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{{f5samples
{{f5samples
|F5samples=
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|ancestors_in_anatomy_facet=UBERON:0000060,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000077,UBERON:0000119,UBERON:0000161,UBERON:0000162,UBERON:0000163,UBERON:0000164,UBERON:0000344,UBERON:0000365,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000486,UBERON:0000489,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001007,UBERON:0001008,UBERON:0001046,UBERON:0001062,UBERON:0001255,UBERON:0001256,UBERON:0001259,UBERON:0001353,UBERON:0001555,UBERON:0001556,UBERON:0002050,UBERON:0002075,UBERON:0002100,UBERON:0002323,UBERON:0002532,UBERON:0002553,UBERON:0003064,UBERON:0003103,UBERON:0003104,UBERON:0003350,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004122,UBERON:0004185,UBERON:0004458,UBERON:0004645,UBERON:0004921,UBERON:0004923,UBERON:0005177,UBERON:0005423,UBERON:0005910,UBERON:0005911,UBERON:0006554,UBERON:0006866,UBERON:0007026,UBERON:0009142
|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:0100792,FF:0101120
|fonse_cell_line=FF:0100792,FF:0101120
|fonse_cell_line_closure=FF:0100792,FF:0101120
|fonse_cell_line_closure=FF:0100792,FF:0101120

Revision as of 16:31, 29 March 2012


Name:transitional-cell carcinoma cell line:5637
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 stage68 year old adult
sexmale
age68
cell typeunclassifiable
cell line5637
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-penis-0.0715
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-lymphoma0.581
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs10735

Jaspar motifP-value
MA0002.27.93003e-4
MA0003.10.134
MA0004.10.949
MA0006.10.902
MA0007.10.272
MA0009.10.503
MA0014.10.431
MA0017.10.136
MA0018.20.14
MA0019.10.904
MA0024.11.64207e-6
MA0025.10.262
MA0027.10.507
MA0028.10.0176
MA0029.10.839
MA0030.10.204
MA0031.10.939
MA0035.20.959
MA0038.15.2855e-4
MA0039.20.39
MA0040.10.74
MA0041.10.655
MA0042.10.307
MA0043.10.0186
MA0046.10.987
MA0047.20.469
MA0048.10.573
MA0050.10.792
MA0051.10.415
MA0052.10.605
MA0055.10.0257
MA0057.10.952
MA0058.10.912
MA0059.10.505
MA0060.11.92872e-10
MA0061.10.478
MA0062.20.0104
MA0065.20.0763
MA0066.10.0317
MA0067.10.461
MA0068.10.774
MA0069.10.563
MA0070.10.199
MA0071.10.196
MA0072.10.651
MA0073.10.918
MA0074.10.5
MA0076.10.0083
MA0077.10.0376
MA0078.10.86
MA0079.20.845
MA0080.20.0214
MA0081.10.195
MA0083.10.137
MA0084.10.351
MA0087.10.329
MA0088.10.299
MA0090.10.149
MA0091.10.00212
MA0092.10.276
MA0093.10.964
MA0099.20.106
MA0100.10.583
MA0101.10.27
MA0102.20.517
MA0103.10.0467
MA0104.20.924
MA0105.10.00146
MA0106.10.302
MA0107.10.324
MA0108.20.00165
MA0111.10.653
MA0112.21.66475e-4
MA0113.10.0338
MA0114.10.51
MA0115.10.854
MA0116.15.66215e-4
MA0117.10.437
MA0119.10.21
MA0122.10.693
MA0124.10.683
MA0125.10.00765
MA0131.10.306
MA0135.10.694
MA0136.10.812
MA0137.20.912
MA0138.20.0105
MA0139.10.345
MA0140.10.457
MA0141.10.0159
MA0142.10.362
MA0143.10.967
MA0144.10.468
MA0145.10.193
MA0146.10.0473
MA0147.10.901
MA0148.10.957
MA0149.10.94
MA0150.10.138
MA0152.10.525
MA0153.10.861
MA0154.10.0153
MA0155.10.0988
MA0156.10.307
MA0157.10.5
MA0159.10.304
MA0160.10.342
MA0162.10.472
MA0163.14.3509e-7
MA0164.10.655
MA0258.10.0012
MA0259.10.833



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: CNhs10735

Novel motifP-value
10.0423
100.312
1000.801
1010.255
1020.969
1030.136
1040.895
1050.419
1060.0492
1070.363
1080.698
1090.3
110.0206
1100.407
1110.704
1120.0196
1130.699
1140.0197
1150.652
1160.225
1170.243
1180.216
1190.054
120.878
1200.59
1210.498
1220.819
1230.184
1240.0803
1250.824
1260.561
1270.449
1280.0107
1290.79
130.977
1300.445
1310.146
1320.922
1330.0168
1340.27
1350.0205
1360.279
1370.0719
1380.141
1390.0019
140.963
1400.659
1410.299
1420.486
1430.00634
1440.0341
1450.195
1460.747
1470.67
1480.216
1490.00546
150.165
1500.87
1510.452
1520.162
1530.576
1540.774
1550.651
1560.911
1570.769
1580.83
1590.332
160.271
1600.253
1610.755
1620.571
1630.568
1640.124
1650.961
1660.403
1670.644
1680.966
1690.0113
170.166
180.0687
190.0458
20.69
200.403
210.374
220.091
230.103
240.812
250.631
260.337
270.184
280.852
290.319
30.034
300.908
310.228
320.00121
330.752
340.418
350.0695
360.574
370.0609
380.417
390.848
40.576
400.845
410.201
420.252
430.0655
440.0472
450.82
460.0458
470.176
480.217
490.124
50.164
500.77
510.266
520.711
530.423
540.178
550.562
560.658
570.512
580.297
590.0235
60.508
600.211
610.602
620.048
630.427
640.258
650.103
660.272
670.375
680.0283
690.283
70.661
700.0146
710.172
720.191
730.0794
740.251
750.113
760.943
770.22
781
792.55589e-4
80.0344
800.29
810.0553
826.17331e-4
830.514
840.771
850.00139
860.167
870.915
880.614
890.0515
90.325
900.305
910.589
920.0621
930.874
940.00405
950.584
960.00717
970.535
980.0823
990.972



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: CNhs10735


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)

UBERON: Anatomy
0000060 (anatomical wall)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000119 (cell layer)
0000161 (orifice)
0000162 (cloaca)
0000163 (embryonic cloaca)
0000164 (primitive urogenital sinus)
0000344 (mucosa)
0000365 (urothelium)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000489 (cavitated compound organ)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001007 (digestive system)
0001008 (renal system)
0001046 (hindgut)
0001062 (anatomical entity)
0001255 (urinary bladder)
0001256 (wall of urinary bladder)
0001259 (mucosa of urinary bladder)
0001353 (anal region)
0001555 (digestive tract)
0001556 (lower urinary tract)
0002050 (embryonic structure)
0002075 (viscus)
0002100 (trunk)
0002323 (body cavity)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003064 (intermediate mesoderm)
0003103 (compound organ)
0003104 (mesenchyme)
0003350 (epithelium of mucosa)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004122 (genitourinary system)
0004185 (endodermal part of digestive tract)
0004458 (body cavity or lining)
0004645 (urinary bladder urothelium)
0004921 (subdivision of digestive tract)
0004923 (organ component layer)
0005177 (trunk region element)
0005423 (developing anatomical structure)
0005910 (transitional epithelium)
0005911 (endo-epithelium)
0006554 (urinary system structure)
0006866 (terminal part of digestive tract)
0007026 (primitive gut)
0009142 (entire embryonic mesenchyme)

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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