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FF:763-44D9

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Name:testis, neonate N10
Species:Mouse (Mus musculus)
Library ID:CNhs11204
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 stage10 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  SAMD00004951
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11204 CAGE DRX009109 DRR009983
Accession ID Mm9

Library idBAMCTSS
CNhs11204 DRZ001408 DRZ002791
Accession ID Mm10

Library idBAMCTSS
CNhs11204 DRZ012758 DRZ014141
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 sample
Ranked 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 sample
Ranked 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

CNhs11204

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 -0.0155
1001 0.0663
1002 0.0785
1003 0.00516
1004 0
1005 -0.122
1006 0.0823
1007 0.134
1008 0
1009 0.185
101 0.178
1010 0
1011 -0.0642
1012 0.0433
1013 -0.126
1014 0.0433
1015 0.0472
1016 0.112
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0433
1022 0.0484
1023 0
1024 -0.0899
1025 0
1026 0
1027 0
1028 0.0433
1029 0.0045
103 0.147
1030 0
1031 -0.0596
1032 -0.121
1033 0.0769
1034 0
1035 0.152
1036 -0.01
1037 0
1038 -0.0592
1039 -0.0153
104 0
1040 -0.0776
1041 0.0433



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs11204
Jaspar motif P-value
MA0002.2 3.4027e-4
MA0003.1 0.783
MA0004.1 0.163
MA0006.1 0.114
MA0007.1 0.941
MA0009.1 0.472
MA0014.1 0.384
MA0017.1 0.0239
MA0018.2 0.255
MA0019.1 0.27
MA0024.1 1.08537e-4
MA0025.1 0.793
MA0027.1 0.685
MA0028.1 0.00267
MA0029.1 0.648
MA0030.1 0.577
MA0031.1 0.57
MA0035.2 0.97
MA0038.1 0.0153
MA0039.2 0.0287
MA0040.1 0.67
MA0041.1 0.608
MA0042.1 0.743
MA0043.1 0.0235
MA0046.1 9.29886e-20
MA0047.2 0.0375
MA0048.1 0.225
MA0050.1 0.355
MA0051.1 0.993
MA0052.1 0.0135
MA0055.1 0.0325
MA0057.1 0.296
MA0058.1 0.0842
MA0059.1 0.294
MA0060.1 2.43626e-16
MA0061.1 0.0384
MA0062.2 8.04837e-5
MA0065.2 0.0451
MA0066.1 0.00932
MA0067.1 0.295
MA0068.1 0.677
MA0069.1 0.516
MA0070.1 0.181
MA0071.1 0.951
MA0072.1 0.599
MA0073.1 0.664
MA0074.1 0.389
MA0076.1 1.37694e-4
MA0077.1 0.893
MA0078.1 0.241
MA0079.2 0.138
MA0080.2 5.24999e-6
MA0081.1 0.44
MA0083.1 0.113
MA0084.1 0.608
MA0087.1 0.952
MA0088.1 0.849
MA0090.1 0.599
MA0091.1 0.0823
MA0092.1 0.118
MA0093.1 0.114
MA0099.2 8.11781e-4
MA0100.1 0.166
MA0101.1 0.512
MA0102.2 0.568
MA0103.1 0.0531
MA0104.2 0.0218
MA0105.1 1.02361e-6
MA0106.1 0.885
MA0107.1 0.209
MA0108.2 7.271e-4
MA0111.1 0.257
MA0112.2 8.78513e-5
MA0113.1 0.894
MA0114.1 0.0171
MA0115.1 0.407
MA0116.1 0.00135
MA0117.1 0.683
MA0119.1 0.0802
MA0122.1 0.576
MA0124.1 0.341
MA0125.1 0.978
MA0131.1 0.189
MA0135.1 0.94
MA0136.1 0.205
MA0137.2 0.769
MA0138.2 0.0118
MA0139.1 0.299
MA0140.1 0.133
MA0141.1 0.726
MA0142.1 0.00595
MA0143.1 0.117
MA0144.1 0.162
MA0145.1 0.0112
MA0146.1 0.531
MA0147.1 0.0294
MA0148.1 0.00909
MA0149.1 0.61
MA0150.1 0.0145
MA0152.1 0.302
MA0153.1 1.74566e-14
MA0154.1 0.00237
MA0155.1 0.319
MA0156.1 0.238
MA0157.1 0.0918
MA0159.1 0.00752
MA0160.1 0.909
MA0162.1 0.0513
MA0163.1 0.061
MA0164.1 0.641
MA0258.1 0.00216
MA0259.1 0.0192



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs11204
Novel motif P-value
1 0.178
10 0.679
100 0.744
101 0.257
102 0.769
103 0.343
104 0.955
105 0.202
106 0.00106
107 0.00567
108 0.53
109 0.689
11 0.271
110 0.773
111 0.53
112 0.529
113 0.511
114 0.064
115 0.603
116 0.209
117 0.568
118 0.984
119 0.108
12 0.568
120 0.244
121 0.433
122 0.833
123 0.08
124 0.234
125 0.144
126 0.977
127 0.313
128 0.0012
129 0.232
13 0.82
130 0.704
131 0.507
132 0.121
133 0.103
134 0.615
135 0.243
136 0.0171
137 0.592
138 0.576
139 0.0911
14 0.103
140 0.283
141 0.0672
142 0.787
143 0.0224
144 0.499
145 0.565
146 0.479
147 0.601
148 0.0636
149 0.237
15 0.153
150 0.711
151 0.131
152 0.232
153 0.214
154 0.955
155 0.758
156 0.00441
157 0.264
158 0.643
159 0.654
160 0.265
161 0.745
162 0.366
163 0.0663
164 0.746
165 0.0742
166 0.713
167 0.845
168 0.0931
169 0.0491
17 0.104
18 0.198
19 0.449
2 0.245
20 0.356
21 0.92
22 0.412
23 0.101
24 0.958
25 0.907
26 0.274
27 0.165
28 0.339
29 0.883
3 0.156
30 0.507
31 0.0991
32 0.146
33 0.951
34 0.525
35 0.189
36 0.267
37 0.16
38 0.637
39 0.672
4 0.899
40 0.839
41 0.091
42 0.325
43 0.143
44 0.141
45 0.446
46 0.109
47 0.359
48 0.509
49 0.18
5 0.0876
50 0.831
51 0.627
52 0.0848
53 0.448
54 0.485
55 0.483
56 0.181
57 0.397
58 0.309
59 0.0556
6 0.643
60 0.0606
61 0.649
62 0.199
63 0.173
64 0.583
65 0.114
66 0.317
67 0.959
68 0.0533
69 0.534
7 0.542
70 0.0683
71 0.171
72 0.556
73 0.55
74 0.369
75 0.457
76 0.627
77 0.261
78 0.288
79 0.436
8 0.185
80 0.368
81 0.288
82 0.354
83 0.967
84 0.378
85 0.0219
86 0.25
87 0.274
88 0.206
89 0.0622
9 0.628
90 0.727
91 0.0503
92 0.273
93 0.917
94 0.0715
95 0.729
96 0.432
97 0.666
98 0.0823
99 0.325



de novo motifs identified by HOMER in promoters active in this sample
Summary:The result of HOMER in this sample is shown.
Analyst:NA

library id: CNhs11204


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)
0000305 (mouse neonate N10 sample)
0011422 (mouse testis- neonate N10 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)