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FF:659-23C6

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Name:whole body, neonate N01
Species:Mouse (Mus musculus)
Library ID:CNhs10576
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 stage1 day 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  SAMD00005246
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10576 CAGE DRX009152 DRR010026
Accession ID Mm9

Library idBAMCTSS
CNhs10576 DRZ001451 DRZ002834
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

CNhs10576

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.076
10 0
100 0
1000 0.417
1001 0.228
1002 0.12
1003 0.323
1004 0
1005 0.0432
1006 0.464
1007 --0.0102
1008 0
1009 0.168
101 --0.0143
1010 0
1011 0.141
1012 0
1013 --0.0868
1014 0.425
1015 --0.101
1016 0.182
1017 0
1018 0.247
1019 0
102 0
1020 0
1021 0
1022 0.541
1023 0
1024 0.281
1025 0
1026 0.257
1027 0.186
1028 0
1029 0.217
103 0.856
1030 0
1031 0.335
1032 0.124
1033 0
1034 0
1035 0.076
1036 --0.0791
1037 0
1038 --0.0034
1039 0.142
104 0
1040 0.316
1041 0.247



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: CNhs10576

Jaspar motif P-value
MA0002.2 0.174
MA0003.1 0.0662
MA0004.1 0.052
MA0006.1 0.247
MA0007.1 0.926
MA0009.1 0.573
MA0014.1 0.315
MA0017.1 9.00354e-5
MA0018.2 0.00644
MA0019.1 0.898
MA0024.1 0.0061
MA0025.1 0.328
MA0027.1 0.292
MA0028.1 5.64394e-10
MA0029.1 0.595
MA0030.1 0.502
MA0031.1 0.437
MA0035.2 0.0117
MA0038.1 0.966
MA0039.2 0.968
MA0040.1 0.598
MA0041.1 0.633
MA0042.1 0.848
MA0043.1 0.063
MA0046.1 6.1736e-12
MA0047.2 0.105
MA0048.1 6.68495e-4
MA0050.1 1.91433e-4
MA0051.1 0.00408
MA0052.1 1.06638e-35
MA0055.1 9.53084e-6
MA0057.1 0.794
MA0058.1 0.0151
MA0059.1 7.11451e-4
MA0060.1 1.69234e-5
MA0061.1 0.448
MA0062.2 1.30901e-15
MA0065.2 0.828
MA0066.1 0.789
MA0067.1 0.107
MA0068.1 0.233
MA0069.1 0.444
MA0070.1 0.191
MA0071.1 0.0726
MA0072.1 0.0486
MA0073.1 0.577
MA0074.1 0.62
MA0076.1 7.32157e-11
MA0077.1 0.557
MA0078.1 0.169
MA0079.2 0.0107
MA0080.2 4.62952e-5
MA0081.1 0.21
MA0083.1 5.89067e-11
MA0084.1 0.619
MA0087.1 0.239
MA0088.1 0.0325
MA0090.1 0.0297
MA0091.1 0.782
MA0092.1 0.372
MA0093.1 0.0405
MA0099.2 0.272
MA0100.1 0.00265
MA0101.1 0.0514
MA0102.2 0.71
MA0103.1 0.00886
MA0104.2 0.0146
MA0105.1 0.716
MA0106.1 0.185
MA0107.1 0.212
MA0108.2 4.41876e-22
MA0111.1 0.817
MA0112.2 0.392
MA0113.1 0.817
MA0114.1 1.13502e-4
MA0115.1 0.00237
MA0116.1 0.831
MA0117.1 0.395
MA0119.1 0.905
MA0122.1 0.794
MA0124.1 0.254
MA0125.1 0.125
MA0131.1 0.288
MA0135.1 0.148
MA0136.1 6.89067e-8
MA0137.2 0.00467
MA0138.2 0.00144
MA0139.1 0.157
MA0140.1 0.00988
MA0141.1 0.264
MA0142.1 0.0375
MA0143.1 0.14
MA0144.1 0.204
MA0145.1 0.0475
MA0146.1 0.993
MA0147.1 0.0188
MA0148.1 0.092
MA0149.1 0.00606
MA0150.1 0.0976
MA0152.1 0.34
MA0153.1 2.91015e-12
MA0154.1 0.438
MA0155.1 0.0914
MA0156.1 1.5524e-12
MA0157.1 0.273
MA0159.1 0.278
MA0160.1 0.183
MA0162.1 0.42
MA0163.1 0.838
MA0164.1 0.322
MA0258.1 0.732
MA0259.1 0.129



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: CNhs10576

Novel motif P-value
1 0.337
10 0.157
100 0.997
101 0.316
102 0.995
103 0.0373
104 0.893
105 0.388
106 0.176
107 0.0598
108 0.374
109 0.625
11 0.402
110 0.515
111 0.262
112 0.139
113 0.751
114 0.951
115 0.259
116 0.287
117 0.0293
118 0.179
119 0.799
12 0.25
120 0.958
121 0.211
122 0.396
123 0.268
124 0.709
125 0.761
126 0.06
127 0.341
128 0.254
129 0.412
13 0.234
130 0.751
131 0.349
132 0.721
133 0.679
134 0.475
135 0.419
136 0.51
137 0.778
138 0.198
139 0.409
14 0.411
140 0.737
141 0.33
142 0.979
143 0.486
144 0.0249
145 0.127
146 0.996
147 0.911
148 0.351
149 0.532
15 0.0172
150 0.906
151 0.656
152 0.0468
153 0.242
154 0.564
155 0.27
156 0.021
157 0.482
158 0.0481
159 0.526
160 0.384
161 0.0232
162 0.894
163 0.638
164 0.111
165 0.913
166 0.316
167 0.0269
168 0.0324
169 0.0919
17 0.356
18 0.513
19 0.323
2 0.00814
20 0.0579
21 0.777
22 0.522
23 0.469
24 0.461
25 0.462
26 0.29
27 0.998
28 0.52
29 0.0146
3 0.218
30 0.214
31 0.541
32 0.139
33 0.176
34 0.134
35 0.11
36 0.0406
37 0.749
38 0.699
39 0.905
4 0.846
40 0.0688
41 0.211
42 0.264
43 0.901
44 0.343
45 0.162
46 0.927
47 0.47
48 0.22
49 0.31
5 0.991
50 0.194
51 0.966
52 0.185
53 0.398
54 0.355
55 0.881
56 0.552
57 0.42
58 0.766
59 0.0442
6 0.271
60 0.318
61 0.283
62 0.647
63 0.421
64 0.65
65 0.866
66 0.838
67 0.683
68 0.262
69 0.188
7 0.818
70 0.595
71 0.371
72 0.437
73 0.629
74 0.943
75 0.107
76 0.0359
77 0.224
78 0.659
79 0.171
8 0.289
80 0.557
81 0.355
82 0.345
83 0.876
84 0.453
85 0.117
86 0.709
87 0.739
88 0.856
89 0.476
9 0.247
90 0.0123
91 0.453
92 0.575
93 0.0405
94 0.882
95 0.536
96 0.76
97 0.518
98 0.599
99 0.381



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: CNhs10576


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)
0000304 (mouse neonate N0 sample)
0000734 (mouse neonate N1 sample)
0011399 (mouse whole body- neonate N01 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)