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FF:503-18G5

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Name:testis, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs11027
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
tissuetestis
dev stage18 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  SAMD00005973
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11027 CAGE DRX009106 DRR009980
Accession ID Mm9

Library idBAMCTSS
CNhs11027 DRZ001405 DRZ002788
Accession ID Mm10

Library idBAMCTSS
CNhs11027 DRZ012755 DRZ014138
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

CNhs11027

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.00141
1001 0.0615
1002 0.813
1003 0.25
1004 0
1005 0
1006 0
1007 0.036
1008 0
1009 0.066
101 0.0691
1010 0
1011 0.0186
1012 0.126
1013 --0.139
1014 0.474
1015 0.137
1016 0.321
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.0678
1023 0
1024 --0.0221
1025 0.0173
1026 0
1027 0
1028 0
1029 0.225
103 0.266
1030 0
1031 0.427
1032 --0.0213
1033 0.0013
1034 0
1035 0.126
1036 0.0511
1037 0
1038 0
1039 --0.0443
104 0
1040 0.0421
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: CNhs11027

Jaspar motif P-value
MA0002.2 0.00167
MA0003.1 0.972
MA0004.1 0.472
MA0006.1 0.0949
MA0007.1 0.818
MA0009.1 0.527
MA0014.1 0.856
MA0017.1 4.87936e-4
MA0018.2 0.102
MA0019.1 0.403
MA0024.1 1.84804e-6
MA0025.1 0.425
MA0027.1 0.956
MA0028.1 0.157
MA0029.1 0.794
MA0030.1 0.0272
MA0031.1 0.0334
MA0035.2 0.25
MA0038.1 0.0416
MA0039.2 0.19
MA0040.1 0.0623
MA0041.1 0.158
MA0042.1 0.378
MA0043.1 0.737
MA0046.1 3.78685e-24
MA0047.2 0.00787
MA0048.1 0.0108
MA0050.1 0.0796
MA0051.1 0.0329
MA0052.1 3.36375e-4
MA0055.1 0.00511
MA0057.1 0.22
MA0058.1 0.238
MA0059.1 0.162
MA0060.1 1.42891e-7
MA0061.1 0.33
MA0062.2 0.977
MA0065.2 0.00463
MA0066.1 0.0772
MA0067.1 0.587
MA0068.1 0.59
MA0069.1 0.78
MA0070.1 0.965
MA0071.1 0.788
MA0072.1 0.254
MA0073.1 0.229
MA0074.1 0.72
MA0076.1 0.131
MA0077.1 0.454
MA0078.1 0.0444
MA0079.2 0.487
MA0080.2 1.23917e-6
MA0081.1 0.301
MA0083.1 0.181
MA0084.1 0.397
MA0087.1 0.248
MA0088.1 0.754
MA0090.1 0.647
MA0091.1 0.993
MA0092.1 0.574
MA0093.1 0.356
MA0099.2 3.10009e-6
MA0100.1 0.715
MA0101.1 0.47
MA0102.2 0.803
MA0103.1 2.80116e-4
MA0104.2 0.0329
MA0105.1 0.19
MA0106.1 0.521
MA0107.1 0.261
MA0108.2 1.59278e-4
MA0111.1 0.283
MA0112.2 0.0356
MA0113.1 0.419
MA0114.1 7.87553e-4
MA0115.1 0.103
MA0116.1 0.404
MA0117.1 0.13
MA0119.1 0.97
MA0122.1 0.623
MA0124.1 0.127
MA0125.1 0.469
MA0131.1 0.559
MA0135.1 0.104
MA0136.1 1.16699e-5
MA0137.2 0.246
MA0138.2 0.0178
MA0139.1 0.867
MA0140.1 0.779
MA0141.1 0.0175
MA0142.1 0.0134
MA0143.1 0.852
MA0144.1 0.16
MA0145.1 0.00995
MA0146.1 0.416
MA0147.1 0.0488
MA0148.1 0.00141
MA0149.1 0.264
MA0150.1 1.21479e-4
MA0152.1 0.0239
MA0153.1 4.0512e-16
MA0154.1 0.0783
MA0155.1 0.971
MA0156.1 0.0321
MA0157.1 0.0915
MA0159.1 2.27186e-5
MA0160.1 0.729
MA0162.1 0.0816
MA0163.1 0.327
MA0164.1 0.731
MA0258.1 0.0018
MA0259.1 0.0341



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: CNhs11027

Novel motif P-value
1 0.275
10 0.922
100 0.527
101 0.71
102 0.375
103 0.641
104 0.928
105 0.226
106 1.24604e-4
107 0.0108
108 0.714
109 0.758
11 0.426
110 0.595
111 0.831
112 0.941
113 0.365
114 0.0465
115 0.503
116 0.27
117 0.525
118 0.465
119 0.22
12 0.427
120 0.364
121 0.946
122 0.955
123 0.235
124 0.328
125 0.261
126 0.811
127 0.412
128 6.17341e-4
129 0.19
13 0.77
130 0.391
131 0.59
132 0.788
133 0.537
134 0.988
135 0.178
136 0.227
137 0.879
138 0.635
139 0.201
14 0.127
140 0.741
141 0.0983
142 0.145
143 0.145
144 0.0138
145 0.726
146 0.208
147 0.612
148 0.214
149 0.457
15 0.127
150 0.979
151 0.0576
152 0.241
153 0.773
154 0.564
155 0.644
156 0.716
157 0.534
158 0.327
159 0.663
160 0.562
161 0.657
162 0.431
163 0.0415
164 0.597
165 0.0427
166 0.652
167 0.929
168 0.226
169 0.843
17 0.167
18 0.201
19 0.68
2 0.238
20 0.6
21 0.425
22 0.891
23 0.111
24 0.998
25 0.41
26 0.791
27 0.248
28 0.408
29 0.192
3 0.434
30 0.594
31 0.214
32 0.734
33 0.744
34 0.879
35 0.103
36 0.45
37 0.328
38 0.676
39 0.937
4 0.622
40 0.576
41 0.0129
42 0.705
43 0.401
44 0.59
45 0.186
46 0.15
47 0.676
48 0.409
49 0.207
5 0.136
50 0.781
51 0.844
52 0.0934
53 0.703
54 0.338
55 0.199
56 0.313
57 0.767
58 0.385
59 0.187
6 0.924
60 0.0283
61 0.841
62 0.124
63 0.309
64 0.836
65 0.262
66 0.771
67 0.192
68 0.00212
69 0.256
7 0.618
70 0.0113
71 0.469
72 0.543
73 0.281
74 0.701
75 0.851
76 0.489
77 0.521
78 0.429
79 0.85
8 0.264
80 0.0161
81 0.422
82 0.874
83 0.771
84 0.252
85 0.0103
86 0.0934
87 0.137
88 0.7
89 0.0266
9 0.745
90 0.545
91 0.481
92 0.277
93 0.293
94 0.494
95 0.909
96 0.678
97 0.949
98 0.123
99 0.88



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: CNhs11027


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)
0000473 (testis)
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)
0003135 (male reproductive organ)
0003133 (reproductive organ)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0003101 (male organism)
0000079 (male reproductive 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)
0000302 (mouse embryonic day 18 sample)
0011377 (mouse testis- embryo E18 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:0009117 (indifferent gonad)
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)