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FF:11714-123C4

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Name:Mouse hepatocyte, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs13078
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
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 numberRNA2060
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004776
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13078 CAGE DRX008857 DRR009729
Accession ID Mm9

Library idBAMCTSS
CNhs13078 DRZ001154 DRZ002539
Accession ID Mm10

Library idBAMCTSS
CNhs13078 DRZ012504 DRZ013889
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

CNhs13078

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0394
1002 --0.116
1003 0.00925
1004 0
1005 0
1006 --0.143
1007 --0.481
1008 0
1009 --0.19
101 0.0841
1010 0
1011 --0.126
1012 0
1013 0.306
1014 --0.0874
1015 --0.303
1016 --0.379
1017 0
1018 0
1019 0
102 0
1020 0.289
1021 0
1022 0.303
1023 0
1024 --0.0776
1025 0
1026 0
1027 --0.048
1028 0
1029 --0.176
103 --0.0887
1030 0
1031 --0.775
1032 --0.43
1033 0.225
1034 0.285
1035 0
1036 0.0729
1037 0
1038 --0.219
1039 0.505
104 0
1040 --0.538
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: CNhs13078

Jaspar motif P-value
MA0002.2 0.089
MA0003.1 0.68
MA0004.1 0.197
MA0006.1 0.57
MA0007.1 0.038
MA0009.1 0.982
MA0014.1 0.214
MA0017.1 8.66483e-14
MA0018.2 0.514
MA0019.1 0.998
MA0024.1 1.64244e-4
MA0025.1 0.019
MA0027.1 0.845
MA0028.1 0.981
MA0029.1 0.337
MA0030.1 0.0459
MA0031.1 0.00211
MA0035.2 0.0284
MA0038.1 0.0033
MA0039.2 0.471
MA0040.1 0.78
MA0041.1 0.314
MA0042.1 0.792
MA0043.1 0.37
MA0046.1 5.458e-63
MA0047.2 1.08072e-5
MA0048.1 0.246
MA0050.1 0.553
MA0051.1 0.243
MA0052.1 0.548
MA0055.1 0.297
MA0057.1 0.42
MA0058.1 0.134
MA0059.1 0.00703
MA0060.1 1.94261e-9
MA0061.1 0.333
MA0062.2 0.587
MA0065.2 6.37281e-12
MA0066.1 0.0171
MA0067.1 0.508
MA0068.1 0.431
MA0069.1 0.126
MA0070.1 0.317
MA0071.1 3.38577e-5
MA0072.1 0.00241
MA0073.1 0.919
MA0074.1 0.165
MA0076.1 0.601
MA0077.1 0.165
MA0078.1 0.478
MA0079.2 0.0959
MA0080.2 0.00182
MA0081.1 0.164
MA0083.1 0.159
MA0084.1 0.534
MA0087.1 0.481
MA0088.1 0.959
MA0090.1 0.354
MA0091.1 0.846
MA0092.1 0.306
MA0093.1 0.239
MA0099.2 1.48312e-6
MA0100.1 0.961
MA0101.1 0.508
MA0102.2 0.272
MA0103.1 0.0355
MA0104.2 0.118
MA0105.1 0.0621
MA0106.1 0.11
MA0107.1 0.803
MA0108.2 0.46
MA0111.1 0.741
MA0112.2 2.20028e-5
MA0113.1 0.175
MA0114.1 1.33348e-14
MA0115.1 1.07137e-9
MA0116.1 0.049
MA0117.1 0.213
MA0119.1 0.113
MA0122.1 0.458
MA0124.1 0.807
MA0125.1 0.249
MA0131.1 0.871
MA0135.1 0.874
MA0136.1 0.0147
MA0137.2 0.048
MA0138.2 0.478
MA0139.1 0.165
MA0140.1 0.902
MA0141.1 1.84412e-5
MA0142.1 0.305
MA0143.1 0.167
MA0144.1 0.12
MA0145.1 0.148
MA0146.1 0.0664
MA0147.1 0.0639
MA0148.1 3.21286e-7
MA0149.1 0.00335
MA0150.1 9.07196e-6
MA0152.1 0.537
MA0153.1 1.09216e-44
MA0154.1 0.16
MA0155.1 0.984
MA0156.1 0.0589
MA0157.1 0.0133
MA0159.1 3.17121e-4
MA0160.1 5.06551e-6
MA0162.1 0.375
MA0163.1 0.00109
MA0164.1 0.984
MA0258.1 6.94323e-4
MA0259.1 0.418



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: CNhs13078

Novel motif P-value
1 0.0963
10 0.261
100 0.276
101 0.915
102 0.789
103 0.0214
104 0.492
105 0.765
106 0.0118
107 0.0561
108 0.664
109 0.0853
11 0.0871
110 0.0639
111 0.00253
112 0.0203
113 0.764
114 0.00365
115 0.383
116 0.915
117 0.0453
118 0.585
119 0.0822
12 0.443
120 0.827
121 0.584
122 0.658
123 0.443
124 0.287
125 0.486
126 0.221
127 0.622
128 0.00666
129 0.79
13 0.0014
130 0.0461
131 0.905
132 0.428
133 0.197
134 0.691
135 0.408
136 0.438
137 0.793
138 0.838
139 0.187
14 0.837
140 0.219
141 0.117
142 0.426
143 0.285
144 0.433
145 0.15
146 0.566
147 0.423
148 0.842
149 0.408
15 0.153
150 0.247
151 0.525
152 0.0878
153 0.692
154 0.89
155 0.547
156 0.319
157 0.806
158 0.538
159 0.615
160 0.396
161 0.83
162 0.364
163 0.255
164 0.0802
165 0.651
166 0.82
167 0.413
168 0.713
169 0.00245
17 0.0547
18 0.399
19 0.189
2 0.966
20 0.363
21 0.792
22 0.198
23 0.194
24 0.319
25 0.546
26 0.00836
27 0.829
28 0.334
29 0.158
3 0.116
30 0.986
31 0.268
32 0.0487
33 0.234
34 0.804
35 0.18
36 0.0908
37 0.0536
38 0.448
39 0.314
4 0.631
40 0.14
41 0.525
42 0.518
43 0.0855
44 0.00167
45 0.686
46 0.0615
47 0.507
48 0.225
49 0.0534
5 0.168
50 0.868
51 0.237
52 0.419
53 0.507
54 0.257
55 0.913
56 0.48
57 0.761
58 0.306
59 0.184
6 0.678
60 0.0701
61 0.375
62 0.0776
63 0.133
64 0.537
65 0.253
66 0.554
67 0.709
68 0.108
69 0.921
7 0.267
70 0.0133
71 0.0191
72 0.933
73 0.0247
74 0.839
75 0.009
76 0.382
77 0.255
78 0.013
79 0.682
8 0.0123
80 0.813
81 0.841
82 0.0321
83 0.207
84 0.049
85 0.0678
86 0.101
87 0.164
88 0.954
89 0.2
9 0.927
90 0.412
91 0.621
92 0.0457
93 0.44
94 0.815
95 0.148
96 0.369
97 0.649
98 0.476
99 0.393



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: CNhs13078


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)