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FF:1300-22B7

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Name:testis, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11189
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 stage0 day 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  SAMD00005755
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11189 CAGE DRX009107 DRR009981
Accession ID Mm9

Library idBAMCTSS
CNhs11189 DRZ001406 DRZ002789
Accession ID Mm10

Library idBAMCTSS
CNhs11189 DRZ012756 DRZ014139
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

CNhs11189

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.0398
1002 0.695
1003 0.167
1004 0.0482
1005 --0.0249
1006 0.0482
1007 0.121
1008 0
1009 0.147
101 0.0758
1010 0
1011 0.0268
1012 0.0482
1013 --0.16
1014 0.556
1015 0.102
1016 0.336
1017 0
1018 0
1019 0
102 0
1020 0.00655
1021 0.0932
1022 0.0482
1023 0
1024 --0.0064
1025 0.0482
1026 0.0188
1027 0.0482
1028 0
1029 0.226
103 0.313
1030 0
1031 0.348
1032 --0.0928
1033 0.0369
1034 0
1035 0.131
1036 0.0184
1037 0
1038 0.0745
1039 --0.071
104 0
1040 0.216
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: CNhs11189

Jaspar motif P-value
MA0002.2 0.00106
MA0003.1 0.811
MA0004.1 0.683
MA0006.1 0.264
MA0007.1 0.681
MA0009.1 0.565
MA0014.1 0.73
MA0017.1 4.30614e-4
MA0018.2 0.143
MA0019.1 0.56
MA0024.1 1.97254e-5
MA0025.1 0.769
MA0027.1 0.748
MA0028.1 0.736
MA0029.1 0.929
MA0030.1 0.435
MA0031.1 0.643
MA0035.2 0.437
MA0038.1 0.231
MA0039.2 0.854
MA0040.1 0.27
MA0041.1 0.243
MA0042.1 0.396
MA0043.1 0.955
MA0046.1 1.07324e-24
MA0047.2 0.0646
MA0048.1 0.0784
MA0050.1 0.232
MA0051.1 0.188
MA0052.1 3.61132e-4
MA0055.1 0.0947
MA0057.1 0.064
MA0058.1 0.603
MA0059.1 0.885
MA0060.1 0.00428
MA0061.1 0.265
MA0062.2 0.482
MA0065.2 0.00315
MA0066.1 0.067
MA0067.1 0.666
MA0068.1 0.144
MA0069.1 0.995
MA0070.1 0.963
MA0071.1 0.915
MA0072.1 0.283
MA0073.1 0.322
MA0074.1 0.464
MA0076.1 0.532
MA0077.1 0.677
MA0078.1 0.109
MA0079.2 0.353
MA0080.2 8.55654e-6
MA0081.1 0.243
MA0083.1 0.762
MA0084.1 0.738
MA0087.1 0.36
MA0088.1 0.142
MA0090.1 0.573
MA0091.1 0.912
MA0092.1 0.403
MA0093.1 0.626
MA0099.2 3.40157e-4
MA0100.1 0.776
MA0101.1 0.571
MA0102.2 0.826
MA0103.1 2.21859e-4
MA0104.2 0.467
MA0105.1 9.61683e-4
MA0106.1 0.811
MA0107.1 0.525
MA0108.2 2.32371e-4
MA0111.1 0.303
MA0112.2 0.00255
MA0113.1 0.763
MA0114.1 2.66168e-4
MA0115.1 0.0731
MA0116.1 0.0383
MA0117.1 0.251
MA0119.1 0.438
MA0122.1 0.432
MA0124.1 0.148
MA0125.1 0.331
MA0131.1 0.456
MA0135.1 0.214
MA0136.1 6.87064e-5
MA0137.2 0.202
MA0138.2 0.00182
MA0139.1 0.234
MA0140.1 0.566
MA0141.1 0.175
MA0142.1 0.0282
MA0143.1 0.983
MA0144.1 0.191
MA0145.1 0.03
MA0146.1 0.825
MA0147.1 0.518
MA0148.1 0.0174
MA0149.1 0.195
MA0150.1 6.74283e-4
MA0152.1 0.0149
MA0153.1 7.25968e-14
MA0154.1 0.0248
MA0155.1 0.586
MA0156.1 0.0575
MA0157.1 0.838
MA0159.1 1.8363e-5
MA0160.1 0.997
MA0162.1 0.0412
MA0163.1 0.572
MA0164.1 0.522
MA0258.1 0.00259
MA0259.1 0.332



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: CNhs11189

Novel motif P-value
1 0.151
10 0.444
100 0.602
101 0.618
102 0.789
103 0.937
104 0.995
105 0.286
106 0.0184
107 0.143
108 0.685
109 0.419
11 0.211
110 0.857
111 0.311
112 0.604
113 0.406
114 0.0914
115 0.512
116 0.218
117 0.915
118 0.723
119 0.0879
12 0.189
120 0.325
121 0.601
122 0.863
123 0.152
124 0.457
125 0.135
126 0.608
127 0.119
128 0.00531
129 0.291
13 0.667
130 0.493
131 0.34
132 0.549
133 0.429
134 0.835
135 0.615
136 0.294
137 0.808
138 0.466
139 0.238
14 0.199
140 0.695
141 0.304
142 0.209
143 0.028
144 0.0223
145 0.837
146 0.369
147 0.639
148 0.228
149 0.494
15 0.0879
150 0.897
151 0.0423
152 0.417
153 0.639
154 0.981
155 0.252
156 0.902
157 0.597
158 0.417
159 0.478
160 0.752
161 0.835
162 0.523
163 0.0472
164 0.801
165 0.0531
166 0.605
167 0.974
168 0.271
169 0.556
17 0.167
18 0.212
19 0.738
2 0.547
20 0.8
21 0.383
22 0.727
23 0.125
24 0.73
25 0.226
26 0.814
27 0.326
28 0.287
29 0.858
3 0.316
30 0.64
31 0.293
32 0.418
33 0.749
34 0.793
35 0.117
36 0.377
37 0.133
38 0.609
39 0.847
4 0.773
40 0.481
41 0.0183
42 0.585
43 0.32
44 0.109
45 0.35
46 0.225
47 0.274
48 0.188
49 0.166
5 0.0973
50 0.896
51 0.798
52 0.277
53 0.712
54 0.371
55 0.197
56 0.284
57 0.766
58 0.262
59 0.163
6 0.577
60 0.109
61 0.796
62 0.0613
63 0.241
64 0.553
65 0.162
66 0.903
67 0.617
68 9.4639e-5
69 0.487
7 0.431
70 0.00823
71 0.213
72 0.484
73 0.34
74 0.669
75 0.254
76 0.383
77 0.326
78 0.403
79 0.892
8 0.143
80 0.0398
81 0.396
82 0.656
83 0.826
84 0.435
85 0.00877
86 0.122
87 0.106
88 0.985
89 0.0335
9 0.835
90 0.127
91 0.535
92 0.264
93 0.798
94 0.411
95 0.672
96 0.204
97 0.507
98 0.111
99 0.929



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: CNhs11189


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)
0000304 (mouse neonate N0 sample)
0011509 (mouse testis- neonate N00 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)