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FF:1289-20F7

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Name:intestine, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs10526
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 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  SAMD00005646
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10526 CAGE DRX008995 DRR009869
Accession ID Mm9

Library idBAMCTSS
CNhs10526 DRZ001294 DRZ002677
Accession ID Mm10

Library idBAMCTSS
CNhs10526 DRZ012644 DRZ014027
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

CNhs10526

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0756
1001 0
1002 0.168
1003 --0.0672
1004 0
1005 0.266
1006 --0.00239
1007 --0.039
1008 0.0756
1009 0.0555
101 --0.0482
1010 0.0756
1011 --0.0106
1012 0
1013 0.161
1014 0.111
1015 --0.0385
1016 --0.0487
1017 0
1018 0.335
1019 0
102 0
1020 0
1021 0
1022 --0.0777
1023 0
1024 0.0946
1025 0.626
1026 0
1027 0.0147
1028 0
1029 0.22
103 0.0756
1030 0
1031 0.174
1032 0.199
1033 0
1034 0
1035 0
1036 --0.105
1037 0
1038 --0.0724
1039 --0.0487
104 0
1040 --0.0452
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: CNhs10526

Jaspar motif P-value
MA0002.2 0.199
MA0003.1 0.144
MA0004.1 0.32
MA0006.1 0.0537
MA0007.1 0.546
MA0009.1 0.764
MA0014.1 0.544
MA0017.1 9.03868e-33
MA0018.2 0.00652
MA0019.1 0.133
MA0024.1 0.109
MA0025.1 0.15
MA0027.1 0.12
MA0028.1 0.404
MA0029.1 0.96
MA0030.1 0.247
MA0031.1 0.334
MA0035.2 3.31046e-10
MA0038.1 0.377
MA0039.2 7.50531e-5
MA0040.1 0.0628
MA0041.1 0.163
MA0042.1 0.393
MA0043.1 0.00425
MA0046.1 8.99535e-109
MA0047.2 4.89959e-5
MA0048.1 0.891
MA0050.1 0.0476
MA0051.1 0.108
MA0052.1 0.00626
MA0055.1 0.528
MA0057.1 0.192
MA0058.1 0.0462
MA0059.1 0.95
MA0060.1 0.0296
MA0061.1 0.679
MA0062.2 0.368
MA0065.2 8.22535e-11
MA0066.1 0.284
MA0067.1 0.3
MA0068.1 0.354
MA0069.1 0.032
MA0070.1 0.579
MA0071.1 0.93
MA0072.1 0.614
MA0073.1 0.775
MA0074.1 0.116
MA0076.1 0.271
MA0077.1 0.441
MA0078.1 0.24
MA0079.2 0.28
MA0080.2 0.02
MA0081.1 0.11
MA0083.1 0.0157
MA0084.1 0.619
MA0087.1 0.989
MA0088.1 0.343
MA0090.1 0.331
MA0091.1 0.646
MA0092.1 0.194
MA0093.1 0.214
MA0099.2 0.142
MA0100.1 0.00867
MA0101.1 0.592
MA0102.2 0.328
MA0103.1 3.93249e-5
MA0104.2 0.288
MA0105.1 0.632
MA0106.1 0.386
MA0107.1 0.484
MA0108.2 7.75867e-5
MA0111.1 0.346
MA0112.2 0.00535
MA0113.1 0.762
MA0114.1 3.50262e-39
MA0115.1 2.45094e-8
MA0116.1 0.35
MA0117.1 0.741
MA0119.1 0.189
MA0122.1 0.775
MA0124.1 0.322
MA0125.1 0.488
MA0131.1 0.774
MA0135.1 0.0037
MA0136.1 0.111
MA0137.2 0.0845
MA0138.2 0.374
MA0139.1 0.0105
MA0140.1 1.23902e-4
MA0141.1 0.00495
MA0142.1 0.0239
MA0143.1 0.122
MA0144.1 0.0148
MA0145.1 0.0126
MA0146.1 0.102
MA0147.1 0.0957
MA0148.1 1.82876e-6
MA0149.1 0.0819
MA0150.1 0.801
MA0152.1 0.755
MA0153.1 1.46858e-68
MA0154.1 0.0511
MA0155.1 0.0693
MA0156.1 0.0537
MA0157.1 0.611
MA0159.1 0.0236
MA0160.1 0.0218
MA0162.1 0.34
MA0163.1 0.0672
MA0164.1 0.613
MA0258.1 0.131
MA0259.1 0.217



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: CNhs10526

Novel motif P-value
1 0.617
10 0.752
100 0.44
101 0.697
102 0.39
103 0.228
104 0.969
105 0.331
106 0.0422
107 0.0436
108 0.983
109 0.0407
11 0.366
110 0.613
111 0.564
112 0.0498
113 0.56
114 0.753
115 0.934
116 0.245
117 0.998
118 0.685
119 0.227
12 0.726
120 0.624
121 0.534
122 0.988
123 0.213
124 0.399
125 0.446
126 0.0936
127 0.408
128 0.221
129 0.705
13 7.92339e-4
130 0.831
131 0.1
132 0.202
133 0.214
134 0.641
135 0.578
136 0.0728
137 0.694
138 0.101
139 0.145
14 0.774
140 0.0536
141 0.332
142 0.294
143 0.046
144 0.262
145 0.181
146 0.116
147 0.625
148 0.227
149 0.137
15 0.579
150 0.248
151 0.656
152 0.03
153 0.0423
154 0.439
155 0.76
156 0.0104
157 0.354
158 0.212
159 0.759
160 0.0781
161 0.369
162 0.39
163 0.141
164 0.418
165 0.609
166 0.788
167 0.28
168 0.218
169 0.0722
17 0.253
18 0.177
19 0.0435
2 0.0859
20 0.316
21 0.835
22 0.171
23 0.292
24 0.803
25 0.784
26 0.0403
27 0.437
28 0.971
29 0.758
3 0.605
30 0.123
31 0.766
32 0.198
33 0.253
34 0.265
35 0.604
36 0.924
37 0.134
38 0.35
39 0.443
4 0.186
40 0.0988
41 0.56
42 0.868
43 0.327
44 0.584
45 0.0881
46 0.65
47 0.485
48 0.436
49 0.682
5 0.881
50 0.442
51 0.689
52 0.0384
53 0.549
54 0.667
55 0.224
56 0.393
57 0.135
58 0.562
59 0.12
6 0.754
60 0.0569
61 0.464
62 0.915
63 0.499
64 0.526
65 0.226
66 0.869
67 0.0711
68 0.894
69 0.611
7 0.0758
70 0.616
71 0.23
72 0.286
73 0.166
74 0.906
75 0.528
76 0.164
77 0.0118
78 0.0466
79 0.981
8 0.932
80 0.595
81 0.782
82 0.305
83 0.926
84 0.237
85 0.192
86 0.521
87 0.0908
88 0.652
89 0.149
9 0.652
90 0.641
91 0.463
92 0.607
93 0.513
94 0.0966
95 0.203
96 0.352
97 0.517
98 0.935
99 0.0271



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: CNhs10526


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)
0000302 (mouse embryonic day 18 sample)
0011511 (mouse intestine- 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)