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FF:11402-118D7: 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 17:06, 29 March 2012


Name:Mesothelial Cells, donor3
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 stage24 years old adult
sexfemale
age24
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-penis0.336
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-0.147
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs12012

Jaspar motifP-value
MA0002.20.00773
MA0003.10.937
MA0004.10.0185
MA0006.10.0164
MA0007.10.869
MA0009.10.464
MA0014.10.539
MA0017.10.443
MA0018.21.38964e-4
MA0019.10.124
MA0024.13.80044e-5
MA0025.10.157
MA0027.10.576
MA0028.10.0265
MA0029.10.315
MA0030.10.213
MA0031.10.0628
MA0035.20.0852
MA0038.10.00423
MA0039.20.371
MA0040.10.771
MA0041.10.654
MA0042.10.885
MA0043.10.00202
MA0046.10.299
MA0047.20.0128
MA0048.10.517
MA0050.10.0485
MA0051.10.176
MA0052.19.3182e-4
MA0055.10.616
MA0057.10.556
MA0058.10.00248
MA0059.10.0549
MA0060.12.10689e-6
MA0061.10.243
MA0062.22.07675e-5
MA0065.20.181
MA0066.10.762
MA0067.10.00436
MA0068.10.692
MA0069.10.608
MA0070.10.554
MA0071.10.274
MA0072.10.0459
MA0073.10.837
MA0074.10.701
MA0076.10.0114
MA0077.10.304
MA0078.10.767
MA0079.20.094
MA0080.25.23532e-10
MA0081.10.00458
MA0083.10.0817
MA0084.10.175
MA0087.10.877
MA0088.10.135
MA0090.11.63451e-5
MA0091.10.2
MA0092.10.674
MA0093.10.0257
MA0099.20.611
MA0100.14.25854e-4
MA0101.10.115
MA0102.20.422
MA0103.10.569
MA0104.20.00114
MA0105.10.0408
MA0106.10.276
MA0107.10.525
MA0108.20.337
MA0111.10.249
MA0112.20.132
MA0113.10.77
MA0114.10.33
MA0115.10.902
MA0116.10.00847
MA0117.10.264
MA0119.10.692
MA0122.10.236
MA0124.10.00881
MA0125.10.733
MA0131.10.0772
MA0135.10.0616
MA0136.11.86886e-12
MA0137.20.431
MA0138.20.0676
MA0139.10.392
MA0140.10.844
MA0141.10.0995
MA0142.10.182
MA0143.10.582
MA0144.10.396
MA0145.10.113
MA0146.10.853
MA0147.15.91101e-4
MA0148.10.19
MA0149.10.806
MA0150.10.473
MA0152.10.788
MA0153.10.653
MA0154.10.227
MA0155.10.156
MA0156.15.62263e-7
MA0157.10.108
MA0159.10.975
MA0160.10.0246
MA0162.10.83
MA0163.10.00132
MA0164.10.219
MA0258.10.166
MA0259.10.00193



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: CNhs12012

Novel motifP-value
10.0977
100.0168
1000.324
1010.933
1020.535
1030.915
1040.289
1050.251
1060.0951
1070.0175
1080.868
1090.179
110.577
1100.621
1110.00575
1120.878
1130.043
1140.603
1150.048
1160.399
1170.109
1180.656
1190.721
120.232
1200.681
1210.991
1220.496
1230.00182
1240.235
1250.194
1260.207
1270.724
1280.0614
1290.616
130.195
1300.486
1310.126
1320.0353
1330.204
1340.937
1350.0382
1360.365
1370.498
1380.998
1390.979
140.991
1400.744
1410.0283
1420.168
1430.272
1440.445
1450.445
1460.228
1470.36
1480.742
1490.494
150.601
1500.179
1510.867
1520.00364
1530.46
1540.685
1550.218
1560.709
1570.695
1580.0183
1590.778
160.367
1600.809
1610.963
1620.345
1630.0153
1640.344
1650.233
1660.708
1670.263
1680.604
1690.53
170.904
180.678
190.695
20.256
200.707
210.749
220.864
230.588
240.928
250.0342
260.539
270.833
280.599
290.515
30.47
300.353
310.95
320.211
330.335
340.844
350.107
360.00476
370.69
380.597
390.319
40.259
400.0432
410.0558
420.257
430.43
440.313
450.47
460.429
470.452
480.611
490.0706
50.0916
500.85
510.829
520.184
530.219
540.415
550.231
560.918
570.802
580.13
590.529
60.844
600.715
610.216
620.126
630.446
640.154
650.976
660.357
670.852
680.753
690.174
70.0349
700.308
710.0531
720.408
730.119
740.88
750.329
760.703
770.0264
780.652
790.0672
80.821
800.104
810.994
820.741
830.664
840.599
850.352
860.613
870.116
880.539
890.247
90.647
900.44
910.503
920.982
930.817
940.247
950.23
960.724
970.551
980.0764
990.0417



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: CNhs12012


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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