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FF:355-15F8

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Name:liver, embryo E12
Species:Mouse (Mus musculus)
Library ID:CNhs10601
Sample type:developmental
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 stage12 days embryo
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005264
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10601 CAGE DRX009015 DRR009889
Accession ID Mm9

Library idBAMCTSS
CNhs10601 DRZ001314 DRZ002697
Accession ID Mm10

Library idBAMCTSS
CNhs10601 DRZ012664 DRZ014047
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

CNhs10601

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0119
1002 0.0674
1003 --0.152
1004 0
1005 --0.0389
1006 --0.0976
1007 0.0314
1008 0
1009 --0.133
101 0.244
1010 0
1011 --0.0343
1012 0
1013 --0.0943
1014 0.176
1015 0.00886
1016 --0.044
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.176
1022 --0.248
1023 0
1024 --0.0145
1025 0.144
1026 0
1027 0
1028 0
1029 2.64663e-4
103 --0.035
1030 0
1031 0.0165
1032 --0.318
1033 0.125
1034 0
1035 0
1036 0.395
1037 0
1038 --0.267
1039 --0.151
104 0
1040 --0.142
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: CNhs10601

Jaspar motif P-value
MA0002.2 0.195
MA0003.1 0.97
MA0004.1 0.0512
MA0006.1 0.86
MA0007.1 0.922
MA0009.1 0.222
MA0014.1 0.525
MA0017.1 2.1055e-6
MA0018.2 0.0389
MA0019.1 0.407
MA0024.1 1.04296e-17
MA0025.1 0.327
MA0027.1 0.479
MA0028.1 7.01873e-7
MA0029.1 0.0146
MA0030.1 0.962
MA0031.1 0.237
MA0035.2 2.15279e-37
MA0038.1 0.0651
MA0039.2 0.749
MA0040.1 0.422
MA0041.1 0.16
MA0042.1 0.608
MA0043.1 0.361
MA0046.1 3.62489e-17
MA0047.2 0.327
MA0048.1 0.00251
MA0050.1 0.00184
MA0051.1 0.00176
MA0052.1 0.0018
MA0055.1 4.04903e-4
MA0057.1 0.927
MA0058.1 0.0317
MA0059.1 0.00234
MA0060.1 1.20975e-12
MA0061.1 0.394
MA0062.2 1.78831e-8
MA0065.2 0.00327
MA0066.1 0.119
MA0067.1 0.336
MA0068.1 0.0422
MA0069.1 0.00727
MA0070.1 0.973
MA0071.1 0.54
MA0072.1 0.377
MA0073.1 0.805
MA0074.1 0.722
MA0076.1 3.56772e-6
MA0077.1 0.812
MA0078.1 0.773
MA0079.2 0.0543
MA0080.2 0.0279
MA0081.1 0.281
MA0083.1 0.958
MA0084.1 0.288
MA0087.1 0.0617
MA0088.1 0.0226
MA0090.1 0.266
MA0091.1 0.278
MA0092.1 0.647
MA0093.1 0.0599
MA0099.2 0.665
MA0100.1 0.00572
MA0101.1 0.441
MA0102.2 0.928
MA0103.1 0.0277
MA0104.2 0.0163
MA0105.1 0.00314
MA0106.1 0.984
MA0107.1 0.957
MA0108.2 0.422
MA0111.1 0.526
MA0112.2 0.225
MA0113.1 0.226
MA0114.1 2.61278e-5
MA0115.1 8.70248e-4
MA0116.1 0.00544
MA0117.1 0.858
MA0119.1 0.928
MA0122.1 0.959
MA0124.1 0.959
MA0125.1 0.718
MA0131.1 0.295
MA0135.1 0.489
MA0136.1 0.00303
MA0137.2 0.599
MA0138.2 6.91924e-4
MA0139.1 0.517
MA0140.1 2.3086e-81
MA0141.1 0.362
MA0142.1 0.169
MA0143.1 0.21
MA0144.1 0.745
MA0145.1 0.292
MA0146.1 0.196
MA0147.1 0.00623
MA0148.1 0.0651
MA0149.1 0.298
MA0150.1 0.017
MA0152.1 0.535
MA0153.1 7.66012e-14
MA0154.1 0.286
MA0155.1 0.534
MA0156.1 2.05802e-4
MA0157.1 0.0412
MA0159.1 0.0587
MA0160.1 0.135
MA0162.1 0.395
MA0163.1 1.20157e-5
MA0164.1 0.174
MA0258.1 0.873
MA0259.1 0.0904



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: CNhs10601

Novel motif P-value
1 0.373
10 0.0976
100 0.133
101 0.206
102 0.759
103 0.247
104 0.804
105 0.743
106 0.61
107 0.583
108 0.696
109 0.0323
11 0.226
110 0.066
111 0.00887
112 0.167
113 0.443
114 0.882
115 0.661
116 0.942
117 0.00193
118 0.037
119 0.762
12 0.84
120 0.972
121 0.163
122 0.708
123 0.0127
124 0.0608
125 0.658
126 0.114
127 0.0614
128 0.99
129 0.61
13 4.84845e-6
130 0.546
131 0.81
132 0.00609
133 0.425
134 0.0838
135 0.19
136 0.371
137 0.303
138 0.333
139 0.464
14 0.268
140 0.768
141 0.0335
142 0.185
143 0.869
144 0.525
145 0.00803
146 0.939
147 0.617
148 0.174
149 0.174
15 0.114
150 0.27
151 0.72
152 0.493
153 0.724
154 0.44
155 0.589
156 0.00635
157 0.785
158 0.0589
159 0.854
160 0.732
161 0.0179
162 0.62
163 0.74
164 0.00155
165 0.253
166 0.0774
167 0.267
168 0.809
169 0.259
17 0.857
18 0.506
19 0.575
2 0.221
20 0.00383
21 0.493
22 0.869
23 0.113
24 0.638
25 0.482
26 6.82155e-4
27 0.601
28 0.806
29 0.00157
3 0.0782
30 0.63
31 0.603
32 0.996
33 0.305
34 0.807
35 0.665
36 0.123
37 0.386
38 0.957
39 0.536
4 0.384
40 0.264
41 0.646
42 0.0751
43 0.285
44 0.853
45 0.735
46 0.173
47 0.26
48 0.351
49 0.229
5 0.247
50 0.763
51 0.99
52 0.526
53 0.653
54 0.863
55 0.575
56 0.955
57 0.445
58 0.932
59 0.794
6 0.876
60 0.92
61 0.393
62 0.346
63 0.898
64 0.781
65 0.777
66 0.115
67 0.14
68 0.899
69 0.609
7 0.0331
70 0.439
71 0.00323
72 0.734
73 0.552
74 0.395
75 0.13
76 0.321
77 0.227
78 0.0162
79 0.0985
8 0.00793
80 0.0951
81 0.964
82 0.453
83 0.289
84 0.685
85 0.485
86 0.547
87 0.3
88 0.175
89 0.821
9 0.865
90 0.234
91 0.836
92 0.876
93 0.344
94 0.277
95 0.0366
96 0.231
97 0.229
98 0.611
99 0.848



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: CNhs10601


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002107 (liver)
0002100 (trunk)
0000479 (tissue)
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)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000295 (mouse embryonic day 12 sample)
0011320 (mouse liver- embryo E12 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:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)