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FF:12156-128G5: 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 17:14, 29 March 2012


Name:Mesothelial Cells, donor2
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
sexfemale
age42 year old adult
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-penis-0.168
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-0.471
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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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: CNhs12197

Jaspar motifP-value
MA0002.20.182
MA0003.10.473
MA0004.10.415
MA0006.10.0678
MA0007.10.88
MA0009.10.36
MA0014.10.945
MA0017.10.7
MA0018.20.00364
MA0019.10.0388
MA0024.17.1048e-13
MA0025.10.907
MA0027.10.899
MA0028.10.289
MA0029.10.176
MA0030.10.504
MA0031.10.905
MA0035.20.00468
MA0038.10.0308
MA0039.20.489
MA0040.10.302
MA0041.10.253
MA0042.10.485
MA0043.10.218
MA0046.10.835
MA0047.20.888
MA0048.10.714
MA0050.10.0193
MA0051.10.955
MA0052.10.766
MA0055.10.82
MA0057.10.272
MA0058.10.431
MA0059.10.625
MA0060.10.00383
MA0061.10.872
MA0062.20.127
MA0065.20.633
MA0066.10.193
MA0067.10.0801
MA0068.10.658
MA0069.10.881
MA0070.10.784
MA0071.10.66
MA0072.10.784
MA0073.10.867
MA0074.10.507
MA0076.10.551
MA0077.10.464
MA0078.10.649
MA0079.20.273
MA0080.20.00216
MA0081.10.0639
MA0083.10.00195
MA0084.10.663
MA0087.10.682
MA0088.10.592
MA0090.14.74557e-5
MA0091.10.886
MA0092.10.0576
MA0093.10.506
MA0099.21.30331e-13
MA0100.10.0145
MA0101.10.939
MA0102.20.37
MA0103.10.963
MA0104.20.0363
MA0105.10.893
MA0106.10.0532
MA0107.10.458
MA0108.20.00199
MA0111.10.382
MA0112.20.202
MA0113.10.249
MA0114.10.24
MA0115.10.606
MA0116.10.354
MA0117.10.381
MA0119.10.702
MA0122.10.525
MA0124.10.0644
MA0125.10.365
MA0131.10.0386
MA0135.10.616
MA0136.10.0514
MA0137.20.277
MA0138.20.107
MA0139.10.702
MA0140.10.0942
MA0141.10.728
MA0142.10.956
MA0143.10.124
MA0144.10.585
MA0145.10.0461
MA0146.10.667
MA0147.10.0175
MA0148.10.265
MA0149.10.283
MA0150.10.00291
MA0152.10.691
MA0153.10.0602
MA0154.10.211
MA0155.10.014
MA0156.10.336
MA0157.10.701
MA0159.10.256
MA0160.10.281
MA0162.10.255
MA0163.10.566
MA0164.10.558
MA0258.10.995
MA0259.10.0382



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: CNhs12197

Novel motifP-value
10.69
100.00895
1000.371
1010.493
1020.794
1030.407
1040.577
1050.259
1060.0332
1070.0378
1080.749
1090.615
110.272
1100.656
1110.0218
1120.414
1130.302
1140.422
1150.313
1160.897
1170.136
1180.854
1190.379
120.995
1200.568
1210.568
1220.37
1231.62797e-5
1240.741
1250.0387
1260.941
1270.514
1280.0925
1290.0945
130.928
1300.511
1310.166
1320.664
1330.059
1340.254
1350.686
1360.339
1370.592
1380.791
1390.269
140.707
1400.86
1410.0915
1420.814
1430.3
1440.922
1450.402
1460.295
1470.869
1480.661
1490.0537
150.149
1500.329
1510.401
1520.0101
1530.929
1540.34
1550.0437
1560.504
1570.353
1580.381
1590.488
160.288
1600.865
1610.807
1620.85
1630.0262
1640.925
1650.269
1660.611
1670.442
1680.582
1690.0804
170.335
180.23
190.496
20.205
200.132
210.11
220.137
230.0383
240.359
250.316
260.354
270.116
280.5
290.911
30.969
300.135
310.26
320.348
330.984
340.388
350.787
360.463
370.162
380.762
390.463
40.649
400.944
410.441
420.825
430.242
440.792
450.028
460.625
470.838
480.654
490.356
50.66
500.995
510.637
520.144
530.632
540.315
550.0472
560.536
570.69
580.431
590.287
60.212
600.359
610.282
620.613
630.555
640.928
650.312
660.69
670.669
680.8
690.0941
70.784
700.074
710.513
720.405
730.0301
740.472
750.444
760.503
770.00753
780.894
790.458
80.441
800.204
810.63
820.261
830.235
840.991
850.215
860.937
870.119
880.788
890.0311
90.603
900.928
910.992
920.437
930.399
940.818
950.154
960.555
970.034
980.331
990.258



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: CNhs12197


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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