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FF:11681-122H7: 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 17:12, 29 March 2012


Name:Urothelial 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
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 numberNA
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-penis0.103
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-0.333
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: CNhs12122

Jaspar motifP-value
MA0002.20.526
MA0003.10.39
MA0004.10.584
MA0006.10.138
MA0007.10.32
MA0009.10.345
MA0014.10.641
MA0017.10.0987
MA0018.20.008
MA0019.10.294
MA0024.10.00284
MA0025.10.559
MA0027.10.897
MA0028.10.00903
MA0029.10.256
MA0030.10.34
MA0031.10.0715
MA0035.20.336
MA0038.10.331
MA0039.20.0365
MA0040.10.314
MA0041.10.352
MA0042.10.664
MA0043.10.00798
MA0046.10.0845
MA0047.20.287
MA0048.10.92
MA0050.10.00186
MA0051.10.00791
MA0052.10.273
MA0055.10.328
MA0057.10.084
MA0058.10.286
MA0059.10.855
MA0060.10.11
MA0061.10.62
MA0062.22.48301e-5
MA0065.20.00833
MA0066.10.0209
MA0067.10.0461
MA0068.10.0147
MA0069.10.807
MA0070.10.893
MA0071.10.668
MA0072.10.619
MA0073.10.918
MA0074.10.45
MA0076.10.0011
MA0077.10.179
MA0078.10.504
MA0079.20.506
MA0080.22.93898e-4
MA0081.10.0107
MA0083.10.603
MA0084.10.173
MA0087.10.622
MA0088.10.721
MA0090.10.0139
MA0091.10.542
MA0092.10.265
MA0093.10.457
MA0099.23.53475e-9
MA0100.10.0417
MA0101.10.63
MA0102.20.0602
MA0103.16.56207e-5
MA0104.20.295
MA0105.10.47
MA0106.11.11382e-5
MA0107.10.955
MA0108.20.00364
MA0111.10.965
MA0112.20.00476
MA0113.10.464
MA0114.10.0712
MA0115.10.812
MA0116.10.21
MA0117.10.324
MA0119.10.081
MA0122.10.976
MA0124.10.457
MA0125.10.268
MA0131.10.157
MA0135.10.046
MA0136.17.74112e-5
MA0137.20.00281
MA0138.20.0469
MA0139.10.433
MA0140.10.829
MA0141.10.327
MA0142.10.219
MA0143.10.689
MA0144.10.556
MA0145.10.0411
MA0146.10.063
MA0147.10.403
MA0148.10.231
MA0149.10.0599
MA0150.10.629
MA0152.10.00288
MA0153.10.0802
MA0154.10.108
MA0155.10.198
MA0156.10.00137
MA0157.10.185
MA0159.10.224
MA0160.10.462
MA0162.10.0933
MA0163.10.431
MA0164.10.619
MA0258.10.031
MA0259.10.388



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: CNhs12122

Novel motifP-value
10.563
100.54
1000.708
1010.292
1020.323
1030.206
1040.264
1050.108
1060.0139
1070.00651
1080.187
1090.0478
110.134
1100.256
1110.189
1120.329
1130.243
1140.367
1150.1
1160.552
1170.716
1180.796
1190.0598
120.663
1200.0726
1210.547
1220.355
1230.962
1240.296
1250.451
1260.691
1270.1
1280.0299
1290.0317
130.296
1300.474
1310.873
1320.247
1330.0158
1340.339
1350.44
1360.913
1370.284
1380.8
1390.219
140.675
1400.444
1410.913
1420.0151
1430.256
1440.553
1450.124
1460.0438
1470.38
1480.839
1490.248
150.596
1500.243
1510.275
1520.034
1530.473
1540.713
1550.266
1560.0934
1570.336
1580.851
1590.853
160.152
1600.0917
1610.306
1620.104
1630.931
1640.851
1650.326
1660.861
1670.357
1680.469
1690.0449
170.103
180.215
190.348
20.139
200.709
210.919
220.207
230.0928
240.259
250.689
260.261
270.336
280.941
290.653
30.442
300.203
310.375
320.419
330.538
340.385
350.544
360.829
370.453
380.252
390.272
40.334
400.0114
410.816
420.763
430.293
440.217
450.167
460.31
470.376
480.23
490.446
50.79
500.45
510.449
520.2
530.962
540.356
550.315
560.286
570.328
580.729
590.0325
60.513
600.126
610.848
620.76
630.151
640.275
650.0622
660.82
670.732
680.665
690.0422
70.638
702.50053e-4
710.364
720.876
730.0572
740.0225
750.401
760.626
770.0157
780.157
790.161
80.147
800.824
810.774
820.191
830.71
840.855
850.134
860.934
870.359
880.223
890.0732
90.503
900.341
910.252
920.176
930.853
940.371
950.249
960.899
970.908
980.418
990.0375



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: CNhs12122


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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