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FF:1322-23E9

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Name:intestine, neonate N01
Species:Mouse (Mus musculus)
Library ID:CNhs11192
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 stage1 day 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  SAMD00005547
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11192 CAGE DRX008997 DRR009871
Accession ID Mm9

Library idBAMCTSS
CNhs11192 DRZ001296 DRZ002679
Accession ID Mm10

Library idBAMCTSS
CNhs11192 DRZ012646 DRZ014029
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

CNhs11192

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.106
1001 0.0318
1002 0.3
1003 --0.0445
1004 0
1005 0.174
1006 --0.0532
1007 --0.158
1008 0.174
1009 0.117
101 --0.0476
1010 0
1011 --0.108
1012 0
1013 0.273
1014 0.365
1015 --0.173
1016 --0.0993
1017 0
1018 0.298
1019 0
102 0
1020 0
1021 0.0662
1022 --0.00418
1023 0
1024 0.0338
1025 0.642
1026 0.0942
1027 0
1028 0
1029 0.146
103 0.085
1030 0
1031 0.126
1032 0.307
1033 0
1034 0
1035 0
1036 --0.0474
1037 0
1038 0.0371
1039 --0.0257
104 0.0662
1040 --0.0865
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: CNhs11192

Jaspar motif P-value
MA0002.2 0.227
MA0003.1 0.166
MA0004.1 0.572
MA0006.1 0.0497
MA0007.1 0.883
MA0009.1 0.447
MA0014.1 0.573
MA0017.1 2.67145e-32
MA0018.2 6.04303e-4
MA0019.1 0.137
MA0024.1 0.00825
MA0025.1 0.142
MA0027.1 0.22
MA0028.1 0.263
MA0029.1 0.836
MA0030.1 0.422
MA0031.1 0.277
MA0035.2 1.52642e-6
MA0038.1 0.354
MA0039.2 4.89281e-4
MA0040.1 0.245
MA0041.1 0.261
MA0042.1 0.868
MA0043.1 0.00918
MA0046.1 2.08841e-71
MA0047.2 0.00384
MA0048.1 0.496
MA0050.1 0.00157
MA0051.1 0.0194
MA0052.1 6.51544e-5
MA0055.1 0.24
MA0057.1 0.115
MA0058.1 0.386
MA0059.1 0.994
MA0060.1 1.13221e-4
MA0061.1 0.717
MA0062.2 0.169
MA0065.2 2.40831e-14
MA0066.1 0.296
MA0067.1 0.28
MA0068.1 0.389
MA0069.1 0.0783
MA0070.1 0.118
MA0071.1 0.805
MA0072.1 0.485
MA0073.1 0.805
MA0074.1 0.0345
MA0076.1 0.134
MA0077.1 0.219
MA0078.1 0.174
MA0079.2 0.555
MA0080.2 0.125
MA0081.1 0.0701
MA0083.1 0.294
MA0084.1 0.659
MA0087.1 0.499
MA0088.1 0.965
MA0090.1 0.204
MA0091.1 0.708
MA0092.1 0.114
MA0093.1 0.557
MA0099.2 0.0025
MA0100.1 0.00871
MA0101.1 0.514
MA0102.2 0.979
MA0103.1 1.09265e-5
MA0104.2 0.175
MA0105.1 0.423
MA0106.1 0.936
MA0107.1 0.334
MA0108.2 0.0882
MA0111.1 0.383
MA0112.2 2.63798e-4
MA0113.1 0.929
MA0114.1 3.14273e-39
MA0115.1 1.52012e-10
MA0116.1 0.392
MA0117.1 0.698
MA0119.1 0.24
MA0122.1 0.72
MA0124.1 0.282
MA0125.1 0.66
MA0131.1 0.708
MA0135.1 0.00977
MA0136.1 0.407
MA0137.2 0.472
MA0138.2 0.61
MA0139.1 0.0183
MA0140.1 0.0402
MA0141.1 4.77283e-4
MA0142.1 0.0159
MA0143.1 0.141
MA0144.1 0.0312
MA0145.1 0.0132
MA0146.1 0.125
MA0147.1 0.102
MA0148.1 1.314e-4
MA0149.1 0.0526
MA0150.1 0.648
MA0152.1 0.328
MA0153.1 2.6911e-57
MA0154.1 0.0161
MA0155.1 0.0557
MA0156.1 0.318
MA0157.1 0.574
MA0159.1 0.0153
MA0160.1 0.00991
MA0162.1 0.232
MA0163.1 0.00395
MA0164.1 0.922
MA0258.1 0.0499
MA0259.1 0.155



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: CNhs11192

Novel motif P-value
1 0.373
10 0.276
100 0.609
101 0.898
102 0.454
103 0.227
104 0.812
105 0.717
106 0.0148
107 0.0287
108 0.503
109 0.0536
11 0.242
110 0.494
111 0.265
112 0.0213
113 0.392
114 0.128
115 0.696
116 0.18
117 0.541
118 0.337
119 0.211
12 0.768
120 0.847
121 0.989
122 0.826
123 0.258
124 0.364
125 0.721
126 0.0783
127 0.4
128 0.066
129 0.437
13 0.00149
130 0.969
131 0.127
132 0.424
133 0.932
134 0.373
135 0.963
136 0.037
137 0.925
138 0.17
139 0.0258
14 0.764
140 0.411
141 0.334
142 0.882
143 0.195
144 0.732
145 0.142
146 0.161
147 0.31
148 0.09
149 0.0781
15 0.209
150 0.302
151 0.686
152 0.0301
153 0.369
154 0.985
155 0.488
156 0.00216
157 0.621
158 0.442
159 0.761
160 0.0882
161 0.487
162 0.287
163 0.061
164 0.124
165 0.49
166 0.72
167 0.49
168 0.357
169 0.0297
17 0.0757
18 0.507
19 0.0427
2 0.0752
20 0.633
21 0.727
22 0.331
23 0.243
24 0.818
25 0.73
26 0.0135
27 0.54
28 0.892
29 0.581
3 0.264
30 0.251
31 0.568
32 0.0195
33 0.109
34 0.432
35 0.909
36 0.924
37 0.0407
38 0.383
39 0.162
4 0.392
40 0.254
41 0.894
42 0.93
43 0.256
44 0.316
45 0.206
46 0.43
47 0.465
48 0.407
49 0.424
5 0.819
50 0.34
51 0.788
52 0.0264
53 0.851
54 0.725
55 0.125
56 0.392
57 0.602
58 0.6
59 0.0926
6 0.74
60 0.023
61 0.338
62 0.695
63 0.29
64 0.567
65 0.185
66 0.376
67 0.243
68 0.232
69 0.807
7 0.0465
70 0.0546
71 0.0888
72 0.554
73 0.128
74 0.825
75 0.206
76 0.912
77 0.0249
78 0.0438
79 0.596
8 0.466
80 0.212
81 0.416
82 0.122
83 0.652
84 0.241
85 0.0612
86 0.381
87 0.287
88 0.796
89 0.163
9 0.712
90 0.595
91 0.626
92 0.167
93 0.928
94 0.229
95 0.107
96 0.736
97 0.553
98 0.866
99 0.0395



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: CNhs11192


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)
0000304 (mouse neonate N0 sample)
0000734 (mouse neonate N1 sample)
0011504 (mouse intestine- neonate N01 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)