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FF:462-17F5

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Name:liver, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs10523
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 stage16 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  SAMD00005920
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10523 CAGE DRX009019 DRR009893
Accession ID Mm9

Library idBAMCTSS
CNhs10523 DRZ001318 DRZ002701
Accession ID Mm10

Library idBAMCTSS
CNhs10523 DRZ012668 DRZ014051
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

CNhs10523

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0749
1002 --0.0692
1003 --0.102
1004 0
1005 0.216
1006 --0.127
1007 --0.0917
1008 0
1009 --0.0888
101 0.0662
1010 0
1011 --0.108
1012 0
1013 0.0742
1014 0.078
1015 --0.13
1016 --0.251
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 --0.0266
1023 0
1024 --0.0707
1025 0.293
1026 0
1027 0
1028 0
1029 --0.0538
103 --0.0528
1030 0
1031 --0.156
1032 --0.262
1033 0
1034 0.175
1035 0
1036 0.119
1037 0
1038 --0.134
1039 --0.00475
104 0
1040 --0.21
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: CNhs10523

Jaspar motif P-value
MA0002.2 0.0152
MA0003.1 0.328
MA0004.1 0.447
MA0006.1 0.297
MA0007.1 0.583
MA0009.1 0.133
MA0014.1 0.529
MA0017.1 7.03595e-14
MA0018.2 1.15666e-4
MA0019.1 0.4
MA0024.1 7.5671e-4
MA0025.1 0.473
MA0027.1 0.557
MA0028.1 0.133
MA0029.1 0.0218
MA0030.1 0.156
MA0031.1 0.21
MA0035.2 6.46673e-25
MA0038.1 0.564
MA0039.2 0.0166
MA0040.1 0.0486
MA0041.1 0.13
MA0042.1 0.755
MA0043.1 0.166
MA0046.1 6.28856e-54
MA0047.2 1.72892e-5
MA0048.1 0.0877
MA0050.1 0.84
MA0051.1 0.784
MA0052.1 1.11283e-4
MA0055.1 0.043
MA0057.1 0.422
MA0058.1 0.349
MA0059.1 0.105
MA0060.1 6.05646e-5
MA0061.1 0.204
MA0062.2 0.0247
MA0065.2 2.40325e-7
MA0066.1 0.0296
MA0067.1 0.251
MA0068.1 0.818
MA0069.1 0.0621
MA0070.1 0.614
MA0071.1 0.0607
MA0072.1 0.0125
MA0073.1 0.864
MA0074.1 0.459
MA0076.1 0.314
MA0077.1 0.249
MA0078.1 0.431
MA0079.2 0.253
MA0080.2 1.48882e-4
MA0081.1 0.516
MA0083.1 0.247
MA0084.1 0.0744
MA0087.1 0.0269
MA0088.1 0.0539
MA0090.1 0.624
MA0091.1 0.569
MA0092.1 0.243
MA0093.1 0.443
MA0099.2 0.959
MA0100.1 0.166
MA0101.1 0.417
MA0102.2 0.0505
MA0103.1 0.59
MA0104.2 0.502
MA0105.1 0.00348
MA0106.1 0.81
MA0107.1 0.827
MA0108.2 0.0905
MA0111.1 0.943
MA0112.2 0.00113
MA0113.1 0.299
MA0114.1 3.23703e-12
MA0115.1 7.10274e-7
MA0116.1 0.00283
MA0117.1 0.836
MA0119.1 0.0284
MA0122.1 0.357
MA0124.1 0.48
MA0125.1 0.706
MA0131.1 0.751
MA0135.1 0.71
MA0136.1 8.42845e-4
MA0137.2 0.799
MA0138.2 0.273
MA0139.1 0.18
MA0140.1 4.01466e-52
MA0141.1 0.0186
MA0142.1 0.19
MA0143.1 0.16
MA0144.1 0.831
MA0145.1 0.739
MA0146.1 0.0607
MA0147.1 0.459
MA0148.1 2.16433e-7
MA0149.1 0.0429
MA0150.1 0.00121
MA0152.1 0.618
MA0153.1 5.43147e-42
MA0154.1 0.0224
MA0155.1 0.995
MA0156.1 0.00582
MA0157.1 0.519
MA0159.1 0.0151
MA0160.1 0.0142
MA0162.1 0.398
MA0163.1 1.00197e-5
MA0164.1 0.472
MA0258.1 0.0685
MA0259.1 0.868



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: CNhs10523

Novel motif P-value
1 0.137
10 0.131
100 0.457
101 0.63
102 0.394
103 0.0259
104 0.982
105 0.627
106 0.166
107 0.289
108 0.582
109 0.0074
11 0.0732
110 0.0743
111 0.0243
112 0.013
113 0.864
114 0.419
115 0.968
116 0.883
117 0.00496
118 0.0318
119 0.0913
12 0.999
120 0.837
121 0.53
122 0.901
123 0.0486
124 0.888
125 0.759
126 0.124
127 0.515
128 0.0739
129 0.924
13 9.40702e-5
130 0.354
131 0.113
132 0.237
133 0.568
134 0.433
135 0.326
136 0.156
137 0.373
138 0.553
139 0.564
14 0.821
140 0.263
141 0.754
142 0.0802
143 0.678
144 0.948
145 0.0294
146 0.385
147 0.891
148 0.515
149 0.906
15 0.0425
150 0.192
151 0.439
152 0.282
153 0.954
154 0.68
155 0.516
156 0.0694
157 0.569
158 0.493
159 0.43
160 0.147
161 0.133
162 0.746
163 0.87
164 0.00473
165 0.299
166 0.677
167 0.313
168 0.338
169 0.00897
17 0.187
18 0.553
19 0.0959
2 0.757
20 0.168
21 0.916
22 0.265
23 0.999
24 0.282
25 0.501
26 3.35138e-4
27 0.54
28 0.271
29 0.0227
3 0.0167
30 0.864
31 0.777
32 0.237
33 0.138
34 0.841
35 0.732
36 0.0452
37 0.155
38 0.568
39 0.798
4 0.553
40 0.085
41 0.931
42 0.0639
43 0.0702
44 0.63
45 0.936
46 0.107
47 0.101
48 0.119
49 0.044
5 0.101
50 0.608
51 0.55
52 0.479
53 0.971
54 0.631
55 0.197
56 0.508
57 0.606
58 0.49
59 0.171
6 0.758
60 0.149
61 0.255
62 0.118
63 0.229
64 0.336
65 0.443
66 0.204
67 0.418
68 0.63
69 0.44
7 0.0389
70 0.381
71 0.0253
72 0.405
73 0.178
74 0.824
75 0.0468
76 0.673
77 0.778
78 0.00494
79 0.871
8 0.012
80 0.0722
81 0.818
82 0.576
83 0.404
84 0.811
85 0.29
86 0.267
87 0.0412
88 0.81
89 0.527
9 0.651
90 0.198
91 0.28
92 0.412
93 0.591
94 0.439
95 0.0468
96 0.0789
97 0.837
98 0.183
99 0.459



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: CNhs10523


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)
0000299 (mouse embryonic day 16 sample)
0011361 (mouse liver- embryo E16 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)