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FF:10848-111F2: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100400,FF:0100453,FF:0102424
|fonse_cell_line=FF:0100400,FF:0100453,FF:0102424
|fonse_cell_line_closure=FF:0100400,FF:0100453,FF:0102424
|fonse_cell_line_closure=FF:0100400,FF:0100453,FF:0102424

Revision as of 17:28, 29 March 2012


Name:mesothelioma cell line:NCI-H2452
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuemesothelium
dev stageNA
sexmale
ageunknown
cell typemesothelial cell
cell lineNCI-H2452
companyATCC
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
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-penis0.146
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-lymphoma0.433
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 no result for this sample


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: CNhs13064

Jaspar motifP-value
MA0002.20.0106
MA0003.10.736
MA0004.10.202
MA0006.10.317
MA0007.10.485
MA0009.10.4
MA0014.10.331
MA0017.10.743
MA0018.22.81789e-5
MA0019.10.466
MA0024.14.6241e-5
MA0025.10.0541
MA0027.10.529
MA0028.16.83421e-5
MA0029.10.935
MA0030.10.00946
MA0031.17.3226e-4
MA0035.20.505
MA0038.10.364
MA0039.20.463
MA0040.10.413
MA0041.10.552
MA0042.10.182
MA0043.11.28896e-4
MA0046.10.0116
MA0047.20.00923
MA0048.10.0488
MA0050.11.07474e-20
MA0051.11.56099e-17
MA0052.10.00219
MA0055.18.17818e-6
MA0057.10.911
MA0058.10.0561
MA0059.10.146
MA0060.19.23243e-4
MA0061.10.706
MA0062.22.44826e-4
MA0065.20.0899
MA0066.10.975
MA0067.10.0281
MA0068.10.00884
MA0069.10.964
MA0070.10.796
MA0071.10.703
MA0072.10.0316
MA0073.10.912
MA0074.10.282
MA0076.18.75121e-5
MA0077.10.029
MA0078.10.145
MA0079.20.0729
MA0080.24.44031e-8
MA0081.10.179
MA0083.10.00217
MA0084.10.672
MA0087.10.318
MA0088.10.0182
MA0090.10.00413
MA0091.10.0973
MA0092.10.504
MA0093.10.12
MA0099.28.78258e-4
MA0100.10.807
MA0101.10.829
MA0102.20.0712
MA0103.10.0435
MA0104.20.0739
MA0105.10.153
MA0106.10.772
MA0107.10.752
MA0108.20.00318
MA0111.10.696
MA0112.20.441
MA0113.10.912
MA0114.10.0757
MA0115.10.00365
MA0116.10.251
MA0117.10.476
MA0119.10.072
MA0122.10.863
MA0124.10.271
MA0125.10.95
MA0131.10.804
MA0135.10.00456
MA0136.10.00153
MA0137.20.878
MA0138.20.151
MA0139.10.617
MA0140.10.389
MA0141.10.581
MA0142.10.805
MA0143.10.666
MA0144.10.749
MA0145.10.836
MA0146.10.0162
MA0147.10.0417
MA0148.10.0513
MA0149.10.174
MA0150.10.00472
MA0152.10.361
MA0153.10.285
MA0154.10.485
MA0155.10.428
MA0156.10.939
MA0157.10.00813
MA0159.10.064
MA0160.10.258
MA0162.10.201
MA0163.10.516
MA0164.10.265
MA0258.10.392
MA0259.10.5



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: CNhs13064

Novel motifP-value
10.00744
100.115
1000.192
1010.54
1020.793
1030.418
1040.467
1050.466
1060.0102
1070.147
1080.509
1090.137
110.507
1100.0328
1110.708
1120.266
1130.0302
1140.527
1150.745
1160.998
1170.0218
1180.102
1190.792
120.453
1200.453
1210.181
1220.75
1230.752
1240.121
1250.783
1260.714
1270.93
1280.00832
1290.34
136.04063e-4
1300.641
1310.606
1320.681
1330.157
1340.054
1350.0236
1360.0375
1370.394
1380.843
1390.0841
140.736
1400.93
1410.526
1420.109
1430.0558
1440.753
1450.646
1460.858
1470.136
1480.705
1490.296
150.179
1500.403
1510.925
1520.515
1530.223
1540.319
1550.234
1560.912
1570.708
1580.187
1590.685
160.921
1600.446
1610.387
1620.878
1630.581
1640.0138
1650.354
1660.669
1670.58
1680.0248
1690.055
170.585
180.361
190.762
20.898
200.364
210.366
220.339
230.0661
240.251
250.352
260.21
270.866
280.496
298.46049e-4
30.249
300.307
310.105
320.162
330.172
340.184
350.674
360.3
370.595
380.811
390.309
40.249
400.058
410.0272
420.469
430.803
440.85
450.513
460.884
470.125
480.0625
490.321
50.26
500.742
510.825
520.298
530.76
540.477
550.712
560.308
570.34
580.357
590.907
60.566
600.18
610.211
620.168
630.533
640.414
650.242
660.0324
670.446
680.531
690.423
70.827
700.718
710.00154
720.523
730.52
740.477
750.00441
760.314
770.206
780.275
790.449
80.421
800.0875
810.564
820.748
830.973
840.651
850.0407
860.301
870.0481
880.765
890.894
90.429
900.552
910.612
920.0413
930.873
940.393
950.541
960.982
970.893
980.999
990.0831



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: CNhs13064


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000066 (epithelial cell)
0000076 (squamous epithelial cell)
0000077 (mesothelial cell)
0000134 (mesenchymal cell)
0000213 (lining cell)
0000215 (barrier cell)
0000219 (motile cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002321 (embryonic cell)
0002371 (somatic cell)

DOID: Disease
0050687 (cell type cancer)
1115 (sarcoma)
14566 (disease of cellular proliferation)
162 (cancer)
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

FF: FANTOM5
NA

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
NA

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