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FF:726-26I4

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Name:testis, neonate N07
Species:Mouse (Mus musculus)
Library ID:CNhs11222
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 stage7 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  SAMD00005949
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11222 CAGE DRX009108 DRR009982
Accession ID Mm9

Library idBAMCTSS
CNhs11222 DRZ001407 DRZ002790
Accession ID Mm10

Library idBAMCTSS
CNhs11222 DRZ012757 DRZ014140
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

CNhs11222

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.127
1002 0.398
1003 0.194
1004 0.122
1005 --0.117
1006 0.00663
1007 0.171
1008 0
1009 0.193
101 0.0911
1010 0
1011 --0.0307
1012 0.0842
1013 --0.116
1014 0.158
1015 0.14
1016 0.222
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.074
1022 0.0938
1023 0
1024 --0.039
1025 0.0394
1026 0
1027 0
1028 0
1029 0.274
103 0.337
1030 0
1031 0.211
1032 --0.00152
1033 0
1034 0.0532
1035 0.143
1036 0.0265
1037 0
1038 0.0544
1039 --0.0161
104 0
1040 --0.0508
1041 0.0532



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: CNhs11222

Jaspar motif P-value
MA0002.2 3.72239e-5
MA0003.1 0.926
MA0004.1 0.332
MA0006.1 0.242
MA0007.1 0.972
MA0009.1 0.309
MA0014.1 0.705
MA0017.1 0.161
MA0018.2 0.362
MA0019.1 0.228
MA0024.1 2.9624e-7
MA0025.1 0.941
MA0027.1 0.835
MA0028.1 0.202
MA0029.1 0.627
MA0030.1 0.915
MA0031.1 0.482
MA0035.2 0.594
MA0038.1 0.0596
MA0039.2 0.187
MA0040.1 0.468
MA0041.1 0.532
MA0042.1 0.786
MA0043.1 0.737
MA0046.1 0.464
MA0047.2 0.574
MA0048.1 0.107
MA0050.1 0.257
MA0051.1 0.275
MA0052.1 0.00662
MA0055.1 0.0249
MA0057.1 0.425
MA0058.1 0.299
MA0059.1 0.537
MA0060.1 2.86206e-12
MA0061.1 0.0957
MA0062.2 0.397
MA0065.2 0.056
MA0066.1 0.0376
MA0067.1 0.961
MA0068.1 0.861
MA0069.1 0.674
MA0070.1 0.28
MA0071.1 0.7
MA0072.1 0.846
MA0073.1 0.457
MA0074.1 0.276
MA0076.1 0.0513
MA0077.1 0.643
MA0078.1 0.168
MA0079.2 0.185
MA0080.2 5.44773e-8
MA0081.1 0.106
MA0083.1 0.965
MA0084.1 0.522
MA0087.1 0.292
MA0088.1 0.371
MA0090.1 0.764
MA0091.1 0.221
MA0092.1 0.429
MA0093.1 0.284
MA0099.2 2.15536e-4
MA0100.1 0.565
MA0101.1 0.444
MA0102.2 0.961
MA0103.1 0.00637
MA0104.2 0.136
MA0105.1 9.10474e-6
MA0106.1 0.927
MA0107.1 0.284
MA0108.2 0.158
MA0111.1 0.243
MA0112.2 1.1295e-4
MA0113.1 0.434
MA0114.1 0.13
MA0115.1 0.545
MA0116.1 0.00357
MA0117.1 0.289
MA0119.1 0.351
MA0122.1 0.232
MA0124.1 0.15
MA0125.1 0.901
MA0131.1 0.246
MA0135.1 0.279
MA0136.1 1.81738e-5
MA0137.2 0.0959
MA0138.2 0.0272
MA0139.1 0.079
MA0140.1 0.847
MA0141.1 0.261
MA0142.1 0.00807
MA0143.1 0.83
MA0144.1 0.1
MA0145.1 0.0238
MA0146.1 0.609
MA0147.1 0.178
MA0148.1 0.324
MA0149.1 0.522
MA0150.1 0.00233
MA0152.1 0.0637
MA0153.1 0.525
MA0154.1 0.0096
MA0155.1 0.551
MA0156.1 0.085
MA0157.1 0.221
MA0159.1 2.90154e-4
MA0160.1 0.883
MA0162.1 0.0437
MA0163.1 0.0983
MA0164.1 0.711
MA0258.1 5.958e-4
MA0259.1 0.115



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: CNhs11222

Novel motif P-value
1 0.125
10 0.425
100 0.642
101 0.42
102 0.9
103 0.655
104 0.758
105 0.505
106 0.00581
107 0.0825
108 0.335
109 0.554
11 0.19
110 0.752
111 0.362
112 0.797
113 0.607
114 0.0225
115 0.344
116 0.124
117 0.88
118 0.911
119 0.153
12 0.445
120 0.135
121 0.727
122 0.834
123 0.151
124 0.613
125 0.0513
126 0.859
127 0.159
128 0.00658
129 0.326
13 0.99
130 0.572
131 0.708
132 0.416
133 0.0485
134 0.781
135 0.331
136 0.0479
137 0.856
138 0.227
139 0.0457
14 0.142
140 0.656
141 0.0461
142 0.176
143 0.0319
144 0.12
145 0.766
146 0.488
147 0.791
148 0.0494
149 0.209
15 0.0743
150 0.984
151 0.0488
152 0.407
153 0.29
154 0.988
155 0.32
156 0.00292
157 0.57
158 0.443
159 0.394
160 0.587
161 0.845
162 0.583
163 0.0426
164 0.806
165 0.05
166 0.238
167 0.363
168 0.367
169 0.185
17 0.142
18 0.164
19 0.769
2 0.559
20 0.779
21 0.707
22 0.75
23 0.187
24 0.986
25 0.427
26 0.908
27 0.255
28 0.359
29 0.974
3 0.233
30 0.739
31 0.162
32 0.332
33 0.8
34 0.726
35 0.0637
36 0.0985
37 0.136
38 0.869
39 0.812
4 0.959
40 0.587
41 0.0195
42 0.4
43 0.223
44 0.128
45 0.448
46 0.107
47 0.241
48 0.344
49 0.211
5 0.078
50 0.972
51 0.828
52 0.215
53 0.544
54 0.513
55 0.392
56 0.145
57 0.465
58 0.19
59 0.111
6 0.613
60 0.0696
61 0.543
62 0.0667
63 0.185
64 0.619
65 0.155
66 0.537
67 0.935
68 0.024
69 0.388
7 0.476
70 0.00679
71 0.215
72 0.517
73 0.379
74 0.913
75 0.219
76 0.986
77 0.434
78 0.3
79 0.64
8 0.148
80 0.102
81 0.27
82 0.399
83 0.668
84 0.441
85 0.0122
86 0.153
87 0.774
88 0.87
89 0.0582
9 0.858
90 0.205
91 0.411
92 0.354
93 0.74
94 0.233
95 0.772
96 0.254
97 0.609
98 0.0742
99 0.822



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: CNhs11222


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)
0000313 (mouse neonate N7 sample)
0011412 (mouse testis- neonate N07 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)