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FF:10845-111E8: 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-H28
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
age48
cell typemesothelial cell
cell lineNCI-H28
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-penis0.363
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-lymphoma0.443
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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 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: CNhs13061

Jaspar motifP-value
MA0002.20.0222
MA0003.10.047
MA0004.10.832
MA0006.10.605
MA0007.10.564
MA0009.10.965
MA0014.10.659
MA0017.10.037
MA0018.24.21886e-4
MA0019.10.744
MA0024.12.64967e-5
MA0025.10.43
MA0027.10.245
MA0028.12.27953e-11
MA0029.10.563
MA0030.10.306
MA0031.10.121
MA0035.20.172
MA0038.10.817
MA0039.20.118
MA0040.10.918
MA0041.10.0647
MA0042.10.0137
MA0043.10.42
MA0046.13.95335e-36
MA0047.20.253
MA0048.10.0183
MA0050.13.00954e-6
MA0051.10.00564
MA0052.15.44262e-4
MA0055.12.30107e-4
MA0057.10.681
MA0058.10.518
MA0059.10.158
MA0060.10.054
MA0061.10.375
MA0062.21.59011e-11
MA0065.20.0147
MA0066.10.893
MA0067.10.0419
MA0068.18.4021e-4
MA0069.10.781
MA0070.10.0853
MA0071.10.0151
MA0072.10.776
MA0073.10.871
MA0074.10.7
MA0076.19.44856e-13
MA0077.10.989
MA0078.10.621
MA0079.20.435
MA0080.29.67819e-9
MA0081.10.232
MA0083.11.13901e-4
MA0084.10.0549
MA0087.10.589
MA0088.10.0383
MA0090.10.812
MA0091.10.0757
MA0092.10.172
MA0093.10.676
MA0099.20.0877
MA0100.10.256
MA0101.10.66
MA0102.20.254
MA0103.10.0119
MA0104.20.0829
MA0105.10.898
MA0106.10.418
MA0107.10.15
MA0108.28.66783e-14
MA0111.10.905
MA0112.20.549
MA0113.10.601
MA0114.12.65405e-4
MA0115.10.00721
MA0116.10.574
MA0117.10.397
MA0119.10.377
MA0122.10.457
MA0124.10.359
MA0125.10.893
MA0131.10.355
MA0135.10.773
MA0136.15.51278e-5
MA0137.20.0884
MA0138.20.179
MA0139.10.184
MA0140.10.45
MA0141.16.10029e-5
MA0142.10.41
MA0143.10.826
MA0144.10.0682
MA0145.10.252
MA0146.10.934
MA0147.10.0306
MA0148.10.267
MA0149.10.184
MA0150.10.103
MA0152.10.496
MA0153.12.55133e-26
MA0154.10.328
MA0155.10.0992
MA0156.10.217
MA0157.10.0203
MA0159.10.0578
MA0160.10.195
MA0162.10.6
MA0163.10.0763
MA0164.10.807
MA0258.10.26
MA0259.10.0601



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: CNhs13061

Novel motifP-value
10.153
100.112
1000.076
1010.312
1020.286
1030.4
1040.651
1050.345
1060.026
1070.0537
1080.423
1090.255
110.826
1100.401
1110.306
1120.354
1130.0997
1140.522
1150.729
1160.505
1170.264
1180.0799
1190.905
120.65
1200.776
1210.824
1220.745
1230.278
1240.284
1250.726
1260.939
1270.205
1285.87253e-4
1290.331
131.03006e-4
1300.827
1310.777
1320.246
1330.032
1340.327
1350.369
1360.00678
1370.149
1380.344
1390.203
140.551
1400.155
1410.542
1420.674
1430.0442
1440.969
1450.346
1460.827
1470.848
1480.919
1490.692
150.629
1500.878
1510.588
1520.028
1530.511
1540.394
1550.78
1560.823
1570.619
1580.532
1590.845
160.914
1600.365
1610.91
1620.696
1630.815
1640.836
1650.732
1660.739
1670.2
1680.87
1690.79
170.278
180.401
190.383
20.0778
200.164
210.964
220.619
230.0628
240.159
250.77
260.309
270.614
280.542
290.189
30.845
300.199
310.595
320.0705
330.656
340.0856
350.648
360.463
370.916
380.858
390.39
40.918
400.612
410.0128
420.788
430.576
440.107
450.564
460.56
470.473
480.734
490.525
50.202
500.902
510.327
520.0779
530.242
540.722
550.805
560.878
570.359
580.657
590.725
60.851
600.159
610.194
620.465
630.927
640.847
650.312
660.443
670.865
680.635
690.254
70.755
700.784
710.169
720.54
730.235
740.31
750.237
760.75
770.466
780.0162
790.355
80.931
800.00414
810.438
820.275
830.197
840.229
850.257
860.655
870.217
880.523
890.645
90.0378
900.37
910.0857
920.0887
930.989
940.134
950.791
960.582
970.469
980.602
990.768



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: CNhs13061


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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