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FF:1352-25E3

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Name:intestine, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11121
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 stage25 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  SAMD00004971
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11121 CAGE DRX009002 DRR009876
Accession ID Mm9

Library idBAMCTSS
CNhs11121 DRZ001301 DRZ002684
Accession ID Mm10

Library idBAMCTSS
CNhs11121 DRZ012651 DRZ014034
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

CNhs11121

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.114
1001 0.0979
1002 0.125
1003 --0.0856
1004 0
1005 0.215
1006 0
1007 --0.0276
1008 2.076
1009 0.027
101 --0.109
1010 0
1011 --0.118
1012 0.0582
1013 0.266
1014 --0.00956
1015 --0.256
1016 --0.323
1017 0
1018 0.4
1019 0
102 0
1020 0
1021 --0.0487
1022 0.0156
1023 0
1024 --0.00489
1025 0.619
1026 0
1027 --0.00439
1028 0
1029 0.612
103 0.085
1030 0.085
1031 --0.12
1032 0.612
1033 --0.0752
1034 0.223
1035 0
1036 --0.0979
1037 0
1038 0.0291
1039 0.0997
104 0.361
1040 --0.222
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: CNhs11121

Jaspar motif P-value
MA0002.2 0.0622
MA0003.1 0.284
MA0004.1 0.587
MA0006.1 0.0566
MA0007.1 0.823
MA0009.1 0.316
MA0014.1 0.311
MA0017.1 4.25992e-20
MA0018.2 0.0187
MA0019.1 0.374
MA0024.1 0.0361
MA0025.1 0.243
MA0027.1 0.989
MA0028.1 0.758
MA0029.1 0.886
MA0030.1 0.84
MA0031.1 0.5
MA0035.2 0.00171
MA0038.1 0.589
MA0039.2 0.00362
MA0040.1 0.176
MA0041.1 0.249
MA0042.1 0.774
MA0043.1 0.084
MA0046.1 4.67169e-32
MA0047.2 0.0018
MA0048.1 0.473
MA0050.1 2.28517e-7
MA0051.1 3.30636e-5
MA0052.1 5.76546e-5
MA0055.1 0.304
MA0057.1 0.162
MA0058.1 0.416
MA0059.1 0.943
MA0060.1 0.0083
MA0061.1 0.294
MA0062.2 0.711
MA0065.2 2.63168e-12
MA0066.1 0.131
MA0067.1 0.192
MA0068.1 0.0948
MA0069.1 0.182
MA0070.1 0.0449
MA0071.1 0.297
MA0072.1 0.63
MA0073.1 0.824
MA0074.1 0.274
MA0076.1 0.302
MA0077.1 0.297
MA0078.1 0.31
MA0079.2 0.142
MA0080.2 0.00117
MA0081.1 0.331
MA0083.1 0.787
MA0084.1 0.675
MA0087.1 0.935
MA0088.1 0.747
MA0090.1 0.974
MA0091.1 0.773
MA0092.1 0.477
MA0093.1 0.535
MA0099.2 0.00766
MA0100.1 0.175
MA0101.1 0.901
MA0102.2 0.18
MA0103.1 3.02485e-5
MA0104.2 0.0813
MA0105.1 0.0639
MA0106.1 0.201
MA0107.1 0.982
MA0108.2 0.626
MA0111.1 0.877
MA0112.2 9.72318e-6
MA0113.1 0.937
MA0114.1 1.48986e-26
MA0115.1 1.11528e-10
MA0116.1 0.173
MA0117.1 0.865
MA0119.1 0.0219
MA0122.1 0.606
MA0124.1 0.45
MA0125.1 0.153
MA0131.1 0.476
MA0135.1 0.374
MA0136.1 0.00307
MA0137.2 0.988
MA0138.2 0.428
MA0139.1 0.0661
MA0140.1 0.163
MA0141.1 6.8322e-5
MA0142.1 0.173
MA0143.1 0.167
MA0144.1 0.147
MA0145.1 0.0039
MA0146.1 0.308
MA0147.1 0.141
MA0148.1 3.92859e-4
MA0149.1 0.0369
MA0150.1 0.52
MA0152.1 0.171
MA0153.1 5.05642e-29
MA0154.1 0.0316
MA0155.1 0.542
MA0156.1 0.0723
MA0157.1 0.993
MA0159.1 0.0049
MA0160.1 0.00934
MA0162.1 0.272
MA0163.1 0.0831
MA0164.1 0.997
MA0258.1 0.0097
MA0259.1 0.241



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: CNhs11121

Novel motif P-value
1 0.1
10 0.131
100 0.846
101 0.934
102 0.893
103 0.16
104 0.858
105 0.459
106 0.0111
107 0.0246
108 0.923
109 0.0611
11 0.179
110 0.199
111 0.0565
112 0.0202
113 0.415
114 0.0495
115 0.62
116 0.361
117 0.267
118 0.516
119 0.175
12 0.941
120 0.515
121 0.789
122 0.879
123 0.245
124 0.934
125 0.484
126 0.0871
127 0.455
128 0.0399
129 0.337
13 9.72606e-4
130 0.932
131 0.0692
132 0.695
133 0.881
134 0.833
135 0.303
136 0.37
137 0.794
138 0.612
139 0.0459
14 0.725
140 0.112
141 0.22
142 0.734
143 0.205
144 0.649
145 0.153
146 0.376
147 0.237
148 0.179
149 0.626
15 0.167
150 0.348
151 0.364
152 0.0578
153 0.61
154 0.304
155 0.541
156 0.491
157 0.85
158 0.563
159 0.164
160 0.187
161 0.624
162 0.783
163 0.451
164 0.106
165 0.476
166 0.995
167 0.734
168 0.77
169 0.00378
17 0.0476
18 0.113
19 0.048
2 0.37
20 0.851
21 0.886
22 0.328
23 0.285
24 0.758
25 0.735
26 0.00271
27 0.712
28 0.45
29 0.245
3 0.206
30 0.531
31 0.732
32 0.0283
33 0.233
34 0.821
35 0.683
36 0.78
37 0.0234
38 0.362
39 0.129
4 0.635
40 0.436
41 0.502
42 0.481
43 0.222
44 0.226
45 0.43
46 0.168
47 0.321
48 0.294
49 0.138
5 0.409
50 0.48
51 0.615
52 0.0792
53 0.89
54 0.525
55 0.583
56 0.384
57 0.768
58 0.293
59 0.275
6 0.659
60 0.0459
61 0.157
62 0.277
63 0.168
64 0.725
65 0.213
66 0.374
67 0.459
68 0.158
69 0.628
7 0.0622
70 0.0781
71 0.0857
72 0.596
73 0.109
74 0.934
75 0.106
76 0.914
77 0.169
78 0.0467
79 0.919
8 0.181
80 0.782
81 0.663
82 0.124
83 0.266
84 0.494
85 0.0309
86 0.226
87 0.878
88 0.592
89 0.352
9 0.725
90 0.159
91 0.28
92 0.355
93 0.671
94 0.872
95 0.144
96 0.772
97 0.875
98 0.854
99 0.0829



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: CNhs11121


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)
0000309 (mouse neonate N25 sample)
0011480 (mouse intestine- neonate N25 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)