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FF:839-18H3

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Name:testis, neonate N20
Species:Mouse (Mus musculus)
Library ID:CNhs11110
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 stage20 days neonate
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  SAMD00004759
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11110 CAGE DRX009110 DRR009984
Accession ID Mm9

Library idBAMCTSS
CNhs11110 DRZ001409 DRZ002792
Accession ID Mm10

Library idBAMCTSS
CNhs11110 DRZ012759 DRZ014142
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

CNhs11110

MCL coexpression id Coexpression dpi cluster scores median value
0 0.505
1 0
10 0
100 0
1000 0.047
1001 0.392
1002 2.087892e-4
1003 0.00324
1004 0
1005 --0.304
1006 --0.0253
1007 0.232
1008 0
1009 0.18
101 0.13
1010 0
1011 0.854
1012 0.094
1013 0.00566
1014 --0.0851
1015 0.472
1016 --0.205
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0
1023 0
1024 --0.14
1025 0
1026 0.968
1027 0.033
1028 0
1029 0.0236
103 0.0275
1030 0
1031 --0.456
1032 --0.418
1033 0.0188
1034 0
1035 0.294
1036 --0.129
1037 0
1038 --0.15
1039 --0.0783
104 0
1040 --0.469
1041 0.237



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: CNhs11110

Jaspar motif P-value
MA0002.2 0.032
MA0003.1 0.801
MA0004.1 0.268
MA0006.1 0.0883
MA0007.1 0.946
MA0009.1 0.37
MA0014.1 0.344
MA0017.1 0.139
MA0018.2 0.045
MA0019.1 0.226
MA0024.1 0.0692
MA0025.1 0.776
MA0027.1 0.768
MA0028.1 4.81754e-5
MA0029.1 0.184
MA0030.1 0.965
MA0031.1 0.798
MA0035.2 0.0759
MA0038.1 0.143
MA0039.2 0.282
MA0040.1 0.392
MA0041.1 0.948
MA0042.1 0.959
MA0043.1 0.0289
MA0046.1 4.39153e-15
MA0047.2 0.00849
MA0048.1 0.0542
MA0050.1 0.00881
MA0051.1 0.611
MA0052.1 1.63504e-4
MA0055.1 8.53065e-4
MA0057.1 0.398
MA0058.1 0.139
MA0059.1 0.0286
MA0060.1 1.266e-11
MA0061.1 0.0218
MA0062.2 1.72785e-7
MA0065.2 0.704
MA0066.1 0.0392
MA0067.1 0.578
MA0068.1 0.698
MA0069.1 0.282
MA0070.1 0.496
MA0071.1 0.774
MA0072.1 0.448
MA0073.1 0.831
MA0074.1 0.638
MA0076.1 1.23549e-6
MA0077.1 0.948
MA0078.1 0.661
MA0079.2 0.703
MA0080.2 1.03555e-4
MA0081.1 0.329
MA0083.1 0.0145
MA0084.1 0.568
MA0087.1 0.503
MA0088.1 0.0813
MA0090.1 0.216
MA0091.1 0.437
MA0092.1 0.0967
MA0093.1 0.225
MA0099.2 0.00316
MA0100.1 2.20814e-15
MA0101.1 0.467
MA0102.2 0.228
MA0103.1 0.401
MA0104.2 6.35214e-4
MA0105.1 7.89549e-4
MA0106.1 0.0483
MA0107.1 0.0823
MA0108.2 1.09506e-5
MA0111.1 0.887
MA0112.2 0.0197
MA0113.1 0.794
MA0114.1 0.107
MA0115.1 0.266
MA0116.1 0.0195
MA0117.1 0.846
MA0119.1 0.0829
MA0122.1 0.428
MA0124.1 0.903
MA0125.1 0.169
MA0131.1 0.0197
MA0135.1 0.0508
MA0136.1 0.719
MA0137.2 0.612
MA0138.2 0.0182
MA0139.1 0.231
MA0140.1 0.00608
MA0141.1 0.842
MA0142.1 0.00503
MA0143.1 0.456
MA0144.1 0.317
MA0145.1 0.0112
MA0146.1 0.0326
MA0147.1 0.00182
MA0148.1 5.50124e-4
MA0149.1 0.214
MA0150.1 0.134
MA0152.1 0.832
MA0153.1 8.6966e-7
MA0154.1 0.00484
MA0155.1 0.101
MA0156.1 0.0658
MA0157.1 0.339
MA0159.1 0.424
MA0160.1 0.485
MA0162.1 0.455
MA0163.1 0.516
MA0164.1 0.328
MA0258.1 0.08
MA0259.1 0.0079



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: CNhs11110

Novel motif P-value
1 0.799
10 0.219
100 0.254
101 0.389
102 0.534
103 0.554
104 0.918
105 0.0192
106 5.31924e-5
107 5.0949e-4
108 0.2
109 0.703
11 0.962
110 0.607
111 0.18
112 0.809
113 0.181
114 0.925
115 0.465
116 0.633
117 0.0199
118 0.449
119 0.253
12 0.836
120 0.894
121 0.0858
122 0.208
123 0.0488
124 0.0812
125 0.481
126 0.443
127 0.438
128 1.91663e-4
129 0.233
13 0.519
130 0.78
131 0.0787
132 0.279
133 0.251
134 0.78
135 0.0287
136 0.00915
137 0.868
138 0.973
139 0.967
14 0.122
140 0.205
141 0.0055
142 0.244
143 0.11
144 0.399
145 0.968
146 0.668
147 0.27
148 0.0966
149 0.0198
15 0.263
150 0.735
151 0.105
152 0.135
153 0.486
154 0.994
155 0.233
156 0.0311
157 0.421
158 0.618
159 0.273
160 0.0938
161 0.308
162 0.329
163 0.244
164 0.589
165 0.143
166 0.73
167 0.428
168 0.0512
169 0.364
17 0.259
18 0.408
19 0.439
2 0.0171
20 0.0213
21 0.515
22 0.44
23 0.12
24 0.119
25 0.567
26 0.665
27 0.0314
28 0.546
29 0.214
3 0.493
30 0.193
31 0.0798
32 0.374
33 0.64
34 0.504
35 0.912
36 0.363
37 0.492
38 0.507
39 0.501
4 0.953
40 0.414
41 0.998
42 0.581
43 0.205
44 0.323
45 0.244
46 0.332
47 0.833
48 0.828
49 0.355
5 0.252
50 0.709
51 0.387
52 0.0399
53 0.254
54 0.315
55 0.253
56 0.0875
57 0.657
58 0.851
59 0.0561
6 0.654
60 0.111
61 0.691
62 0.642
63 0.262
64 0.861
65 0.0987
66 0.012
67 0.137
68 0.758
69 0.866
7 0.967
70 0.895
71 0.524
72 0.711
73 0.776
74 0.866
75 0.815
76 0.0641
77 0.289
78 0.0282
79 0.221
8 0.776
80 0.372
81 0.199
82 0.346
83 0.842
84 0.358
85 0.302
86 0.86
87 0.119
88 0.282
89 0.223
9 0.768
90 0.7
91 0.0793
92 0.299
93 0.909
94 0.349
95 0.336
96 0.932
97 0.603
98 0.291
99 0.421



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: CNhs11110


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000308 (mouse neonate N20 sample)
0011433 (mouse testis- neonate N20 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)