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FF:10850-111F4: 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-25
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
age60
cell typemesothelial cell
cell lineMero-25
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-penis0.155
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-lymphoma0.169
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: CNhs13066

Jaspar motifP-value
MA0002.20.069
MA0003.10.941
MA0004.10.00949
MA0006.10.763
MA0007.10.934
MA0009.10.357
MA0014.10.248
MA0017.10.223
MA0018.20.0124
MA0019.10.531
MA0024.10.0197
MA0025.10.384
MA0027.10.574
MA0028.11.55755e-14
MA0029.10.82
MA0030.10.473
MA0031.10.00487
MA0035.20.167
MA0038.10.455
MA0039.20.174
MA0040.10.484
MA0041.10.61
MA0042.10.595
MA0043.10.00397
MA0046.10.316
MA0047.20.0536
MA0048.10.00301
MA0050.15.67887e-4
MA0051.11.91751e-7
MA0052.10.0954
MA0055.10.00235
MA0057.10.635
MA0058.10.00811
MA0059.12.42819e-4
MA0060.10.0157
MA0061.10.813
MA0062.22.16146e-16
MA0065.20.0331
MA0066.10.413
MA0067.10.53
MA0068.10.417
MA0069.10.914
MA0070.10.0485
MA0071.10.751
MA0072.10.498
MA0073.10.847
MA0074.10.663
MA0076.11.24193e-12
MA0077.10.337
MA0078.10.617
MA0079.20.312
MA0080.21.7572e-7
MA0081.10.901
MA0083.10.997
MA0084.10.416
MA0087.10.272
MA0088.10.0121
MA0090.10.253
MA0091.10.113
MA0092.10.871
MA0093.10.00534
MA0099.20.0653
MA0100.10.368
MA0101.10.273
MA0102.20.72
MA0103.10.115
MA0104.20.00409
MA0105.10.485
MA0106.10.72
MA0107.10.37
MA0108.20.319
MA0111.10.353
MA0112.20.316
MA0113.10.179
MA0114.10.551
MA0115.10.596
MA0116.10.579
MA0117.10.581
MA0119.10.0905
MA0122.10.439
MA0124.10.0306
MA0125.10.344
MA0131.10.284
MA0135.10.837
MA0136.10.0297
MA0137.20.751
MA0138.20.381
MA0139.10.684
MA0140.10.286
MA0141.10.467
MA0142.10.238
MA0143.10.0496
MA0144.10.0678
MA0145.10.611
MA0146.10.0412
MA0147.10.00102
MA0148.10.212
MA0149.10.158
MA0150.10.111
MA0152.10.608
MA0153.10.738
MA0154.10.162
MA0155.10.102
MA0156.10.0499
MA0157.10.0137
MA0159.10.067
MA0160.10.709
MA0162.10.0877
MA0163.10.875
MA0164.10.159
MA0258.10.421
MA0259.10.0525



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: CNhs13066

Novel motifP-value
10.566
100.883
1000.047
1010.279
1020.82
1030.989
1040.725
1050.122
1060.259
1070.493
1080.6
1090.15
110.715
1100.403
1110.988
1120.397
1130.00315
1140.213
1150.676
1160.908
1170.196
1180.328
1190.699
120.631
1200.0311
1210.797
1220.199
1230.0605
1240.0193
1250.599
1260.874
1270.468
1280.00105
1290.137
130.00211
1300.909
1310.816
1320.768
1330.677
1340.161
1350.00415
1360.00709
1370.0202
1380.317
1390.0682
140.249
1400.302
1410.434
1420.793
1430.149
1440.685
1450.0776
1460.459
1470.929
1480.0433
1490.299
150.726
1500.306
1510.213
1520.00617
1530.0798
1540.0835
1550.945
1560.631
1570.588
1580.296
1590.992
160.93
1600.541
1610.319
1620.8
1630.934
1640.0275
1650.15
1660.302
1670.488
1680.092
1690.458
170.695
180.25
190.379
20.319
200.117
210.826
220.619
230.0213
240.799
250.424
260.645
270.287
280.809
290.123
30.309
300.485
310.972
320.153
330.159
340.344
350.735
360.515
370.125
380.601
390.661
40.861
400.0149
410.0416
420.762
430.261
440.704
450.537
460.751
470.581
480.629
490.233
50.0272
500.782
510.643
520.129
530.111
540.336
550.0397
560.914
570.765
580.104
590.778
60.305
600.13
610.388
620.0814
630.632
640.914
650.172
660.0884
670.896
680.446
690.945
70.575
700.338
710.83
720.41
730.0101
740.036
750.0511
760.393
770.76
780.717
790.44
80.833
800.0715
810.416
820.115
830.366
840.0899
850.0672
860.928
870.0269
880.85
890.794
90.189
900.00206
910.0175
920.0143
930.559
940.969
950.0417
960.215
970.782
980.374
990.901



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: CNhs13066


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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