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FF:409-16E1

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Name:liver, embryo E14
Species:Mouse (Mus musculus)
Library ID:CNhs10594
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 stage14 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  SAMD00005338
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10594 CAGE DRX009017 DRR009891
Accession ID Mm9

Library idBAMCTSS
CNhs10594 DRZ001316 DRZ002699
Accession ID Mm10

Library idBAMCTSS
CNhs10594 DRZ012666 DRZ014049
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 sample
Ranked 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 sample
Ranked 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

CNhs10594

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 -0.0355
1001 0
1002 -0.00274
1003 -0.112
1004 0
1005 0
1006 -0.143
1007 4.236979e-4
1008 0
1009 -0.172
101 0.208
1010 0
1011 -0.108
1012 0
1013 -0.176
1014 0.0683
1015 -0.0558
1016 -0.291
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0881
1022 -0.186
1023 0
1024 -0.00178
1025 0.253
1026 0
1027 -0.048
1028 0
1029 0.0471
103 -0.0595
1030 0
1031 -0.184
1032 -0.333
1033 0.0129
1034 0
1035 0
1036 0.358
1037 0
1038 -0.342
1039 -0.0945
104 0
1040 -0.211
1041 0



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs10594
Jaspar motif P-value
MA0002.2 0.042
MA0003.1 0.999
MA0004.1 0.234
MA0006.1 0.634
MA0007.1 0.408
MA0009.1 0.084
MA0014.1 0.891
MA0017.1 1.57093e-8
MA0018.2 0.0073
MA0019.1 0.294
MA0024.1 1.03426e-8
MA0025.1 0.344
MA0027.1 0.839
MA0028.1 6.06458e-4
MA0029.1 0.0477
MA0030.1 0.907
MA0031.1 0.682
MA0035.2 1.2573e-25
MA0038.1 0.169
MA0039.2 0.351
MA0040.1 0.431
MA0041.1 0.367
MA0042.1 0.547
MA0043.1 0.0762
MA0046.1 6.92154e-25
MA0047.2 0.0406
MA0048.1 0.0253
MA0050.1 0.542
MA0051.1 0.38
MA0052.1 7.61991e-7
MA0055.1 0.00887
MA0057.1 0.666
MA0058.1 0.176
MA0059.1 0.00959
MA0060.1 2.12546e-4
MA0061.1 0.204
MA0062.2 4.98778e-5
MA0065.2 7.48039e-5
MA0066.1 0.0272
MA0067.1 0.357
MA0068.1 0.0203
MA0069.1 0.0526
MA0070.1 0.655
MA0071.1 0.175
MA0072.1 0.106
MA0073.1 0.766
MA0074.1 0.735
MA0076.1 0.00326
MA0077.1 0.258
MA0078.1 0.813
MA0079.2 0.0558
MA0080.2 0.002
MA0081.1 0.572
MA0083.1 0.0263
MA0084.1 0.0569
MA0087.1 0.0333
MA0088.1 0.0211
MA0090.1 0.287
MA0091.1 0.281
MA0092.1 0.6
MA0093.1 0.233
MA0099.2 0.973
MA0100.1 0.024
MA0101.1 0.399
MA0102.2 0.695
MA0103.1 0.783
MA0104.2 0.121
MA0105.1 8.80262e-4
MA0106.1 0.458
MA0107.1 0.955
MA0108.2 0.012
MA0111.1 0.97
MA0112.2 0.00734
MA0113.1 0.161
MA0114.1 6.22236e-8
MA0115.1 1.49902e-5
MA0116.1 6.49299e-4
MA0117.1 0.861
MA0119.1 0.165
MA0122.1 0.241
MA0124.1 0.875
MA0125.1 0.676
MA0131.1 0.43
MA0135.1 0.395
MA0136.1 0.00107
MA0137.2 0.402
MA0138.2 0.0179
MA0139.1 0.165
MA0140.1 3.16649e-59
MA0141.1 0.0419
MA0142.1 0.0759
MA0143.1 0.365
MA0144.1 0.676
MA0145.1 0.712
MA0146.1 0.11
MA0147.1 0.0711
MA0148.1 3.27097e-4
MA0149.1 0.0293
MA0150.1 0.0011
MA0152.1 0.747
MA0153.1 2.77384e-22
MA0154.1 0.0673
MA0155.1 0.692
MA0156.1 0.00128
MA0157.1 0.442
MA0159.1 0.0625
MA0160.1 0.0393
MA0162.1 0.237
MA0163.1 1.59989e-6
MA0164.1 0.218
MA0258.1 0.219
MA0259.1 0.274



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs10594
Novel motif P-value
1 0.103
10 0.0411
100 0.211
101 0.623
102 0.858
103 0.016
104 0.901
105 0.813
106 0.667
107 0.858
108 0.372
109 0.011
11 0.103
110 0.0458
111 0.00491
112 0.0279
113 0.628
114 0.39
115 0.518
116 0.878
117 0.00153
118 0.0291
119 0.346
12 0.943
120 0.995
121 0.334
122 0.91
123 0.0469
124 0.268
125 0.36
126 0.104
127 0.204
128 0.625
129 0.586
13 1.03034e-4
130 0.563
131 0.606
132 0.0883
133 0.254
134 0.249
135 0.215
136 0.512
137 0.277
138 0.896
139 0.714
14 0.839
140 0.328
141 0.274
142 0.128
143 0.883
144 0.797
145 0.00775
146 0.581
147 0.906
148 0.316
149 0.634
15 0.0364
150 0.246
151 0.546
152 0.885
153 0.792
154 0.963
155 0.196
156 3.71578e-7
157 0.722
158 0.078
159 0.315
160 0.38
161 0.0317
162 0.837
163 0.937
164 0.00155
165 0.702
166 0.249
167 0.0718
168 0.602
169 0.0287
17 0.547
18 0.292
19 0.291
2 0.337
20 0.0244
21 0.814
22 0.525
23 0.397
24 0.479
25 0.389
26 7.86077e-4
27 0.974
28 0.411
29 0.0031
3 0.025
30 0.734
31 0.939
32 0.812
33 0.14
34 0.95
35 0.944
36 0.0222
37 0.184
38 0.835
39 0.682
4 0.677
40 0.108
41 0.665
42 0.0565
43 0.119
44 0.965
45 0.783
46 0.103
47 0.167
48 0.169
49 0.0663
5 0.041
50 0.873
51 0.591
52 0.914
53 0.767
54 0.746
55 0.319
56 0.727
57 0.345
58 0.498
59 0.557
6 0.88
60 0.467
61 0.297
62 0.127
63 0.48
64 0.369
65 0.818
66 0.338
67 0.4
68 0.724
69 0.748
7 0.0445
70 0.552
71 0.00619
72 0.439
73 0.31
74 0.499
75 0.0296
76 0.36
77 0.857
78 0.00883
79 0.435
8 0.00718
80 0.0909
81 0.874
82 0.832
83 0.645
84 0.971
85 0.648
86 0.465
87 0.59
88 0.696
89 0.8
9 0.992
90 0.0678
91 0.335
92 0.617
93 0.679
94 0.207
95 0.0359
96 0.116
97 0.567
98 0.214
99 0.776



de novo motifs identified by HOMER in promoters active in this sample
Summary:The result of HOMER in this sample is shown.
Analyst:NA

library id: CNhs10594


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)
0000296 (mouse embryonic day 14 sample)
0011340 (mouse liver- embryo E14 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)