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FF:1286-20C6

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Name:stomach, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs10999
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 stage18 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  SAMD00005926
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10999 CAGE DRX009095 DRR009969
Accession ID Mm9

Library idBAMCTSS
CNhs10999 DRZ001394 DRZ002777
Accession ID Mm10

Library idBAMCTSS
CNhs10999 DRZ012744 DRZ014127
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

CNhs10999

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.122
1001 0.0822
1002 0.428
1003 0.0939
1004 0
1005 0.197
1006 --0.0659
1007 --0.0227
1008 0
1009 0.121
101 0.00106
1010 0
1011 0
1012 0
1013 0.0443
1014 0.538
1015 --0.00708
1016 0.0847
1017 0.852
1018 0.631
1019 0
102 0
1020 0
1021 0
1022 0.0154
1023 0
1024 0.0565
1025 0.757
1026 0.0563
1027 0
1028 0
1029 0.304
103 0.273
1030 0
1031 0.349
1032 0.219
1033 0
1034 0
1035 0
1036 0.0466
1037 0
1038 0.0126
1039 --0.0106
104 0
1040 0.0979
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: CNhs10999

Jaspar motif P-value
MA0002.2 0.415
MA0003.1 0.285
MA0004.1 0.304
MA0006.1 0.0852
MA0007.1 0.778
MA0009.1 0.0502
MA0014.1 0.757
MA0017.1 0.063
MA0018.2 2.66634e-5
MA0019.1 0.623
MA0024.1 0.23
MA0025.1 9.49205e-4
MA0027.1 0.0179
MA0028.1 0.00178
MA0029.1 0.915
MA0030.1 0.289
MA0031.1 0.718
MA0035.2 0.168
MA0038.1 0.589
MA0039.2 0.00315
MA0040.1 0.587
MA0041.1 0.127
MA0042.1 0.193
MA0043.1 3.14172e-4
MA0046.1 4.18051e-24
MA0047.2 1.65062e-6
MA0048.1 0.585
MA0050.1 0.467
MA0051.1 0.033
MA0052.1 0.00366
MA0055.1 0.373
MA0057.1 0.0668
MA0058.1 0.114
MA0059.1 0.444
MA0060.1 0.0846
MA0061.1 0.829
MA0062.2 2.16164e-8
MA0065.2 0.086
MA0066.1 0.166
MA0067.1 0.159
MA0068.1 0.0671
MA0069.1 0.0434
MA0070.1 0.494
MA0071.1 0.0529
MA0072.1 0.323
MA0073.1 0.606
MA0074.1 0.963
MA0076.1 1.61676e-4
MA0077.1 0.306
MA0078.1 0.233
MA0079.2 0.475
MA0080.2 0.0317
MA0081.1 0.00121
MA0083.1 1.50976e-5
MA0084.1 0.945
MA0087.1 0.298
MA0088.1 0.178
MA0090.1 0.0801
MA0091.1 0.679
MA0092.1 0.213
MA0093.1 0.261
MA0099.2 2.81008e-5
MA0100.1 0.00702
MA0101.1 0.343
MA0102.2 0.769
MA0103.1 5.42171e-5
MA0104.2 0.181
MA0105.1 0.0674
MA0106.1 0.0927
MA0107.1 0.379
MA0108.2 1.44913e-7
MA0111.1 0.855
MA0112.2 0.00455
MA0113.1 0.509
MA0114.1 0.00241
MA0115.1 0.976
MA0116.1 0.0415
MA0117.1 0.194
MA0119.1 0.0986
MA0122.1 0.182
MA0124.1 0.997
MA0125.1 0.576
MA0131.1 0.238
MA0135.1 0.355
MA0136.1 7.20797e-5
MA0137.2 0.737
MA0138.2 0.745
MA0139.1 0.25
MA0140.1 0.318
MA0141.1 0.361
MA0142.1 0.0504
MA0143.1 0.138
MA0144.1 0.185
MA0145.1 0.00923
MA0146.1 0.655
MA0147.1 0.153
MA0148.1 2.06192e-7
MA0149.1 0.491
MA0150.1 0.602
MA0152.1 0.728
MA0153.1 1.20894e-16
MA0154.1 0.00876
MA0155.1 0.275
MA0156.1 0.0023
MA0157.1 0.321
MA0159.1 0.89
MA0160.1 0.194
MA0162.1 0.255
MA0163.1 0.0139
MA0164.1 0.834
MA0258.1 0.17
MA0259.1 0.177



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: CNhs10999

Novel motif P-value
1 0.532
10 0.439
100 0.604
101 0.717
102 0.789
103 0.0414
104 0.868
105 0.779
106 0.00757
107 0.0151
108 0.637
109 0.199
11 0.657
110 0.479
111 0.505
112 0.161
113 0.517
114 0.995
115 0.931
116 0.167
117 0.617
118 0.366
119 0.159
12 0.83
120 0.523
121 0.454
122 0.341
123 0.629
124 0.768
125 0.876
126 0.117
127 0.569
128 0.0188
129 0.945
13 0.0231
130 0.461
131 0.845
132 0.322
133 0.77
134 0.402
135 0.998
136 0.807
137 0.887
138 0.00633
139 0.49
14 0.768
140 0.045
141 0.369
142 0.677
143 0.0809
144 0.207
145 0.0916
146 0.346
147 0.787
148 0.559
149 0.213
15 0.825
150 0.456
151 0.773
152 0.0833
153 0.563
154 0.868
155 0.946
156 0.00513
157 0.275
158 0.807
159 0.151
160 0.0384
161 0.22
162 0.256
163 0.978
164 0.519
165 0.784
166 0.225
167 0.29
168 0.0739
169 0.025
17 0.0374
18 0.685
19 0.0316
2 0.244
20 0.24
21 0.274
22 0.215
23 0.134
24 0.615
25 0.358
26 0.0161
27 0.693
28 0.879
29 0.921
3 0.57
30 0.103
31 0.902
32 0.0412
33 0.727
34 0.72
35 0.697
36 0.371
37 0.193
38 0.69
39 0.156
4 0.198
40 0.765
41 0.379
42 0.659
43 0.216
44 0.774
45 0.266
46 0.299
47 0.531
48 0.762
49 0.457
5 0.517
50 0.526
51 0.421
52 0.0431
53 0.275
54 0.21
55 0.961
56 0.377
57 0.387
58 0.626
59 0.226
6 0.17
60 0.0538
61 0.438
62 0.759
63 0.408
64 0.873
65 0.365
66 0.528
67 0.901
68 0.0774
69 0.319
7 0.246
70 0.875
71 0.0785
72 0.572
73 0.306
74 0.517
75 0.715
76 0.121
77 0.00339
78 0.245
79 0.915
8 0.687
80 0.181
81 0.592
82 0.285
83 0.988
84 0.897
85 0.17
86 0.556
87 0.484
88 0.145
89 0.352
9 0.265
90 0.846
91 0.671
92 0.113
93 0.266
94 0.522
95 0.656
96 0.43
97 0.266
98 0.871
99 0.0344



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: CNhs10999


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)
0000302 (mouse embryonic day 18 sample)
0011514 (mouse stomach- embryo E18 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)