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FF:490-9F9

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Name:whole body, embryo E17.5
Species:Mouse (Mus musculus)
Library ID:CNhs10513
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 stage17.5 days embryo
sexmale
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  SAMD00004978
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10513 CAGE DRX009148 DRR010022
Accession ID Mm9

Library idBAMCTSS
CNhs10513 DRZ001447 DRZ002830
Accession ID Mm10

Library idBAMCTSS
CNhs10513 DRZ012797 DRZ014180
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

CNhs10513

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.103
10 0
100 0.0766
1000 0.0737
1001 0.0651
1002 --0.0468
1003 0.0602
1004 0
1005 0.0479
1006 0.187
1007 0.00857
1008 0
1009 0.0353
101 --0.0221
1010 0
1011 0.1
1012 0.0438
1013 --0.0355
1014 0.401
1015 0.0117
1016 0.169
1017 0
1018 0.371
1019 0
102 0
1020 0
1021 0
1022 0.247
1023 0
1024 0.16
1025 0.437
1026 0.145
1027 0.15
1028 0
1029 --0.1
103 0.442
1030 0
1031 0.344
1032 --0.022
1033 0
1034 0.198
1035 0.129
1036 --0.0113
1037 0
1038 0.0613
1039 0.0638
104 0
1040 0.124
1041 0.198



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: CNhs10513

Jaspar motif P-value
MA0002.2 0.368
MA0003.1 0.0865
MA0004.1 0.0685
MA0006.1 0.513
MA0007.1 0.132
MA0009.1 0.527
MA0014.1 0.214
MA0017.1 0.388
MA0018.2 1.83182e-4
MA0019.1 0.83
MA0024.1 0.475
MA0025.1 0.205
MA0027.1 0.505
MA0028.1 5.29781e-9
MA0029.1 0.549
MA0030.1 0.422
MA0031.1 0.755
MA0035.2 0.0998
MA0038.1 0.0126
MA0039.2 0.113
MA0040.1 0.831
MA0041.1 0.494
MA0042.1 0.7
MA0043.1 0.0627
MA0046.1 1.97535e-19
MA0047.2 0.0839
MA0048.1 0.003
MA0050.1 1.90546e-7
MA0051.1 1.39622e-5
MA0052.1 2.16537e-16
MA0055.1 3.31586e-5
MA0057.1 0.638
MA0058.1 0.0104
MA0059.1 0.00463
MA0060.1 0.0385
MA0061.1 0.106
MA0062.2 1.94351e-16
MA0065.2 0.66
MA0066.1 0.694
MA0067.1 0.0696
MA0068.1 0.351
MA0069.1 0.236
MA0070.1 0.21
MA0071.1 0.0247
MA0072.1 0.175
MA0073.1 0.986
MA0074.1 0.192
MA0076.1 4.3881e-10
MA0077.1 0.717
MA0078.1 0.0563
MA0079.2 0.012
MA0080.2 4.3656e-7
MA0081.1 0.0311
MA0083.1 5.08059e-10
MA0084.1 0.818
MA0087.1 0.113
MA0088.1 0.132
MA0090.1 0.0408
MA0091.1 0.763
MA0092.1 0.29
MA0093.1 0.0589
MA0099.2 0.683
MA0100.1 0.00591
MA0101.1 0.00669
MA0102.2 0.199
MA0103.1 0.804
MA0104.2 0.0822
MA0105.1 0.775
MA0106.1 0.289
MA0107.1 0.0361
MA0108.2 1.05129e-53
MA0111.1 0.647
MA0112.2 0.664
MA0113.1 0.15
MA0114.1 0.846
MA0115.1 0.169
MA0116.1 0.873
MA0117.1 0.165
MA0119.1 0.211
MA0122.1 0.73
MA0124.1 0.871
MA0125.1 0.0137
MA0131.1 0.231
MA0135.1 0.0571
MA0136.1 1.06296e-13
MA0137.2 0.00105
MA0138.2 2.11122e-6
MA0139.1 0.194
MA0140.1 0.00369
MA0141.1 0.0379
MA0142.1 0.783
MA0143.1 0.781
MA0144.1 0.0941
MA0145.1 0.0786
MA0146.1 0.255
MA0147.1 0.0633
MA0148.1 0.0449
MA0149.1 0.00532
MA0150.1 0.183
MA0152.1 0.932
MA0153.1 3.53897e-9
MA0154.1 0.377
MA0155.1 0.145
MA0156.1 1.26058e-12
MA0157.1 0.932
MA0159.1 0.0416
MA0160.1 0.0516
MA0162.1 0.965
MA0163.1 0.232
MA0164.1 0.16
MA0258.1 0.377
MA0259.1 0.207



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: CNhs10513

Novel motif P-value
1 0.508
10 0.0806
100 0.532
101 0.1
102 0.0485
103 0.0386
104 0.73
105 0.462
106 0.581
107 0.024
108 0.813
109 0.372
11 0.313
110 0.292
111 0.018
112 0.106
113 0.633
114 0.196
115 0.863
116 0.371
117 0.00415
118 0.144
119 0.694
12 0.358
120 0.384
121 0.291
122 0.248
123 0.401
124 0.646
125 0.099
126 0.124
127 0.78
128 0.532
129 0.804
13 0.0371
130 0.471
131 0.0527
132 0.943
133 0.0828
134 0.482
135 0.739
136 0.176
137 0.55
138 0.762
139 0.696
14 0.389
140 0.725
141 0.838
142 0.749
143 0.144
144 0.817
145 0.359
146 0.204
147 0.95
148 0.28
149 0.858
15 0.0267
150 0.88
151 0.776
152 0.534
153 0.298
154 0.415
155 0.0295
156 0.0797
157 0.134
158 0.00395
159 0.0657
160 0.126
161 0.118
162 0.274
163 0.817
164 0.0362
165 0.395
166 0.118
167 0.00395
168 0.00139
169 0.639
17 0.966
18 0.245
19 0.444
2 0.0189
20 0.00368
21 0.342
22 0.834
23 0.274
24 0.156
25 0.695
26 0.511
27 0.464
28 0.819
29 0.0228
3 0.411
30 0.072
31 0.683
32 0.754
33 0.19
34 0.349
35 0.151
36 0.0629
37 0.257
38 0.702
39 0.711
4 0.914
40 0.211
41 0.205
42 0.619
43 0.999
44 0.205
45 0.201
46 0.737
47 0.827
48 0.415
49 0.515
5 0.536
50 0.683
51 0.857
52 0.199
53 0.14
54 0.476
55 0.743
56 0.586
57 0.529
58 0.833
59 0.133
6 0.91
60 0.804
61 0.308
62 0.792
63 0.865
64 0.951
65 0.87
66 0.999
67 0.916
68 0.53
69 0.771
7 0.794
70 0.0118
71 0.393
72 0.504
73 0.142
74 0.788
75 0.0411
76 0.0016
77 0.336
78 0.683
79 0.836
8 0.407
80 0.901
81 0.587
82 0.833
83 0.558
84 0.705
85 0.921
86 0.963
87 0.58
88 0.363
89 0.419
9 0.489
90 0.0119
91 0.505
92 0.684
93 0.0316
94 0.968
95 0.0238
96 0.866
97 0.576
98 0.748
99 0.138



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: CNhs10513


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)
0000301 (mouse embryonic day 17.5 sample)
0011374 (mouse whole body- embryo E17.5 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)