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FF:372-23H2

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Name:whole body, embryo E13
Species:Mouse (Mus musculus)
Library ID:CNhs10512
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
tissuewhole body
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  SAMD00006017
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10512 CAGE DRX009144 DRR010018
Accession ID Mm9

Library idBAMCTSS
CNhs10512 DRZ001443 DRZ002826
Accession ID Mm10

Library idBAMCTSS
CNhs10512 DRZ012793 DRZ014176
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

CNhs10512

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.114
10 0
100 0.18
1000 --0.00125
1001 --0.0749
1002 0.0979
1003 0.0046
1004 0.154
1005 --0.0402
1006 0.0468
1007 0.0839
1008 0
1009 --0.0105
101 0.101
1010 0
1011 0.0424
1012 0
1013 --0.169
1014 0.338
1015 0.27
1016 0.193
1017 0
1018 0.0685
1019 0
102 0
1020 0
1021 -7.232784e-4
1022 --0.0188
1023 0
1024 --0.066
1025 0.18
1026 0.039
1027 0.268
1028 0
1029 --0.0553
103 0.104
1030 0
1031 0.317
1032 --0.177
1033 0.104
1034 0
1035 0
1036 0.197
1037 0
1038 --0.0722
1039 --0.123
104 0
1040 --0.00904
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: CNhs10512

Jaspar motif P-value
MA0002.2 9.71032e-5
MA0003.1 0.276
MA0004.1 0.651
MA0006.1 0.267
MA0007.1 0.141
MA0009.1 0.182
MA0014.1 0.188
MA0017.1 1.45862e-5
MA0018.2 0.496
MA0019.1 0.866
MA0024.1 4.24535e-4
MA0025.1 0.01
MA0027.1 0.0335
MA0028.1 0.534
MA0029.1 0.944
MA0030.1 0.135
MA0031.1 0.00862
MA0035.2 0.327
MA0038.1 0.00734
MA0039.2 0.14
MA0040.1 0.343
MA0041.1 0.515
MA0042.1 0.567
MA0043.1 0.389
MA0046.1 0.0135
MA0047.2 0.00531
MA0048.1 0.573
MA0050.1 6.33008e-6
MA0051.1 4.16219e-5
MA0052.1 0.845
MA0055.1 0.686
MA0057.1 0.0745
MA0058.1 0.758
MA0059.1 0.435
MA0060.1 2.05506e-16
MA0061.1 0.101
MA0062.2 0.052
MA0065.2 1.99506e-6
MA0066.1 0.0697
MA0067.1 0.488
MA0068.1 0.0731
MA0069.1 0.635
MA0070.1 0.114
MA0071.1 0.0334
MA0072.1 0.0146
MA0073.1 0.929
MA0074.1 0.281
MA0076.1 0.832
MA0077.1 0.0867
MA0078.1 0.896
MA0079.2 0.542
MA0080.2 1.45991e-10
MA0081.1 0.226
MA0083.1 0.331
MA0084.1 0.825
MA0087.1 0.323
MA0088.1 0.263
MA0090.1 0.533
MA0091.1 0.915
MA0092.1 0.466
MA0093.1 0.743
MA0099.2 2.86669e-5
MA0100.1 0.694
MA0101.1 0.145
MA0102.2 0.533
MA0103.1 0.0013
MA0104.2 0.821
MA0105.1 0.121
MA0106.1 0.0431
MA0107.1 0.108
MA0108.2 2.16709e-4
MA0111.1 0.424
MA0112.2 2.13946e-6
MA0113.1 0.245
MA0114.1 6.07343e-5
MA0115.1 0.0048
MA0116.1 0.0397
MA0117.1 0.424
MA0119.1 0.0992
MA0122.1 0.74
MA0124.1 0.94
MA0125.1 0.00591
MA0131.1 0.57
MA0135.1 0.214
MA0136.1 7.29847e-10
MA0137.2 0.0275
MA0138.2 0.435
MA0139.1 0.0895
MA0140.1 0.00415
MA0141.1 9.61289e-5
MA0142.1 0.186
MA0143.1 0.0249
MA0144.1 0.0551
MA0145.1 0.0316
MA0146.1 0.0229
MA0147.1 0.988
MA0148.1 0.00299
MA0149.1 8.17113e-4
MA0150.1 0.00659
MA0152.1 0.915
MA0153.1 0.0174
MA0154.1 0.00365
MA0155.1 0.768
MA0156.1 6.41909e-5
MA0157.1 0.0107
MA0159.1 3.26423e-4
MA0160.1 0.00126
MA0162.1 0.435
MA0163.1 0.00234
MA0164.1 0.952
MA0258.1 1.14377e-4
MA0259.1 0.909



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: CNhs10512

Novel motif P-value
1 0.0575
10 0.0793
100 0.952
101 0.766
102 0.44
103 0.0294
104 0.662
105 0.484
106 0.0168
107 0.119
108 0.887
109 0.0324
11 0.0645
110 0.105
111 0.0052
112 0.00662
113 0.901
114 0.0101
115 0.41
116 0.47
117 0.0194
118 0.539
119 0.107
12 0.846
120 0.885
121 0.677
122 0.817
123 0.987
124 0.667
125 0.0933
126 0.116
127 0.065
128 0.0674
129 0.236
13 0.00961
130 0.196
131 0.748
132 0.285
133 0.434
134 0.966
135 0.668
136 0.0951
137 0.562
138 0.838
139 0.0269
14 0.572
140 0.0152
141 0.0535
142 0.623
143 0.216
144 0.652
145 0.0881
146 0.72
147 0.617
148 0.227
149 0.341
15 0.0496
150 0.284
151 0.23
152 0.0399
153 0.162
154 0.566
155 0.179
156 8.55989e-6
157 0.847
158 0.0885
159 0.0966
160 0.538
161 0.29
162 0.827
163 0.299
164 0.0269
165 0.155
166 0.39
167 0.744
168 0.608
169 0.00257
17 0.0444
18 0.467
19 0.175
2 0.914
20 0.45
21 0.671
22 0.173
23 0.264
24 0.177
25 0.412
26 0.0147
27 0.563
28 0.337
29 0.0982
3 0.0957
30 0.843
31 0.528
32 0.215
33 0.215
34 0.963
35 0.25
36 0.222
37 0.018
38 0.311
39 0.36
4 0.626
40 0.236
41 0.346
42 0.354
43 0.118
44 0.0398
45 0.55
46 0.121
47 0.13
48 0.0768
49 0.0991
5 0.151
50 0.898
51 0.599
52 0.411
53 0.985
54 0.639
55 0.382
56 0.403
57 0.488
58 0.214
59 0.0699
6 0.65
60 0.0429
61 0.22
62 0.0718
63 0.13
64 0.5
65 0.18
66 0.679
67 0.984
68 0.176
69 0.488
7 0.116
70 1.78847e-4
71 0.0508
72 0.384
73 0.0205
74 0.367
75 0.0146
76 0.552
77 0.12
78 0.0911
79 0.715
8 0.0866
80 0.386
81 0.558
82 0.0305
83 0.322
84 0.252
85 0.0166
86 0.232
87 0.514
88 0.434
89 0.209
9 0.614
90 0.084
91 0.464
92 0.0798
93 0.119
94 0.898
95 0.0231
96 0.408
97 0.556
98 0.395
99 0.745



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: CNhs10512


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)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

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)
0011326 (mouse whole body- 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

FF:0000294 (mouse embryonic day 11 sample)