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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005469
 
|DRA_sample_Accession=CAGE@SAMD00005469
|accession_numbers=CAGE;DRX008859;DRR009731;DRZ001156;DRZ002541
+
|accession_numbers=CAGE;DRX008859;DRR009731;DRZ001156;DRZ002541;DRZ012506;DRZ013891
 
|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

Latest revision as of 12:17, 10 August 2017


Name:Mouse hepatocyte, donor6
Species:Mouse (Mus musculus)
Library ID:CNhs13090
Sample type:primary cells
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stageNA
sexmale
ageNA
cell typehepatocyte
cell lineNA
companyNA
collaborationSoichi Kojima (RIKEN ASI)
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  SAMD00005469
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13090 CAGE DRX008859 DRR009731
Accession ID Mm9

Library idBAMCTSS
CNhs13090 DRZ001156 DRZ002541
Accession ID Mm10

Library idBAMCTSS
CNhs13090 DRZ012506 DRZ013891
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
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

CNhs13090

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0371
1001 0.162
1002 --0.116
1003 0.254
1004 0
1005 0
1006 --0.143
1007 --0.203
1008 0
1009 --0.0572
101 --0.0456
1010 0
1011 --0.298
1012 0
1013 0.658
1014 --0.0874
1015 --0.396
1016 --0.377
1017 0
1018 0
1019 0
102 0
1020 0.75
1021 0
1022 0.628
1023 0
1024 --0.14
1025 0.201
1026 0
1027 0
1028 0
1029 --0.0989
103 --0.0887
1030 0
1031 --0.41
1032 --0.395
1033 --0.0665
1034 1.113
1035 0
1036 --0.271
1037 0
1038 --0.276
1039 0.82
104 0
1040 --0.216
1041 0



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: CNhs13090

Jaspar motif P-value
MA0002.2 0.182
MA0003.1 0.7
MA0004.1 0.516
MA0006.1 0.321
MA0007.1 0.136
MA0009.1 0.956
MA0014.1 0.0738
MA0017.1 8.87184e-20
MA0018.2 8.03987e-4
MA0019.1 0.945
MA0024.1 1.45855e-4
MA0025.1 0.28
MA0027.1 0.9
MA0028.1 0.548
MA0029.1 0.329
MA0030.1 0.0438
MA0031.1 0.0173
MA0035.2 0.142
MA0038.1 0.33
MA0039.2 0.832
MA0040.1 0.747
MA0041.1 0.406
MA0042.1 0.682
MA0043.1 0.275
MA0046.1 1.22483e-70
MA0047.2 2.26766e-6
MA0048.1 0.24
MA0050.1 0.42
MA0051.1 0.079
MA0052.1 0.016
MA0055.1 0.257
MA0057.1 0.695
MA0058.1 0.407
MA0059.1 0.0378
MA0060.1 2.82413e-6
MA0061.1 0.514
MA0062.2 0.988
MA0065.2 1.43332e-13
MA0066.1 0.0302
MA0067.1 0.241
MA0068.1 0.447
MA0069.1 0.098
MA0070.1 0.311
MA0071.1 3.48778e-5
MA0072.1 1.23577e-4
MA0073.1 0.913
MA0074.1 0.186
MA0076.1 0.959
MA0077.1 0.0389
MA0078.1 0.968
MA0079.2 0.169
MA0080.2 0.00639
MA0081.1 0.27
MA0083.1 0.00298
MA0084.1 0.329
MA0087.1 0.365
MA0088.1 0.227
MA0090.1 0.729
MA0091.1 0.873
MA0092.1 0.169
MA0093.1 0.565
MA0099.2 0.8
MA0100.1 0.584
MA0101.1 0.916
MA0102.2 0.522
MA0103.1 0.0598
MA0104.2 0.595
MA0105.1 0.038
MA0106.1 0.00865
MA0107.1 0.614
MA0108.2 1.17946e-6
MA0111.1 0.87
MA0112.2 8.05884e-6
MA0113.1 0.379
MA0114.1 1.81009e-18
MA0115.1 1.32566e-11
MA0116.1 0.0807
MA0117.1 0.539
MA0119.1 0.025
MA0122.1 0.222
MA0124.1 0.963
MA0125.1 0.302
MA0131.1 0.771
MA0135.1 0.431
MA0136.1 0.0266
MA0137.2 0.0267
MA0138.2 0.297
MA0139.1 0.122
MA0140.1 0.522
MA0141.1 5.70523e-7
MA0142.1 0.31
MA0143.1 0.208
MA0144.1 0.217
MA0145.1 0.153
MA0146.1 0.0825
MA0147.1 0.43
MA0148.1 3.22163e-8
MA0149.1 0.00312
MA0150.1 0.00593
MA0152.1 0.467
MA0153.1 4.15652e-57
MA0154.1 0.154
MA0155.1 0.938
MA0156.1 0.156
MA0157.1 0.00671
MA0159.1 4.8844e-4
MA0160.1 1.79782e-5
MA0162.1 0.277
MA0163.1 0.00103
MA0164.1 0.945
MA0258.1 0.00159
MA0259.1 0.92



