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FF:11216-116B1: 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 16:33, 29 March 2012


Name:Urothelial cells, donor0
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
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog number4325
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-0.0791
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-0.138
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
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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: CNhs10843

Jaspar motifP-value
MA0002.20.317
MA0003.10.951
MA0004.10.126
MA0006.10.02
MA0007.10.959
MA0009.10.207
MA0014.10.184
MA0017.10.498
MA0018.20.00202
MA0019.10.499
MA0024.16.16908e-4
MA0025.10.113
MA0027.10.688
MA0028.10.0676
MA0029.10.156
MA0030.10.407
MA0031.10.85
MA0035.20.901
MA0038.10.562
MA0039.20.00302
MA0040.10.388
MA0041.10.675
MA0042.10.549
MA0043.10.00236
MA0046.10.45
MA0047.20.13
MA0048.10.724
MA0050.10.106
MA0051.10.307
MA0052.10.014
MA0055.10.0139
MA0057.10.0702
MA0058.10.0154
MA0059.10.322
MA0060.10.00615
MA0061.10.656
MA0062.21.81499e-4
MA0065.20.26
MA0066.10.116
MA0067.10.0173
MA0068.10.0247
MA0069.10.492
MA0070.10.77
MA0071.10.541
MA0072.10.892
MA0073.10.527
MA0074.10.613
MA0076.10.0101
MA0077.10.276
MA0078.10.555
MA0079.20.615
MA0080.20.00161
MA0081.10.00605
MA0083.10.96
MA0084.10.107
MA0087.10.782
MA0088.10.293
MA0090.15.25117e-5
MA0091.10.541
MA0092.10.569
MA0093.10.0708
MA0099.21.41735e-10
MA0100.10.269
MA0101.10.675
MA0102.20.102
MA0103.13.10592e-6
MA0104.20.0201
MA0105.10.472
MA0106.11.57338e-10
MA0107.10.955
MA0108.20.107
MA0111.10.755
MA0112.20.124
MA0113.10.88
MA0114.10.263
MA0115.10.674
MA0116.10.674
MA0117.10.487
MA0119.10.043
MA0122.10.991
MA0124.10.886
MA0125.10.0143
MA0131.10.393
MA0135.10.262
MA0136.10.0293
MA0137.20.0384
MA0138.20.208
MA0139.10.383
MA0140.10.658
MA0141.10.401
MA0142.10.347
MA0143.10.171
MA0144.10.78
MA0145.10.0286
MA0146.10.559
MA0147.10.0464
MA0148.10.0806
MA0149.10.0403
MA0150.10.416
MA0152.10.263
MA0153.10.63
MA0154.10.135
MA0155.10.681
MA0156.10.131
MA0157.10.451
MA0159.10.595
MA0160.10.698
MA0162.10.168
MA0163.10.842
MA0164.10.978
MA0258.10.811
MA0259.10.104



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: CNhs10843

Novel motifP-value
10.859
100.382
1000.563
1010.481
1020.382
1030.0634
1040.721
1050.46
1060.0323
1070.00757
1080.176
1090.0662
110.471
1100.464
1110.0255
1120.592
1130.0146
1140.135
1150.341
1160.756
1170.506
1180.592
1190.107
120.405
1200.00942
1210.587
1220.971
1230.64
1240.131
1250.334
1260.47
1270.168
1280.0839
1290.0621
130.672
1300.247
1310.715
1320.168
1330.0548
1340.112
1350.559
1360.64
1370.265
1380.818
1390.951
140.828
1400.419
1410.714
1420.638
1430.978
1440.646
1450.0972
1460.122
1470.265
1480.139
1490.555
150.6
1500.129
1510.276
1520.0126
1530.818
1540.646
1550.613
1560.589
1570.721
1580.663
1590.894
160.179
1600.702
1610.976
1620.894
1630.717
1640.764
1650.662
1660.688
1670.223
1680.146
1690.0976
170.0636
180.31
190.881
20.223
200.792
210.552
220.545
230.0131
240.0809
250.68
260.545
270.529
280.389
290.456
30.252
300.154
310.476
320.239
330.399
340.901
350.175
360.854
370.495
380.218
390.264
40.74
400.124
410.871
420.46
430.37
440.26
450.0948
460.511
470.594
480.26
490.587
50.641
500.332
510.429
520.184
530.657
540.419
550.321
560.219
570.521
580.823
590.249
60.229
600.255
610.953
620.981
630.124
640.937
650.212
660.504
670.513
680.265
690.26
70.71
700.00937
710.582
720.896
730.0202
740.171
750.181
760.671
770.046
780.0291
790.874
80.543
800.781
810.91
820.604
830.657
840.562
850.33
860.475
870.73
880.578
890.0306
90.846
900.683
910.472
920.228
930.958
940.522
950.336
960.956
970.921
980.826
990.286



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: CNhs10843


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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