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FF:11824-124F6

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Name:Mouse hepatocyte, donor8
Species:Mouse (Mus musculus)
Library ID:CNhs13091
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  SAMD00005803
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13091 CAGE DRX008860 DRR009732
Accession ID Mm9

Library idBAMCTSS
CNhs13091 DRZ001157 DRZ002542
Accession ID Mm10

Library idBAMCTSS
CNhs13091 DRZ012507 DRZ013892
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

CNhs13091

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.126
1002 --0.116
1003 0.0584
1004 0
1005 0
1006 --0.143
1007 --0.266
1008 0
1009 --0.2
101 --0.0453
1010 0
1011 --0.137
1012 0
1013 0.566
1014 --0.0874
1015 --0.41
1016 --0.433
1017 0
1018 0
1019 0
102 0
1020 0.805
1021 0.0209
1022 0.768
1023 0
1024 --0.14
1025 0.0996
1026 0
1027 --0.0213
1028 0
1029 --0.148
103 --0.0887
1030 0
1031 --0.615
1032 --0.588
1033 --0.0665
1034 1.051
1035 0
1036 --0.476
1037 0
1038 --0.193
1039 0.884
104 0
1040 --0.261
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: CNhs13091

Jaspar motif P-value
MA0002.2 0.187
MA0003.1 0.67
MA0004.1 0.24
MA0006.1 0.359
MA0007.1 0.0503
MA0009.1 0.875
MA0014.1 0.0635
MA0017.1 8.16951e-23
MA0018.2 0.00169
MA0019.1 0.65
MA0024.1 8.81409e-5
MA0025.1 0.00807
MA0027.1 0.733
MA0028.1 0.52
MA0029.1 0.508
MA0030.1 0.00671
MA0031.1 0.00164
MA0035.2 0.162
MA0038.1 0.253
MA0039.2 0.941
MA0040.1 0.589
MA0041.1 0.304
MA0042.1 0.517
MA0043.1 0.807
MA0046.1 2.98191e-79
MA0047.2 1.81016e-6
MA0048.1 0.241
MA0050.1 0.542
MA0051.1 0.112
MA0052.1 0.0327
MA0055.1 0.275
MA0057.1 0.753
MA0058.1 0.162
MA0059.1 0.0321
MA0060.1 3.48052e-6
MA0061.1 0.692
MA0062.2 0.899
MA0065.2 1.2165e-16
MA0066.1 0.0436
MA0067.1 0.289
MA0068.1 0.782
MA0069.1 0.0813
MA0070.1 0.22
MA0071.1 2.78459e-5
MA0072.1 7.57913e-4
MA0073.1 0.943
MA0074.1 0.206
MA0076.1 0.893
MA0077.1 0.0709
MA0078.1 0.968
MA0079.2 0.202
MA0080.2 0.0132
MA0081.1 0.326
MA0083.1 0.00118
MA0084.1 0.324
MA0087.1 0.222
MA0088.1 0.207
MA0090.1 0.59
MA0091.1 0.506
MA0092.1 0.209
MA0093.1 0.278
MA0099.2 0.809
MA0100.1 0.83
MA0101.1 0.883
MA0102.2 0.292
MA0103.1 0.0548
MA0104.2 0.401
MA0105.1 0.186
MA0106.1 0.0202
MA0107.1 0.437
MA0108.2 2.57838e-6
MA0111.1 0.876
MA0112.2 3.77533e-5
MA0113.1 0.169
MA0114.1 1.06343e-22
MA0115.1 1.04495e-13
MA0116.1 0.157
MA0117.1 0.495
MA0119.1 0.0615
MA0122.1 0.231
MA0124.1 0.897
MA0125.1 0.576
MA0131.1 0.82
MA0135.1 0.942
MA0136.1 0.0405
MA0137.2 0.0165
MA0138.2 0.484
MA0139.1 0.337
MA0140.1 0.854
MA0141.1 1.78178e-7
MA0142.1 0.312
MA0143.1 0.186
MA0144.1 0.145
MA0145.1 0.191
MA0146.1 0.0727
MA0147.1 0.283
MA0148.1 3.15129e-8
MA0149.1 0.00388
MA0150.1 0.00164
MA0152.1 0.323
MA0153.1 1.08799e-56
MA0154.1 0.237
MA0155.1 0.928
MA0156.1 0.158
MA0157.1 0.00102
MA0159.1 2.72201e-4
MA0160.1 1.5975e-6
MA0162.1 0.553
MA0163.1 0.0036
MA0164.1 0.981
MA0258.1 0.00269
MA0259.1 0.775



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: CNhs13091

Novel motif P-value
1 0.0769
10 0.173
100 0.424
101 0.98
102 0.194
103 0.00265
104 0.803
105 0.753
106 0.174
107 0.127
108 0.958
109 0.0679
11 0.103
110 0.0369
111 0.0103
112 0.018
113 0.738
114 0.00183
115 0.617
116 0.706
117 0.0578
118 0.373
119 0.101
12 0.33
120 0.73
121 0.793
122 0.479
123 0.47
124 0.56
125 0.719
126 0.172
127 0.879
128 0.0706
129 0.966
13 2.32566e-4
130 0.389
131 0.879
132 0.593
133 0.719
134 0.874
135 0.343
136 0.777
137 0.958
138 0.591
139 0.325
14 0.638
140 0.117
141 0.362
142 0.158
143 0.73
144 0.474
145 0.111
146 0.492
147 0.366
148 0.738
149 0.192
15 0.119
150 0.217
151 0.401
152 0.175
153 0.354
154 0.898
155 0.535
156 2.90989e-4
157 0.859
158 0.921
159 0.772
160 0.25
161 0.934
162 0.447
163 0.289
164 0.045
165 0.472
166 0.44
167 0.17
168 0.899
169 0.00449
17 0.087
18 0.922
19 0.119
2 0.994
20 0.337
21 0.633
22 0.166
23 0.428
24 0.211
25 0.417
26 0.00589
27 0.743
28 0.355
29 0.154
3 0.0857
30 0.935
31 0.393
32 0.133
33 0.316
34 0.84
35 0.156
36 0.115
37 0.0628
38 0.55
39 0.315
4 0.817
40 0.19
41 0.895
42 0.447
43 0.0905
44 0.00299
45 0.842
46 0.108
47 0.499
48 0.182
49 0.0387
5 0.0614
50 0.833
51 0.237
52 0.673
53 0.477
54 0.316
55 0.507
56 0.492
57 0.819
58 0.284
59 0.415
6 0.701
60 0.157
61 0.345
62 0.0797
63 0.128
64 0.491
65 0.405
66 0.691
67 0.726
68 0.214
69 0.909
7 0.171
70 0.0122
71 0.029
72 0.85
73 0.045
74 0.665
75 0.0062
76 0.657
77 0.456
78 0.0146
79 0.761
8 0.0139
80 0.86
81 0.734
82 0.00922
83 0.338
84 0.0287
85 0.0269
86 0.0672
87 0.31
88 0.963
89 0.153
9 0.986
90 0.0982
91 0.741
92 0.147
93 0.0937
94 0.7
95 0.197
96 0.36
97 0.477
98 0.532
99 0.223



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: CNhs13091


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)