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FF:11600-120H7: 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 17:11, 29 March 2012


Name:Urothelial 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
tissuebladder
dev stageNA
sexNA
ageNA
cell typeurothelial cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:4521
catalog numberSC4325
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-0.362
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: CNhs12091

Jaspar motifP-value
MA0002.20.0572
MA0003.10.351
MA0004.10.812
MA0006.10.316
MA0007.10.271
MA0009.10.389
MA0014.10.829
MA0017.10.0384
MA0018.20.00357
MA0019.10.665
MA0024.10.00276
MA0025.10.0619
MA0027.10.871
MA0028.10.00639
MA0029.10.0903
MA0030.10.154
MA0031.10.0648
MA0035.20.0993
MA0038.10.207
MA0039.20.341
MA0040.10.389
MA0041.10.3
MA0042.10.671
MA0043.10.00188
MA0046.10.201
MA0047.20.43
MA0048.10.77
MA0050.10.0179
MA0051.10.0496
MA0052.10.677
MA0055.10.63
MA0057.10.0915
MA0058.10.569
MA0059.10.452
MA0060.10.0315
MA0061.10.18
MA0062.28.10521e-5
MA0065.20.00172
MA0066.10.0102
MA0067.10.109
MA0068.10.00269
MA0069.10.948
MA0070.10.938
MA0071.10.667
MA0072.10.888
MA0073.10.638
MA0074.10.675
MA0076.19.89388e-4
MA0077.10.714
MA0078.10.291
MA0079.20.799
MA0080.20.0206
MA0081.10.0509
MA0083.10.402
MA0084.10.00585
MA0087.10.442
MA0088.10.694
MA0090.10.0634
MA0091.10.358
MA0092.10.241
MA0093.10.683
MA0099.21.37955e-6
MA0100.10.181
MA0101.10.87
MA0102.20.0413
MA0103.19.97051e-4
MA0104.20.787
MA0105.10.027
MA0106.12.30621e-5
MA0107.10.58
MA0108.20.0672
MA0111.10.629
MA0112.21.92183e-4
MA0113.10.435
MA0114.10.0558
MA0115.10.793
MA0116.10.0182
MA0117.10.493
MA0119.10.0318
MA0122.10.58
MA0124.10.398
MA0125.10.336
MA0131.10.0747
MA0135.10.979
MA0136.10.00333
MA0137.20.0246
MA0138.20.0233
MA0139.10.302
MA0140.10.327
MA0141.10.13
MA0142.10.103
MA0143.10.287
MA0144.10.932
MA0145.10.082
MA0146.10.121
MA0147.10.987
MA0148.10.135
MA0149.10.0281
MA0150.10.384
MA0152.10.0976
MA0153.10.0229
MA0154.10.0251
MA0155.10.206
MA0156.10.0314
MA0157.10.278
MA0159.10.0485
MA0160.10.154
MA0162.10.0693
MA0163.10.0339
MA0164.10.704
MA0258.10.00462
MA0259.10.672



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: CNhs12091

Novel motifP-value
10.283
100.872
1000.744
1010.921
1020.591
1030.158
1040.399
1050.0732
1060.0109
1070.0187
1080.298
1090.0996
110.0807
1100.224
1110.154
1120.29
1130.464
1140.151
1150.719
1160.438
1170.476
1180.663
1190.0853
120.776
1200.0509
1210.409
1220.254
1230.317
1240.989
1250.408
1260.506
1270.0447
1280.0352
1290.0681
130.217
1300.869
1310.947
1320.195
1330.0264
1340.45
1350.0172
1360.692
1370.699
1380.439
1390.117
140.631
1400.0599
1410.396
1420.0379
1430.0612
1440.945
1450.119
1460.144
1470.143
1480.217
1490.145
150.223
1500.391
1510.179
1520.0661
1530.85
1540.834
1550.372
1560.0123
1570.538
1580.933
1590.671
160.172
1600.0555
1610.421
1620.291
1630.837
1640.822
1650.772
1660.863
1670.743
1680.443
1690.0298
170.0753
180.082
190.329
20.238
200.641
210.773
220.247
230.0592
240.291
250.979
260.186
270.177
280.924
290.502
30.258
300.315
310.36
320.293
330.542
340.457
350.698
360.238
370.301
380.235
390.274
40.351
400.0427
410.522
420.585
430.234
440.149
450.218
460.134
470.209
480.197
490.224
50.469
500.583
510.4
520.266
530.806
540.329
550.297
560.378
570.234
580.519
590.042
60.632
600.137
610.796
620.355
630.149
640.173
650.0449
660.731
670.36
680.706
690.142
70.499
700.00173
710.146
720.721
730.124
740.466
750.258
760.767
770.0359
780.123
790.118
80.0863
800.67
810.465
820.16
830.322
840.659
850.0567
860.833
870.55
880.204
890.018
90.528
900.917
910.0657
920.099
930.543
940.0823
950.245
960.481
970.91
980.152
990.115



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: CNhs12091


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)
0000244 (transitional epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000731 (urothelial cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000119 (cell layer)
0000365 (urothelium)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001008 (renal system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0005423 (developing anatomical structure)
0005910 (transitional epithelium)
0005911 (endo-epithelium)
0006554 (urinary system structure)

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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