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: CNhs13090

Novel motif P-value
1 0.0617
10 0.151
100 0.452
101 0.997
102 0.294
103 0.00526
104 0.876
105 0.775
106 0.125
107 0.134
108 0.957
109 0.0679
11 0.0628
110 0.0382
111 0.00343
112 0.0192
113 0.916
114 0.00204
115 0.762
116 0.92
117 0.0633
118 0.468
119 0.0855
12 0.431
120 0.77
121 0.876
122 0.56
123 0.517
124 0.365
125 0.82
126 0.225
127 0.782
128 0.0449
129 0.749
13 5.36286e-4
130 0.5
131 0.715
132 0.396
133 0.78
134 0.909
135 0.428
136 0.732
137 0.855
138 0.813
139 0.262
14 0.616
140 0.0863
141 0.407
142 0.0816
143 0.536
144 0.653
145 0.0875
146 0.591
147 0.461
148 0.519
149 0.132
15 0.103
150 0.285
151 0.457
152 0.183
153 0.344
154 0.875
155 0.505
156 0.264
157 0.924
158 0.822
159 0.753
160 0.257
161 0.687
162 0.527
163 0.33
164 0.0827
165 0.697
166 0.522
167 0.0801
168 0.822
169 0.00159
17 0.0768
18 0.81
19 0.0828
2 0.953
20 0.409
21 0.716
22 0.172
23 0.323
24 0.22
25 0.502
26 0.00737
27 0.787
28 0.392
29 0.135
3 0.0661
30 0.934
31 0.392
32 0.109
33 0.379
34 0.836
35 0.214
36 0.119
37 0.0645
38 0.439
39 0.245
4 0.896
40 0.266
41 0.996
42 0.392
43 0.0778
44 0.00142
45 0.833
46 0.106
47 0.342
48 0.173
49 0.049
5 0.0921
50 0.902
51 0.314
52 0.626
53 0.487
54 0.259
55 0.621
56 0.421
57 0.598
58 0.352
59 0.404
6 0.835
60 0.185
61 0.303
62 0.0969
63 0.15
64 0.423
65 0.256
66 0.438
67 0.875
68 0.122
69 0.833
7 0.215
70 0.0187
71 0.0342
72 0.749
73 0.0714
74 0.531
75 0.0108
76 0.765
77 0.431
78 0.0209
79 0.564
8 0.0099
80 0.943
81 0.756
82 0.0127
83 0.352
84 0.0709
85 0.0114
86 0.1
87 0.45
88 0.774
89 0.156
9 0.981
90 0.0704
91 0.581
92 0.1
93 0.0389
94 0.667
95 0.203
96 0.373
97 0.58
98 0.397
99 0.165



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: CNhs13090


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)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000109 (mouse 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)