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FF:443-27C5

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Name:testis, embryo E15
Species:Mouse (Mus musculus)
Library ID:CNhs11034
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 stage15 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  SAMD00005707
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11034 CAGE DRX009103 DRR009977
Accession ID Mm9

Library idBAMCTSS
CNhs11034 DRZ001402 DRZ002785
Accession ID Mm10

Library idBAMCTSS
CNhs11034 DRZ012752 DRZ014135
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

CNhs11034

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0749
1002 0.363
1003 --0.0745
1004 0
1005 --0.132
1006 --0.0582
1007 0.0483
1008 0
1009 0.00927
101 0.0999
1010 0
1011 0
1012 0
1013 --0.163
1014 0
1015 0.298
1016 0.377
1017 0
1018 0.0665
1019 0
102 0
1020 0
1021 0
1022 0
1023 0
1024 0
1025 0
1026 0
1027 0.00553
1028 0
1029 --0.0518
103 0.0557
1030 0
1031 0.242
1032 --0.0163
1033 0
1034 0
1035 0.0665
1036 --0.0236
1037 0
1038 --0.0566
1039 0.0195
104 0
1040 --0.0544
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: CNhs11034

Jaspar motif P-value
MA0002.2 0.0331
MA0003.1 0.631
MA0004.1 0.264
MA0006.1 0.189
MA0007.1 0.656
MA0009.1 0.878
MA0014.1 0.609
MA0017.1 0.0182
MA0018.2 0.604
MA0019.1 0.326
MA0024.1 1.18078e-7
MA0025.1 0.547
MA0027.1 0.144
MA0028.1 8.87583e-4
MA0029.1 0.678
MA0030.1 0.0311
MA0031.1 0.0905
MA0035.2 0.264
MA0038.1 0.0335
MA0039.2 0.0423
MA0040.1 0.332
MA0041.1 0.379
MA0042.1 0.414
MA0043.1 0.661
MA0046.1 3.63769e-24
MA0047.2 0.08
MA0048.1 0.0185
MA0050.1 2.09459e-4
MA0051.1 4.80874e-4
MA0052.1 0.00452
MA0055.1 4.75198e-4
MA0057.1 0.387
MA0058.1 0.0706
MA0059.1 0.0605
MA0060.1 5.51409e-15
MA0061.1 0.109
MA0062.2 0.00603
MA0065.2 0.0483
MA0066.1 0.0911
MA0067.1 0.646
MA0068.1 0.0348
MA0069.1 0.827
MA0070.1 0.439
MA0071.1 0.586
MA0072.1 0.427
MA0073.1 0.845
MA0074.1 0.655
MA0076.1 6.1391e-4
MA0077.1 0.548
MA0078.1 0.593
MA0079.2 0.488
MA0080.2 1.53644e-5
MA0081.1 0.887
MA0083.1 0.0815
MA0084.1 0.925
MA0087.1 0.546
MA0088.1 0.521
MA0090.1 0.79
MA0091.1 0.659
MA0092.1 0.485
MA0093.1 0.207
MA0099.2 1.37722e-4
MA0100.1 0.399
MA0101.1 0.626
MA0102.2 0.091
MA0103.1 0.00101
MA0104.2 0.0128
MA0105.1 0.0257
MA0106.1 0.608
MA0107.1 0.168
MA0108.2 0.0671
MA0111.1 0.176
MA0112.2 0.00514
MA0113.1 0.869
MA0114.1 0.0122
MA0115.1 0.363
MA0116.1 0.382
MA0117.1 0.0952
MA0119.1 0.432
MA0122.1 0.86
MA0124.1 0.315
MA0125.1 0.944
MA0131.1 0.278
MA0135.1 0.902
MA0136.1 0.122
MA0137.2 0.405
MA0138.2 0.00233
MA0139.1 0.729
MA0140.1 0.244
MA0141.1 0.0342
MA0142.1 0.415
MA0143.1 0.253
MA0144.1 0.311
MA0145.1 0.028
MA0146.1 0.22
MA0147.1 0.00945
MA0148.1 0.00703
MA0149.1 0.633
MA0150.1 0.00234
MA0152.1 0.701
MA0153.1 7.91459e-16
MA0154.1 0.0591
MA0155.1 0.819
MA0156.1 0.63
MA0157.1 0.106
MA0159.1 9.5101e-4
MA0160.1 0.317
MA0162.1 0.317
MA0163.1 0.711
MA0164.1 0.381
MA0258.1 0.00306
MA0259.1 0.0478



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: CNhs11034

Novel motif P-value
1 0.181
10 0.589
100 0.506
101 0.639
102 0.549
103 0.44
104 0.988
105 0.172
106 6.43075e-4
107 0.0172
108 0.964
109 0.802
11 0.586
110 0.703
111 0.516
112 0.399
113 0.306
114 0.177
115 0.577
116 0.688
117 0.46
118 0.703
119 0.261
12 0.655
120 0.656
121 0.534
122 0.913
123 0.193
124 0.0665
125 0.0943
126 0.989
127 0.239
128 8.21339e-4
129 0.031
13 0.668
130 0.236
131 0.813
132 0.183
133 0.864
134 0.249
135 0.981
136 0.0724
137 0.662
138 0.693
139 0.116
14 0.129
140 0.457
141 0.0484
142 0.886
143 0.116
144 0.088
145 0.973
146 0.363
147 0.377
148 0.0612
149 0.371
15 0.184
150 0.953
151 0.0427
152 0.648
153 0.244
154 0.93
155 0.666
156 6.94651e-5
157 0.591
158 0.227
159 0.0504
160 0.884
161 0.75
162 0.636
163 0.073
164 0.615
165 0.168
166 0.918
167 0.794
168 0.181
169 0.78
17 0.141
18 0.235
19 0.866
2 0.396
20 0.374
21 0.477
22 0.874
23 0.0399
24 0.652
25 0.4
26 0.939
27 0.224
28 0.252
29 0.521
3 0.407
30 0.714
31 0.163
32 0.192
33 0.404
34 0.989
35 0.0664
36 0.698
37 0.405
38 0.831
39 0.836
4 0.711
40 0.765
41 0.245
42 0.701
43 0.221
44 0.392
45 0.354
46 0.192
47 0.549
48 0.512
49 0.128
5 0.072
50 0.832
51 0.805
52 0.139
53 0.634
54 0.373
55 0.744
56 0.253
57 0.9
58 0.299
59 0.394
6 0.833
60 0.0336
61 0.593
62 0.166
63 0.215
64 0.885
65 0.255
66 0.312
67 0.345
68 5.76279e-4
69 0.707
7 0.444
70 0.0167
71 0.367
72 0.896
73 0.855
74 0.452
75 0.957
76 0.364
77 0.443
78 0.328
79 0.861
8 0.507
80 0.158
81 0.256
82 0.48
83 0.642
84 0.146
85 0.00771
86 0.316
87 0.213
88 0.675
89 0.0352
9 0.643
90 0.26
91 0.285
92 0.0629
93 0.645
94 0.176
95 0.361
96 0.395
97 0.891
98 0.0724
99 0.653



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: CNhs11034


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)
0000298 (mouse embryonic day 15 sample)
0011352 (mouse testis- embryo E15 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)