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FF:324-5I8

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Name:whole body, embryo E11
Species:Mouse (Mus musculus)
Library ID:CNhs11014
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 stage11 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  SAMD00004694
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11014 CAGE DRX009142 DRR010016
Accession ID Mm9

Library idBAMCTSS
CNhs11014 DRZ001441 DRZ002824
Accession ID Mm10

Library idBAMCTSS
CNhs11014 DRZ012791 DRZ014174
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 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

CNhs11014

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.00413
10 0
100 0.227
1000 --0.0157
1001 --0.0239
1002 0.156
1003 --0.121
1004 0.116
1005 --0.223
1006 --0.105
1007 0.231
1008 0
1009 --0.108
101 0.194
1010 0
1011 --0.117
1012 0
1013 --0.4
1014 0.193
1015 0.4
1016 0.105
1017 0
1018 0.0429
1019 0
102 0
1020 0
1021 0.0019
1022 --0.252
1023 0
1024 --0.0576
1025 0.21
1026 0
1027 0.3
1028 0
1029 --0.115
103 --0.0802
1030 0
1031 --0.0459
1032 --0.396
1033 0.0344
1034 0
1035 0
1036 0.0745
1037 0
1038 --0.0517
1039 --0.062
104 0
1040 --0.00315
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: CNhs11014

Jaspar motif P-value
MA0002.2 1.52861e-4
MA0003.1 0.0789
MA0004.1 0.963
MA0006.1 0.238
MA0007.1 0.199
MA0009.1 0.537
MA0014.1 0.241
MA0017.1 8.41182e-4
MA0018.2 0.0472
MA0019.1 0.605
MA0024.1 6.95345e-6
MA0025.1 0.0661
MA0027.1 0.236
MA0028.1 0.0474
MA0029.1 0.701
MA0030.1 0.0688
MA0031.1 0.0085
MA0035.2 0.0366
MA0038.1 1.06987e-4
MA0039.2 4.70676e-4
MA0040.1 0.412
MA0041.1 0.762
MA0042.1 0.328
MA0043.1 0.00391
MA0046.1 5.63481e-13
MA0047.2 0.0131
MA0048.1 0.0675
MA0050.1 4.28676e-7
MA0051.1 8.05779e-6
MA0052.1 0.00354
MA0055.1 0.0665
MA0057.1 0.0285
MA0058.1 0.678
MA0059.1 0.478
MA0060.1 1.88308e-20
MA0061.1 0.116
MA0062.2 0.168
MA0065.2 0.00283
MA0066.1 0.244
MA0067.1 0.715
MA0068.1 0.183
MA0069.1 0.708
MA0070.1 0.729
MA0071.1 0.138
MA0072.1 0.17
MA0073.1 0.869
MA0074.1 0.48
MA0076.1 0.036
MA0077.1 0.00727
MA0078.1 0.0211
MA0079.2 0.124
MA0080.2 1.2062e-9
MA0081.1 0.353
MA0083.1 0.919
MA0084.1 0.857
MA0087.1 0.222
MA0088.1 0.717
MA0090.1 0.196
MA0091.1 0.927
MA0092.1 0.268
MA0093.1 0.948
MA0099.2 5.43705e-6
MA0100.1 0.295
MA0101.1 0.53
MA0102.2 0.545
MA0103.1 0.00411
MA0104.2 0.22
MA0105.1 0.354
MA0106.1 0.204
MA0107.1 0.261
MA0108.2 0.255
MA0111.1 0.665
MA0112.2 2.04525e-4
MA0113.1 0.339
MA0114.1 0.00514
MA0115.1 0.535
MA0116.1 0.0466
MA0117.1 0.804
MA0119.1 0.0318
MA0122.1 0.737
MA0124.1 0.847
MA0125.1 0.245
MA0131.1 0.173
MA0135.1 0.847
MA0136.1 5.42465e-4
MA0137.2 0.252
MA0138.2 0.00573
MA0139.1 0.0477
MA0140.1 0.167
MA0141.1 0.0199
MA0142.1 0.0172
MA0143.1 9.66636e-5
MA0144.1 0.158
MA0145.1 0.0102
MA0146.1 0.278
MA0147.1 0.268
MA0148.1 0.00101
MA0149.1 0.00404
MA0150.1 0.0264
MA0152.1 0.221
MA0153.1 2.82423e-8
MA0154.1 0.00558
MA0155.1 0.574
MA0156.1 0.0396
MA0157.1 0.0248
MA0159.1 0.047
MA0160.1 0.103
MA0162.1 0.701
MA0163.1 0.0752
MA0164.1 0.241
MA0258.1 0.0129
MA0259.1 0.269



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: CNhs11014

Novel motif P-value
1 0.131
10 0.505
100 0.774
101 0.553
102 0.767
103 0.056
104 0.697
105 0.0727
106 0.00537
107 0.0819
108 0.98
109 0.0308
11 0.155
110 0.486
111 0.0387
112 0.0466
113 0.422
114 0.0784
115 0.257
116 0.848
117 0.848
118 0.968
119 0.00719
12 0.591
120 0.544
121 0.684
122 0.77
123 0.199
124 0.14
125 0.999
126 0.66
127 0.0979
128 0.0226
129 0.263
13 0.158
130 0.976
131 0.113
132 0.207
133 0.198
134 0.995
135 0.292
136 0.391
137 0.552
138 0.645
139 0.00658
14 0.17
140 0.0188
141 0.0689
142 0.938
143 0.697
144 0.953
145 0.513
146 0.351
147 0.516
148 0.246
149 0.0728
15 0.092
150 0.543
151 0.119
152 0.0294
153 0.186
154 0.741
155 0.631
156 3.6311e-7
157 0.924
158 0.511
159 0.0182
160 0.58
161 0.647
162 0.695
163 0.115
164 0.128
165 0.676
166 0.617
167 0.797
168 0.804
169 0.00853
17 0.0677
18 0.94
19 0.0625
2 0.312
20 0.482
21 0.594
22 0.152
23 0.0686
24 0.233
25 0.648
26 0.158
27 0.361
28 0.381
29 0.939
3 0.326
30 0.482
31 0.47
32 0.0502
33 0.497
34 0.535
35 0.978
36 0.439
37 0.134
38 0.109
39 0.362
4 0.478
40 0.17
41 0.621
42 0.653
43 0.153
44 0.866
45 0.314
46 0.31
47 0.151
48 0.149
49 0.137
5 0.241
50 0.589
51 0.582
52 0.166
53 0.325
54 0.587
55 0.79
56 0.317
57 0.717
58 0.193
59 0.0538
6 0.555
60 0.054
61 0.714
62 0.146
63 0.0702
64 0.48
65 0.0754
66 0.229
67 0.914
68 0.218
69 0.235
7 0.248
70 4.32794e-4
71 0.373
72 0.303
73 0.0866
74 0.544
75 0.384
76 0.863
77 0.212
78 0.381
79 0.337
8 0.373
80 0.588
81 0.323
82 0.094
83 0.793
84 0.99
85 0.0151
86 0.457
87 0.662
88 0.924
89 0.148
9 0.398
90 0.321
91 0.555
92 0.086
93 0.296
94 0.714
95 0.0996
96 0.339
97 0.391
98 0.146
99 0.444



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: CNhs11014


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)
0000294 (mouse embryonic day 11 sample)
0011311 (mouse whole body- embryo E11 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)