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FF:459-17D4

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Name:stomach, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs11022
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 stage16 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  SAMD00005650
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11022 CAGE DRX009093 DRR009967
Accession ID Mm9

Library idBAMCTSS
CNhs11022 DRZ001392 DRZ002775
Accession ID Mm10

Library idBAMCTSS
CNhs11022 DRZ012742 DRZ014125
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

CNhs11022

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.00282
10 0
100 0
1000 0.0479
1001 0.00312
1002 0.47
1003 0.086
1004 0
1005 0.0849
1006 --0.114
1007 0.0605
1008 0
1009 0.15
101 0.074
1010 0.122
1011 --0.063
1012 0.0445
1013 --0.0608
1014 0.649
1015 0.125
1016 0.149
1017 0.799
1018 0.418
1019 0
102 0
1020 0
1021 --0.00415
1022 --0.0704
1023 0
1024 --0.0177
1025 0.821
1026 0.0151
1027 0.0666
1028 0
1029 0.285
103 0.257
1030 0
1031 0.367
1032 0.0745
1033 0.0232
1034 0.101
1035 0
1036 0.135
1037 0
1038 0.0166
1039 --0.074
104 0
1040 0.0604
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: CNhs11022

Jaspar motif P-value
MA0002.2 0.00757
MA0003.1 0.69
MA0004.1 0.233
MA0006.1 0.285
MA0007.1 0.84
MA0009.1 0.245
MA0014.1 0.912
MA0017.1 0.715
MA0018.2 1.91569e-4
MA0019.1 0.443
MA0024.1 9.8003e-7
MA0025.1 1.85249e-4
MA0027.1 0.015
MA0028.1 0.00957
MA0029.1 0.855
MA0030.1 0.899
MA0031.1 0.227
MA0035.2 0.876
MA0038.1 0.45
MA0039.2 0.0889
MA0040.1 0.741
MA0041.1 0.154
MA0042.1 0.273
MA0043.1 5.35077e-4
MA0046.1 1.80805e-20
MA0047.2 0.00782
MA0048.1 0.015
MA0050.1 0.0154
MA0051.1 4.36365e-4
MA0052.1 1.28973e-6
MA0055.1 0.239
MA0057.1 0.343
MA0058.1 0.0239
MA0059.1 0.338
MA0060.1 0.00334
MA0061.1 0.287
MA0062.2 1.37405e-6
MA0065.2 0.0308
MA0066.1 0.511
MA0067.1 0.016
MA0068.1 0.279
MA0069.1 0.0703
MA0070.1 0.424
MA0071.1 0.00176
MA0072.1 0.0218
MA0073.1 0.432
MA0074.1 0.89
MA0076.1 0.00137
MA0077.1 0.748
MA0078.1 0.259
MA0079.2 0.886
MA0080.2 1.74044e-4
MA0081.1 0.00844
MA0083.1 6.81589e-7
MA0084.1 0.557
MA0087.1 0.502
MA0088.1 0.405
MA0090.1 0.36
MA0091.1 0.968
MA0092.1 0.442
MA0093.1 0.176
MA0099.2 0.461
MA0100.1 0.00575
MA0101.1 0.077
MA0102.2 0.825
MA0103.1 0.0164
MA0104.2 0.166
MA0105.1 0.535
MA0106.1 0.489
MA0107.1 0.0348
MA0108.2 0.253
MA0111.1 0.685
MA0112.2 0.949
MA0113.1 0.621
MA0114.1 0.77
MA0115.1 0.365
MA0116.1 0.362
MA0117.1 0.00281
MA0119.1 0.842
MA0122.1 0.103
MA0124.1 0.734
MA0125.1 0.983
MA0131.1 0.771
MA0135.1 0.714
MA0136.1 3.38478e-6
MA0137.2 0.105
MA0138.2 0.0417
MA0139.1 0.29
MA0140.1 0.79
MA0141.1 1.32523e-4
MA0142.1 0.233
MA0143.1 0.658
MA0144.1 0.485
MA0145.1 0.288
MA0146.1 0.527
MA0147.1 0.11
MA0148.1 0.00623
MA0149.1 0.88
MA0150.1 0.00176
MA0152.1 0.31
MA0153.1 2.10491e-14
MA0154.1 0.228
MA0155.1 0.159
MA0156.1 0.00149
MA0157.1 0.368
MA0159.1 0.163
MA0160.1 5.57235e-4
MA0162.1 0.222
MA0163.1 0.0777
MA0164.1 0.971
MA0258.1 0.0597
MA0259.1 0.401



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: CNhs11022

Novel motif P-value
1 0.423
10 0.877
100 0.637
101 0.49
102 0.504
103 0.696
104 0.725
105 0.891
106 0.183
107 0.0903
108 0.931
109 0.582
11 0.173
110 0.932
111 0.141
112 0.929
113 0.119
114 0.0124
115 0.619
116 0.441
117 0.19
118 0.174
119 0.459
12 0.443
120 0.423
121 0.138
122 0.798
123 0.247
124 0.429
125 0.419
126 0.31
127 0.613
128 0.883
129 0.487
13 0.0235
130 0.211
131 0.326
132 0.687
133 0.644
134 0.428
135 0.927
136 0.922
137 0.72
138 0.00316
139 0.379
14 0.465
140 0.2
141 0.955
142 0.909
143 0.206
144 0.472
145 0.388
146 0.567
147 0.411
148 0.597
149 0.86
15 0.0398
150 0.414
151 0.0992
152 0.358
153 0.216
154 0.982
155 0.541
156 0.017
157 0.434
158 0.432
159 0.0834
160 0.0168
161 0.387
162 0.924
163 0.638
164 0.513
165 0.735
166 0.0613
167 0.772
168 0.271
169 0.565
17 0.626
18 0.0681
19 0.103
2 0.936
20 0.292
21 0.605
22 0.594
23 0.619
24 0.585
25 0.0437
26 0.0525
27 0.68
28 0.235
29 0.711
3 0.608
30 0.37
31 0.488
32 0.691
33 0.861
34 0.991
35 0.0662
36 0.682
37 0.858
38 0.572
39 0.248
4 0.275
40 0.945
41 0.0575
42 0.968
43 0.498
44 0.296
45 0.77
46 0.795
47 0.653
48 0.322
49 0.17
5 0.515
50 0.361
51 0.945
52 0.0792
53 0.506
54 0.999
55 0.485
56 0.577
57 0.591
58 0.44
59 0.541
6 0.39
60 0.383
61 0.612
62 0.0531
63 0.5
64 0.507
65 0.496
66 0.508
67 0.385
68 0.0923
69 0.0499
7 0.721
70 0.0192
71 0.574
72 0.948
73 0.501
74 0.483
75 0.375
76 0.413
77 0.149
78 0.987
79 0.813
8 0.225
80 0.184
81 0.544
82 0.134
83 0.402
84 0.393
85 0.142
86 0.997
87 0.00533
88 0.181
89 0.672
9 0.499
90 0.25
91 0.566
92 0.881
93 0.696
94 0.229
95 0.335
96 0.736
97 0.662
98 0.082
99 0.128



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: CNhs11022


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)
0000299 (mouse embryonic day 16 sample)
0011358 (mouse stomach- embryo E16 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)