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FF:761-6B4

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Name:whole body, neonate N10
Species:Mouse (Mus musculus)
Library ID:CNhs10518
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
tissuewhole body
dev stage10 days neonate
sexmixture
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  SAMD00005787
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10518 CAGE DRX009154 DRR010028
Accession ID Mm9

Library idBAMCTSS
CNhs10518 DRZ001453 DRZ002836
Accession ID Mm10

Library idBAMCTSS
CNhs10518 DRZ012803 DRZ014186
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

CNhs10518

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.0646
10 0
100 0
1000 0.435
1001 0.182
1002 --0.0513
1003 0.162
1004 0
1005 0.0881
1006 0.491
1007 --0.0888
1008 0
1009 0.144
101 --0.0158
1010 0
1011 0.0366
1012 0
1013 --0.0689
1014 0.165
1015 --0.0559
1016 0.0298
1017 0
1018 0.0871
1019 0
102 0
1020 0
1021 0.0419
1022 0.55
1023 0
1024 0.239
1025 0
1026 0.136
1027 0.152
1028 0
1029 --0.0114
103 0.74
1030 0.165
1031 0.262
1032 0.197
1033 0
1034 0
1035 0.285
1036 --0.036
1037 0
1038 --0.0453
1039 0.244
104 0
1040 0.126
1041 0.49



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: CNhs10518

Jaspar motif P-value
MA0002.2 0.0662
MA0003.1 0.0108
MA0004.1 0.0918
MA0006.1 0.143
MA0007.1 0.553
MA0009.1 0.698
MA0014.1 0.941
MA0017.1 0.133
MA0018.2 0.0181
MA0019.1 0.112
MA0024.1 0.0784
MA0025.1 0.583
MA0027.1 0.208
MA0028.1 2.12603e-4
MA0029.1 0.785
MA0030.1 0.733
MA0031.1 0.721
MA0035.2 0.821
MA0038.1 0.13
MA0039.2 0.188
MA0040.1 0.0696
MA0041.1 0.309
MA0042.1 0.49
MA0043.1 0.0185
MA0046.1 3.23452e-8
MA0047.2 0.218
MA0048.1 0.00154
MA0050.1 0.147
MA0051.1 0.665
MA0052.1 2.10008e-53
MA0055.1 4.83338e-4
MA0057.1 0.503
MA0058.1 0.0519
MA0059.1 0.0157
MA0060.1 0.192
MA0061.1 0.709
MA0062.2 1.98761e-7
MA0065.2 0.0252
MA0066.1 0.799
MA0067.1 0.166
MA0068.1 0.956
MA0069.1 0.289
MA0070.1 0.755
MA0071.1 0.836
MA0072.1 0.307
MA0073.1 0.611
MA0074.1 0.845
MA0076.1 2.39175e-5
MA0077.1 0.664
MA0078.1 0.0317
MA0079.2 0.0283
MA0080.2 0.66
MA0081.1 0.893
MA0083.1 3.17325e-9
MA0084.1 0.366
MA0087.1 0.778
MA0088.1 0.935
MA0090.1 0.284
MA0091.1 0.186
MA0092.1 0.132
MA0093.1 0.0995
MA0099.2 0.576
MA0100.1 0.0235
MA0101.1 0.458
MA0102.2 0.457
MA0103.1 0.00435
MA0104.2 0.0379
MA0105.1 0.464
MA0106.1 0.589
MA0107.1 0.632
MA0108.2 1.96658e-42
MA0111.1 0.843
MA0112.2 0.00159
MA0113.1 0.74
MA0114.1 0.242
MA0115.1 0.0056
MA0116.1 0.215
MA0117.1 0.961
MA0119.1 0.215
MA0122.1 0.149
MA0124.1 0.686
MA0125.1 0.146
MA0131.1 0.283
MA0135.1 0.176
MA0136.1 0.0036
MA0137.2 0.0111
MA0138.2 6.34727e-4
MA0139.1 0.969
MA0140.1 0.0119
MA0141.1 0.178
MA0142.1 0.226
MA0143.1 0.107
MA0144.1 0.381
MA0145.1 0.0174
MA0146.1 0.697
MA0147.1 0.0655
MA0148.1 0.794
MA0149.1 0.0199
MA0150.1 0.937
MA0152.1 0.367
MA0153.1 2.10136e-8
MA0154.1 0.0348
MA0155.1 0.095
MA0156.1 0.0027
MA0157.1 0.824
MA0159.1 0.663
MA0160.1 0.416
MA0162.1 0.201
MA0163.1 0.135
MA0164.1 0.112
MA0258.1 0.0539
MA0259.1 0.116



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: CNhs10518

Novel motif P-value
1 0.966
10 0.546
100 0.983
101 0.149
102 0.758
103 0.406
104 0.515
105 0.105
106 0.138
107 0.189
108 0.678
109 0.235
11 0.691
110 0.852
111 0.242
112 0.663
113 0.269
114 0.776
115 0.823
116 0.0882
117 0.1
118 0.384
119 0.412
12 0.0662
120 0.68
121 0.754
122 0.846
123 0.11
124 0.725
125 0.784
126 0.493
127 0.377
128 0.282
129 0.519
13 0.566
130 0.603
131 0.312
132 0.972
133 0.138
134 0.827
135 0.211
136 0.772
137 0.168
138 0.451
139 0.365
14 0.191
140 0.935
141 0.241
142 0.102
143 0.934
144 0.0844
145 0.309
146 0.407
147 0.978
148 0.98
149 0.137
15 0.549
150 0.818
151 0.127
152 0.0495
153 0.539
154 0.555
155 0.511
156 0.798
157 0.114
158 0.274
159 0.146
160 0.12
161 0.287
162 0.811
163 0.78
164 0.165
165 0.191
166 0.56
167 0.0202
168 0.0457
169 0.00677
17 0.437
18 0.504
19 0.049
2 0.0385
20 0.0289
21 0.616
22 0.243
23 0.36
24 0.715
25 0.545
26 0.63
27 0.486
28 0.823
29 0.156
3 0.894
30 0.306
31 0.501
32 0.032
33 0.339
34 0.098
35 0.243
36 0.163
37 0.263
38 0.644
39 0.539
4 0.881
40 0.975
41 0.278
42 0.68
43 0.576
44 0.92
45 0.214
46 0.842
47 0.758
48 0.94
49 0.795
5 0.4
50 0.48
51 0.734
52 0.212
53 0.142
54 0.29
55 0.908
56 0.399
57 0.672
58 0.621
59 0.00787
6 0.628
60 0.349
61 0.416
62 0.482
63 0.336
64 0.787
65 0.471
66 0.465
67 0.526
68 0.449
69 0.305
7 0.381
70 0.875
71 0.425
72 0.998
73 0.187
74 0.435
75 0.513
76 0.0181
77 0.245
78 0.111
79 0.308
8 0.897
80 0.208
81 0.166
82 0.204
83 0.213
84 0.493
85 0.0969
86 0.671
87 0.175
88 0.551
89 0.347
9 0.22
90 0.0614
91 0.143
92 0.378
93 0.385
94 0.761
95 0.361
96 0.808
97 0.873
98 0.981
99 0.342



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: CNhs10518


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)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

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)
0011420 (mouse whole body- 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

FF:0000294 (mouse embryonic day 11 sample)