0009.10.587
MA0014.10.914
MA0017.10.967
MA0018.24.65276e-4
MA0019.10.858
MA0024.10.395
MA0025.10.00455
MA0027.10.172
MA0028.11.79114e-6
MA0029.10.706
MA0030.10.0138
MA0031.10.0116
MA0035.20.527
MA0038.10.603
MA0039.20.0366
MA0040.10.444
MA0041.10.529
MA0042.10.711
MA0043.13.98492e-7
MA0046.10.122
MA0047.20.00298
MA0048.10.449
MA0050.10.0404
MA0051.10.627
MA0052.17.77123e-5
MA0055.10.176
MA0057.10.0374
MA0058.10.459
MA0059.10.127
MA0060.10.845
MA0061.10.0151
MA0062.21.3248e-5
MA0065.20.77
MA0066.10.658
MA0067.10.00102
MA0068.12.20101e-4
MA0069.10.292
MA0070.10.698
MA0071.10.282
MA0072.10.106
MA0073.10.257
MA0074.10.956
MA0076.11.0573e-5
MA0077.10.418
MA0078.10.494
MA0079.20.318
MA0080.28.74823e-12
MA0081.10.0698
MA0083.10.189
MA0084.10.499
MA0087.10.549
MA0088.10.388
MA0090.12.16634e-5
MA0091.10.161
MA0092.10.89
MA0093.10.715
MA0099.20.00203
MA0100.10.707
MA0101.10.0324
MA0102.23.77894e-8
MA0103.10.264
MA0104.20.589
MA0105.10.0392
MA0106.10.0266
MA0107.10.00501
MA0108.20.0152
MA0111.10.77
MA0112.20.537
MA0113.10.603
MA0114.10.744
MA0115.10.0946
MA0116.10.103
MA0117.10.698
MA0119.10.757
MA0122.10.988
MA0124.10.0386
MA0125.10.372
MA0131.10.215
MA0135.10.0381
MA0136.14.78903e-9
MA0137.20.022
MA0138.20.0968
MA0139.10.616
MA0140.10.627
MA0141.10.257
MA0142.10.442
MA0143.10.283
MA0144.10.0556
MA0145.10.77
MA0146.10.718
MA0147.10.615
MA0148.10.00703
MA0149.10.436
MA0150.10.959
MA0152.10.985
MA0153.10.0924
MA0154.10.0383
MA0155.10.177
MA0156.10.171
MA0157.10.195
MA0159.10.366
MA0160.10.118
MA0162.10.139
MA0163.10.818
MA0164.10.509
MA0258.10.211
MA0259.10.329



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: CNhs13068

Novel motifP-value
10.924
100.474
1000.836
1010.194
1020.648
1030.447
1040.306
1050.0216
1060.0685
1070.746
1080.847
1090.744
110.823
1100.966
1110.567
1120.519
1130.0152
1140.331
1150.326
1160.548
1170.956
1180.0646
1190.62
120.694
1200.0481
1210.17
1220.648
1230.00645
1240.0401
1250.217
1260.55
1270.123
1280.00783
1290.372
130.577
1300.565
1310.149
1320.762
1330.908
1340.243
1350.0972
1360.252
1370.0484
1380.419
1390.184
140.439
1400.313
1410.0331
1420.511
1430.215
1440.854
1450.212
1460.778
1470.32
1480.6
1490.222
150.562
1500.171
1510.9
1520.0811
1530.768
1540.304
1550.0224
1560.442
1570.643
1580.013
1590.834
160.716
1600.787
1610.052
1620.433
1630.21
1640.0268
1650.398
1660.603
1670.783
1680.913
1690.362
170.355
180.458
190.807
20.767
200.307
210.0851
220.432
230.712
240.295
250.717
260.232
270.701
280.613
290.0215
30.595
300.684
310.568
320.0833
330.975
340.239
350.118
360.139
370.454
380.702
390.953
40.429
400.62
410.0749
420.858
430.0602
440.245
450.178
460.986
470.595
480.737
490.0565
50.205
500.781
510.673
520.347
530.236
540.599
550.153
560.874
570.378
580.338
590.794
60.642
600.151
610.43
620.741
630.408
640.546
650.278
660.251
670.933
680.539
690.282
70.302
700.832
710.778
720.597
730.0422
740.641
750.636
760.849
770.851
780.755
790.611
80.864
800.1
810.679
820.277
830.409
840.192
850.02
860.0352
870.189
880.601
890.836
90.146
900.295
910.748
920.452
930.415
940.773
950.674
960.977
970.996
980.0458
990.031



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: CNhs13068


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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