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FF:1391-42E2

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Name:testis, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11130
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 stage30 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  SAMD00005568
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11130 CAGE DRX009111 DRR009985
Accession ID Mm9

Library idBAMCTSS
CNhs11130 DRZ001410 DRZ002793
Accession ID Mm10

Library idBAMCTSS
CNhs11130 DRZ012760 DRZ014143
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

CNhs11130

MCL coexpression id Coexpression dpi cluster scores median value
0 1.145
1 0
10 0
100 0
1000 0.456
1001 0.339
1002 0
1003 --0.0132
1004 0
1005 --0.0389
1006 0.27
1007 0.336
1008 0
1009 0.276
101 0.0798
1010 0
1011 0.971
1012 0
1013 --0.174
1014 --0.0874
1015 0.494
1016 --0.261
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.312
1023 0
1024 --0.14
1025 0
1026 1.077
1027 0
1028 0
1029 --0.0661
103 0.0521
1030 0.198
1031 --0.517
1032 --0.232
1033 0
1034 0
1035 0.702
1036 --0.187
1037 0
1038 --0.188
1039 0.18
104 0
1040 --0.269
1041 0.333



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: CNhs11130

Jaspar motif P-value
MA0002.2 0.176
MA0003.1 0.867
MA0004.1 0.431
MA0006.1 0.167
MA0007.1 0.985
MA0009.1 0.539
MA0014.1 0.473
MA0017.1 0.401
MA0018.2 8.65971e-12
MA0019.1 0.0575
MA0024.1 0.447
MA0025.1 0.73
MA0027.1 0.455
MA0028.1 0.00439
MA0029.1 0.704
MA0030.1 0.917
MA0031.1 0.387
MA0035.2 0.0216
MA0038.1 0.912
MA0039.2 0.118
MA0040.1 0.402
MA0041.1 0.206
MA0042.1 0.976
MA0043.1 9.71983e-4
MA0046.1 5.9641e-11
MA0047.2 0.00666
MA0048.1 0.0731
MA0050.1 1.88638e-4
MA0051.1 0.505
MA0052.1 0.824
MA0055.1 6.25948e-5
MA0057.1 0.546
MA0058.1 0.397
MA0059.1 0.0188
MA0060.1 7.00114e-7
MA0061.1 0.0124
MA0062.2 0.00182
MA0065.2 0.1
MA0066.1 0.715
MA0067.1 0.324
MA0068.1 0.867
MA0069.1 0.684
MA0070.1 0.864
MA0071.1 0.516
MA0072.1 0.693
MA0073.1 0.986
MA0074.1 0.939
MA0076.1 0.00156
MA0077.1 4.68677e-4
MA0078.1 8.22671e-10
MA0079.2 0.185
MA0080.2 2.22589e-7
MA0081.1 0.0567
MA0083.1 0.482
MA0084.1 0.621
MA0087.1 0.133
MA0088.1 0.0416
MA0090.1 0.687
MA0091.1 0.498
MA0092.1 0.0967
MA0093.1 0.519
MA0099.2 0.0721
MA0100.1 8.59338e-18
MA0101.1 0.181
MA0102.2 0.185
MA0103.1 0.874
MA0104.2 0.00167
MA0105.1 0.00694
MA0106.1 0.0331
MA0107.1 0.0128
MA0108.2 0.041
MA0111.1 0.365
MA0112.2 0.987
MA0113.1 0.72
MA0114.1 0.22
MA0115.1 0.27
MA0116.1 0.162
MA0117.1 0.851
MA0119.1 0.13
MA0122.1 0.868
MA0124.1 0.933
MA0125.1 0.149
MA0131.1 0.0471
MA0135.1 0.12
MA0136.1 8.90673e-4
MA0137.2 0.128
MA0138.2 0.0721
MA0139.1 0.194
MA0140.1 5.92681e-4
MA0141.1 0.387
MA0142.1 0.948
MA0143.1 3.43409e-4
MA0144.1 0.106
MA0145.1 0.00936
MA0146.1 0.00207
MA0147.1 0.00174
MA0148.1 0.00175
MA0149.1 0.387
MA0150.1 0.876
MA0152.1 0.212
MA0153.1 2.82563e-5
MA0154.1 0.0476
MA0155.1 0.191
MA0156.1 0.0534
MA0157.1 0.304
MA0159.1 0.234
MA0160.1 2.83736e-4
MA0162.1 0.928
MA0163.1 0.0172
MA0164.1 0.488
MA0258.1 0.305
MA0259.1 0.0236



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: CNhs11130

Novel motif P-value
1 0.585
10 0.107
100 0.0524
101 0.952
102 0.182
103 0.67
104 0.739
105 0.399
106 4.07231e-4
107 5.70932e-4
108 0.27
109 0.184
11 0.412
110 0.285
111 0.0206
112 0.248
113 0.405
114 0.255
115 0.951
116 0.895
117 0.00499
118 0.142
119 0.892
12 0.836
120 0.968
121 0.0404
122 0.765
123 0.33
124 0.224
125 0.927
126 0.167
127 0.878
128 0.00326
129 0.45
13 0.085
130 0.983
131 0.184
132 0.699
133 0.771
134 0.575
135 0.0318
136 0.00101
137 0.543
138 0.614
139 0.363
14 0.31
140 0.949
141 0.142
142 0.713
143 0.697
144 0.163
145 0.267
146 0.796
147 0.241
148 0.0751
149 0.0743
15 0.701
150 0.2
151 0.192
152 0.431
153 0.299
154 0.725
155 0.225
156 0.0352
157 0.783
158 6.68628e-6
159 0.22
160 0.161
161 0.166
162 0.732
163 0.366
164 0.19
165 0.469
166 0.602
167 0.67
168 0.438
169 0.515
17 0.646
18 0.884
19 0.762
2 6.26518e-4
20 0.00436
21 0.429
22 0.986
23 0.416
24 0.118
25 0.336
26 0.886
27 0.00867
28 0.9
29 0.0559
3 0.911
30 0.246
31 0.28
32 0.745
33 0.268
34 0.839
35 0.631
36 0.187
37 0.822
38 0.866
39 0.52
4 0.759
40 0.129
41 4.24996e-4
42 0.8
43 0.639
44 0.823
45 0.366
46 0.891
47 0.328
48 0.379
49 0.944
5 0.821
50 0.886
51 0.55
52 0.174
53 0.267
54 0.508
55 0.677
56 0.233
57 0.974
58 0.557
59 0.222
6 0.556
60 0.447
61 0.649
62 0.744
63 0.695
64 0.661
65 0.229
66 0.0452
67 0.639
68 0.319
69 0.192
7 0.637
70 0.374
71 0.983
72 0.262
73 0.523
74 0.894
75 0.366
76 0.0186
77 0.671
78 0.0079
79 0.604
8 0.0423
80 0.306
81 0.2
82 0.989
83 0.899
84 0.627
85 0.889
86 0.855
87 0.0214
88 0.78
89 0.578
9 0.738
90 0.591
91 0.211
92 0.666
93 0.237
94 0.824
95 0.0866
96 0.39
97 0.256
98 0.976
99 0.247



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: CNhs11130


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)
0000310 (mouse neonate N30 sample)
0011495 (mouse testis- neonate N30 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)