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FF:641-24F4

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Name:liver, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11117
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
tissueliver
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  SAMD00005838
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11117 CAGE DRX009022 DRR009896
Accession ID Mm9

Library idBAMCTSS
CNhs11117 DRZ001321 DRZ002704
Accession ID Mm10

Library idBAMCTSS
CNhs11117 DRZ012671 DRZ014054
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

CNhs11117

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 -0.00285
1001 0.0581
1002 0.061
1003 -0.102
1004 0
1005 0.219
1006 -0.143
1007 -0.0684
1008 0
1009 -0.0406
101 0.104
1010 0
1011 -0.165
1012 0.0147
1013 0.0802
1014 0.208
1015 -0.233
1016 -0.261
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0653
1022 0.0653
1023 0
1024 0.122
1025 0.454
1026 0
1027 -0.00994
1028 0
1029 0.185
103 -0.00602
1030 0.172
1031 0.00115
1032 -0.21
1033 -0.00124
1034 0.644
1035 0
1036 0.083
1037 0
1038 -0.126
1039 0.353
104 0
1040 -0.0869
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: CNhs11117
Jaspar motif P-value
MA0002.2 0.156
MA0003.1 0.702
MA0004.1 0.547
MA0006.1 0.26
MA0007.1 0.18
MA0009.1 0.189
MA0014.1 0.883
MA0017.1 1.02945e-12
MA0018.2 4.62858e-5
MA0019.1 0.301
MA0024.1 0.987
MA0025.1 0.78
MA0027.1 0.651
MA0028.1 0.781
MA0029.1 0.129
MA0030.1 0.0296
MA0031.1 0.04
MA0035.2 9.49523e-6
MA0038.1 0.0309
MA0039.2 0.621
MA0040.1 0.209
MA0041.1 0.369
MA0042.1 0.962
MA0043.1 0.01
MA0046.1 1.92565e-27
MA0047.2 4.44081e-6
MA0048.1 0.213
MA0050.1 0.0949
MA0051.1 0.488
MA0052.1 3.24587e-5
MA0055.1 0.55
MA0057.1 0.829
MA0058.1 0.579
MA0059.1 0.125
MA0060.1 0.00581
MA0061.1 0.214
MA0062.2 0.686
MA0065.2 3.03421e-9
MA0066.1 0.00572
MA0067.1 0.231
MA0068.1 0.973
MA0069.1 0.193
MA0070.1 0.777
MA0071.1 0.00209
MA0072.1 0.0345
MA0073.1 0.478
MA0074.1 0.15
MA0076.1 0.314
MA0077.1 0.0335
MA0078.1 0.455
MA0079.2 0.103
MA0080.2 0.00693
MA0081.1 0.688
MA0083.1 0.0382
MA0084.1 0.065
MA0087.1 0.0186
MA0088.1 0.596
MA0090.1 0.51
MA0091.1 0.316
MA0092.1 0.11
MA0093.1 0.618
MA0099.2 0.585
MA0100.1 0.995
MA0101.1 0.677
MA0102.2 0.144
MA0103.1 0.261
MA0104.2 0.956
MA0105.1 0.00123
MA0106.1 0.155
MA0107.1 0.918
MA0108.2 2.16129e-4
MA0111.1 0.781
MA0112.2 2.41757e-6
MA0113.1 0.129
MA0114.1 1.8395e-10
MA0115.1 4.4174e-8
MA0116.1 0.0125
MA0117.1 0.996
MA0119.1 0.0259
MA0122.1 0.134
MA0124.1 0.938
MA0125.1 0.575
MA0131.1 0.996
MA0135.1 0.049
MA0136.1 0.557
MA0137.2 0.997
MA0138.2 0.885
MA0139.1 0.125
MA0140.1 4.55036e-12
MA0141.1 3.84837e-5
MA0142.1 0.351
MA0143.1 0.227
MA0144.1 0.61
MA0145.1 0.487
MA0146.1 0.195
MA0147.1 0.738
MA0148.1 9.44022e-9
MA0149.1 0.00571
MA0150.1 0.0828
MA0152.1 0.283
MA0153.1 5.88437e-20
MA0154.1 0.0235
MA0155.1 0.445
MA0156.1 0.741
MA0157.1 0.0222
MA0159.1 0.00704
MA0160.1 0.00195
MA0162.1 0.314
MA0163.1 1.8764e-6
MA0164.1 0.431
MA0258.1 0.00361
MA0259.1 0.871



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: CNhs11117
Novel motif P-value
1 0.153
10 0.0893
100 0.499
101 0.376
102 0.471
103 0.00394
104 0.917
105 0.905
106 0.0128
107 0.0169
108 0.883
109 0.0714
11 0.098
110 0.0784
111 0.0297
112 0.00167
113 0.996
114 0.0253
115 0.719
116 0.828
117 0.0157
118 0.106
119 0.118
12 0.509
120 0.945
121 0.979
122 0.658
123 0.531
124 0.104
125 0.464
126 0.118
127 0.702
128 0.00948
129 0.471
13 0.00207
130 0.791
131 0.67
132 0.759
133 0.144
134 0.971
135 0.985
136 0.442
137 0.299
138 0.303
139 0.657
14 0.91
140 0.00693
141 0.498
142 0.0538
143 0.31
144 0.798
145 0.0168
146 0.486
147 0.733
148 0.56
149 0.71
15 0.0678
150 0.157
151 0.417
152 0.186
153 0.137
154 0.544
155 0.796
156 0.156
157 0.904
158 0.851
159 0.765
160 0.131
161 0.603
162 0.637
163 0.587
164 0.0138
165 0.353
166 0.926
167 0.169
168 0.955
169 0.00294
17 0.0334
18 0.455
19 0.0564
2 0.93
20 0.231
21 0.793
22 0.238
23 0.463
24 0.442
25 0.945
26 1.08956e-4
27 0.722
28 0.412
29 0.145
3 0.0169
30 0.805
31 0.348
32 0.143
33 0.23
34 0.957
35 0.504
36 0.0421
37 0.0579
38 0.616
39 0.211
4 0.389
40 0.274
41 0.627
42 0.157
43 0.0436
44 0.104
45 0.879
46 0.045
47 0.459
48 0.222
49 0.0424
5 0.0501
50 0.471
51 0.339
52 0.296
53 0.702
54 0.36
55 0.829
56 0.384
57 0.435
58 0.49
59 0.2
6 0.827
60 0.0788
61 0.151
62 0.112
63 0.115
64 0.46
65 0.326
66 0.706
67 0.662
68 0.132
69 0.348
7 0.164
70 0.172
71 0.0232
72 0.57
73 0.105
74 0.957
75 0.0225
76 0.539
77 0.599
78 0.00727
79 0.619
8 0.0106
80 0.246
81 0.728
82 0.103
83 0.454
84 0.905
85 0.131
86 0.185
87 0.676
88 0.927
89 0.566
9 0.702
90 0.061
91 0.184
92 0.0906
93 0.793
94 0.8
95 0.0998
96 0.0915
97 0.683
98 0.284
99 0.27



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: CNhs11117


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)
0002107 (liver)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary 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)
0011395 (mouse liver- 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:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)