Personal tools

FF:857-27C9

From FANTOM5_SSTAR

Jump to: navigation, search


Name:whole body, embryo E12
Species:Mouse (Mus musculus)
Library ID:CNhs10587
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 stage12 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  SAMD00005965
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10587 CAGE DRX009143 DRR010017
Accession ID Mm9

Library idBAMCTSS
CNhs10587 DRZ001442 DRZ002825
Accession ID Mm10

Library idBAMCTSS
CNhs10587 DRZ012792 DRZ014175
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

CNhs10587

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.112
10 0
100 0.146
1000 0
1001 --0.0749
1002 0.309
1003 0.0362
1004 0.255
1005 --0.0507
1006 --0.00509
1007 0.107
1008 0
1009 --0.143
101 0.101
1010 0
1011 0.122
1012 0
1013 --0.124
1014 0.0585
1015 0.251
1016 0.439
1017 0
1018 0.0503
1019 0
102 0
1020 0
1021 --0.0487
1022 --0.0924
1023 0
1024 --0.0523
1025 0.146
1026 0
1027 0.353
1028 0
1029 0.237
103 0
1030 0
1031 0.231
1032 --0.184
1033 0.0912
1034 0
1035 0
1036 0.0659
1037 0
1038 0.0417
1039 --0.238
104 0
1040 0.0835
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: CNhs10587

Jaspar motif P-value
MA0002.2 8.29221e-4
MA0003.1 0.254
MA0004.1 0.788
MA0006.1 0.319
MA0007.1 0.133
MA0009.1 0.391
MA0014.1 0.167
MA0017.1 9.60547e-6
MA0018.2 0.149
MA0019.1 0.801
MA0024.1 0.00235
MA0025.1 0.174
MA0027.1 0.179
MA0028.1 0.579
MA0029.1 0.495
MA0030.1 0.733
MA0031.1 0.0569
MA0035.2 0.745
MA0038.1 0.0121
MA0039.2 0.0788
MA0040.1 0.829
MA0041.1 0.24
MA0042.1 0.722
MA0043.1 0.109
MA0046.1 1.45241e-4
MA0047.2 0.0164
MA0048.1 0.469
MA0050.1 3.79834e-8
MA0051.1 4.73854e-4
MA0052.1 0.236
MA0055.1 0.809
MA0057.1 0.0816
MA0058.1 0.809
MA0059.1 0.333
MA0060.1 3.57506e-16
MA0061.1 0.0699
MA0062.2 0.132
MA0065.2 1.51986e-5
MA0066.1 0.104
MA0067.1 0.737
MA0068.1 0.713
MA0069.1 0.688
MA0070.1 0.3
MA0071.1 0.0433
MA0072.1 0.0282
MA0073.1 0.968
MA0074.1 0.445
MA0076.1 0.939
MA0077.1 0.0244
MA0078.1 0.686
MA0079.2 0.451
MA0080.2 6.86274e-11
MA0081.1 0.292
MA0083.1 0.717
MA0084.1 0.639
MA0087.1 0.893
MA0088.1 0.203
MA0090.1 0.353
MA0091.1 0.748
MA0092.1 0.374
MA0093.1 0.832
MA0099.2 3.60048e-4
MA0100.1 0.982
MA0101.1 0.125
MA0102.2 0.791
MA0103.1 0.00612
MA0104.2 0.993
MA0105.1 0.00643
MA0106.1 0.0811
MA0107.1 0.0892
MA0108.2 0.0114
MA0111.1 0.37
MA0112.2 3.59556e-6
MA0113.1 0.222
MA0114.1 1.61361e-4
MA0115.1 0.00539
MA0116.1 0.00889
MA0117.1 0.572
MA0119.1 0.0161
MA0122.1 0.804
MA0124.1 0.658
MA0125.1 0.0114
MA0131.1 0.652
MA0135.1 0.0417
MA0136.1 6.02806e-9
MA0137.2 0.0734
MA0138.2 0.321
MA0139.1 0.0532
MA0140.1 0.2
MA0141.1 1.6363e-4
MA0142.1 0.219
MA0143.1 0.00825
MA0144.1 0.063
MA0145.1 0.0475
MA0146.1 0.114
MA0147.1 0.765
MA0148.1 0.00211
MA0149.1 0.00131
MA0150.1 0.0144
MA0152.1 0.946
MA0153.1 2.86602e-4
MA0154.1 0.00295
MA0155.1 0.735
MA0156.1 0.00213
MA0157.1 0.0836
MA0159.1 0.00364
MA0160.1 0.00414
MA0162.1 0.307
MA0163.1 2.14579e-4
MA0164.1 0.994
MA0258.1 4.73581e-4
MA0259.1 0.973



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: CNhs10587

Novel motif P-value
1 0.039
10 0.0687
100 0.942
101 0.735
102 0.64
103 0.0304
104 0.904
105 0.313
106 0.0324
107 0.197
108 0.782
109 0.0139
11 0.0393
110 0.068
111 0.0207
112 0.00814
113 0.958
114 0.0169
115 0.484
116 0.28
117 0.0225
118 0.565
119 0.127
12 0.954
120 0.924
121 0.464
122 0.895
123 0.61
124 0.653
125 0.273
126 0.209
127 0.226
128 0.0524
129 0.147
13 0.00838
130 0.883
131 0.781
132 0.26
133 0.42
134 0.983
135 0.718
136 0.093
137 0.582
138 0.852
139 0.0139
14 0.471
140 0.0138
141 0.208
142 0.852
143 0.196
144 0.799
145 0.129
146 0.672
147 0.627
148 0.0864
149 0.155
15 0.0751
150 0.356
151 0.328
152 0.0722
153 0.193
154 0.542
155 0.585
156 0.0538
157 0.731
158 0.359
159 0.551
160 0.365
161 0.223
162 0.979
163 0.436
164 0.0267
165 0.344
166 0.84
167 0.306
168 0.898
169 0.00198
17 0.051
18 0.612
19 0.147
2 0.999
20 0.589
21 0.596
22 0.201
23 0.262
24 0.171
25 0.371
26 0.0378
27 0.592
28 0.478
29 0.12
3 0.0807
30 0.825
31 0.594
32 0.2
33 0.24
34 0.891
35 0.332
36 0.14
37 0.0204
38 0.274
39 0.345
4 0.72
40 0.191
41 0.44
42 0.332
43 0.119
44 0.0169
45 0.788
46 0.139
47 0.079
48 0.0535
49 0.115
5 0.135
50 0.85
51 0.473
52 0.51
53 0.946
54 0.602
55 0.354
56 0.397
57 0.293
58 0.168
59 0.0893
6 0.562
60 0.1
61 0.231
62 0.0623
63 0.113
64 0.431
65 0.155
66 0.902
67 0.665
68 0.18
69 0.623
7 0.106
70 2.14811e-4
71 0.0446
72 0.498
73 0.0341
74 0.351
75 0.021
76 0.554
77 0.178
78 0.115
79 0.0875
8 0.0524
80 0.559
81 0.536
82 0.0834
83 0.117
84 0.711
85 0.0331
86 0.251
87 0.263
88 0.553
89 0.176
9 0.553
90 0.00561
91 0.352
92 0.0787
93 0.454
94 0.582
95 0.0553
96 0.379
97 0.604
98 0.482
99 0.565



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: CNhs10587


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)
0000295 (mouse embryonic day 12 sample)
0011434 (mouse whole body- embryo E12 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)