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FF:11520-119H8: 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 16:45, 29 March 2012


Name:Urothelial 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
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:4494
catalog numberSC4325
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-0.0861
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-0.315
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: CNhs11334

Jaspar motifP-value
MA0002.20.291
MA0003.10.331
MA0004.10.602
MA0006.10.168
MA0007.10.335
MA0009.10.231
MA0014.10.784
MA0017.10.0745
MA0018.20.00767
MA0019.10.39
MA0024.18.56035e-4
MA0025.10.151
MA0027.10.739
MA0028.10.0726
MA0029.10.123
MA0030.10.302
MA0031.10.0622
MA0035.20.137
MA0038.10.55
MA0039.20.0822
MA0040.10.593
MA0041.10.389
MA0042.10.783
MA0043.10.0076
MA0046.10.0245
MA0047.20.441
MA0048.10.949
MA0050.10.0235
MA0051.10.131
MA0052.10.853
MA0055.10.188
MA0057.10.0542
MA0058.10.331
MA0059.10.709
MA0060.10.115
MA0061.10.323
MA0062.20.00265
MA0065.20.00724
MA0066.10.0972
MA0067.10.0319
MA0068.10.0241
MA0069.10.61
MA0070.10.662
MA0071.10.449
MA0072.10.818
MA0073.10.96
MA0074.10.69
MA0076.10.01
MA0077.10.35
MA0078.10.352
MA0079.20.694
MA0080.20.0446
MA0081.10.081
MA0083.10.154
MA0084.10.0364
MA0087.10.729
MA0088.10.813
MA0090.10.00655
MA0091.10.72
MA0092.10.23
MA0093.10.477
MA0099.21.35115e-11
MA0100.10.149
MA0101.10.882
MA0102.20.00517
MA0103.13.43029e-4
MA0104.20.495
MA0105.10.228
MA0106.16.70879e-6
MA0107.10.631
MA0108.20.00214
MA0111.10.95
MA0112.20.00286
MA0113.10.601
MA0114.10.0337
MA0115.10.571
MA0116.10.142
MA0117.10.351
MA0119.10.0578
MA0122.10.837
MA0124.10.882
MA0125.10.0868
MA0131.10.215
MA0135.10.216
MA0136.10.0884
MA0137.20.0104
MA0138.20.0916
MA0139.10.36
MA0140.10.533
MA0141.10.332
MA0142.10.281
MA0143.10.232
MA0144.10.902
MA0145.10.0343
MA0146.10.117
MA0147.10.694
MA0148.10.0952
MA0149.10.0369
MA0150.10.201
MA0152.10.0179
MA0153.10.0156
MA0154.10.0711
MA0155.10.171
MA0156.10.119
MA0157.10.201
MA0159.10.175
MA0160.10.248
MA0162.10.0657
MA0163.10.197
MA0164.10.71
MA0258.10.0495
MA0259.10.581



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: CNhs11334

Novel motifP-value
10.588
100.695
1000.911
1010.618
1020.427
1030.173
1040.409
1050.0342
1060.0106
1070.0132
1080.323
1090.0421
110.122
1100.222
1110.104
1120.296
1130.171
1140.215
1150.775
1160.573
1170.494
1180.667
1190.127
120.653
1200.201
1210.592
1220.399
1230.858
1240.857
1250.318
1260.529
1270.0342
1280.0326
1290.0414
130.364
1300.591
1310.875
1320.23
1330.00787
1340.786
1350.245
1360.906
1370.369
1380.967
1390.441
140.609
1400.464
1410.703
1420.0811
1430.287
1440.858
1450.116
1460.0599
1470.224
1480.968
1490.224
150.455
1500.26
1510.3
1520.0402
1530.638
1540.437
1550.61
1560.0242
1570.466
1580.683
1590.727
160.212
1600.091
1610.46
1620.33
1630.857
1640.971
1650.625
1660.769
1670.229
1680.482
1690.0386
170.094
180.116
190.338
20.174
200.726
210.834
220.218
230.0504
240.24
250.856
260.334
270.259
280.915
290.832
30.333
300.213
310.375
320.575
330.451
340.376
350.626
360.622
370.335
380.218
390.191
40.195
400.014
410.486
420.465
430.249
440.606
450.16
460.242
470.297
480.171
490.319
50.519
500.417
510.339
520.255
530.976
540.355
550.189
560.268
570.354
580.613
590.0504
60.474
600.118
610.747
620.576
630.115
640.285
650.0561
660.608
670.562
680.996
690.0894
70.513
705.38074e-4
710.281
720.964
730.0479
740.431
750.33
760.683
770.021
780.187
790.736
80.151
800.668
810.807
820.215
830.578
840.409
850.169
860.895
870.442
880.235
890.0174
90.516
900.316
910.0969
920.31
930.907
940.205
950.256
960.705
970.786
980.376
990.107



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: CNhs11334


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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