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FF:482-18D3

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Name:intestine, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs10582
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
tissueintestine
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  SAMD00005044
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10582 CAGE DRX008994 DRR009868
Accession ID Mm9

Library idBAMCTSS
CNhs10582 DRZ001293 DRZ002676
Accession ID Mm10

Library idBAMCTSS
CNhs10582 DRZ012643 DRZ014026
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

CNhs10582

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0501
1001 0
1002 0.243
1003 -0.038
1004 0
1005 0.194
1006 -0.0554
1007 -0.0136
1008 0.0872
1009 -0.00584
101 -0.00728
1010 0
1011 -0.0758
1012 0
1013 0.0458
1014 0.16
1015 -0.0332
1016 -0.0214
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 -0.0631
1023 0
1024 -0.00267
1025 0.822
1026 0
1027 0
1028 0
1029 0.332
103 0.0825
1030 0
1031 0.267
1032 0.115
1033 0
1034 0
1035 0
1036 -0.00419
1037 0
1038 0.0039
1039 -0.189
104 0
1040 -0.0454
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: CNhs10582
Jaspar motif P-value
MA0002.2 0.751
MA0003.1 0.234
MA0004.1 0.118
MA0006.1 0.0783
MA0007.1 0.386
MA0009.1 0.913
MA0014.1 0.895
MA0017.1 5.44395e-35
MA0018.2 4.04319e-4
MA0019.1 0.191
MA0024.1 0.837
MA0025.1 0.0371
MA0027.1 0.267
MA0028.1 0.258
MA0029.1 0.963
MA0030.1 0.738
MA0031.1 0.985
MA0035.2 1.3355e-7
MA0038.1 0.297
MA0039.2 9.50032e-4
MA0040.1 0.384
MA0041.1 0.987
MA0042.1 0.862
MA0043.1 0.0114
MA0046.1 1.20518e-94
MA0047.2 0.00308
MA0048.1 0.409
MA0050.1 0.818
MA0051.1 0.596
MA0052.1 7.09562e-4
MA0055.1 0.529
MA0057.1 0.293
MA0058.1 0.0107
MA0059.1 0.782
MA0060.1 0.00821
MA0061.1 0.776
MA0062.2 0.239
MA0065.2 1.21566e-8
MA0066.1 0.401
MA0067.1 0.219
MA0068.1 0.102
MA0069.1 0.0553
MA0070.1 0.354
MA0071.1 0.801
MA0072.1 0.614
MA0073.1 0.958
MA0074.1 0.0303
MA0076.1 0.152
MA0077.1 0.938
MA0078.1 0.395
MA0079.2 0.494
MA0080.2 0.0586
MA0081.1 0.0497
MA0083.1 0.0269
MA0084.1 0.768
MA0087.1 0.777
MA0088.1 0.365
MA0090.1 0.364
MA0091.1 0.342
MA0092.1 0.355
MA0093.1 0.0618
MA0099.2 0.517
MA0100.1 0.00519
MA0101.1 0.545
MA0102.2 0.287
MA0103.1 1.8157e-5
MA0104.2 0.496
MA0105.1 0.703
MA0106.1 0.581
MA0107.1 0.397
MA0108.2 0.155
MA0111.1 0.218
MA0112.2 0.00822
MA0113.1 0.927
MA0114.1 1.74528e-44
MA0115.1 9.13058e-8
MA0116.1 0.28
MA0117.1 0.215
MA0119.1 0.206
MA0122.1 0.704
MA0124.1 0.316
MA0125.1 0.504
MA0131.1 0.994
MA0135.1 0.0163
MA0136.1 0.252
MA0137.2 0.588
MA0138.2 0.754
MA0139.1 0.0153
MA0140.1 0.0242
MA0141.1 0.00417
MA0142.1 0.0471
MA0143.1 0.165
MA0144.1 0.0717
MA0145.1 0.0888
MA0146.1 0.153
MA0147.1 0.192
MA0148.1 3.47321e-4
MA0149.1 0.243
MA0150.1 0.191
MA0152.1 0.855
MA0153.1 4.47003e-60
MA0154.1 0.077
MA0155.1 0.042
MA0156.1 0.069
MA0157.1 0.667
MA0159.1 0.0553
MA0160.1 0.0298
MA0162.1 0.196
MA0163.1 0.0293
MA0164.1 0.565
MA0258.1 0.238
MA0259.1 0.391



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: CNhs10582
Novel motif P-value
1 0.714
10 0.457
100 0.363
101 0.906
102 0.228
103 0.643
104 0.976
105 0.381
106 0.0748
107 0.151
108 0.93
109 0.297
11 0.609
110 0.434
111 0.612
112 0.0438
113 0.186
114 0.864
115 0.906
116 0.483
117 0.913
118 0.53
119 0.897
12 0.543
120 0.645
121 0.702
122 0.638
123 0.0156
124 0.162
125 0.908
126 0.0344
127 0.908
128 0.44
129 0.933
13 4.97818e-5
130 0.481
131 0.344
132 0.459
133 0.53
134 0.402
135 0.311
136 0.223
137 0.815
138 0.0538
139 0.227
14 0.948
140 0.255
141 0.221
142 0.295
143 0.0769
144 0.191
145 0.208
146 0.0564
147 0.438
148 0.0733
149 0.101
15 0.761
150 0.276
151 0.972
152 0.0685
153 0.13
154 0.257
155 0.837
156 0.914
157 0.636
158 0.828
159 0.0636
160 0.0505
161 0.495
162 0.629
163 0.364
164 0.586
165 0.592
166 0.621
167 0.662
168 0.229
169 0.115
17 0.334
18 0.0511
19 0.0281
2 0.181
20 0.618
21 0.94
22 0.227
23 0.725
24 0.443
25 0.975
26 0.0253
27 0.587
28 0.579
29 0.621
3 0.657
30 0.273
31 0.988
32 0.307
33 0.299
34 0.31
35 0.436
36 0.849
37 0.23
38 0.63
39 0.244
4 0.306
40 0.0994
41 0.348
42 0.782
43 0.502
44 0.567
45 0.0778
46 0.702
47 0.807
48 0.687
49 0.811
5 0.662
50 0.351
51 0.874
52 0.0195
53 0.664
54 0.754
55 0.0547
56 0.497
57 0.122
58 0.729
59 0.362
6 0.962
60 0.0728
61 0.409
62 0.541
63 0.604
64 0.719
65 0.502
66 0.86
67 0.0663
68 0.584
69 0.582
7 0.0659
70 0.664
71 0.113
72 0.446
73 0.419
74 0.818
75 0.504
76 0.473
77 0.0201
78 0.113
79 0.562
8 0.734
80 0.377
81 0.629
82 0.795
83 0.356
84 0.498
85 0.382
86 0.472
87 0.895
88 0.553
89 0.209
9 0.722
90 0.785
91 0.333
92 0.612
93 0.618
94 0.0714
95 0.657
96 0.384
97 0.343
98 0.958
99 0.0718



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: CNhs10582


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)
0000160 (intestine)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
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)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)

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)
0011370 (mouse intestine- 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)