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FF:755-23A5

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Name:intestine, neonate N10
Species:Mouse (Mus musculus)
Library ID:CNhs11098
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 stage10 days neonate
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  SAMD00004753
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11098 CAGE DRX009000 DRR009874
Accession ID Mm9

Library idBAMCTSS
CNhs11098 DRZ001299 DRZ002682
Accession ID Mm10

Library idBAMCTSS
CNhs11098 DRZ012649 DRZ014032
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

CNhs11098

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0774
1001 0.024
1002 0.149
1003 --0.025
1004 0
1005 0.2
1006 0
1007 --0.00978
1008 0.548
1009 0.18
101 --0.0687
1010 0.0774
1011 --0.0357
1012 0
1013 0.201
1014 0.107
1015 --0.146
1016 --0.0493
1017 0
1018 0.374
1019 0
102 0
1020 0
1021 --0.0487
1022 0.00697
1023 0
1024 0.156
1025 0.784
1026 0
1027 0
1028 0
1029 0.348
103 0.15
1030 0
1031 0.0506
1032 0.325
1033 --0.0665
1034 0.0156
1035 0
1036 --0.102
1037 0
1038 0.0514
1039 0.018
104 0.143
1040 --0.0438
1041 0.0774



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: CNhs11098

Jaspar motif P-value
MA0002.2 0.0861
MA0003.1 0.121
MA0004.1 0.843
MA0006.1 0.0266
MA0007.1 0.415
MA0009.1 0.463
MA0014.1 0.799
MA0017.1 8.48901e-28
MA0018.2 0.00228
MA0019.1 0.212
MA0024.1 0.0187
MA0025.1 0.336
MA0027.1 0.193
MA0028.1 0.133
MA0029.1 0.789
MA0030.1 0.319
MA0031.1 0.218
MA0035.2 2.88729e-6
MA0038.1 0.814
MA0039.2 1.19223e-4
MA0040.1 0.0606
MA0041.1 0.37
MA0042.1 0.911
MA0043.1 0.00215
MA0046.1 3.88361e-75
MA0047.2 3.47291e-5
MA0048.1 0.722
MA0050.1 5.69282e-8
MA0051.1 7.40381e-6
MA0052.1 0.00146
MA0055.1 0.184
MA0057.1 0.118
MA0058.1 0.595
MA0059.1 0.69
MA0060.1 0.0222
MA0061.1 0.559
MA0062.2 0.0726
MA0065.2 9.17153e-12
MA0066.1 0.319
MA0067.1 0.41
MA0068.1 0.785
MA0069.1 0.0303
MA0070.1 0.117
MA0071.1 0.736
MA0072.1 0.665
MA0073.1 0.739
MA0074.1 0.181
MA0076.1 0.0661
MA0077.1 0.115
MA0078.1 0.113
MA0079.2 0.235
MA0080.2 0.00357
MA0081.1 0.14
MA0083.1 0.134
MA0084.1 0.646
MA0087.1 0.987
MA0088.1 0.948
MA0090.1 0.376
MA0091.1 0.561
MA0092.1 0.172
MA0093.1 0.745
MA0099.2 0.0118
MA0100.1 0.00708
MA0101.1 0.584
MA0102.2 0.601
MA0103.1 1.55215e-5
MA0104.2 0.0716
MA0105.1 0.73
MA0106.1 0.815
MA0107.1 0.653
MA0108.2 0.00599
MA0111.1 0.51
MA0112.2 4.64534e-4
MA0113.1 0.621
MA0114.1 3.83109e-33
MA0115.1 3.47783e-8
MA0116.1 0.691
MA0117.1 0.993
MA0119.1 0.0673
MA0122.1 0.88
MA0124.1 0.208
MA0125.1 0.613
MA0131.1 0.329
MA0135.1 0.029
MA0136.1 0.053
MA0137.2 0.588
MA0138.2 0.711
MA0139.1 0.0268
MA0140.1 0.037
MA0141.1 0.0215
MA0142.1 0.062
MA0143.1 0.0352
MA0144.1 0.0431
MA0145.1 0.00596
MA0146.1 0.122
MA0147.1 0.0366
MA0148.1 6.41801e-7
MA0149.1 0.124
MA0150.1 0.773
MA0152.1 0.593
MA0153.1 8.24325e-48
MA0154.1 0.0244
MA0155.1 0.0561
MA0156.1 0.0789
MA0157.1 0.32
MA0159.1 0.00971
MA0160.1 0.132
MA0162.1 0.316
MA0163.1 0.0634
MA0164.1 0.895
MA0258.1 0.102
MA0259.1 0.0594



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: CNhs11098

Novel motif P-value
1 0.448
10 0.455
100 0.389
101 0.948
102 0.571
103 0.209
104 0.676
105 0.645
106 0.0127
107 0.00777
108 0.754
109 0.0802
11 0.409
110 0.615
111 0.273
112 0.0257
113 0.403
114 0.488
115 0.473
116 0.212
117 0.91
118 0.725
119 0.274
12 0.9
120 0.997
121 0.5
122 0.662
123 0.0804
124 0.623
125 0.832
126 0.133
127 0.903
128 0.0603
129 0.436
13 0.00109
130 0.518
131 0.0948
132 0.165
133 0.405
134 0.337
135 0.978
136 0.0866
137 0.766
138 0.0265
139 0.0663
14 0.567
140 0.805
141 0.319
142 0.374
143 0.106
144 0.427
145 0.212
146 0.095
147 0.855
148 0.101
149 0.0574
15 0.247
150 0.27
151 0.576
152 0.0159
153 0.429
154 0.737
155 0.719
156 0.107
157 0.556
158 0.663
159 0.134
160 0.13
161 0.244
162 0.57
163 0.0325
164 0.233
165 0.242
166 0.933
167 0.286
168 0.242
169 0.0193
17 0.126
18 0.757
19 0.0525
2 0.0562
20 0.342
21 0.833
22 0.209
23 0.314
24 0.712
25 0.921
26 0.00754
27 0.498
28 0.777
29 0.839
3 0.487
30 0.18
31 0.62
32 0.0179
33 0.263
34 0.351
35 0.913
36 0.477
37 0.0729
38 0.36
39 0.161
4 0.417
40 0.427
41 0.348
42 0.96
43 0.24
44 0.936
45 0.173
46 0.463
47 0.596
48 0.424
49 0.373
5 0.686
50 0.449
51 0.622
52 0.0284
53 0.607
54 0.595
55 0.417
56 0.383
57 0.346
58 0.541
59 0.094
6 0.638
60 0.034
61 0.391
62 0.868
63 0.287
64 0.878
65 0.25
66 0.382
67 0.251
68 0.564
69 0.89
7 0.126
70 0.291
71 0.224
72 0.714
73 0.149
74 0.804
75 0.425
76 0.286
77 0.0326
78 0.0553
79 0.817
8 0.733
80 0.742
81 0.52
82 0.171
83 0.91
84 0.565
85 0.12
86 0.337
87 0.19
88 0.996
89 0.151
9 0.536
90 0.697
91 0.854
92 0.399
93 0.99
94 0.113
95 0.241
96 0.5
97 0.378
98 0.805
99 0.0576



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: CNhs11098


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000305 (mouse neonate N10 sample)
0011418 (mouse intestine- neonate N10 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)