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FF:10853-111F7: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0102424
|fonse_cell_line=FF:0102424
|fonse_cell_line_closure=FF:0102424
|fonse_cell_line_closure=FF:0102424

Revision as of 17:28, 29 March 2012


Name:mesothelioma cell line:Mero-82
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 lineMero-82
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
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-penis0.315
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-lymphoma0.331
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs13069

Jaspar motifP-value
MA0002.20.00356
MA0003.10.145
MA0004.10.23
MA0006.10.795
MA0007.10.242
MA0009.10.277
MA0014.10.542
MA0017.10.393
MA0018.20.13
MA0019.10.218
MA0024.10.0297
MA0025.10.745
MA0027.10.989
MA0028.13.44168e-7
MA0029.10.333
MA0030.10.207
MA0031.10.996
MA0035.20.387
MA0038.10.35
MA0039.20.597
MA0040.10.115
MA0041.10.3
MA0042.10.227
MA0043.10.198
MA0046.10.0994
MA0047.20.0425
MA0048.16.41999e-4
MA0050.12.62327e-18
MA0051.14.57081e-16
MA0052.15.51366e-4
MA0055.18.09558e-4
MA0057.10.699
MA0058.10.329
MA0059.10.00578
MA0060.12.29672e-12
MA0061.10.587
MA0062.22.26742e-5
MA0065.20.257
MA0066.10.614
MA0067.10.0638
MA0068.10.0453
MA0069.10.828
MA0070.10.11
MA0071.10.523
MA0072.10.622
MA0073.10.491
MA0074.10.421
MA0076.11.12357e-6
MA0077.10.675
MA0078.10.64
MA0079.20.385
MA0080.24.15633e-9
MA0081.10.0708
MA0083.10.924
MA0084.10.3
MA0087.10.0512
MA0088.10.0117
MA0090.10.0876
MA0091.10.166
MA0092.10.154
MA0093.10.209
MA0099.20.00517
MA0100.10.715
MA0101.10.648
MA0102.20.0324
MA0103.10.313
MA0104.20.0801
MA0105.10.617
MA0106.10.865
MA0107.10.765
MA0108.20.225
MA0111.10.981
MA0112.20.707
MA0113.10.256
MA0114.10.783
MA0115.10.0497
MA0116.10.877
MA0117.10.369
MA0119.10.859
MA0122.10.264
MA0124.10.707
MA0125.10.789
MA0131.10.215
MA0135.10.00692
MA0136.18.04602e-5
MA0137.20.16
MA0138.20.0915
MA0139.10.677
MA0140.10.0373
MA0141.10.408
MA0142.10.144
MA0143.10.319
MA0144.10.269
MA0145.10.251
MA0146.10.042
MA0147.10.0282
MA0148.10.16
MA0149.10.114
MA0150.10.0212
MA0152.10.732
MA0153.10.0785
MA0154.10.0423
MA0155.10.387
MA0156.10.653
MA0157.10.166
MA0159.10.728
MA0160.10.281
MA0162.10.463
MA0163.10.133
MA0164.10.0777
MA0258.10.48
MA0259.10.118



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: CNhs13069

Novel motifP-value
10.445
100.161
1000.0817
1010.651
1020.322
1030.646
1040.677
1050.0323
1060.557
1070.903
1080.957
1090.209
110.789
1100.223
1110.321
1120.0421
1130.0459
1140.834
1150.614
1160.582
1170.0421
1180.155
1190.726
120.0782
1200.344
1210.894
1220.961
1230.472
1240.63
1250.906
1260.558
1270.871
1280.114
1290.915
130.0217
1300.72
1310.567
1320.656
1330.5
1340.174
1350.0311
1360.045
1370.241
1380.214
1390.108
140.2
1400.849
1410.59
1420.369
1430.943
1440.8
1450.668
1460.384
1470.403
1480.462
1490.123
150.646
1500.0968
1510.395
1520.0188
1530.907
1540.371
1550.87
1560.81
1570.28
1580.396
1590.746
160.868
1600.834
1610.686
1620.247
1630.391
1640.892
1650.43
1660.191
1670.069
1680.603
1690.408
170.931
180.288
190.218
20.148
200.177
210.0651
220.763
230.0203
240.75
250.577
260.609
270.743
280.7
290.044
30.509
300.628
310.383
320.978
330.589
340.113
350.813
360.511
370.0582
380.955
390.992
40.11
400.552
410.0331
420.734
430.735
440.377
450.283
460.997
470.577
480.55
490.99
50.123
500.331
510.784
520.262
530.282
540.955
550.886
560.949
570.846
580.536
590.448
60.42
600.309
610.0292
620.403
630.947
640.981
650.609
663.20764e-9
670.886
680.774
690.346
70.427
700.561
710.242
720.866
730.0293
740.228
750.00811
760.101
770.189
780.576
790.977
80.861
800.0283
810.615
820.223
830.642
840.328
850.214
860.86
870.0818
880.852
890.193
90.165
900.2
910.171
920.143
930.336
940.618
950.04
960.317
970.705
980.413
990.327



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: CNhs13069


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)
0000066 (epithelial cell)
0000076 (squamous epithelial cell)
0000077 (mesothelial cell)
0000213 (lining cell)
0000215 (barrier cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002321 (embryonic cell)

DOID: Disease
4 (disease)
7 (disease of anatomical entity)

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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