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FF:395-14B1

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Name:whole body, embryo E14
Species:Mouse (Mus musculus)
Library ID:CNhs10519
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 stage14 days embryo
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  SAMD00005034
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10519 CAGE DRX009146 DRR010020
Accession ID Mm9

Library idBAMCTSS
CNhs10519 DRZ001445 DRZ002828
Accession ID Mm10

Library idBAMCTSS
CNhs10519 DRZ012795 DRZ014178
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

CNhs10519

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.0826
10 0
100 0.0826
1000 0.00421
1001 -0.0749
1002 0.0663
1003 0.0441
1004 0.0413
1005 0
1006 0.0826
1007 -0.012
1008 0
1009 -0.117
101 0.0734
1010 0
1011 0.0136
1012 0
1013 -0.3
1014 0.264
1015 0.139
1016 0.0255
1017 0
1018 0.0826
1019 0
102 0
1020 0
1021 0
1022 -0.124
1023 0
1024 -0.0427
1025 0.191
1026 0.0272
1027 0.0627
1028 0
1029 -0.115
103 0.00443
1030 0
1031 0.128
1032 -0.109
1033 -0.0665
1034 0.0826
1035 0.033
1036 -0.0152
1037 0
1038 -0.119
1039 -0.00323
104 0
1040 -0.00376
1041 0



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: CNhs10519
Jaspar motif P-value
MA0002.2 0.00987
MA0003.1 0.834
MA0004.1 0.344
MA0006.1 0.213
MA0007.1 0.00723
MA0009.1 0.446
MA0014.1 0.0914
MA0017.1 0.00956
MA0018.2 0.437
MA0019.1 0.619
MA0024.1 8.72663e-6
MA0025.1 0.276
MA0027.1 0.567
MA0028.1 0.0161
MA0029.1 0.276
MA0030.1 0.505
MA0031.1 0.24
MA0035.2 6.23234e-4
MA0038.1 0.00913
MA0039.2 0.526
MA0040.1 0.88
MA0041.1 0.302
MA0042.1 0.732
MA0043.1 0.659
MA0046.1 4.38127e-7
MA0047.2 0.898
MA0048.1 0.0806
MA0050.1 1.78165e-7
MA0051.1 2.79483e-6
MA0052.1 2.45646e-5
MA0055.1 0.0276
MA0057.1 0.305
MA0058.1 0.473
MA0059.1 0.182
MA0060.1 2.14359e-16
MA0061.1 0.117
MA0062.2 1.17664e-5
MA0065.2 0.00976
MA0066.1 0.106
MA0067.1 0.024
MA0068.1 0.547
MA0069.1 0.926
MA0070.1 0.502
MA0071.1 0.0293
MA0072.1 0.148
MA0073.1 0.962
MA0074.1 0.0636
MA0076.1 0.0324
MA0077.1 0.208
MA0078.1 0.689
MA0079.2 0.281
MA0080.2 4.26206e-10
MA0081.1 0.137
MA0083.1 3.75769e-4
MA0084.1 0.599
MA0087.1 0.336
MA0088.1 0.402
MA0090.1 0.669
MA0091.1 0.772
MA0092.1 0.535
MA0093.1 0.396
MA0099.2 0.00806
MA0100.1 0.36
MA0101.1 0.0413
MA0102.2 0.727
MA0103.1 0.00207
MA0104.2 0.778
MA0105.1 0.441
MA0106.1 0.0435
MA0107.1 0.0456
MA0108.2 2.46842e-24
MA0111.1 0.258
MA0112.2 1.37628e-5
MA0113.1 0.088
MA0114.1 0.0543
MA0115.1 0.444
MA0116.1 0.134
MA0117.1 0.791
MA0119.1 0.679
MA0122.1 0.763
MA0124.1 0.253
MA0125.1 0.0122
MA0131.1 0.831
MA0135.1 0.00431
MA0136.1 3.63734e-10
MA0137.2 0.00188
MA0138.2 0.337
MA0139.1 0.0581
MA0140.1 1.65826e-6
MA0141.1 1.56043e-4
MA0142.1 0.229
MA0143.1 0.0231
MA0144.1 0.0261
MA0145.1 0.165
MA0146.1 0.0881
MA0147.1 0.817
MA0148.1 0.885
MA0149.1 0.00399
MA0150.1 0.0656
MA0152.1 0.996
MA0153.1 8.96608e-4
MA0154.1 0.0245
MA0155.1 0.931
MA0156.1 5.26285e-8
MA0157.1 0.105
MA0159.1 0.0217
MA0160.1 0.0353
MA0162.1 0.763
MA0163.1 0.0065
MA0164.1 0.707
MA0258.1 4.00149e-4
MA0259.1 0.791



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: CNhs10519
Novel motif P-value
1 0.0472
10 0.0265
100 0.788
101 0.878
102 0.271
103 0.019
104 0.815
105 0.586
106 0.0235
107 0.395
108 0.579
109 0.0103
11 0.0655
110 0.0532
111 0.00119
112 0.0155
113 0.584
114 0.0144
115 0.719
116 0.895
117 0.021
118 0.397
119 0.0208
12 0.834
120 0.899
121 0.903
122 0.735
123 0.701
124 0.624
125 0.0912
126 0.0973
127 0.134
128 0.26
129 0.344
13 0.00126
130 0.419
131 0.0245
132 0.365
133 0.0196
134 0.451
135 0.787
136 0.028
137 0.576
138 0.654
139 0.00261
14 0.696
140 0.291
141 0.173
142 0.477
143 0.515
144 0.802
145 0.0369
146 0.995
147 0.627
148 0.0292
149 0.703
15 0.0443
150 0.156
151 0.23
152 0.0847
153 0.146
154 0.206
155 0.233
156 0.418
157 0.774
158 0.0299
159 0.0114
160 0.934
161 0.199
162 0.427
163 0.746
164 0.0133
165 0.445
166 0.62
167 0.417
168 0.214
169 0.00828
17 0.0779
18 0.783
19 0.283
2 0.556
20 0.022
21 0.676
22 0.316
23 0.821
24 0.207
25 0.685
26 0.00492
27 0.612
28 0.311
29 0.046
3 0.0743
30 0.288
31 0.749
32 0.065
33 0.355
34 0.643
35 0.351
36 0.496
37 0.0129
38 0.172
39 0.201
4 0.703
40 0.556
41 0.73
42 0.487
43 0.091
44 0.244
45 0.99
46 0.145
47 0.199
48 0.0492
49 0.0404
5 0.327
50 0.533
51 0.711
52 0.811
53 0.444
54 0.959
55 0.893
56 0.657
57 0.492
58 0.312
59 0.254
6 0.53
60 0.063
61 0.12
62 0.251
63 0.0996
64 0.786
65 0.29
66 0.235
67 0.704
68 0.248
69 0.379
7 0.16
70 0.00363
71 0.0463
72 0.51
73 0.0081
74 0.67
75 0.0352
76 0.0177
77 0.305
78 0.312
79 0.657
8 0.173
80 0.468
81 0.872
82 0.085
83 0.825
84 0.479
85 0.0273
86 0.138
87 0.578
88 0.204
89 0.828
9 0.893
90 0.0203
91 0.958
92 0.244
93 0.23
94 0.955
95 0.00351
96 0.863
97 0.649
98 0.704
99 0.916



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: CNhs10519


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)
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)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000296 (mouse embryonic day 14 sample)
0011333 (mouse whole body- embryo E14 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)