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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005118
 
|DRA_sample_Accession=CAGE@SAMD00005118
|accession_numbers=CAGE;DRX007833;DRR008705;DRZ000130;DRZ001515
+
|accession_numbers=CAGE;DRX007833;DRR008705;DRZ000130;DRZ001515;DRZ011480;DRZ012865
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002394,UBERON:0000058,UBERON:0001007,UBERON:0004119,UBERON:0000062,UBERON:0004111,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003928,UBERON:0010317,UBERON:0002294,UBERON:0001173,UBERON:0002423
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002394,UBERON:0000058,UBERON:0001007,UBERON:0004119,UBERON:0000062,UBERON:0004111,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003928,UBERON:0010317,UBERON:0002294,UBERON:0001173,UBERON:0002423
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000255
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000255
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|profile_rnaseq=
 
|profile_rnaseq=
 
|profile_srnaseq=,,,
 
|profile_srnaseq=,,,
|refex=http://refex.dbcls.jp/genelist.php?lang=en&db=human&roku_valid=1&rk[]=&order_key=score
+
|refex=http://refex.dbcls.jp/genelist.php?lang
 
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Latest revision as of 10:19, 10 August 2017

Name:bile duct carcinoma cell line:HuCCT1
Species:Human (Homo sapiens)
Library ID:CNhs10750
Sample type:cell lines
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
RefEX:Specific genes
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

Accession numbers
MethodSample accession id
CAGE  SAMD00005118
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10750 CAGE DRX007833 DRR008705
Accession ID Hg19

Library idBAMCTSS
CNhs10750 DRZ000130 DRZ001515
Accession ID Hg38

Library idBAMCTSS
CNhs10750 DRZ011480 DRZ012865
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload


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.
Analyst:NA

link to dataset.
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
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C83-choriocarcinoma-pancreatic-placenta-chorionic-HES3GFP-testicular-amniotic0
C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
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 sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs10750

Jaspar motif P-value
MA0002.2 0.302
MA0003.1 0.396
MA0004.1 0.889
MA0006.1 0.485
MA0007.1 0.488
MA0009.1 0.179
MA0014.1 0.0352
MA0017.1 0.676
MA0018.2 0.362
MA0019.1 0.166
MA0024.1 1.01958e-4
MA0025.1 0.698
MA0027.1 0.37
MA0028.1 1.57796e-6
MA0029.1 0.317
MA0030.1 0.13
MA0031.1 0.512
MA0035.2 0.00962
MA0038.1 0.134
MA0039.2 0.00314
MA0040.1 0.418
MA0041.1 0.929
MA0042.1 0.535
MA0043.1 0.93
MA0046.1 0.00122
MA0047.2 0.042
MA0048.1 0.35
MA0050.1 0.0784
MA0051.1 6.79664e-4
MA0052.1 0.478
MA0055.1 0.0035
MA0057.1 0.51
MA0058.1 0.673
MA0059.1 0.58
MA0060.1 6.95478e-5
MA0061.1 0.613
MA0062.2 4.58742e-6
MA0065.2 0.784
MA0066.1 0.588
MA0067.1 0.0928
MA0068.1 0.0334
MA0069.1 0.79
MA0070.1 0.522
MA0071.1 0.23
MA0072.1 0.747
MA0073.1 0.46
MA0074.1 0.635
MA0076.1 1.96464e-4
MA0077.1 0.687
MA0078.1 0.646
MA0079.2 0.804
MA0080.2 0.188
MA0081.1 0.622
MA0083.1 0.0366
MA0084.1 0.152
MA0087.1 0.898
MA0088.1 0.631
MA0090.1 0.00175
MA0091.1 0.00135
MA0092.1 0.307
MA0093.1 0.83
MA0099.2 2.71604e-11
MA0100.1 0.335
MA0101.1 0.628
MA0102.2 0.896
MA0103.1 3.64938e-9
MA0104.2 0.148
MA0105.1 0.0186
MA0106.1 0.806
MA0107.1 0.529
MA0108.2 0.429
MA0111.1 0.808
MA0112.2 0.512
MA0113.1 0.0346
MA0114.1 0.282
MA0115.1 0.251
MA0116.1 0.208
MA0117.1 0.311
MA0119.1 0.904
MA0122.1 0.727
MA0124.1 0.462
MA0125.1 0.466
MA0131.1 0.262
MA0135.1 0.394
MA0136.1 0.44
MA0137.2 0.321
MA0138.2 0.0246
MA0139.1 0.374
MA0140.1 0.117
MA0141.1 0.413
MA0142.1 0.748
MA0143.1 0.173
MA0144.1 0.644
MA0145.1 0.661
MA0146.1 0.374
MA0147.1 0.0592
MA0148.1 0.0667
MA0149.1 0.0943
MA0150.1 0.168
MA0152.1 0.181
MA0153.1 3.56894e-4
MA0154.1 0.0851
MA0155.1 0.0122
MA0156.1 0.0172
MA0157.1 0.472
MA0159.1 0.505
MA0160.1 0.709
MA0162.1 0.973
MA0163.1 0.0124
MA0164.1 0.753
MA0258.1 0.0418
MA0259.1 0.615



FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs10750

Novel motif P-value
1 0.688
10 0.77
100 0.306
101 0.167
102 0.641
103 0.52
104 0.791
105 0.4
106 0.912
107 0.638
108 0.922
109 0.117
11 0.0887
110 0.705
111 0.802
112 0.0492
113 0.0269
114 0.307
115 0.236
116 0.147
117 0.694
118 0.976
119 0.232
12 0.595
120 0.549
121 0.139
122 0.215
123 0.771
124 0.365
125 0.309
126 0.683
127 0.996
128 0.00119
129 0.365
13 0.0545
130 0.118
131 0.41
132 0.9
133 0.0588
134 0.468
135 0.0301
136 0.0151
137 0.27
138 0.884
139 0.0622
14 0.77
140 0.646
141 0.0717
142 0.787
143 0.0846
144 0.159
145 0.395
146 0.606
147 0.781
148 0.993
149 0.149
15 0.76
150 0.537
151 0.743
152 0.618
153 0.291
154 0.769
155 0.276
156 0.186
157 0.453
158 0.357
159 0.58
16 0.695
160 0.585
161 0.935
162 0.203
163 0.611
164 0.722
165 0.37
166 0.49
167 0.965
168 0.29
169 0.986
17 0.614
18 0.188
19 0.2
2 0.629
20 0.0779
21 0.253
22 0.154
23 0.0849
24 0.415
25 0.852
26 0.36
27 0.637
28 0.487
29 0.3
3 0.23
30 0.609
31 0.194
32 1.84694e-4
33 0.12
34 0.165
35 0.106
36 0.546
37 0.461
38 0.985
39 0.57
4 0.918
40 0.452
41 0.213
42 0.91
43 0.161
44 0.441
45 0.974
46 0.273
47 0.992
48 0.589
49 0.178
5 0.33
50 0.176
51 0.561
52 0.75
53 0.525
54 0.409
55 0.782
56 0.713
57 0.833
58 0.759
59 0.33
6 0.493
60 0.877
61 0.293
62 0.179
63 0.222
64 0.303
65 0.184
66 0.0266
67 0.881
68 0.00293
69 0.438
7 0.492
70 0.142
71 0.533
72 0.231
73 0.585
74 0.898
75 0.531
76 0.514
77 0.745
78 0.106
79 0.0013
8 0.391
80 0.253
81 0.0242
82 3.57767e-5
83 0.164
84 0.576
85 0.0057
86 0.717
87 0.0119
88 0.523
89 0.255
9 0.127
90 0.477
91 0.122
92 0.088
93 0.759
94 0.0963
95 0.283
96 0.122
97 0.621
98 0.343
99 0.646



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs10750


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0000255 (eukaryotic cell)

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)
0002394 (bile duct)
0000058 (duct)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0004111 (anatomical conduit)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003928 (digestive system duct)
0010317 (germ layer / neural crest derived structure)
0002294 (biliary system)
0001173 (biliary tree)
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)
0103910 (bile duct cancer cell line sample)
0103911 (HuCCT-1 cell sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)