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FF:470-26G5

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Name:testis, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs11033
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 stage16 days embryo
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  SAMD00005676
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11033 CAGE DRX009104 DRR009978
Accession ID Mm9

Library idBAMCTSS
CNhs11033 DRZ001403 DRZ002786
Accession ID Mm10

Library idBAMCTSS
CNhs11033 DRZ012753 DRZ014136
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

CNhs11033

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 -2.109203e-4
1002 0.645
1003 0.0233
1004 0
1005 --0.0389
1006 0.0538
1007 0.16
1008 0
1009 0.18
101 0.0674
1010 0
1011 0.0703
1012 0
1013 --0.156
1014 0.143
1015 0.152
1016 0.335
1017 0
1018 0.0772
1019 0
102 0
1020 0
1021 --0.0487
1022 0.0723
1023 0
1024 --0.0624
1025 0
1026 0.0477
1027 0
1028 0
1029 --0.0196
103 0.248
1030 0
1031 0.437
1032 7.252914e-4
1033 0
1034 0
1035 0
1036 0.0663
1037 0
1038 --0.0304
1039 --0.0195
104 0
1040 0.105
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: CNhs11033

Jaspar motif P-value
MA0002.2 0.00447
MA0003.1 0.812
MA0004.1 0.329
MA0006.1 0.123
MA0007.1 0.421
MA0009.1 0.749
MA0014.1 0.76
MA0017.1 0.00218
MA0018.2 0.708
MA0019.1 0.379
MA0024.1 8.08751e-6
MA0025.1 0.857
MA0027.1 0.664
MA0028.1 0.146
MA0029.1 0.799
MA0030.1 0.135
MA0031.1 0.34
MA0035.2 0.846
MA0038.1 0.00902
MA0039.2 0.0346
MA0040.1 0.305
MA0041.1 0.424
MA0042.1 0.559
MA0043.1 0.154
MA0046.1 4.47548e-25
MA0047.2 0.0469
MA0048.1 0.197
MA0050.1 0.00181
MA0051.1 0.00497
MA0052.1 0.00689
MA0055.1 0.0182
MA0057.1 0.446
MA0058.1 0.108
MA0059.1 0.456
MA0060.1 2.18761e-18
MA0061.1 0.131
MA0062.2 0.284
MA0065.2 0.00787
MA0066.1 0.0617
MA0067.1 0.775
MA0068.1 0.15
MA0069.1 0.777
MA0070.1 0.154
MA0071.1 0.682
MA0072.1 0.413
MA0073.1 0.931
MA0074.1 0.633
MA0076.1 0.0313
MA0077.1 0.929
MA0078.1 0.132
MA0079.2 0.0947
MA0080.2 1.16179e-4
MA0081.1 0.633
MA0083.1 0.588
MA0084.1 0.979
MA0087.1 0.518
MA0088.1 0.995
MA0090.1 0.933
MA0091.1 0.307
MA0092.1 0.333
MA0093.1 0.216
MA0099.2 5.83726e-4
MA0100.1 0.334
MA0101.1 0.518
MA0102.2 0.76
MA0103.1 0.00125
MA0104.2 0.0566
MA0105.1 9.40138e-5
MA0106.1 0.345
MA0107.1 0.343
MA0108.2 0.0716
MA0111.1 0.368
MA0112.2 8.67024e-5
MA0113.1 0.338
MA0114.1 0.00297
MA0115.1 0.052
MA0116.1 0.0201
MA0117.1 0.206
MA0119.1 0.314
MA0122.1 0.965
MA0124.1 0.169
MA0125.1 0.929
MA0131.1 0.632
MA0135.1 0.625
MA0136.1 0.0213
MA0137.2 0.261
MA0138.2 0.006
MA0139.1 0.56
MA0140.1 0.839
MA0141.1 0.537
MA0142.1 0.00344
MA0143.1 0.828
MA0144.1 0.156
MA0145.1 0.0463
MA0146.1 0.346
MA0147.1 0.137
MA0148.1 0.00176
MA0149.1 0.0869
MA0150.1 0.00299
MA0152.1 0.235
MA0153.1 6.02754e-18
MA0154.1 0.00597
MA0155.1 0.709
MA0156.1 0.769
MA0157.1 0.264
MA0159.1 6.64849e-5
MA0160.1 0.968
MA0162.1 0.0387
MA0163.1 0.163
MA0164.1 0.339
MA0258.1 3.72e-4
MA0259.1 0.0828



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: CNhs11033

Novel motif P-value
1 0.108
10 0.229
100 0.725
101 0.569
102 0.648
103 0.291
104 0.834
105 0.395
106 2.95835e-4
107 0.00349
108 0.722
109 0.697
11 0.343
110 0.792
111 0.415
112 0.431
113 0.397
114 0.035
115 0.613
116 0.478
117 0.642
118 0.909
119 0.169
12 0.463
120 0.463
121 0.51
122 0.716
123 0.127
124 0.119
125 0.0584
126 0.939
127 0.261
128 1.61625e-4
129 0.142
13 0.471
130 0.423
131 0.829
132 0.568
133 0.962
134 0.645
135 0.491
136 0.0657
137 0.852
138 0.538
139 0.0532
14 0.171
140 0.5
141 0.125
142 0.888
143 0.109
144 0.133
145 0.627
146 0.429
147 0.763
148 0.0513
149 0.326
15 0.111
150 0.858
151 0.0713
152 0.266
153 0.315
154 0.799
155 0.71
156 5.53283e-4
157 0.293
158 0.215
159 0.0388
160 0.79
161 0.659
162 0.609
163 0.128
164 0.937
165 0.0354
166 0.846
167 0.268
168 0.215
169 0.453
17 0.0895
18 0.185
19 0.975
2 0.556
20 0.731
21 0.674
22 0.803
23 0.134
24 0.983
25 0.42
26 0.39
27 0.313
28 0.339
29 0.957
3 0.199
30 0.93
31 0.148
32 0.467
33 0.726
34 0.957
35 0.0477
36 0.204
37 0.127
38 0.663
39 0.801
4 0.637
40 0.722
41 0.139
42 0.466
43 0.183
44 0.276
45 0.496
46 0.132
47 0.47
48 0.358
49 0.104
5 0.0561
50 0.913
51 0.784
52 0.0999
53 0.912
54 0.428
55 0.236
56 0.196
57 0.561
58 0.292
59 0.174
6 0.815
60 0.0345
61 0.967
62 0.0849
63 0.179
64 0.734
65 0.218
66 0.286
67 0.8
68 1.1007e-4
69 0.461
7 0.401
70 0.0139
71 0.114
72 0.765
73 0.302
74 0.654
75 0.275
76 0.787
77 0.316
78 0.341
79 0.533
8 0.0957
80 0.118
81 0.237
82 0.504
83 0.426
84 0.302
85 0.00602
86 0.09
87 0.411
88 0.857
89 0.0434
9 0.737
90 0.179
91 0.45
92 0.117
93 0.667
94 0.24
95 0.933
96 0.235
97 0.639
98 0.118
99 0.975



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: CNhs11033


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)
0000922 (embryo)
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)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000299 (mouse embryonic day 16 sample)
0011364 (mouse testis- embryo E16 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)