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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00004984
 
|DRA_sample_Accession=CAGE@SAMD00004984
|accession_numbers=CAGE;DRX008309;DRR009181;DRZ000606;DRZ001991
+
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00004984
 +
|accession_numbers=CAGE;DRX008309;DRR009181;DRZ000606;DRZ001991;DRZ011956;DRZ013341
 +
|accession_numbers_RNASeq=sRNA-Seq;DRX037268;DRR041634;DRZ007276
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002107,UBERON:0002100,UBERON:0001007,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0002365,UBERON:0005172,UBERON:0006925,UBERON:0002530,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0002330,UBERON:0000916,UBERON:0002423
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002107,UBERON:0002100,UBERON:0001007,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0002365,UBERON:0005172,UBERON:0006925,UBERON:0002530,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0002330,UBERON:0000916,UBERON:0002423
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000181,CL:0000417,CL:0000668,CL:0000412,CL:0000255,CL:0000182
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000181,CL:0000417,CL:0000668,CL:0000412,CL:0000255,CL:0000182
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|library_id=CNhs12626
 
|library_id=CNhs12626
 
|library_id_phase_based=2:CNhs12626
 
|library_id_phase_based=2:CNhs12626
 +
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11684
 +
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10066.ATGTCA.11684
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11684
 +
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10066.ATGTCA.11684
 
|name=Hepatocyte, donor3
 
|name=Hepatocyte, donor3
 
|namespace=FANTOM5
 
|namespace=FANTOM5
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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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|repeat_enrich_byfamily=0,0.201612826790636,0,0,0,0,0,0.0412947967042498,0.201612826790636,0.14781743869182,0.425301637616317,0,0,0,0,0,0,0,0,0,0,0,0,0,0.504185978865094,0,0,0,0,0,0.240813210061876,0,0,0.393790891083462,0,0,0,0,0,0,0,0,0,0,0,0,0.244911409606796,0.201612826790636,0,0,0,0,0,0,0,0.0765913922824835,0,0,0,0.201612826790636,0,0,0,0.241778745087328,0,0,-0.097343627213097,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.383596618641401,0.100806413395318,0,0,0.201612826790636,0,0.00305139826687684,0.0817155200045978,0.270191966560285,0,0.00654846188167335,0.105756991539787,0.45243552853594,0.169385553164967,0,0.100806413395318,0.338771106329934,-0.0980353512377064,0.0829483726069465,0,0,0,0,0,0,0,0,0,0,0,0.201612826790636,0,0,0,0,0,0.2323809006843,0,0,0,0.227167489876042,0.229558257259108,0,0,0.0218625117952507,0.078786051332105,0,0
 
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Line 74: Line 82:
 
|rna_tube_id=122I1
 
|rna_tube_id=122I1
 
|rna_weight_ug=10
 
|rna_weight_ug=10
 +
|rnaseq_library_id=SRhi10066.ATGTCA
 
|sample_age=
 
|sample_age=
 
|sample_category=primary cells
 
|sample_category=primary cells

Latest revision as of 06:56, 17 October 2017

Name:Hepatocyte, donor3
Species:Human (Homo sapiens)
Library ID:CNhs12626
Sample type:primary cells
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samplessRNA samples)
Excluding candidate novel miRNAs(CAGE samplessRNA samples)
RefEX:Specific genes
FANTOM CAT:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueliver
dev stageNA
sexNA
ageNA
cell typehepatocyte
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNA1057
catalog numberSC5205
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004984
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12626 CAGE DRX008309 DRR009181
Accession ID Hg19

Library idBAMCTSS
CNhs12626 DRZ000606 DRZ001991
Accession ID Hg38

Library idBAMCTSS
CNhs12626 DRZ011956 DRZ013341
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00004984
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10066.ATGTCA sRNA-Seq DRX037268 DRR041634
Accession ID Hg19

Library idBAMCTSS
SRhi10066.ATGTCA DRZ007276


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
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
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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: CNhs12626

