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|rna_box=107
|rna_box=107

Revision as of 16:57, 21 September 2012


Name:cholangiocellular carcinoma cell line:HuH-28
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueliver
dev stageNA
sexunknown
ageNA
cell typeduct cell, bile duct
cell lineHuH-28
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-0.0355
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



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: CNhs11283

Jaspar motifP-value
MA0002.20.332
MA0003.10.0754
MA0004.10.897
MA0006.10.814
MA0007.10.64
MA0009.10.204
MA0014.10.783
MA0017.10.0417
MA0018.20.321
MA0019.10.638
MA0024.10.186
MA0025.10.169
MA0027.10.502
MA0028.11.32001e-8
MA0029.10.101
MA0030.10.333
MA0031.10.906
MA0035.20.462
MA0038.10.0563
MA0039.20.276
MA0040.10.753
MA0041.10.132
MA0042.10.223
MA0043.10.0138
MA0046.10.135
MA0047.20.313
MA0048.10.341
MA0050.10.495
MA0051.10.596
MA0052.10.0471
MA0055.10.228
MA0057.10.103
MA0058.10.925
MA0059.10.492
MA0060.10.0623
MA0061.10.458
MA0062.22.63214e-8
MA0065.20.00723
MA0066.10.136
MA0067.10.129
MA0068.10.559
MA0069.10.993
MA0070.10.412
MA0071.10.905
MA0072.10.248
MA0073.10.48
MA0074.10.453
MA0076.17.75883e-14
MA0077.10.888
MA0078.10.924
MA0079.20.392
MA0080.21.14647e-8
MA0081.10.148
MA0083.10.331
MA0084.10.307
MA0087.10.53
MA0088.10.755
MA0090.10.0196
MA0091.10.354
MA0092.10.407
MA0093.10.85
MA0099.21.58075e-5
MA0100.10.543
MA0101.10.301
MA0102.20.0255
MA0103.10.0012
MA0104.20.773
MA0105.10.215
MA0106.10.625
MA0107.10.356
MA0108.20.0838
MA0111.10.844
MA0112.20.0185
MA0113.10.338
MA0114.10.382
MA0115.10.126
MA0116.10.0101
MA0117.10.859
MA0119.10.861
MA0122.10.541
MA0124.10.498
MA0125.10.731
MA0131.10.484
MA0135.10.0225
MA0136.10.00366
MA0137.20.917
MA0138.20.0252
MA0139.10.748
MA0140.10.326
MA0141.10.847
MA0142.10.15
MA0143.10.481
MA0144.10.731
MA0145.10.344
MA0146.10.0439
MA0147.10.432
MA0148.10.949
MA0149.10.352
MA0150.10.402
MA0152.10.0199
MA0153.10.494
MA0154.10.0278
MA0155.10.054
MA0156.10.0624
MA0157.10.712
MA0159.10.347
MA0160.10.993
MA0162.10.471
MA0163.10.0335
MA0164.10.0181
MA0258.10.116
MA0259.10.787



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: CNhs11283

Novel motifP-value
10.647
100.551
1000.7
1010.558
1020.127
1030.36
1040.228
1050.0313
1060.0526
1070.0766
1080.877
1090.922
110.432
1100.479
1110.81
1120.0637
1130.033
1140.855
1150.836
1160.591
1170.577
1180.953
1190.723
120.806
1200.262
1210.241
1220.583
1230.0272
1240.777
1250.361
1260.472
1270.125
1280.163
1290.178
130.974
1300.226
1310.236
1320.431
1330.111
1340.248
1350.762
1360.618
1370.23
1380.748
1390.634
140.463
1400.307
1410.537
1420.36
1430.235
1440.73
1450.0894
1460.981
1470.798
1480.682
1490.9
150.162
1500.903
1510.413
1520.213
1530.417
1540.654
1550.0431
1560.75
1570.749
1580.29
1590.0954
160.941
1600.171
1610.602
1620.213
1630.0509
1640.851
1650.417
1660.704
1670.00815
1680.0494
1690.109
170.297
180.405
190.471
20.088
200.341
210.464
220.094
230.0585
240.322
250.337
260.75
270.0683
280.362
290.775
30.917
300.234
310.941
320.402
330.619
340.0498
350.959
360.567
370.883
380.218
390.703
40.595
400.943
410.415
420.873
430.388
440.0543
450.454
460.471
470.574
480.228
490.327
50.0625
500.994
510.286
520.0243
530.19
540.948
550.713
560.0788
570.938
580.0703
590.0298
60.673
600.0769
610.589
620.108
630.797
640.4
650.203
660.014
670.209
680.514
690.344
70.52
700.0353
710.976
720.251
730.5
740.00186
750.138
760.121
770.565
780.00647
790.475
80.802
800.451
810.29
820.343
830.618
840.498
850.523
860.893
870.283
880.479
890.412
90.0315
900.464
910.00358
920.157
930.804
940.978
950.156
960.248
970.665
980.0161
990.238



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: CNhs11283


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)
0002371 (somatic cell)
0000181 (metabolising cell)
0000417 (endopolyploid cell)
0000668 (parenchymal cell)
0000412 (polyploid cell)
0000255 (eukaryotic cell)
0000182 (hepatocyte)

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

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
0001282 (intralobular bile duct)
0002394 (bile duct)
0000058 (duct)
0001007 (digestive system)
0000064 (organ part)
0004119 (endoderm-derived structure)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0009842 (acinus)
0000353 (parenchyma)
0003704 (intrahepatic bile duct)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0003928 (digestive system duct)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0001280 (liver parenchyma)
0001171 (portal lobule)
0004647 (liver lobule)
0002294 (biliary system)
0001173 (biliary tree)
0001172 (hepatic acinus)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary system)

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)
0100224 (liver cell line sample)
0100578 (hepatoma cell line sample)
0102842 (cholangioma cell 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
CL:0000134 (mesenchymal cell)
CL:0000223 (endodermal cell)
UBERON:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)

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