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FF:11247-116E5: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 16:34, 29 March 2012


Name:Mesothelial Cells, donor1
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 stage45 years old adult
sexfemale
age45
cell typemesothelial cell
cell lineNA
companyZenbio
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
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
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-lymphoma-0.411
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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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: CNhs10850

Jaspar motifP-value
MA0002.20.44
MA0003.10.62
MA0004.10.276
MA0006.10.0205
MA0007.10.632
MA0009.10.333
MA0014.10.516
MA0017.10.362
MA0018.23.14956e-6
MA0019.10.157
MA0024.12.67172e-14
MA0025.10.16
MA0027.10.573
MA0028.10.432
MA0029.10.0715
MA0030.10.698
MA0031.10.932
MA0035.20.028
MA0038.10.0824
MA0039.20.866
MA0040.10.244
MA0041.10.217
MA0042.10.304
MA0043.10.00531
MA0046.10.456
MA0047.20.179
MA0048.10.987
MA0050.10.928
MA0051.10.13
MA0052.10.00925
MA0055.10.834
MA0057.10.571
MA0058.10.399
MA0059.10.266
MA0060.18.56128e-8
MA0061.11
MA0062.20.0169
MA0065.20.435
MA0066.10.512
MA0067.10.0673
MA0068.10.6
MA0069.10.52
MA0070.10.693
MA0071.10.906
MA0072.10.72
MA0073.10.857
MA0074.10.849
MA0076.10.769
MA0077.10.483
MA0078.10.993
MA0079.20.322
MA0080.22.11909e-8
MA0081.15.36379e-4
MA0083.10.959
MA0084.10.632
MA0087.10.801
MA0088.10.329
MA0090.17.12042e-6
MA0091.10.41
MA0092.10.22
MA0093.10.414
MA0099.21.16287e-7
MA0100.10.00112
MA0101.10.795
MA0102.20.747
MA0103.10.616
MA0104.20.0167
MA0105.10.495
MA0106.10.254
MA0107.10.527
MA0108.20.569
MA0111.10.121
MA0112.20.875
MA0113.10.459
MA0114.10.811
MA0115.10.385
MA0116.10.0422
MA0117.10.157
MA0119.10.77
MA0122.10.424
MA0124.10.144
MA0125.10.877
MA0131.10.192
MA0135.10.0526
MA0136.11.65695e-8
MA0137.20.661
MA0138.20.106
MA0139.10.89
MA0140.10.4
MA0141.10.397
MA0142.10.456
MA0143.10.0851
MA0144.10.872
MA0145.10.0836
MA0146.10.888
MA0147.10.00292
MA0148.10.861
MA0149.10.698
MA0150.10.0851
MA0152.10.273
MA0153.10.328
MA0154.10.961
MA0155.10.131
MA0156.10.00342
MA0157.10.587
MA0159.10.177
MA0160.10.369
MA0162.10.197
MA0163.10.242
MA0164.10.213
MA0258.10.482
MA0259.10.0123



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: CNhs10850

Novel motifP-value
10.192
100.0061
1000.414
1010.768
1020.178
1030.405
1040.718
1050.602
1060.108
1070.064
1080.896
1090.291
110.902
1100.747
1110.00282
1120.336
1130.0655
1140.684
1150.667
1160.939
1170.145
1180.98
1190.517
120.643
1200.839
1210.953
1220.513
1230.00405
1240.73
1250.514
1260.472
1270.678
1280.0646
1290.196
130.729
1300.66
1310.02
1320.393
1330.377
1340.349
1350.325
1360.385
1370.0693
1380.967
1390.13
140.771
1400.574
1410.0329
1420.0842
1430.858
1440.539
1450.0642
1460.884
1470.149
1480.834
1490.159
150.64
1500.318
1510.503
1520.00793
1530.846
1540.676
1550.0484
1560.829
1570.748
1580.0562
1590.462
160.0516
1600.834
1610.574
1620.675
1630.0109
1640.574
1650.338
1660.932
1670.171
1680.553
1690.205
170.582
180.956
190.807
20.31
200.357
210.618
220.505
230.244
240.631
250.0484
260.445
270.398
280.5
290.856
30.767
300.112
310.618
320.104
330.663
340.736
350.575
360.041
370.256
380.643
390.323
40.116
400.336
410.563
420.712
430.822
440.722
450.171
460.385
470.624
480.804
490.243
50.781
500.94
510.869
520.336
530.138
540.346
550.0273
560.949
570.658
580.193
590.858
60.715
600.933
610.348
620.177
630.544
640.0796
650.953
660.318
670.812
680.87
690.553
70.144
700.0294
710.713
720.72
730.0681
740.118
750.896
760.7
770.0285
780.506
790.826
80.584
800.906
810.721
820.636
830.122
840.647
850.168
860.768
870.0527
880.597
890.0424
90.902
900.917
910.658
920.147
930.863
940.521
950.502
960.741
970.133
980.0235
990.153



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: CNhs10850


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)

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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