Jaspar motif P-value
MA0002.2 0.42
MA0003.1 0.0224
MA0004.1 0.797
MA0006.1 0.248
MA0007.1 0.00597
MA0009.1 0.413
MA0014.1 0.626
MA0017.1 3.0979e-25
MA0018.2 0.0177
MA0019.1 0.792
MA0024.1 0.0168
MA0025.1 0.741
MA0027.1 0.776
MA0028.1 0.00341
MA0029.1 0.756
MA0030.1 0.0161
MA0031.1 0.0607
MA0035.2 0.014
MA0038.1 0.497
MA0039.2 0.482
MA0040.1 0.62
MA0041.1 0.894
MA0042.1 0.751
MA0043.1 0.355
MA0046.1 1.327e-69
MA0047.2 4.63124e-5
MA0048.1 0.619
MA0050.1 0.859
MA0051.1 0.955
MA0052.1 0.858
MA0055.1 0.642
MA0057.1 0.196
MA0058.1 0.759
MA0059.1 0.46
MA0060.1 0.0262
MA0061.1 0.0116
MA0062.2 1.62359e-6
MA0065.2 8.17741e-13
MA0066.1 0.568
MA0067.1 0.0191
MA0068.1 0.0567
MA0069.1 0.207
MA0070.1 0.446
MA0071.1 0.265
MA0072.1 0.139
MA0073.1 0.895
MA0074.1 0.402
MA0076.1 1.72196e-4
MA0077.1 0.418
MA0078.1 0.775
MA0079.2 0.943
MA0080.2 3.25646e-5
MA0081.1 0.0277
MA0083.1 0.149
MA0084.1 0.903
MA0087.1 0.342
MA0088.1 0.362
MA0090.1 0.876
MA0091.1 0.911
MA0092.1 0.525
MA0093.1 0.776
MA0099.2 5.93952e-18
MA0100.1 0.154
MA0101.1 6.46738e-4
MA0102.2 0.286
MA0103.1 0.0599
MA0104.2 0.573
MA0105.1 0.0597
MA0106.1 0.71
MA0107.1 5.05165e-4
MA0108.2 0.0657
MA0111.1 0.867
MA0112.2 4.22876e-5
MA0113.1 0.0588
MA0114.1 1.22125e-28
MA0115.1 4.20168e-8
MA0116.1 0.00543
MA0117.1 0.457
MA0119.1 0.0514
MA0122.1 0.861
MA0124.1 0.98
MA0125.1 0.397
MA0131.1 0.334
MA0135.1 0.846
MA0136.1 1.15362e-4
MA0137.2 0.00135
MA0138.2 0.0654
MA0139.1 0.809
MA0140.1 0.564
MA0141.1 2.24522e-4
MA0142.1 0.199
MA0143.1 0.311
MA0144.1 0.00273
MA0145.1 0.362
MA0146.1 0.424
MA0147.1 0.798
MA0148.1 0.00266
MA0149.1 0.801
MA0150.1 0.0874
MA0152.1 6.06755e-4
MA0153.1 1.30752e-36
MA0154.1 0.287
MA0155.1 0.204
MA0156.1 5.53798e-4
MA0157.1 0.379
MA0159.1 1.91505e-4
MA0160.1 0.0147
MA0162.1 0.919
MA0163.1 0.311
MA0164.1 0.472
MA0258.1 0.00162
MA0259.1 0.323



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: CNhs12626

Novel motif P-value
1 0.171
10 0.82
100 0.246
101 0.905
102 0.0634
103 0.319
104 0.505
105 0.43
106 0.00392
107 0.00587
108 0.251
109 0.902
11 0.403
110 0.577
111 0.307
112 0.0129
113 2.31647e-4
114 0.15
115 0.854
116 0.35
117 0.275
118 0.314
119 0.0079
12 0.57
120 0.688
121 0.903
122 0.221
123 0.796
124 0.0803
125 0.118
126 0.553
127 0.0896
128 0.16
129 0.727
13 0.0898
130 0.0127
131 0.981
132 0.0556
133 0.319
134 0.775
135 0.525
136 0.0894
137 0.299
138 0.29
139 0.962
14 0.631
140 0.537
141 0.136
142 0.273
143 0.00249
144 0.445
145 0.265
146 0.47
147 0.948
148 0.175
149 0.146
15 1
150 0.891
151 0.451
152 0.949
153 0.816
154 0.406
155 0.0485
156 0.708
157 0.469
158 0.311
159 0.0708
16 0.603
160 0.503
161 0.973
162 0.589
163 0.598
164 0.378
165 0.00189
166 0.283
167 0.492
168 0.63
169 0.001
17 0.447
18 0.639
19 0.00157
2 0.185
20 0.98
21 0.12
22 0.0783
23 0.0518
24 0.76
25 0.802
26 0.251
27 0.514
28 0.946
29 0.94
3 0.528
30 0.646
31 0.22
32 0.406
33 0.995
34 0.254
35 0.299
36 0.391
37 0.982
38 0.227
39 0.238
4 0.156
40 0.258
41 0.0829
42 0.977
43 0.253
44 0.00459
45 0.332
46 0.254
47 0.818
48 0.488
49 0.151
5 0.285
50 0.399
51 0.937
52 0.0419
53 0.846
54 0.509
55 0.829
56 0.891
57 0.968
58 0.253
59 0.215
6 0.619
60 0.0222
61 0.662
62 0.211
63 0.15
64 0.659
65 0.0753
66 0.0539
67 0.0742
68 0.936
69 0.99
7 0.101
70 0.98
71 0.265
72 0.662
73 0.962
74 0.888
75 0.565
76 0.329
77 0.0271
78 0.175
79 0.829
8 0.137
80 0.984
81 0.721
82 0.307
83 0.972
84 0.45
85 0.00756
86 0.763
87 0.0394
88 0.318
89 0.278
9 0.842
90 0.511
91 0.175
92 0.344
93 0.586
94 0.194
95 0.14
96 0.0451
97 0.92
98 0.957
99 0.0694



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: CNhs12626


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000078 (human hepatocyte 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

CL:0000134 (mesenchymal cell)
CL:0000223 (endodermal cell)