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FF:356-43E3

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Name:stomach, embryo E12
Species:Mouse (Mus musculus)
Library ID:CNhs10588
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
tissuestomach
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  SAMD00005153
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10588 CAGE DRX009091 DRR009965
Accession ID Mm9

Library idBAMCTSS
CNhs10588 DRZ001390 DRZ002773
Accession ID Mm10

Library idBAMCTSS
CNhs10588 DRZ012740 DRZ014123
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

CNhs10588

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0119
1001 --0.0668
1002 0.481
1003 --0.132
1004 0
1005 --0.136
1006 --0.00645
1007 0.17
1008 0
1009 0
101 0.14
1010 0
1011 0
1012 0
1013 --0.217
1014 0.343
1015 0.406
1016 0.315
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0151
1022 --0.124
1023 0
1024 --0.0173
1025 0.665
1026 0
1027 0.0638
1028 0
1029 --0.0838
103 0
1030 0
1031 0.285
1032 --0.0606
1033 0.0441
1034 0
1035 0
1036 0.164
1037 0
1038 0.0106
1039 --0.18
104 0
1040 0.161
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: CNhs10588

Jaspar motif P-value
MA0002.2 0.00101
MA0003.1 0.251
MA0004.1 0.678
MA0006.1 0.362
MA0007.1 0.358
MA0009.1 0.606
MA0014.1 0.418
MA0017.1 3.79694e-4
MA0018.2 0.379
MA0019.1 0.791
MA0024.1 5.09002e-6
MA0025.1 0.0898
MA0027.1 0.0423
MA0028.1 0.0605
MA0029.1 0.515
MA0030.1 0.669
MA0031.1 0.374
MA0035.2 0.275
MA0038.1 0.00823
MA0039.2 0.461
MA0040.1 0.764
MA0041.1 0.337
MA0042.1 0.653
MA0043.1 0.0679
MA0046.1 0.0536
MA0047.2 0.725
MA0048.1 0.238
MA0050.1 1.15441e-6
MA0051.1 3.75459e-5
MA0052.1 8.6983e-6
MA0055.1 0.0419
MA0057.1 0.0891
MA0058.1 0.494
MA0059.1 0.692
MA0060.1 6.80594e-18
MA0061.1 0.0973
MA0062.2 0.12
MA0065.2 0.00109
MA0066.1 0.0795
MA0067.1 0.429
MA0068.1 0.613
MA0069.1 0.946
MA0070.1 0.366
MA0071.1 0.111
MA0072.1 0.158
MA0073.1 0.979
MA0074.1 0.764
MA0076.1 0.0379
MA0077.1 0.0281
MA0078.1 0.572
MA0079.2 0.552
MA0080.2 9.4604e-7
MA0081.1 0.646
MA0083.1 0.197
MA0084.1 0.383
MA0087.1 0.936
MA0088.1 0.98
MA0090.1 0.533
MA0091.1 0.714
MA0092.1 0.433
MA0093.1 0.624
MA0099.2 4.92676e-4
MA0100.1 0.592
MA0101.1 0.635
MA0102.2 0.61
MA0103.1 0.0141
MA0104.2 0.233
MA0105.1 0.00769
MA0106.1 0.193
MA0107.1 0.291
MA0108.2 0.0456
MA0111.1 0.568
MA0112.2 3.30863e-6
MA0113.1 0.817
MA0114.1 0.00281
MA0115.1 0.0534
MA0116.1 0.0093
MA0117.1 0.101
MA0119.1 0.012
MA0122.1 0.929
MA0124.1 0.757
MA0125.1 0.0499
MA0131.1 0.179
MA0135.1 0.203
MA0136.1 0.036
MA0137.2 0.346
MA0138.2 0.0019
MA0139.1 0.282
MA0140.1 0.337
MA0141.1 0.00162
MA0142.1 0.754
MA0143.1 0.0155
MA0144.1 0.293
MA0145.1 0.0221
MA0146.1 0.853
MA0147.1 0.371
MA0148.1 0.123
MA0149.1 0.0259
MA0150.1 0.00348
MA0152.1 0.755
MA0153.1 0.599
MA0154.1 0.00554
MA0155.1 0.952
MA0156.1 0.811
MA0157.1 0.3
MA0159.1 0.0231
MA0160.1 0.0423
MA0162.1 0.662
MA0163.1 0.0876
MA0164.1 0.691
MA0258.1 2.91149e-4
MA0259.1 0.573



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: CNhs10588

Novel motif P-value
1 0.0661
10 0.341
100 0.939
101 0.47
102 0.754
103 0.0691
104 0.901
105 0.276
106 0.00974
107 0.0517
108 0.96
109 0.211
11 0.137
110 0.198
111 0.091
112 0.0843
113 0.424
114 0.0138
115 0.701
116 0.62
117 0.419
118 0.806
119 0.0489
12 0.98
120 0.806
121 0.706
122 0.936
123 0.107
124 0.368
125 0.387
126 0.733
127 0.0884
128 0.0272
129 0.0315
13 0.441
130 0.589
131 0.179
132 0.646
133 0.493
134 0.522
135 0.943
136 0.408
137 0.679
138 0.728
139 0.00441
14 0.333
140 0.059
141 0.281
142 0.327
143 0.452
144 0.692
145 0.51
146 0.503
147 0.561
148 0.224
149 0.206
15 0.0932
150 0.47
151 0.143
152 0.21
153 0.132
154 0.367
155 0.907
156 0.0158
157 0.846
158 0.35
159 0.0806
160 0.519
161 0.667
162 0.612
163 0.213
164 0.445
165 0.144
166 0.679
167 0.936
168 0.315
169 0.00487
17 0.044
18 0.334
19 0.21
2 0.629
20 0.781
21 0.962
22 0.312
23 0.0503
24 0.677
25 0.335
26 0.352
27 0.324
28 0.291
29 0.544
3 0.233
30 0.88
31 0.291
32 0.304
33 0.809
34 0.865
35 0.257
36 0.489
37 0.0915
38 0.435
39 0.882
4 0.613
40 0.659
41 0.601
42 0.538
43 0.14
44 0.101
45 0.634
46 0.231
47 0.138
48 0.195
49 0.108
5 0.144
50 0.894
51 0.54
52 0.329
53 0.598
54 0.43
55 0.969
56 0.36
57 0.436
58 0.248
59 0.0583
6 0.513
60 0.143
61 0.978
62 0.0785
63 0.135
64 0.544
65 0.157
66 0.404
67 0.519
68 0.192
69 0.278
7 0.319
70 0.0011
71 0.298
72 0.562
73 0.206
74 0.223
75 0.267
76 0.77
77 0.228
78 0.258
79 0.287
8 0.149
80 0.251
81 0.298
82 0.0957
83 0.142
84 0.882
85 0.00325
86 0.56
87 0.663
88 0.838
89 0.177
9 0.498
90 0.0465
91 0.175
92 0.083
93 0.981
94 0.166
95 0.316
96 0.209
97 0.908
98 0.264
99 0.77



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: CNhs10588


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)
0000945 (stomach)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010039 (food storage organ)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)
0001041 (foregut)

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)
0011321 (mouse stomach- 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

UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)