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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0000489,UBERON:0000916,UBERON:0000922,UBERON:0001008,UBERON:0001062,UBERON:0002100,UBERON:0002113,UBERON:0002417,UBERON:0003103,UBERON:0005095,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005423,UBERON:0006554,UBERON:0007687
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0000489,UBERON:0000916,UBERON:0000922,UBERON:0001008,UBERON:0001062,UBERON:0002100,UBERON:0002113,UBERON:0002417,UBERON:0003103,UBERON:0005095,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005423,UBERON:0006554,UBERON:0007687
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100067,FF:0101120
|fonse_cell_line=FF:0100067,FF:0101120
|fonse_cell_line_closure=FF:0100067,FF:0101120
|fonse_cell_line_closure=FF:0100067,FF:0101120

Revision as of 16:31, 29 March 2012


Name:renal cell carcinoma cell line:OS-RC-2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuekidney
dev stageNA
sexmale
ageunknown
cell typeunclassifiable
cell lineOS-RC-2
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
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-penis0.0347
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-lymphoma0.396
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
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: CNhs10729

Jaspar motifP-value
MA0002.20.509
MA0003.10.669
MA0004.10.0402
MA0006.10.0232
MA0007.10.431
MA0009.10.926
MA0014.10.151
MA0017.10.0118
MA0018.22.35942e-5
MA0019.10.227
MA0024.10.00124
MA0025.10.253
MA0027.10.452
MA0028.19.47244e-4
MA0029.10.181
MA0030.10.175
MA0031.10.421
MA0035.20.762
MA0038.16.55207e-5
MA0039.28.86766e-4
MA0040.10.951
MA0041.10.2
MA0042.10.727
MA0043.10.0256
MA0046.12.01922e-53
MA0047.20.796
MA0048.10.616
MA0050.10.0102
MA0051.11.7202e-4
MA0052.10.107
MA0055.10.163
MA0057.10.889
MA0058.10.072
MA0059.10.284
MA0060.14.68693e-10
MA0061.10.133
MA0062.20.0158
MA0065.20.562
MA0066.10.574
MA0067.10.00338
MA0068.10.00339
MA0069.10.901
MA0070.10.25
MA0071.10.376
MA0072.10.278
MA0073.10.532
MA0074.10.608
MA0076.10.00648
MA0077.10.598
MA0078.10.16
MA0079.20.122
MA0080.23.60057e-4
MA0081.10.0533
MA0083.10.568
MA0084.10.0635
MA0087.10.622
MA0088.10.0387
MA0090.16.91976e-6
MA0091.10.0319
MA0092.10.992
MA0093.10.0968
MA0099.22.26582e-14
MA0100.10.745
MA0101.10.0869
MA0102.20.272
MA0103.10.101
MA0104.20.191
MA0105.10.834
MA0106.14.88133e-5
MA0107.10.115
MA0108.20.0832
MA0111.10.396
MA0112.20.31
MA0113.10.204
MA0114.10.00605
MA0115.10.529
MA0116.10.405
MA0117.10.58
MA0119.10.0446
MA0122.10.659
MA0124.10.778
MA0125.10.843
MA0131.10.496
MA0135.10.69
MA0136.10.0332
MA0137.20.257
MA0138.20.0335
MA0139.13.39508e-4
MA0140.10.496
MA0141.10.357
MA0142.10.164
MA0143.10.328
MA0144.10.0723
MA0145.10.00909
MA0146.10.399
MA0147.10.126
MA0148.10.109
MA0149.10.981
MA0150.10.0163
MA0152.10.963
MA0153.12.77106e-42
MA0154.10.46
MA0155.10.309
MA0156.10.343
MA0157.10.548
MA0159.10.977
MA0160.10.256
MA0162.10.479
MA0163.10.0153
MA0164.10.891
MA0258.10.993
MA0259.10.203



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: CNhs10729

Novel motifP-value
10.562
100.332
1000.659
1010.151
1020.954
1030.588
1040.579
1050.473
1060.225
1070.701
1080.825
1090.3
110.669
1100.246
1110.314
1120.378
1130.146
1140.301
1150.214
1160.93
1170.302
1180.313
1190.471
120.975
1200.956
1210.931
1220.204
1230.00201
1240.988
1250.564
1260.161
1270.687
1280.446
1290.0945
130.0652
1300.183
1310.479
1320.106
1330.409
1340.699
1350.236
1360.108
1370.307
1380.653
1390.103
140.22
1400.121
1410.923
1420.811
1430.804
1440.972
1450.946
1460.396
1470.58
1480.304
1490.258
150.477
1500.603
1510.504
1520.962
1530.192
1540.781
1550.491
1560.267
1570.959
1580.477
1590.888
160.571
1600.383
1610.315
1620.513
1630.0407
1640.0977
1650.689
1660.664
1670.76
1680.788
1690.103
170.442
180.143
190.464
20.25
200.435
210.284
220.516
230.558
240.168
250.614
260.42
270.992
280.325
290.868
30.936
300.0114
310.801
320.00335
330.711
340.455
350.0149
360.183
370.837
380.922
390.607
40.275
400.829
410.155
420.801
430.951
440.705
450.124
460.902
470.435
480.775
490.12
50.826
500.736
510.788
520.6
530.671
540.639
550.432
560.172
570.298
580.957
590.489
60.873
600.778
610.782
620.456
630.7
640.912
650.592
660.00456
670.471
680.743
690.594
70.28
700.653
710.285
720.907
730.472
740.346
750.369
760.558
770.0557
780.448
790.0338
80.865
800.362
810.318
820.8
830.331
840.252
850.108
860.607
870.226
880.278
890.58
90.535
900.389
910.731
920.847
930.553
940.374
950.13
960.254
970.548
980.512
990.497



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: CNhs10729


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)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
305 (carcinoma)
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000480 (anatomical group)
0000489 (cavitated compound organ)
0000916 (abdomen)
0000922 (embryo)
0001008 (renal system)
0001062 (anatomical entity)
0002100 (trunk)
0002113 (kidney)
0002417 (abdominal segment of trunk)
0003103 (compound organ)
0005095 (kidney rudiment)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005423 (developing anatomical structure)
0006554 (urinary system structure)
0007687 (kidney field)

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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