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FF:1564-45I6

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Name:gonad, embryo E13
Species:Mouse (Mus musculus)
Library ID:CNhs11044
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
tissuegonad
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  SAMD00004837
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11044 CAGE DRX008970 DRR009844
Accession ID Mm9

Library idBAMCTSS
CNhs11044 DRZ001269 DRZ002652
Accession ID Mm10

Library idBAMCTSS
CNhs11044 DRZ012619 DRZ014002
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

CNhs11044

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0322
1001 --0.0356
1002 0.586
1003 --0.102
1004 0.112
1005 --0.0389
1006 --0.0465
1007 0.113
1008 0
1009 --0.00536
101 0.0975
1010 0
1011 --0.0287
1012 0
1013 --0.116
1014 0.358
1015 0.159
1016 0.339
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.0638
1023 0
1024 --0.011
1025 0
1026 0.0494
1027 0
1028 0
1029 0.117
103 0.164
1030 0
1031 0.416
1032 --0.0159
1033 0.0397
1034 0
1035 0.0788
1036 0.132
1037 0
1038 0.0817
1039 --0.108
104 0
1040 0.0559
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: CNhs11044

Jaspar motif P-value
MA0002.2 2.30203e-4
MA0003.1 0.561
MA0004.1 0.601
MA0006.1 0.293
MA0007.1 0.427
MA0009.1 0.775
MA0014.1 0.646
MA0017.1 0.00329
MA0018.2 0.163
MA0019.1 0.906
MA0024.1 3.76289e-6
MA0025.1 0.00118
MA0027.1 0.129
MA0028.1 0.173
MA0029.1 0.986
MA0030.1 0.036
MA0031.1 0.00374
MA0035.2 0.24
MA0038.1 0.153
MA0039.2 0.127
MA0040.1 0.377
MA0041.1 0.244
MA0042.1 0.461
MA0043.1 0.319
MA0046.1 3.95704e-7
MA0047.2 0.0178
MA0048.1 0.0135
MA0050.1 0.0142
MA0051.1 0.0038
MA0052.1 5.56738e-6
MA0055.1 0.00532
MA0057.1 0.128
MA0058.1 0.432
MA0059.1 0.221
MA0060.1 1.93354e-6
MA0061.1 0.121
MA0062.2 0.727
MA0065.2 2.71987e-4
MA0066.1 0.0493
MA0067.1 0.411
MA0068.1 0.00216
MA0069.1 0.541
MA0070.1 0.851
MA0071.1 0.283
MA0072.1 0.0369
MA0073.1 0.655
MA0074.1 0.871
MA0076.1 0.154
MA0077.1 0.982
MA0078.1 0.527
MA0079.2 0.945
MA0080.2 1.85304e-7
MA0081.1 0.345
MA0083.1 0.128
MA0084.1 0.615
MA0087.1 0.318
MA0088.1 0.597
MA0090.1 0.987
MA0091.1 0.578
MA0092.1 0.677
MA0093.1 0.584
MA0099.2 2.69456e-7
MA0100.1 0.781
MA0101.1 0.305
MA0102.2 0.0726
MA0103.1 0.00372
MA0104.2 0.241
MA0105.1 0.0409
MA0106.1 0.226
MA0107.1 0.164
MA0108.2 0.00213
MA0111.1 0.474
MA0112.2 5.7843e-4
MA0113.1 0.463
MA0114.1 0.00204
MA0115.1 0.0459
MA0116.1 0.0482
MA0117.1 0.0299
MA0119.1 0.206
MA0122.1 0.926
MA0124.1 0.283
MA0125.1 0.831
MA0131.1 0.21
MA0135.1 0.273
MA0136.1 3.40985e-4
MA0137.2 0.194
MA0138.2 1.82196e-4
MA0139.1 0.638
MA0140.1 0.623
MA0141.1 0.591
MA0142.1 0.558
MA0143.1 0.111
MA0144.1 0.145
MA0145.1 0.00767
MA0146.1 0.729
MA0147.1 0.242
MA0148.1 0.00783
MA0149.1 0.0488
MA0150.1 3.2078e-4
MA0152.1 0.211
MA0153.1 6.38008e-5
MA0154.1 0.0489
MA0155.1 0.971
MA0156.1 0.0867
MA0157.1 0.0704
MA0159.1 0.0052
MA0160.1 0.149
MA0162.1 0.401
MA0163.1 0.835
MA0164.1 0.964
MA0258.1 0.00208
MA0259.1 0.203



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: CNhs11044

Novel motif P-value
1 0.115
10 0.41
100 0.726
101 0.519
102 0.844
103 0.366
104 0.843
105 0.228
106 0.012
107 0.2
108 0.496
109 0.256
11 0.247
110 0.932
111 0.288
112 0.428
113 0.418
114 0.0418
115 0.437
116 0.463
117 0.374
118 0.844
119 0.205
12 0.516
120 0.818
121 0.273
122 0.737
123 0.106
124 0.169
125 0.415
126 0.957
127 0.0615
128 0.00599
129 0.0312
13 0.973
130 0.224
131 0.222
132 0.569
133 0.527
134 0.595
135 0.932
136 0.697
137 0.698
138 0.488
139 0.0502
14 0.177
140 0.94
141 0.176
142 0.322
143 0.102
144 0.372
145 0.967
146 0.268
147 0.835
148 0.192
149 0.258
15 0.118
150 0.88
151 0.0439
152 0.114
153 0.882
154 0.512
155 0.837
156 2.80617e-4
157 0.574
158 0.334
159 0.198
160 0.747
161 0.862
162 0.997
163 0.00882
164 0.464
165 0.102
166 0.316
167 0.652
168 0.122
169 0.0915
17 0.112
18 0.111
19 0.803
2 0.526
20 0.377
21 0.696
22 0.559
23 0.137
24 0.6
25 0.277
26 0.848
27 0.369
28 0.244
29 0.751
3 0.385
30 0.561
31 0.219
32 0.308
33 0.947
34 0.764
35 0.111
36 0.262
37 0.169
38 0.657
39 0.85
4 0.743
40 0.404
41 0.0598
42 0.767
43 0.224
44 0.0775
45 0.409
46 0.312
47 0.287
48 0.283
49 0.13
5 0.169
50 0.8
51 0.683
52 0.268
53 0.564
54 0.365
55 0.503
56 0.318
57 0.912
58 0.25
59 0.142
6 0.848
60 0.0888
61 0.581
62 0.0705
63 0.194
64 0.657
65 0.206
66 0.967
67 0.821
68 0.0836
69 0.872
7 0.363
70 0.00188
71 0.31
72 0.35
73 0.143
74 0.747
75 0.197
76 0.469
77 0.317
78 0.214
79 0.88
8 0.236
80 0.0706
81 0.315
82 0.217
83 0.346
84 0.0786
85 0.00599
86 0.32
87 0.259
88 0.805
89 0.0947
9 0.753
90 0.104
91 0.517
92 0.125
93 0.681
94 0.364
95 0.188
96 0.503
97 0.908
98 0.131
99 0.799



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: CNhs11044


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)
0000991 (gonad)
0000479 (tissue)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003133 (reproductive organ)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)

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)
0011282 (mouse gonad- 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:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0005564 (gonad primordium)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)