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FF:720-20F2

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Name:intestine, neonate N07
Species:Mouse (Mus musculus)
Library ID:CNhs11095
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 stage7 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  SAMD00005632
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11095 CAGE DRX008999 DRR009873
Accession ID Mm9

Library idBAMCTSS
CNhs11095 DRZ001298 DRZ002681
Accession ID Mm10

Library idBAMCTSS
CNhs11095 DRZ012648 DRZ014031
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
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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

CNhs11095

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.112
1001 0.0408
1002 0.0987
1003 --0.00817
1004 0
1005 0.203
1006 --0.00622
1007 --0.0285
1008 0.203
1009 0.189
101 --0.0869
1010 0
1011 0
1012 0
1013 0.197
1014 0.0788
1015 --0.0848
1016 --0.111
1017 0
1018 0.414
1019 0
102 0
1020 0
1021 --0.0487
1022 0.00841
1023 0
1024 0
1025 0.869
1026 0
1027 0
1028 0
1029 0.226
103 0.145
1030 0
1031 0.0889
1032 0.36
1033 --0.017
1034 0
1035 0
1036 --0.118
1037 0
1038 0.0505
1039 0.073
104 0.101
1040 --0.0702
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: CNhs11095

Jaspar motif P-value
MA0002.2 0.161
MA0003.1 0.0631
MA0004.1 0.81
MA0006.1 0.0375
MA0007.1 0.512
MA0009.1 0.285
MA0014.1 0.866
MA0017.1 2.45371e-28
MA0018.2 5.80675e-4
MA0019.1 0.222
MA0024.1 0.026
MA0025.1 0.279
MA0027.1 0.0915
MA0028.1 0.0782
MA0029.1 0.86
MA0030.1 0.265
MA0031.1 0.141
MA0035.2 1.71543e-6
MA0038.1 0.817
MA0039.2 8.91859e-5
MA0040.1 0.214
MA0041.1 0.755
MA0042.1 0.612
MA0043.1 0.00128
MA0046.1 2.95544e-80
MA0047.2 3.09732e-6
MA0048.1 0.842
MA0050.1 7.35344e-9
MA0051.1 9.16829e-6
MA0052.1 4.05783e-4
MA0055.1 0.0317
MA0057.1 0.126
MA0058.1 0.515
MA0059.1 0.552
MA0060.1 0.029
MA0061.1 0.554
MA0062.2 0.0201
MA0065.2 6.12927e-13
MA0066.1 0.164
MA0067.1 0.384
MA0068.1 0.579
MA0069.1 0.0504
MA0070.1 0.316
MA0071.1 0.683
MA0072.1 0.631
MA0073.1 0.789
MA0074.1 0.267
MA0076.1 0.0314
MA0077.1 0.0848
MA0078.1 0.152
MA0079.2 0.22
MA0080.2 0.00554
MA0081.1 0.0459
MA0083.1 0.122
MA0084.1 0.895
MA0087.1 0.337
MA0088.1 0.98
MA0090.1 0.441
MA0091.1 0.474
MA0092.1 0.2
MA0093.1 0.731
MA0099.2 0.0139
MA0100.1 0.0111
MA0101.1 0.72
MA0102.2 0.49
MA0103.1 3.01343e-5
MA0104.2 0.0955
MA0105.1 0.585
MA0106.1 0.97
MA0107.1 0.714
MA0108.2 4.20206e-5
MA0111.1 0.49
MA0112.2 7.13084e-4
MA0113.1 0.559
MA0114.1 2.55266e-33
MA0115.1 1.17646e-8
MA0116.1 0.522
MA0117.1 0.771
MA0119.1 0.046
MA0122.1 0.867
MA0124.1 0.408
MA0125.1 0.58
MA0131.1 0.433
MA0135.1 0.00854
MA0136.1 0.0626
MA0137.2 0.599
MA0138.2 0.718
MA0139.1 0.0448
MA0140.1 0.0779
MA0141.1 0.0292
MA0142.1 0.106
MA0143.1 0.0338
MA0144.1 0.0352
MA0145.1 0.00827
MA0146.1 0.183
MA0147.1 0.0487
MA0148.1 8.47275e-9
MA0149.1 0.0574
MA0150.1 0.973
MA0152.1 0.805
MA0153.1 7.98129e-50
MA0154.1 0.0174
MA0155.1 0.0369
MA0156.1 0.13
MA0157.1 0.214
MA0159.1 0.0327
MA0160.1 0.154
MA0162.1 0.275
MA0163.1 0.0185
MA0164.1 0.949
MA0258.1 0.102
MA0259.1 0.0577



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: CNhs11095

Novel motif P-value
1 0.548
10 0.564
100 0.475
101 0.651
102 0.433
103 0.302
104 0.75
105 0.75
106 0.00748
107 0.012
108 0.589
109 0.0985
11 0.41
110 0.649
111 0.472
112 0.0355
113 0.53
114 0.588
115 0.352
116 0.225
117 0.974
118 0.664
119 0.304
12 0.951
120 0.966
121 0.39
122 0.878
123 0.319
124 0.924
125 0.738
126 0.133
127 0.803
128 0.0404
129 0.361
13 0.00324
130 0.497
131 0.147
132 0.24
133 0.368
134 0.772
135 0.568
136 0.0693
137 0.891
138 0.0707
139 0.0968
14 0.648
140 0.762
141 0.386
142 0.669
143 0.0551
144 0.336
145 0.206
146 0.113
147 0.999
148 0.136
149 0.165
15 0.213
150 0.26
151 0.453
152 0.0208
153 0.364
154 0.961
155 0.575
156 0.0757
157 0.22
158 0.26
159 0.646
160 0.101
161 0.518
162 0.265
163 0.104
164 0.221
165 0.316
166 0.83
167 0.217
168 0.165
169 0.0244
17 0.133
18 0.738
19 0.0588
2 0.0439
20 0.222
21 0.827
22 0.242
23 0.407
24 0.963
25 0.93
26 0.0115
27 0.371
28 0.78
29 0.979
3 0.506
30 0.152
31 0.497
32 0.0577
33 0.194
34 0.366
35 0.906
36 0.599
37 0.0734
38 0.512
39 0.233
4 0.397
40 0.349
41 0.464
42 0.944
43 0.271
44 0.791
45 0.117
46 0.434
47 0.653
48 0.489
49 0.454
5 0.549
50 0.492
51 0.564
52 0.021
53 0.636
54 0.625
55 0.352
56 0.37
57 0.303
58 0.529
59 0.138
6 0.583
60 0.0353
61 0.661
62 0.738
63 0.333
64 0.808
65 0.305
66 0.341
67 0.175
68 0.922
69 0.86
7 0.145
70 0.181
71 0.184
72 0.422
73 0.153
74 0.811
75 0.455
76 0.202
77 0.0305
78 0.0921
79 0.75
8 0.664
80 0.697
81 0.506
82 0.17
83 0.977
84 0.541
85 0.115
86 0.334
87 0.0638
88 0.912
89 0.146
9 0.591
90 0.89
91 0.634
92 0.383
93 0.435
94 0.16
95 0.339
96 0.561
97 0.333
98 0.894
99 0.0322



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: CNhs11095


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)
0000313 (mouse neonate N7 sample)
0011411 (mouse intestine- neonate N07 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)