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FF:644-26D1

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Name:intestine, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11126
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 stage0 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  SAMD00006001
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11126 CAGE DRX008996 DRR009870
Accession ID Mm9

Library idBAMCTSS
CNhs11126 DRZ001295 DRZ002678
Accession ID Mm10

Library idBAMCTSS
CNhs11126 DRZ012645 DRZ014028
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 sample
Ranked 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 sample
Ranked 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

CNhs11126

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0961
1001 0.0453
1002 0.0516
1003 -0.058
1004 0
1005 0.229
1006 -0.0512
1007 -0.0584
1008 1.878
1009 0.1
101 -0.105
1010 0
1011 -0.154
1012 0
1013 0.304
1014 -0.0874
1015 -0.342
1016 -0.222
1017 0
1018 0.585
1019 0
102 0
1020 0
1021 0
1022 0.0983
1023 0
1024 0
1025 0.584
1026 0
1027 -0.0134
1028 0
1029 0.582
103 0.169
1030 0
1031 -0.172
1032 0.64
1033 0
1034 0
1035 0
1036 -0.183
1037 0
1038 0.0862
1039 -0.043
104 0
1040 -0.216
1041 0



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs11126
Jaspar motif P-value
MA0002.2 0.0106
MA0003.1 0.15
MA0004.1 0.722
MA0006.1 0.0441
MA0007.1 0.578
MA0009.1 0.347
MA0014.1 0.359
MA0017.1 3.73907e-22
MA0018.2 0.00692
MA0019.1 0.384
MA0024.1 0.0286
MA0025.1 0.163
MA0027.1 0.875
MA0028.1 0.343
MA0029.1 0.96
MA0030.1 0.382
MA0031.1 0.576
MA0035.2 4.33673e-6
MA0038.1 0.387
MA0039.2 0.00661
MA0040.1 0.206
MA0041.1 0.21
MA0042.1 0.842
MA0043.1 0.0388
MA0046.1 6.40895e-33
MA0047.2 0.0504
MA0048.1 0.381
MA0050.1 1.5073e-6
MA0051.1 5.58828e-5
MA0052.1 9.27913e-5
MA0055.1 0.387
MA0057.1 0.135
MA0058.1 0.51
MA0059.1 0.97
MA0060.1 0.00217
MA0061.1 0.402
MA0062.2 0.236
MA0065.2 2.03617e-13
MA0066.1 0.127
MA0067.1 0.164
MA0068.1 0.0793
MA0069.1 0.218
MA0070.1 0.239
MA0071.1 0.472
MA0072.1 0.401
MA0073.1 0.693
MA0074.1 0.101
MA0076.1 0.129
MA0077.1 0.793
MA0078.1 0.583
MA0079.2 0.376
MA0080.2 0.00447
MA0081.1 0.311
MA0083.1 0.756
MA0084.1 0.883
MA0087.1 0.735
MA0088.1 0.866
MA0090.1 0.711
MA0091.1 0.846
MA0092.1 0.286
MA0093.1 0.659
MA0099.2 0.0211
MA0100.1 0.148
MA0101.1 0.995
MA0102.2 0.16
MA0103.1 1.28856e-5
MA0104.2 0.11
MA0105.1 0.198
MA0106.1 0.745
MA0107.1 0.869
MA0108.2 0.724
MA0111.1 0.951
MA0112.2 3.47894e-5
MA0113.1 0.677
MA0114.1 2.22337e-26
MA0115.1 1.9569e-10
MA0116.1 0.208
MA0117.1 0.973
MA0119.1 0.0637
MA0122.1 0.712
MA0124.1 0.358
MA0125.1 0.0949
MA0131.1 0.42
MA0135.1 0.267
MA0136.1 0.0248
MA0137.2 0.862
MA0138.2 0.581
MA0139.1 0.0551
MA0140.1 0.0347
MA0141.1 4.98095e-5
MA0142.1 0.42
MA0143.1 0.294
MA0144.1 0.0902
MA0145.1 0.00907
MA0146.1 0.335
MA0147.1 0.182
MA0148.1 0.00428
MA0149.1 0.0236
MA0150.1 0.88
MA0152.1 0.157
MA0153.1 6.91296e-29
MA0154.1 0.0183
MA0155.1 0.249
MA0156.1 0.175
MA0157.1 0.45
MA0159.1 0.00175
MA0160.1 0.00804
MA0162.1 0.127
MA0163.1 0.018
MA0164.1 0.987
MA0258.1 0.00945
MA0259.1 0.25



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs11126
Novel motif P-value
1 0.139
10 0.186
100 0.969
101 0.713
102 0.767
103 0.19
104 0.925
105 0.412
106 0.00942
107 0.0231
108 0.854
109 0.0786
11 0.141
110 0.27
111 0.0395
112 0.0239
113 0.435
114 0.047
115 0.561
116 0.25
117 0.224
118 0.514
119 0.0915
12 0.794
120 0.696
121 0.755
122 0.733
123 0.315
124 0.903
125 0.591
126 0.097
127 0.251
128 0.0757
129 0.408
13 0.00234
130 0.585
131 0.0339
132 0.602
133 0.684
134 0.838
135 0.473
136 0.158
137 0.454
138 0.639
139 0.048
14 0.676
140 0.525
141 0.298
142 0.868
143 0.692
144 0.637
145 0.121
146 0.266
147 0.312
148 0.163
149 0.552
15 0.206
150 0.225
151 0.504
152 0.0324
153 0.71
154 0.346
155 0.193
156 0.738
157 0.869
158 0.731
159 0.399
160 0.237
161 0.35
162 0.919
163 0.396
164 0.141
165 0.398
166 0.614
167 0.942
168 0.801
169 0.0122
17 0.0961
18 0.0823
19 0.0899
2 0.274
20 0.858
21 0.982
22 0.366
23 0.203
24 0.762
25 0.755
26 0.00595
27 0.491
28 0.662
29 0.227
3 0.179
30 0.419
31 0.584
32 0.00355
33 0.282
34 0.809
35 0.533
36 0.774
37 0.0401
38 0.399
39 0.165
4 0.457
40 0.31
41 0.404
42 0.462
43 0.216
44 0.296
45 0.4
46 0.232
47 0.284
48 0.259
49 0.154
5 0.68
50 0.526
51 0.565
52 0.0753
53 0.994
54 0.48
55 0.609
56 0.484
57 0.786
58 0.48
59 0.105
6 0.797
60 0.043
61 0.194
62 0.353
63 0.166
64 0.628
65 0.181
66 0.582
67 0.556
68 0.11
69 0.992
7 0.0827
70 0.0223
71 0.091
72 0.589
73 0.0976
74 0.969
75 0.144
76 0.897
77 0.106
78 0.0441
79 0.579
8 0.136
80 0.492
81 0.641
82 0.061
83 0.785
84 0.466
85 0.0358
86 0.159
87 0.31
88 0.74
89 0.306
9 0.653
90 0.209
91 0.112
92 0.241
93 0.585
94 0.363
95 0.146
96 0.723
97 0.334
98 0.995
99 0.0358



de novo motifs identified by HOMER in promoters active in this sample
Summary:The result of HOMER in this sample is shown.
Analyst:NA

library id: CNhs11126


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)
0011265 (mouse intestine- neonate N00 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)