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FF:1252-16G8

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Name:stomach, embryo E15
Species:Mouse (Mus musculus)
Library ID:CNhs10603
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 stage15 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  SAMD00004695
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10603 CAGE DRX009092 DRR009966
Accession ID Mm9

Library idBAMCTSS
CNhs10603 DRZ001391 DRZ002774
Accession ID Mm10

Library idBAMCTSS
CNhs10603 DRZ012741 DRZ014124
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

CNhs10603

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.00779
1001 0.0474
1002 0.429
1003 0.0564
1004 0
1005 0
1006 --0.0434
1007 0.076
1008 0
1009 0.091
101 0.101
1010 0.482
1011 0.00686
1012 0
1013 --0.0891
1014 0.357
1015 0.263
1016 0.256
1017 0.0804
1018 0.305
1019 0
102 0
1020 0
1021 0
1022 0.00999
1023 0
1024 0.00862
1025 0.773
1026 0
1027 0.146
1028 0
1029 0.269
103 0.157
1030 0
1031 0.435
1032 0.0163
1033 0
1034 0
1035 0
1036 0.119
1037 0
1038 0.0684
1039 --0.141
104 0
1040 0.0799
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: CNhs10603

Jaspar motif P-value
MA0002.2 0.00111
MA0003.1 0.643
MA0004.1 0.572
MA0006.1 0.974
MA0007.1 0.287
MA0009.1 0.433
MA0014.1 0.467
MA0017.1 6.92823e-5
MA0018.2 0.511
MA0019.1 0.746
MA0024.1 3.77252e-7
MA0025.1 0.0389
MA0027.1 0.0139
MA0028.1 0.496
MA0029.1 0.345
MA0030.1 0.248
MA0031.1 0.87
MA0035.2 0.612
MA0038.1 0.00192
MA0039.2 0.416
MA0040.1 0.909
MA0041.1 0.64
MA0042.1 0.668
MA0043.1 0.945
MA0046.1 1.83716e-17
MA0047.2 0.00146
MA0048.1 0.732
MA0050.1 2.01891e-5
MA0051.1 4.26164e-4
MA0052.1 0.00951
MA0055.1 0.531
MA0057.1 0.534
MA0058.1 0.354
MA0059.1 0.15
MA0060.1 1.13476e-13
MA0061.1 0.211
MA0062.2 0.108
MA0065.2 2.71669e-4
MA0066.1 0.0525
MA0067.1 0.127
MA0068.1 0.171
MA0069.1 0.526
MA0070.1 0.271
MA0071.1 0.00605
MA0072.1 0.0236
MA0073.1 0.847
MA0074.1 0.834
MA0076.1 0.657
MA0077.1 0.206
MA0078.1 0.603
MA0079.2 0.119
MA0080.2 1.39501e-4
MA0081.1 0.152
MA0083.1 1.03307e-6
MA0084.1 0.99
MA0087.1 0.397
MA0088.1 0.889
MA0090.1 0.289
MA0091.1 0.853
MA0092.1 0.789
MA0093.1 0.592
MA0099.2 0.228
MA0100.1 0.204
MA0101.1 0.612
MA0102.2 0.905
MA0103.1 0.684
MA0104.2 0.573
MA0105.1 0.0272
MA0106.1 0.719
MA0107.1 0.485
MA0108.2 0.0185
MA0111.1 0.313
MA0112.2 8.61779e-5
MA0113.1 0.66
MA0114.1 8.48374e-4
MA0115.1 0.00347
MA0116.1 0.0186
MA0117.1 0.0218
MA0119.1 0.225
MA0122.1 0.443
MA0124.1 0.801
MA0125.1 0.195
MA0131.1 0.463
MA0135.1 0.0235
MA0136.1 1.97159e-4
MA0137.2 0.34
MA0138.2 0.0404
MA0139.1 0.659
MA0140.1 0.792
MA0141.1 1.32011e-5
MA0142.1 0.755
MA0143.1 0.382
MA0144.1 0.587
MA0145.1 0.526
MA0146.1 0.267
MA0147.1 0.392
MA0148.1 0.00914
MA0149.1 0.0287
MA0150.1 0.0015
MA0152.1 0.393
MA0153.1 1.86046e-11
MA0154.1 0.0531
MA0155.1 0.527
MA0156.1 0.171
MA0157.1 0.666
MA0159.1 0.00544
MA0160.1 0.00154
MA0162.1 0.948
MA0163.1 0.187
MA0164.1 0.687
MA0258.1 8.97642e-5
MA0259.1 0.725



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: CNhs10603

Novel motif P-value
1 0.0464
10 0.123
100 0.7
101 0.577
102 0.606
103 0.0858
104 0.93
105 0.829
106 0.248
107 0.715
108 0.913
109 0.171
11 0.0556
110 0.161
111 0.00479
112 0.0701
113 0.692
114 2.86038e-5
115 0.846
116 0.738
117 0.0335
118 0.202
119 0.0834
12 0.622
120 0.33
121 0.618
122 0.93
123 0.374
124 0.508
125 0.157
126 0.658
127 0.197
128 0.149
129 0.141
13 0.578
130 0.15
131 0.699
132 0.937
133 0.507
134 0.548
135 0.928
136 0.563
137 0.826
138 0.0233
139 0.0224
14 0.577
140 0.778
141 0.754
142 0.472
143 0.0143
144 0.524
145 0.734
146 0.685
147 0.408
148 0.139
149 0.68
15 0.0282
150 0.536
151 0.0748
152 0.822
153 0.194
154 0.446
155 0.195
156 0.076
157 0.82
158 0.227
159 0.122
160 0.977
161 0.505
162 0.548
163 0.359
164 0.145
165 0.473
166 0.229
167 0.48
168 0.326
169 0.0321
17 0.148
18 0.0987
19 0.67
2 0.855
20 0.351
21 0.726
22 0.555
23 0.174
24 0.885
25 0.115
26 0.788
27 0.658
28 0.266
29 0.27
3 0.0767
30 0.625
31 0.379
32 0.202
33 0.824
34 0.877
35 0.027
36 0.128
37 0.0896
38 0.46
39 0.781
4 0.891
40 0.73
41 0.16
42 0.433
43 0.123
44 0.0724
45 0.985
46 0.224
47 0.156
48 0.0884
49 0.0706
5 0.0955
50 0.617
51 0.538
52 0.638
53 0.758
54 0.548
55 0.47
56 0.468
57 0.227
58 0.309
59 0.142
6 0.897
60 0.578
61 0.815
62 0.0279
63 0.208
64 0.36
65 0.285
66 0.655
67 0.357
68 0.0373
69 0.0571
7 0.453
70 5.39113e-4
71 0.169
72 0.786
73 0.136
74 0.824
75 0.0283
76 0.32
77 0.312
78 0.267
79 0.271
8 0.0534
80 0.394
81 0.28
82 0.0535
83 0.176
84 0.901
85 0.00693
86 0.68
87 0.364
88 0.627
89 0.466
9 0.938
90 0.0162
91 0.429
92 0.159
93 0.525
94 0.0286
95 0.085
96 0.18
97 0.707
98 0.286
99 0.724



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: CNhs10603


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)
0000298 (mouse embryonic day 15 sample)
0011523 (mouse stomach- embryo E15 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)