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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000119,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001007,UBERON:0001041,UBERON:0001062,UBERON:0001173,UBERON:0001555,UBERON:0002050,UBERON:0002075,UBERON:0002100,UBERON:0002110,UBERON:0002294,UBERON:0002323,UBERON:0002417,UBERON:0002423,UBERON:0002532,UBERON:0002553,UBERON:0003104,UBERON:0003914,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004458,UBERON:0004912,UBERON:0004921,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0005911,UBERON:0007026,UBERON:0009142
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000119,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001007,UBERON:0001041,UBERON:0001062,UBERON:0001173,UBERON:0001555,UBERON:0002050,UBERON:0002075,UBERON:0002100,UBERON:0002110,UBERON:0002294,UBERON:0002323,UBERON:0002417,UBERON:0002423,UBERON:0002532,UBERON:0002553,UBERON:0003104,UBERON:0003914,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004458,UBERON:0004912,UBERON:0004921,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0005911,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:0101120
|fonse_cell_line=FF:0101120
|fonse_cell_line_closure=FF:0101120
|fonse_cell_line_closure=FF:0101120

Revision as of 16:31, 29 March 2012


Name:gall bladder carcinoma cell line:TGBC2TKB
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuegall bladder
dev stageNA
sexfemale
ageunknown
cell typeunclassifiable
cell lineTGBC2TKB
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-0.0502
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-lymphoma0.0939
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: CNhs10733

Jaspar motifP-value
MA0002.20.66
MA0003.10.55
MA0004.10.525
MA0006.10.469
MA0007.10.504
MA0009.10.434
MA0014.10.0704
MA0017.10.691
MA0018.20.637
MA0019.10.454
MA0024.10.652
MA0025.10.174
MA0027.10.764
MA0028.17.2445e-9
MA0029.10.571
MA0030.10.315
MA0031.10.559
MA0035.20.92
MA0038.10.0758
MA0039.24.8828e-4
MA0040.10.833
MA0041.10.313
MA0042.10.732
MA0043.10.0255
MA0046.10.106
MA0047.20.263
MA0048.10.311
MA0050.10.942
MA0051.10.055
MA0052.10.0163
MA0055.10.00171
MA0057.10.502
MA0058.10.436
MA0059.10.97
MA0060.10.039
MA0061.10.317
MA0062.21.24398e-6
MA0065.20.234
MA0066.10.892
MA0067.10.396
MA0068.16.63606e-4
MA0069.10.731
MA0070.10.285
MA0071.10.212
MA0072.10.67
MA0073.10.439
MA0074.10.435
MA0076.11.04826e-6
MA0077.10.184
MA0078.10.596
MA0079.20.179
MA0080.20.00222
MA0081.10.298
MA0083.10.48
MA0084.10.754
MA0087.10.149
MA0088.10.626
MA0090.12.57356e-4
MA0091.10.0379
MA0092.10.885
MA0093.10.692
MA0099.23.33579e-14
MA0100.10.714
MA0101.10.00415
MA0102.20.748
MA0103.11.32532e-6
MA0104.20.865
MA0105.10.831
MA0106.10.904
MA0107.10.0288
MA0108.20.293
MA0111.10.277
MA0112.20.282
MA0113.10.183
MA0114.10.0635
MA0115.10.947
MA0116.10.0818
MA0117.10.699
MA0119.10.466
MA0122.10.731
MA0124.10.309
MA0125.10.63
MA0131.10.61
MA0135.10.431
MA0136.10.218
MA0137.22.34054e-5
MA0138.20.113
MA0139.12.50149e-4
MA0140.10.38
MA0141.10.158
MA0142.10.91
MA0143.10.479
MA0144.10.00144
MA0145.10.117
MA0146.10.71
MA0147.10.991
MA0148.10.0304
MA0149.10.145
MA0150.17.46974e-5
MA0152.10.208
MA0153.10.499
MA0154.10.974
MA0155.10.163
MA0156.10.0418
MA0157.10.536
MA0159.10.269
MA0160.10.903
MA0162.10.856
MA0163.10.0152
MA0164.10.953
MA0258.10.664
MA0259.10.886



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: CNhs10733

Novel motifP-value
10.944
100.212
1000.637
1010.237
1020.987
1030.778
1040.814
1050.198
1060.145
1070.569
1080.18
1090.913
110.239
1100.586
1110.198
1120.118
1130.0287
1140.892
1150.132
1160.0954
1170.121
1180.503
1190.653
120.454
1200.279
1210.484
1220.952
1230.0141
1240.082
1250.276
1260.167
1270.444
1280.188
1290.404
130.135
1300.466
1310.208
1320.235
1330.0115
1340.638
1350.614
1360.145
1370.0615
1380.959
1390.201
140.625
1400.113
1410.921
1420.65
1430.76
1440.255
1450.0838
1460.339
1470.785
1480.505
1490.261
150.723
1500.704
1510.748
1520.374
1530.441
1540.499
1550.558
1560.144
1570.398
1580.764
1590.868
160.63
1600.204
1610.839
1620.498
1630.326
1640.416
1650.914
1660.453
1670.252
1680.82
1690.971
170.693
180.61
190.684
20.737
200.0925
210.884
220.235
230.741
240.262
250.299
260.586
270.194
280.135
290.803
30.611
300.249
310.369
323.69568e-4
330.28
340.25
350.0445
360.782
370.982
380.855
390.901
40.301
400.887
410.159
420.618
430.197
440.691
450.125
460.196
470.868
480.966
490.141
50.935
500.537
510.942
520.334
530.303
540.873
550.972
560.679
570.908
580.605
590.65
60.895
600.298
610.195
620.189
630.433
640.537
650.486
660.0046
670.433
680.0525
690.261
70.899
700.23
710.789
720.907
730.925
740.289
750.114
760.841
770.316
780.256
790.0256
80.237
800.787
810.00838
820.00176
830.647
840.493
850.0584
860.567
870.124
880.504
890.76
90.3
900.266
910.0325
920.432
930.965
940.174
950.741
960.579
970.182
980.091
990.413



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: CNhs10733


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
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000119 (cell layer)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001007 (digestive system)
0001041 (foregut)
0001062 (anatomical entity)
0001173 (biliary tree)
0001555 (digestive tract)
0002050 (embryonic structure)
0002075 (viscus)
0002100 (trunk)
0002110 (gallbladder)
0002294 (biliary system)
0002323 (body cavity)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003104 (mesenchyme)
0003914 (epithelial tube)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004458 (body cavity or lining)
0004912 (biliary bud)
0004921 (subdivision of digestive tract)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
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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