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FF:1382-42D1

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Name:liver, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11106
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 stage30 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  SAMD00005227
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11106 CAGE DRX009029 DRR009903
Accession ID Mm9

Library idBAMCTSS
CNhs11106 DRZ001328 DRZ002711
Accession ID Mm10

Library idBAMCTSS
CNhs11106 DRZ012678 DRZ014061
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

CNhs11106

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.202
1002 -0.0941
1003 0.0147
1004 0
1005 0
1006 0
1007 -0.0267
1008 0
1009 0.0336
101 -0.0331
1010 0
1011 -0.298
1012 0
1013 0.536
1014 0
1015 -0.266
1016 -0.423
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.646
1023 0
1024 0.0811
1025 0.389
1026 0
1027 0
1028 0
1029 -0.005
103 -0.0659
1030 0
1031 -0.0495
1032 -0.4
1033 -0.0665
1034 1.033
1035 0
1036 -0.324
1037 0
1038 -0.17
1039 0.892
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: CNhs11106
Jaspar motif P-value
MA0002.2 0.587
MA0003.1 0.672
MA0004.1 0.455
MA0006.1 0.216
MA0007.1 0.0981
MA0009.1 0.452
MA0014.1 0.165
MA0017.1 9.97493e-24
MA0018.2 4.48636e-4
MA0019.1 0.481
MA0024.1 2.56906e-4
MA0025.1 0.121
MA0027.1 0.809
MA0028.1 0.569
MA0029.1 0.333
MA0030.1 3.00124e-4
MA0031.1 3.00358e-4
MA0035.2 0.192
MA0038.1 0.682
MA0039.2 0.425
MA0040.1 0.205
MA0041.1 0.809
MA0042.1 0.988
MA0043.1 0.151
MA0046.1 1.24382e-79
MA0047.2 5.42224e-9
MA0048.1 0.28
MA0050.1 0.021
MA0051.1 0.0152
MA0052.1 0.00572
MA0055.1 0.305
MA0057.1 0.612
MA0058.1 0.285
MA0059.1 0.0989
MA0060.1 0.00427
MA0061.1 0.517
MA0062.2 0.74
MA0065.2 2.25501e-17
MA0066.1 0.0239
MA0067.1 0.297
MA0068.1 0.423
MA0069.1 0.407
MA0070.1 0.442
MA0071.1 4.45847e-6
MA0072.1 2.3437e-6
MA0073.1 0.687
MA0074.1 0.0874
MA0076.1 0.944
MA0077.1 0.0537
MA0078.1 0.757
MA0079.2 0.456
MA0080.2 0.402
MA0081.1 0.552
MA0083.1 0.00164
MA0084.1 0.651
MA0087.1 0.421
MA0088.1 0.369
MA0090.1 0.677
MA0091.1 0.917
MA0092.1 0.0976
MA0093.1 0.471
MA0099.2 0.467
MA0100.1 0.569
MA0101.1 0.919
MA0102.2 0.179
MA0103.1 0.166
MA0104.2 0.94
MA0105.1 0.145
MA0106.1 0.062
MA0107.1 0.767
MA0108.2 3.05594e-4
MA0111.1 0.867
MA0112.2 7.07994e-6
MA0113.1 0.247
MA0114.1 3.75978e-23
MA0115.1 4.25869e-11
MA0116.1 0.188
MA0117.1 0.526
MA0119.1 0.0346
MA0122.1 0.219
MA0124.1 0.488
MA0125.1 0.498
MA0131.1 0.939
MA0135.1 0.464
MA0136.1 0.177
MA0137.2 0.081
MA0138.2 0.436
MA0139.1 0.377
MA0140.1 0.643
MA0141.1 1.78798e-8
MA0142.1 0.111
MA0143.1 0.429
MA0144.1 0.199
MA0145.1 0.138
MA0146.1 0.0307
MA0147.1 0.957
MA0148.1 7.11055e-12
MA0149.1 0.00753
MA0150.1 0.00681
MA0152.1 0.564
MA0153.1 3.10829e-56
MA0154.1 0.158
MA0155.1 0.559
MA0156.1 0.677
MA0157.1 3.4051e-4
MA0159.1 4.13464e-4
MA0160.1 5.80247e-6
MA0162.1 0.528
MA0163.1 0.00509
MA0164.1 0.724
MA0258.1 0.00506
MA0259.1 0.656



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: CNhs11106
Novel motif P-value
1 0.106
10 0.206
100 0.596
101 0.665
102 0.241
103 0.0106
104 0.776
105 0.821
106 0.0542
107 0.0922
108 0.531
109 0.0618
11 0.0642
110 0.0592
111 0.0249
112 0.00273
113 0.971
114 0.0118
115 0.274
116 0.653
117 0.0543
118 0.209
119 0.0586
12 0.358
120 0.548
121 0.691
122 0.288
123 0.193
124 0.504
125 0.316
126 0.222
127 0.817
128 0.0466
129 0.816
13 7.69856e-5
130 0.852
131 0.383
132 0.348
133 0.683
134 0.943
135 0.504
136 0.229
137 0.897
138 0.347
139 0.74
14 0.462
140 0.00928
141 0.366
142 0.105
143 0.793
144 0.475
145 0.0378
146 0.323
147 0.474
148 0.335
149 0.319
15 0.17
150 0.164
151 0.52
152 0.121
153 0.241
154 0.716
155 0.546
156 0.0418
157 0.697
158 0.654
159 0.494
160 0.186
161 0.657
162 0.611
163 0.166
164 0.0338
165 0.42
166 0.366
167 0.216
168 0.848
169 0.00331
17 0.065
18 0.907
19 0.0416
2 0.722
20 0.312
21 0.471
22 0.114
23 0.435
24 0.149
25 0.744
26 0.00326
27 0.916
28 0.392
29 0.28
3 0.0754
30 0.928
31 0.394
32 0.127
33 0.344
34 0.937
35 0.504
36 0.0584
37 0.0359
38 0.307
39 0.182
4 0.686
40 0.134
41 0.954
42 0.492
43 0.0821
44 0.0492
45 0.68
46 0.126
47 0.691
48 0.18
49 0.0447
5 0.122
50 0.585
51 0.277
52 0.391
53 0.535
54 0.339
55 0.744
56 0.452
57 0.788
58 0.275
59 0.245
6 0.756
60 0.103
61 0.196
62 0.106
63 0.0868
64 0.55
65 0.222
66 0.594
67 0.949
68 0.149
69 0.878
7 0.186
70 0.0216
71 0.0538
72 0.725
73 0.058
74 0.636
75 0.0155
76 0.894
77 0.451
78 0.0173
79 0.946
8 0.0128
80 0.75
81 0.639
82 0.0255
83 0.434
84 0.289
85 0.0304
86 0.146
87 0.21
88 0.76
89 0.166
9 0.881
90 0.0652
91 0.334
92 0.292
93 0.195
94 0.731
95 0.215
96 0.199
97 0.523
98 0.417
99 0.0914



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: CNhs11106


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)
0000310 (mouse neonate N30 sample)
0011486 (mouse liver- neonate N30 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)