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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000015,UBERON:0000025,UBERON:0000058,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000119,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001173,UBERON:0001555,UBERON:0002050,UBERON:0002100,UBERON:0002294,UBERON:0002394,UBERON:0002423,UBERON:0002532,UBERON:0003104,UBERON:0003894,UBERON:0003914,UBERON:0003928,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004912,UBERON:0004921,UBERON:0005256,UBERON:0005423,UBERON:0005911,UBERON:0006235,UBERON:0007026,UBERON:0008835,UBERON:0009142
|ancestors_in_anatomy_facet=UBERON:0000015,UBERON:0000025,UBERON:0000058,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000119,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001173,UBERON:0001555,UBERON:0002050,UBERON:0002100,UBERON:0002294,UBERON:0002394,UBERON:0002423,UBERON:0002532,UBERON:0003104,UBERON:0003894,UBERON:0003914,UBERON:0003928,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004912,UBERON:0004921,UBERON:0005256,UBERON:0005423,UBERON:0005911,UBERON:0006235,UBERON:0007026,UBERON:0008835,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,FF:0103910
|fonse_cell_line=FF:0101120,FF:0103910
|fonse_cell_line_closure=FF:0101120,FF:0103910
|fonse_cell_line_closure=FF:0101120,FF:0103910

Revision as of 16:42, 29 March 2012


Name:bile duct carcinoma cell line:TFK-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebile duct
dev stageNA
sexmale
age63
cell typeduct cell, bile duct
cell lineTFK-1
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-penis0.0175
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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 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: CNhs11265

Jaspar motifP-value
MA0002.20.106
MA0003.10.5
MA0004.10.543
MA0006.10.873
MA0007.10.635
MA0009.10.174
MA0014.10.0779
MA0017.10.00424
MA0018.20.929
MA0019.10.0534
MA0024.10.389
MA0025.10.00833
MA0027.10.758
MA0028.11.25514e-5
MA0029.10.671
MA0030.10.593
MA0031.10.588
MA0035.20.56
MA0038.10.152
MA0039.20.878
MA0040.10.659
MA0041.10.387
MA0042.10.404
MA0043.10.00322
MA0046.19.36925e-15
MA0047.27.95649e-4
MA0048.10.297
MA0050.10.128
MA0051.10.191
MA0052.10.0116
MA0055.10.00511
MA0057.10.543
MA0058.10.466
MA0059.10.0196
MA0060.10.00188
MA0061.10.678
MA0062.27.04602e-5
MA0065.28.35396e-4
MA0066.10.707
MA0067.10.572
MA0068.10.681
MA0069.10.57
MA0070.10.0885
MA0071.10.206
MA0072.10.924
MA0073.10.87
MA0074.10.694
MA0076.14.59287e-5
MA0077.10.629
MA0078.10.645
MA0079.20.041
MA0080.20.0154
MA0081.10.0608
MA0083.10.00748
MA0084.10.564
MA0087.10.856
MA0088.10.388
MA0090.10.0489
MA0091.10.0224
MA0092.10.627
MA0093.10.46
MA0099.20.00167
MA0100.10.666
MA0101.10.514
MA0102.20.0218
MA0103.19.39981e-9
MA0104.20.0219
MA0105.10.887
MA0106.10.432
MA0107.10.287
MA0108.21.69855e-5
MA0111.10.3
MA0112.26.2226e-4
MA0113.10.506
MA0114.11.28402e-5
MA0115.10.052
MA0116.10.2
MA0117.10.804
MA0119.10.00162
MA0122.10.686
MA0124.10.0675
MA0125.10.742
MA0131.10.634
MA0135.10.00298
MA0136.10.987
MA0137.20.789
MA0138.20.922
MA0139.15.61954e-5
MA0140.10.674
MA0141.10.0154
MA0142.10.501
MA0143.10.845
MA0144.10.172
MA0145.10.126
MA0146.10.897
MA0147.10.00885
MA0148.13.44069e-4
MA0149.10.117
MA0150.11.85729e-5
MA0152.10.259
MA0153.15.31698e-14
MA0154.10.827
MA0155.10.186
MA0156.10.275
MA0157.10.927
MA0159.10.00154
MA0160.10.0634
MA0162.10.233
MA0163.10.336
MA0164.10.277
MA0258.10.0188
MA0259.10.408



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: CNhs11265

Novel motifP-value
10.0566
100.0354
1000.0938
1010.759
1020.466
1030.623
1040.992
1050.516
1060.305
1070.34
1080.299
1090.154
110.787
1100.336
1110.224
1120.483
1130.385
1140.0496
1150.709
1160.418
1170.116
1180.463
1190.0942
120.641
1200.803
1210.0228
1220.423
1230.00433
1240.834
1250.668
1260.995
1270.136
1280.649
1290.72
130.0166
1300.513
1310.337
1320.715
1330.136
1340.771
1350.528
1360.216
1370.134
1380.748
1390.117
140.736
1400.515
1410.27
1420.842
1430.048
1440.318
1450.785
1460.435
1470.73
1480.128
1490.986
150.0845
1500.521
1510.179
1520.604
1530.894
1540.753
1550.675
1560.31
1570.429
1580.419
1590.431
160.379
1600.922
1610.869
1620.705
1630.868
1640.0289
1650.0473
1660.308
1670.412
1680.754
1690.0113
170.287
180.509
190.533
20.864
200.163
210.255
220.913
230.96
240.466
250.603
260.144
270.989
280.606
290.193
30.113
300.859
310.599
320.175
330.109
340.326
350.621
360.12
370.487
380.471
390.41
40.505
400.371
410.0772
420.156
430.603
440.89
450.697
460.304
470.614
480.536
490.496
50.546
500.482
510.887
520.55
530.428
540.652
550.865
560.666
570.232
580.453
590.813
60.895
600.324
610.102
620.537
630.0649
640.393
650.593
660.786
670.745
680.051
690.463
70.193
700.0881
710.0851
720.631
730.951
740.967
750.011
760.255
770.189
780.00119
790.133
80.759
800.31
810.532
820.408
830.581
840.202
850.962
860.375
870.793
880.801
890.34
90.488
900.168
910.189
920.624
930.535
940.74
950.926
960.97
970.616
980.428
990.809



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: CNhs11265


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
0000015 (anatomical boundary)
0000025 (tube)
0000058 (duct)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000119 (cell layer)
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)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001173 (biliary tree)
0001555 (digestive tract)
0002050 (embryonic structure)
0002100 (trunk)
0002294 (biliary system)
0002394 (bile duct)
0002423 (hepatobiliary system)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003894 (liver primordium)
0003914 (epithelial tube)
0003928 (digestive system duct)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004912 (biliary bud)
0004921 (subdivision of digestive tract)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006235 (foregut-midgut junction)
0007026 (primitive gut)
0008835 (hepatic diverticulum)
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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