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FF:688-20B8

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Name:intestine, neonate N06
Species:Mouse (Mus musculus)
Library ID:CNhs11102
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 stage6 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  SAMD00005089
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11102 CAGE DRX008998 DRR009872
Accession ID Mm9

Library idBAMCTSS
CNhs11102 DRZ001297 DRZ002680
Accession ID Mm10

Library idBAMCTSS
CNhs11102 DRZ012647 DRZ014030
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

CNhs11102

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.103
1001 0.0397
1002 0.271
1003 0.00838
1004 0
1005 0.302
1006 0.0644
1007 0.0133
1008 0.353
1009 0.12
101 --0.077
1010 0.0974
1011 0
1012 0
1013 0.224
1014 0.177
1015 --0.126
1016 --0.0806
1017 0
1018 0.399
1019 0
102 0
1020 0
1021 0.0487
1022 0.0251
1023 0
1024 0.0974
1025 0.592
1026 0
1027 0
1028 0
1029 0.515
103 0.149
1030 0
1031 0.0721
1032 0.292
1033 --0.0665
1034 0.0974
1035 0.177
1036 --0.00598
1037 0
1038 0.0926
1039 0.00248
104 0.0974
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: CNhs11102

Jaspar motif P-value
MA0002.2 0.394
MA0003.1 0.126
MA0004.1 0.632
MA0006.1 0.0483
MA0007.1 0.532
MA0009.1 0.636
MA0014.1 0.623
MA0017.1 7.72128e-26
MA0018.2 1.8503e-4
MA0019.1 0.341
MA0024.1 0.0291
MA0025.1 0.0453
MA0027.1 0.15
MA0028.1 0.131
MA0029.1 0.892
MA0030.1 0.631
MA0031.1 0.234
MA0035.2 1.5562e-5
MA0038.1 0.536
MA0039.2 8.60781e-4
MA0040.1 0.493
MA0041.1 0.272
MA0042.1 0.801
MA0043.1 5.05974e-4
MA0046.1 6.68208e-73
MA0047.2 1.55354e-4
MA0048.1 0.367
MA0050.1 3.62317e-5
MA0051.1 0.00278
MA0052.1 3.08707e-6
MA0055.1 0.214
MA0057.1 0.126
MA0058.1 0.411
MA0059.1 0.644
MA0060.1 0.00322
MA0061.1 0.516
MA0062.2 0.0289
MA0065.2 1.17264e-11
MA0066.1 0.216
MA0067.1 0.175
MA0068.1 0.182
MA0069.1 0.0268
MA0070.1 0.227
MA0071.1 0.99
MA0072.1 0.616
MA0073.1 0.777
MA0074.1 0.196
MA0076.1 0.0389
MA0077.1 0.0967
MA0078.1 0.237
MA0079.2 0.732
MA0080.2 0.061
MA0081.1 0.0223
MA0083.1 0.606
MA0084.1 0.86
MA0087.1 0.396
MA0088.1 0.95
MA0090.1 0.637
MA0091.1 0.997
MA0092.1 0.153
MA0093.1 0.581
MA0099.2 0.177
MA0100.1 0.0108
MA0101.1 0.545
MA0102.2 0.754
MA0103.1 1.48839e-5
MA0104.2 0.169
MA0105.1 0.252
MA0106.1 0.688
MA0107.1 0.52
MA0108.2 0.17
MA0111.1 0.825
MA0112.2 1.16896e-4
MA0113.1 0.554
MA0114.1 7.43193e-31
MA0115.1 6.91523e-8
MA0116.1 0.217
MA0117.1 0.679
MA0119.1 0.0397
MA0122.1 0.642
MA0124.1 0.203
MA0125.1 0.591
MA0131.1 0.483
MA0135.1 0.239
MA0136.1 0.714
MA0137.2 0.756
MA0138.2 0.578
MA0139.1 0.00983
MA0140.1 0.0371
MA0141.1 0.00528
MA0142.1 0.108
MA0143.1 0.121
MA0144.1 0.0622
MA0145.1 0.0188
MA0146.1 0.157
MA0147.1 0.137
MA0148.1 5.90408e-6
MA0149.1 0.0368
MA0150.1 0.967
MA0152.1 0.88
MA0153.1 1.0532e-47
MA0154.1 0.0111
MA0155.1 0.043
MA0156.1 0.593
MA0157.1 0.534
MA0159.1 0.00438
MA0160.1 0.1
MA0162.1 0.254
MA0163.1 0.0023
MA0164.1 0.916
MA0258.1 0.0637
MA0259.1 0.141



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: CNhs11102

Novel motif P-value
1 0.311
10 0.184
100 0.689
101 0.906
102 0.444
103 0.1
104 0.807
105 0.587
106 0.0116
107 0.00778
108 0.616
109 0.0904
11 0.26
110 0.346
111 0.15
112 0.0167
113 0.35
114 0.163
115 0.769
116 0.27
117 0.678
118 0.4
119 0.248
12 0.854
120 0.792
121 0.883
122 0.772
123 0.167
124 0.858
125 0.947
126 0.0754
127 0.613
128 0.0442
129 0.485
13 0.00186
130 0.487
131 0.171
132 0.173
133 0.718
134 0.384
135 0.935
136 0.435
137 0.53
138 0.0137
139 0.0771
14 0.596
140 0.857
141 0.309
142 0.995
143 0.183
144 0.594
145 0.102
146 0.231
147 0.598
148 0.0481
149 0.283
15 0.173
150 0.24
151 0.544
152 0.0361
153 0.267
154 0.669
155 0.722
156 0.442
157 0.397
158 0.61
159 0.0978
160 0.0477
161 0.344
162 0.553
163 0.0455
164 0.102
165 0.428
166 0.685
167 0.821
168 0.313
169 0.013
17 0.0836
18 0.971
19 0.0563
2 0.0911
20 0.5
21 0.93
22 0.295
23 0.244
24 0.936
25 0.849
26 0.00495
27 0.539
28 0.813
29 0.609
3 0.286
30 0.359
31 0.51
32 0.0116
33 0.206
34 0.486
35 0.776
36 0.969
37 0.0586
38 0.462
39 0.0946
4 0.375
40 0.444
41 0.391
42 0.824
43 0.151
44 0.789
45 0.277
46 0.401
47 0.466
48 0.358
49 0.206
5 0.422
50 0.457
51 0.59
52 0.0266
53 0.721
54 0.656
55 0.276
56 0.38
57 0.687
58 0.525
59 0.148
6 0.724
60 0.0336
61 0.371
62 0.68
63 0.259
64 0.623
65 0.274
66 0.3
67 0.445
68 0.365
69 0.847
7 0.106
70 0.278
71 0.074
72 0.887
73 0.211
74 0.857
75 0.332
76 0.49
77 0.0638
78 0.106
79 0.645
8 0.321
80 0.552
81 0.566
82 0.173
83 0.921
84 0.994
85 0.0791
86 0.358
87 0.981
88 0.944
89 0.27
9 0.546
90 0.355
91 0.397
92 0.172
93 0.941
94 0.245
95 0.461
96 0.879
97 0.401
98 0.939
99 0.032



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: CNhs11102


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)
0000312 (mouse neonate N6 sample)
0011404 (mouse intestine- neonate N06 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)