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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 16:32, 29 March 2012


Name:bile duct carcinoma cell line:HuCCT1
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 stage56 year old adult
sexunknown
age56
cell typeduct cell, bile duct
cell lineHuCCT1
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-0.0312
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: CNhs10750

Jaspar motifP-value
MA0002.20.302
MA0003.10.396
MA0004.10.889
MA0006.10.485
MA0007.10.488
MA0009.10.179
MA0014.10.0352
MA0017.10.676
MA0018.20.362
MA0019.10.166
MA0024.11.01958e-4
MA0025.10.698
MA0027.10.37
MA0028.11.57796e-6
MA0029.10.317
MA0030.10.13
MA0031.10.512
MA0035.20.00962
MA0038.10.134
MA0039.20.00314
MA0040.10.418
MA0041.10.929
MA0042.10.535
MA0043.10.93
MA0046.10.00122
MA0047.20.042
MA0048.10.35
MA0050.10.0784
MA0051.16.79664e-4
MA0052.10.478
MA0055.10.0035
MA0057.10.51
MA0058.10.673
MA0059.10.58
MA0060.16.95478e-5
MA0061.10.613
MA0062.24.58742e-6
MA0065.20.784
MA0066.10.588
MA0067.10.0928
MA0068.10.0334
MA0069.10.79
MA0070.10.522
MA0071.10.23
MA0072.10.747
MA0073.10.46
MA0074.10.635
MA0076.11.96464e-4
MA0077.10.687
MA0078.10.646
MA0079.20.804
MA0080.20.188
MA0081.10.622
MA0083.10.0366
MA0084.10.152
MA0087.10.898
MA0088.10.631
MA0090.10.00175
MA0091.10.00135
MA0092.10.307
MA0093.10.83
MA0099.22.71604e-11
MA0100.10.335
MA0101.10.628
MA0102.20.896
MA0103.13.64938e-9
MA0104.20.148
MA0105.10.0186
MA0106.10.806
MA0107.10.529
MA0108.20.429
MA0111.10.808
MA0112.20.512
MA0113.10.0346
MA0114.10.282
MA0115.10.251
MA0116.10.208
MA0117.10.311
MA0119.10.904
MA0122.10.727
MA0124.10.462
MA0125.10.466
MA0131.10.262
MA0135.10.394
MA0136.10.44
MA0137.20.321
MA0138.20.0246
MA0139.10.374
MA0140.10.117
MA0141.10.413
MA0142.10.748
MA0143.10.173
MA0144.10.644
MA0145.10.661
MA0146.10.374
MA0147.10.0592
MA0148.10.0667
MA0149.10.0943
MA0150.10.168
MA0152.10.181
MA0153.13.56894e-4
MA0154.10.0851
MA0155.10.0122
MA0156.10.0172
MA0157.10.472
MA0159.10.505
MA0160.10.709
MA0162.10.973
MA0163.10.0124
MA0164.10.753
MA0258.10.0418
MA0259.10.615



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: CNhs10750

Novel motifP-value
10.688
100.77
1000.306
1010.167
1020.641
1030.52
1040.791
1050.4
1060.912
1070.638
1080.922
1090.117
110.0887
1100.705
1110.802
1120.0492
1130.0269
1140.307
1150.236
1160.147
1170.694
1180.976
1190.232
120.595
1200.549
1210.139
1220.215
1230.771
1240.365
1250.309
1260.683
1270.996
1280.00119
1290.365
130.0545
1300.118
1310.41
1320.9
1330.0588
1340.468
1350.0301
1360.0151
1370.27
1380.884
1390.0622
140.77
1400.646
1410.0717
1420.787
1430.0846
1440.159
1450.395
1460.606
1470.781
1480.993
1490.149
150.76
1500.537
1510.743
1520.618
1530.291
1540.769
1550.276
1560.186
1570.453
1580.357
1590.58
160.695
1600.585
1610.935
1620.203
1630.611
1640.722
1650.37
1660.49
1670.965
1680.29
1690.986
170.614
180.188
190.2
20.629
200.0779
210.253
220.154
230.0849
240.415
250.852
260.36
270.637
280.487
290.3
30.23
300.609
310.194
321.84694e-4
330.12
340.165
350.106
360.546
370.461
380.985
390.57
40.918
400.452
410.213
420.91
430.161
440.441
450.974
460.273
470.992
480.589
490.178
50.33
500.176
510.561
520.75
530.525
540.409
550.782
560.713
570.833
580.759
590.33
60.493
600.877
610.293
620.179
630.222
640.303
650.184
660.0266
670.881
680.00293
690.438
70.492
700.142
710.533
720.231
730.585
740.898
750.531
760.514
770.745
780.106
790.0013
80.391
800.253
810.0242
823.57767e-5
830.164
840.576
850.0057
860.717
870.0119
880.523
890.255
90.127
900.477
910.122
920.088
930.759
940.0963
950.283
960.122
970.621
980.343
990.646



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: CNhs10750


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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