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FF:381-16D5

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Name:intestine, embryo E13
Species:Mouse (Mus musculus)
Library ID:CNhs11010
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 stage13 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  SAMD00005002
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11010 CAGE DRX008991 DRR009865
Accession ID Mm9

Library idBAMCTSS
CNhs11010 DRZ001290 DRZ002673
Accession ID Mm10

Library idBAMCTSS
CNhs11010 DRZ012640 DRZ014023
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

CNhs11010

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.0926
1002 0.773
1003 --0.109
1004 0
1005 --0.0389
1006 --0.0304
1007 0.0992
1008 0
1009 0.0395
101 0.129
1010 0
1011 --0.0556
1012 0.0907
1013 --0.234
1014 0.627
1015 0.226
1016 0.142
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0907
1022 --0.0333
1023 0
1024 0.0436
1025 0.833
1026 0
1027 0.00132
1028 0
1029 0.357
103 0.146
1030 0
1031 0.367
1032 --0.184
1033 0.0907
1034 0.0209
1035 0.0467
1036 0.225
1037 0
1038 0.0595
1039 --0.22
104 0
1040 0.109
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: CNhs11010

Jaspar motif P-value
MA0002.2 6.49357e-4
MA0003.1 0.0437
MA0004.1 0.909
MA0006.1 0.256
MA0007.1 0.399
MA0009.1 0.592
MA0014.1 0.276
MA0017.1 0.00381
MA0018.2 0.186
MA0019.1 0.884
MA0024.1 1.26653e-6
MA0025.1 6.76391e-5
MA0027.1 0.0182
MA0028.1 0.698
MA0029.1 0.439
MA0030.1 0.364
MA0031.1 0.0539
MA0035.2 0.435
MA0038.1 0.239
MA0039.2 0.00227
MA0040.1 0.654
MA0041.1 0.186
MA0042.1 0.385
MA0043.1 0.709
MA0046.1 0.739
MA0047.2 0.251
MA0048.1 0.0253
MA0050.1 0.00192
MA0051.1 1.42095e-4
MA0052.1 8.08567e-8
MA0055.1 0.027
MA0057.1 0.0817
MA0058.1 0.96
MA0059.1 0.468
MA0060.1 1.95836e-6
MA0061.1 0.171
MA0062.2 0.327
MA0065.2 9.24534e-6
MA0066.1 0.225
MA0067.1 0.275
MA0068.1 0.532
MA0069.1 0.554
MA0070.1 0.94
MA0071.1 0.0447
MA0072.1 0.0238
MA0073.1 0.584
MA0074.1 0.716
MA0076.1 0.856
MA0077.1 0.845
MA0078.1 0.939
MA0079.2 0.0198
MA0080.2 2.52132e-11
MA0081.1 0.118
MA0083.1 0.0111
MA0084.1 0.597
MA0087.1 0.267
MA0088.1 0.718
MA0090.1 0.864
MA0091.1 0.749
MA0092.1 0.833
MA0093.1 0.924
MA0099.2 1.93002e-6
MA0100.1 0.882
MA0101.1 0.287
MA0102.2 0.465
MA0103.1 0.00524
MA0104.2 0.374
MA0105.1 0.703
MA0106.1 0.506
MA0107.1 0.0881
MA0108.2 0.0535
MA0111.1 0.643
MA0112.2 0.00184
MA0113.1 0.648
MA0114.1 0.00583
MA0115.1 0.304
MA0116.1 0.307
MA0117.1 0.0242
MA0119.1 0.0408
MA0122.1 0.197
MA0124.1 0.405
MA0125.1 0.76
MA0131.1 0.305
MA0135.1 0.111
MA0136.1 3.26584e-8
MA0137.2 0.0961
MA0138.2 1.8949e-4
MA0139.1 0.286
MA0140.1 0.574
MA0141.1 0.00153
MA0142.1 0.768
MA0143.1 0.12
MA0144.1 0.186
MA0145.1 0.00536
MA0146.1 0.131
MA0147.1 0.344
MA0148.1 0.263
MA0149.1 0.127
MA0150.1 6.29089e-4
MA0152.1 0.00838
MA0153.1 0.628
MA0154.1 0.0359
MA0155.1 0.96
MA0156.1 5.45826e-4
MA0157.1 0.0728
MA0159.1 0.0353
MA0160.1 0.00213
MA0162.1 0.933
MA0163.1 0.849
MA0164.1 0.541
MA0258.1 8.36757e-4
MA0259.1 0.282



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: CNhs11010

Novel motif P-value
1 0.216
10 0.734
100 0.724
101 0.474
102 0.564
103 0.24
104 0.906
105 0.296
106 0.0467
107 0.187
108 0.823
109 0.0854
11 0.204
110 0.547
111 0.17
112 0.323
113 0.457
114 0.00723
115 0.683
116 0.425
117 0.858
118 0.939
119 0.0497
12 0.786
120 0.508
121 0.582
122 0.61
123 0.262
124 0.452
125 0.995
126 0.963
127 0.253
128 0.0808
129 0.104
13 0.829
130 0.374
131 0.0594
132 0.973
133 0.329
134 0.897
135 0.686
136 0.232
137 0.84
138 0.299
139 0.0807
14 0.259
140 0.166
141 0.539
142 0.911
143 0.669
144 0.554
145 0.898
146 0.312
147 0.385
148 0.66
149 0.344
15 0.0637
150 0.383
151 0.0881
152 0.0229
153 0.635
154 0.964
155 0.619
156 4.62317e-10
157 0.792
158 0.763
159 0.0681
160 0.487
161 0.961
162 0.692
163 0.14
164 0.526
165 0.0786
166 0.231
167 0.138
168 0.62
169 0.0172
17 0.15
18 0.377
19 0.673
2 0.371
20 0.497
21 0.462
22 0.204
23 0.0801
24 0.0799
25 0.168
26 0.922
27 0.218
28 0.204
29 0.961
3 0.497
30 0.464
31 0.282
32 0.451
33 0.796
34 0.594
35 0.497
36 0.789
37 0.0591
38 0.246
39 0.977
4 0.799
40 0.43
41 0.107
42 0.767
43 0.251
44 0.0172
45 0.295
46 0.439
47 0.253
48 0.154
49 0.239
5 0.357
50 0.952
51 0.607
52 0.529
53 0.53
54 0.51
55 0.461
56 0.292
57 0.954
58 0.323
59 0.0378
6 0.689
60 0.212
61 0.943
62 0.0602
63 0.126
64 0.577
65 0.0893
66 0.794
67 0.871
68 0.349
69 0.345
7 0.298
70 1.95049e-4
71 0.671
72 0.274
73 0.0124
74 0.849
75 0.192
76 0.336
77 0.192
78 0.231
79 0.552
8 0.292
80 0.0468
81 0.365
82 0.108
83 0.304
84 0.512
85 0.0195
86 0.218
87 0.00134
88 0.698
89 0.112
9 0.476
90 0.257
91 0.441
92 0.319
93 0.989
94 0.86
95 0.0334
96 0.466
97 0.708
98 0.233
99 0.892



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: CNhs11010


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)
0000293 (mouse embryonic day 13 sample)
0011330 (mouse intestine- embryo E13 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)