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FF:378-3H6

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Name:liver, embryo E13
Species:Mouse (Mus musculus)
Library ID:CNhs10524
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 stage13 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  SAMD00004746
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10524 CAGE DRX009016 DRR009890
Accession ID Mm9

Library idBAMCTSS
CNhs10524 DRZ001315 DRZ002698
Accession ID Mm10

Library idBAMCTSS
CNhs10524 DRZ012665 DRZ014048
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
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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

CNhs10524

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 -3.848171e-4
1002 0.043
1003 --0.107
1004 0
1005 0
1006 --0.0932
1007 --0.0174
1008 0
1009 --0.19
101 0.235
1010 0
1011 --0.108
1012 0
1013 --0.0359
1014 0.114
1015 --0.0209
1016 --0.108
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0779
1022 0
1023 0
1024 0.00443
1025 0.14
1026 0
1027 --0.048
1028 0
1029 --0.0697
103 --0.0108
1030 0
1031 --0.0914
1032 --0.189
1033 0
1034 0.0779
1035 0
1036 0.314
1037 0
1038 --0.199
1039 --0.155
104 0
1040 --0.138
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: CNhs10524

Jaspar motif P-value
MA0002.2 0.245
MA0003.1 0.722
MA0004.1 0.0739
MA0006.1 0.697
MA0007.1 0.638
MA0009.1 0.0747
MA0014.1 0.851
MA0017.1 2.54864e-9
MA0018.2 0.00368
MA0019.1 0.263
MA0024.1 1.21152e-13
MA0025.1 0.206
MA0027.1 0.711
MA0028.1 1.38137e-5
MA0029.1 0.00514
MA0030.1 0.743
MA0031.1 0.767
MA0035.2 1.76882e-36
MA0038.1 0.197
MA0039.2 0.158
MA0040.1 0.195
MA0041.1 0.107
MA0042.1 0.58
MA0043.1 0.0793
MA0046.1 6.29204e-26
MA0047.2 0.0322
MA0048.1 0.0123
MA0050.1 0.0294
MA0051.1 0.0136
MA0052.1 7.48819e-7
MA0055.1 0.00179
MA0057.1 0.847
MA0058.1 0.0345
MA0059.1 0.00199
MA0060.1 5.84429e-11
MA0061.1 0.297
MA0062.2 1.59903e-6
MA0065.2 2.76216e-4
MA0066.1 0.108
MA0067.1 0.229
MA0068.1 0.381
MA0069.1 0.0273
MA0070.1 0.939
MA0071.1 0.494
MA0072.1 0.271
MA0073.1 0.953
MA0074.1 0.944
MA0076.1 1.8574e-4
MA0077.1 0.662
MA0078.1 0.676
MA0079.2 0.0721
MA0080.2 0.0154
MA0081.1 0.239
MA0083.1 0.265
MA0084.1 0.169
MA0087.1 0.0301
MA0088.1 0.017
MA0090.1 0.191
MA0091.1 0.176
MA0092.1 0.893
MA0093.1 0.0708
MA0099.2 0.833
MA0100.1 0.0381
MA0101.1 0.48
MA0102.2 0.871
MA0103.1 0.164
MA0104.2 0.0316
MA0105.1 0.00259
MA0106.1 0.995
MA0107.1 0.78
MA0108.2 0.279
MA0111.1 0.673
MA0112.2 0.107
MA0113.1 0.256
MA0114.1 1.373e-7
MA0115.1 3.10902e-4
MA0116.1 0.0017
MA0117.1 0.966
MA0119.1 0.225
MA0122.1 0.822
MA0124.1 0.772
MA0125.1 0.569
MA0131.1 0.213
MA0135.1 0.43
MA0136.1 0.00374
MA0137.2 0.555
MA0138.2 0.00388
MA0139.1 0.242
MA0140.1 2.995e-75
MA0141.1 0.344
MA0142.1 0.0668
MA0143.1 0.3
MA0144.1 0.682
MA0145.1 0.555
MA0146.1 0.0764
MA0147.1 0.0128
MA0148.1 0.00278
MA0149.1 0.0579
MA0150.1 7.68936e-4
MA0152.1 0.499
MA0153.1 1.52462e-20
MA0154.1 0.141
MA0155.1 0.675
MA0156.1 6.49087e-4
MA0157.1 0.333
MA0159.1 0.0921
MA0160.1 0.184
MA0162.1 0.295
MA0163.1 1.15471e-6
MA0164.1 0.237
MA0258.1 0.892
MA0259.1 0.213



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: CNhs10524

Novel motif P-value
1 0.255
10 0.0819
100 0.147
101 0.427
102 0.504
103 0.0431
104 0.712
105 0.914
106 0.878
107 0.919
108 0.531
109 0.016
11 0.222
110 0.0985
111 0.00649
112 0.0466
113 0.513
114 0.76
115 0.91
116 0.718
117 0.00203
118 0.0276
119 0.812
12 0.947
120 0.982
121 0.173
122 0.573
123 0.0226
124 0.0742
125 0.745
126 0.0473
127 0.346
128 0.588
129 0.867
13 6.79977e-6
130 0.394
131 0.332
132 0.0268
133 0.299
134 0.0704
135 0.463
136 0.23
137 0.31
138 0.821
139 0.678
14 0.627
140 0.772
141 0.0558
142 0.0805
143 0.829
144 0.819
145 0.00481
146 0.706
147 0.749
148 0.156
149 0.199
15 0.0718
150 0.222
151 0.701
152 0.941
153 0.855
154 0.466
155 0.61
156 0.0279
157 0.974
158 0.282
159 0.562
160 0.506
161 0.00566
162 0.583
163 0.638
164 3.34774e-4
165 0.5
166 0.209
167 0.182
168 0.603
169 0.0833
17 0.922
18 0.439
19 0.343
2 0.344
20 0.00846
21 0.727
22 0.705
23 0.228
24 0.477
25 0.436
26 6.90933e-4
27 0.929
28 0.735
29 0.00227
3 0.0452
30 0.893
31 0.867
32 0.853
33 0.143
34 0.653
35 0.553
36 0.017
37 0.301
38 0.731
39 0.909
4 0.378
40 0.101
41 0.665
42 0.0499
43 0.2
44 0.889
45 0.822
46 0.121
47 0.128
48 0.18
49 0.0988
5 0.196
50 0.739
51 0.917
52 0.853
53 0.827
54 0.948
55 0.172
56 0.924
57 0.467
58 0.826
59 0.587
6 0.897
60 0.529
61 0.62
62 0.214
63 0.687
64 0.598
65 0.862
66 0.148
67 0.193
68 0.761
69 0.439
7 0.0181
70 0.542
71 0.00432
72 0.632
73 0.372
74 0.441
75 0.0787
76 0.381
77 0.424
78 0.0163
79 0.542
8 0.00453
80 0.108
81 0.888
82 0.824
83 0.539
84 0.653
85 0.591
86 0.379
87 0.0369
88 0.682
89 0.957
9 0.74
90 0.251
91 0.838
92 0.983
93 0.795
94 0.244
95 0.0557
96 0.219
97 0.563
98 0.363
99 0.915



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: CNhs10524


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)
0000293 (mouse embryonic day 13 sample)
0011328 (mouse liver- embryo E13 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)