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|rna_box=107
|rna_box=107

Revision as of 20:02, 21 September 2012


Name:transitional-cell carcinoma cell line:JMSU1
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
sexmale
age75
cell typeunclassifiable
cell lineJMSU1
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
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C82-Basophils-CD14-Eosinophils-Natural-Peripheral-immature-CD340
C83-choriocarcinoma-pancreatic-placenta-chorionic-HES3GFP-testicular-amniotic0
C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
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



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: CNhs11261

Jaspar motifP-value
MA0002.20.00658
MA0003.10.27
MA0004.10.0347
MA0006.10.66
MA0007.10.178
MA0009.10.219
MA0014.10.225
MA0017.10.0315
MA0018.20.764
MA0019.10.125
MA0024.16.5711e-5
MA0025.10.985
MA0027.10.621
MA0028.10.0882
MA0029.10.444
MA0030.10.932
MA0031.10.832
MA0035.20.109
MA0038.10.075
MA0039.20.155
MA0040.10.454
MA0041.10.264
MA0042.10.389
MA0043.10.0931
MA0046.10.0934
MA0047.20.102
MA0048.10.0358
MA0050.10.00613
MA0051.10.00688
MA0052.10.396
MA0055.10.0127
MA0057.10.652
MA0058.10.0129
MA0059.10.0448
MA0060.10.00501
MA0061.10.762
MA0062.20.408
MA0065.20.993
MA0066.10.368
MA0067.10.642
MA0068.10.336
MA0069.10.585
MA0070.10.208
MA0071.10.785
MA0072.10.28
MA0073.10.936
MA0074.10.731
MA0076.10.194
MA0077.10.978
MA0078.10.1
MA0079.20.686
MA0080.21.13294e-9
MA0081.10.147
MA0083.10.316
MA0084.10.862
MA0087.10.33
MA0088.10.325
MA0090.10.297
MA0091.10.00341
MA0092.10.209
MA0093.10.0132
MA0099.20.232
MA0100.10.0851
MA0101.10.66
MA0102.20.368
MA0103.10.683
MA0104.21.06785e-4
MA0105.10.648
MA0106.10.766
MA0107.10.957
MA0108.20.173
MA0111.10.624
MA0112.28.10839e-4
MA0113.10.0177
MA0114.10.999
MA0115.10.656
MA0116.10.159
MA0117.10.315
MA0119.10.466
MA0122.10.942
MA0124.10.907
MA0125.10.65
MA0131.10.644
MA0135.10.0409
MA0136.11.1118e-6
MA0137.20.072
MA0138.20.178
MA0139.10.292
MA0140.10.077
MA0141.10.271
MA0142.10.00735
MA0143.10.124
MA0144.10.139
MA0145.10.0739
MA0146.10.23
MA0147.12.17053e-4
MA0148.10.0773
MA0149.10.376
MA0150.10.333
MA0152.10.562
MA0153.10.982
MA0154.10.053
MA0155.10.254
MA0156.10.00975
MA0157.10.664
MA0159.10.517
MA0160.10.0767
MA0162.10.784
MA0163.10.47
MA0164.10.933
MA0258.10.0201
MA0259.10.183



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: CNhs11261

Novel motifP-value
10.568
100.235
1000.153
1010.347
1020.965
1030.0161
1040.757
1050.874
1060.00221
1070.338
1080.449
1090.904
110.536
1100.881
1110.654
1120.0185
1130.0124
1140.166
1150.754
1160.846
1170.447
1180.388
1190.0886
120.799
1200.394
1210.224
1220.591
1230.911
1240.134
1250.928
1260.736
1270.303
1280.0158
1290.188
130.137
1300.436
1310.802
1320.546
1330.621
1340.0751
1350.00589
1360.043
1370.364
1380.629
1390.0483
140.39
1400.0149
1410.604
1420.465
1430.00573
1440.255
1450.377
1460.149
1470.941
1480.156
1490.0609
150.275
1500.886
1510.207
1520.0522
1530.568
1540.954
1550.46
1560.734
1570.8
1580.164
1590.25
160.521
1600.476
1610.845
1620.586
1630.168
1640.152
1650.193
1660.285
1670.88
1680.584
1690.0164
170.37
180.279
190.25
20.282
200.0352
210.053
220.0549
230.11
240.813
250.365
260.702
270.0282
280.385
290.418
30.678
300.583
310.132
320.0775
330.548
340.248
350.213
360.691
370.722
380.358
390.78
40.209
400.766
410.00183
420.756
430.176
440.575
450.122
460.0947
470.959
480.864
490.117
50.0395
500.506
510.363
520.203
530.517
540.306
550.0783
560.69
570.929
580.394
590.106
60.397
600.0496
610.353
620.129
630.865
640.612
650.149
660.417
670.605
680.323
690.109
70.451
700.113
710.833
720.483
730.19
740.796
750.484
760.674
770.338
780.694
790.0361
80.322
800.0724
810.339
820.00186
830.576
840.927
850.0057
860.571
870.219
880.992
890.00445
90.193
900.267
910.0336
920.151
930.541
940.0519
950.66
960.198
970.894
980.138
990.974



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: CNhs11261


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)
0000548 (animal cell)
0000066 (epithelial cell)
0000255 (eukaryotic cell)

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

UBERON: Anatomy
0000483 (epithelium)
0005910 (transitional epithelium)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0005911 (endo-epithelium)
0001062 (anatomical entity)
0000119 (cell layer)
0000486 (multilaminar epithelium)
0010317 (germ layer / neural crest derived structure)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0101120 (epithelial cell line sample)
0102869 (transitional cell carcinoma cell line sample)

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
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)

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