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FF:1035-18D5

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Name:stomach, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs11006
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 stage17 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  SAMD00005724
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11006 CAGE DRX009094 DRR009968
Accession ID Mm9

Library idBAMCTSS
CNhs11006 DRZ001393 DRZ002776
Accession ID Mm10

Library idBAMCTSS
CNhs11006 DRZ012743 DRZ014126
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

CNhs11006

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.152
1001 0.0365
1002 0.505
1003 0.0399
1004 0
1005 0.0825
1006 -0.151
1007 0.0354
1008 0
1009 0.111
101 0.0456
1010 0.0825
1011 0.0462
1012 0
1013 0.0425
1014 0.627
1015 0.074
1016 0.157
1017 1.09
1018 0.427
1019 0
102 0
1020 0
1021 0
1022 -0.0704
1023 0
1024 0.0561
1025 0.862
1026 0.053
1027 0.0908
1028 0
1029 0.391
103 0.311
1030 0.0825
1031 0.365
1032 0.103
1033 0.00724
1034 0.0655
1035 0
1036 0.147
1037 0
1038 0.0245
1039 -0.0782
104 0
1040 0.0578
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: CNhs11006
Jaspar motif P-value
MA0002.2 0.0554
MA0003.1 0.56
MA0004.1 0.19
MA0006.1 0.101
MA0007.1 0.782
MA0009.1 0.0523
MA0014.1 0.977
MA0017.1 0.0363
MA0018.2 1.97629e-6
MA0019.1 0.181
MA0024.1 0.232
MA0025.1 8.61966e-5
MA0027.1 0.059
MA0028.1 1.62471e-4
MA0029.1 0.52
MA0030.1 0.764
MA0031.1 0.541
MA0035.2 0.205
MA0038.1 0.745
MA0039.2 0.0386
MA0040.1 0.628
MA0041.1 0.139
MA0042.1 0.307
MA0043.1 1.20495e-4
MA0046.1 0.00275
MA0047.2 0.00617
MA0048.1 0.0963
MA0050.1 0.00323
MA0051.1 1.77101e-5
MA0052.1 2.35314e-4
MA0055.1 0.883
MA0057.1 0.079
MA0058.1 0.0135
MA0059.1 0.262
MA0060.1 0.887
MA0061.1 0.856
MA0062.2 3.32671e-11
MA0065.2 0.0822
MA0066.1 0.984
MA0067.1 0.0308
MA0068.1 0.102
MA0069.1 0.146
MA0070.1 0.753
MA0071.1 0.00108
MA0072.1 0.0526
MA0073.1 0.652
MA0074.1 0.987
MA0076.1 9.85564e-6
MA0077.1 0.709
MA0078.1 0.197
MA0079.2 0.828
MA0080.2 9.52272e-5
MA0081.1 1.41243e-4
MA0083.1 2.70082e-7
MA0084.1 0.807
MA0087.1 0.334
MA0088.1 0.158
MA0090.1 0.234
MA0091.1 0.731
MA0092.1 0.123
MA0093.1 0.125
MA0099.2 1.71985e-4
MA0100.1 0.00402
MA0101.1 0.085
MA0102.2 0.55
MA0103.1 3.77306e-4
MA0104.2 0.114
MA0105.1 0.126
MA0106.1 0.0763
MA0107.1 0.101
MA0108.2 0.0025
MA0111.1 0.985
MA0112.2 0.0679
MA0113.1 0.695
MA0114.1 0.174
MA0115.1 0.0237
MA0116.1 0.0402
MA0117.1 0.024
MA0119.1 0.521
MA0122.1 0.243
MA0124.1 0.709
MA0125.1 0.429
MA0131.1 0.608
MA0135.1 0.637
MA0136.1 1.57956e-6
MA0137.2 0.127
MA0138.2 0.724
MA0139.1 0.466
MA0140.1 0.181
MA0141.1 1.68576e-4
MA0142.1 0.272
MA0143.1 0.238
MA0144.1 0.918
MA0145.1 0.0773
MA0146.1 0.792
MA0147.1 0.0918
MA0148.1 0.00644
MA0149.1 0.759
MA0150.1 0.0309
MA0152.1 0.0346
MA0153.1 3.61198e-4
MA0154.1 0.0266
MA0155.1 0.294
MA0156.1 5.31489e-5
MA0157.1 0.868
MA0159.1 0.389
MA0160.1 1.27055e-4
MA0162.1 0.193
MA0163.1 0.0239
MA0164.1 0.432
MA0258.1 0.819
MA0259.1 0.259



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: CNhs11006
Novel motif P-value
1 0.603
10 0.459
100 0.532
101 0.836
102 0.903
103 0.13
104 0.755
105 0.922
106 0.00507
107 0.0204
108 0.712
109 0.983
11 0.634
110 0.532
111 0.941
112 0.69
113 0.125
114 0.244
115 0.938
116 0.204
117 0.467
118 0.172
119 0.801
12 0.734
120 0.401
121 0.284
122 0.502
123 0.466
124 0.502
125 0.817
126 0.167
127 0.758
128 0.0546
129 0.546
13 0.0299
130 0.342
131 0.12
132 0.501
133 0.464
134 0.318
135 0.974
136 0.386
137 0.526
138 0.0145
139 0.652
14 0.817
140 0.0488
141 0.421
142 0.521
143 0.235
144 0.291
145 0.212
146 0.486
147 0.545
148 0.75
149 0.728
15 0.231
150 0.48
151 0.884
152 0.164
153 0.714
154 0.907
155 0.962
156 3.31114e-6
157 0.675
158 0.681
159 0.0288
160 0.0373
161 0.251
162 0.541
163 0.55
164 0.804
165 0.615
166 0.199
167 0.536
168 0.162
169 0.0553
17 0.0623
18 0.362
19 0.0262
2 0.609
20 0.358
21 0.107
22 0.315
23 0.537
24 0.516
25 0.0593
26 0.00251
27 0.827
28 0.78
29 0.752
3 0.789
30 0.105
31 0.746
32 0.132
33 0.907
34 0.875
35 0.409
36 0.552
37 0.223
38 0.739
39 0.17
4 0.173
40 0.805
41 0.275
42 0.572
43 0.368
44 0.373
45 0.372
46 0.405
47 0.804
48 0.597
49 0.688
5 0.451
50 0.283
51 0.592
52 0.0382
53 0.34
54 0.627
55 0.89
56 0.532
57 0.529
58 0.934
59 0.684
6 0.133
60 0.0862
61 0.603
62 0.435
63 0.669
64 0.743
65 0.903
66 0.427
67 0.838
68 0.146
69 0.219
7 0.385
70 0.414
71 0.0536
72 0.669
73 0.624
74 0.404
75 0.675
76 0.263
77 0.00157
78 0.629
79 0.884
8 0.873
80 0.164
81 0.761
82 0.85
83 0.995
84 0.414
85 0.742
86 0.672
87 0.00199
88 0.141
89 0.865
9 0.177
90 0.658
91 0.795
92 0.206
93 0.231
94 0.51
95 0.591
96 0.293
97 0.583
98 0.548
99 0.0756



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: CNhs11006


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)
0000300 (mouse embryonic day 17 sample)
0011492 (mouse stomach- embryo E17 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)