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FF:823-25A3

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Name:liver, neonate N20
Species:Mouse (Mus musculus)
Library ID:CNhs11220
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stage20 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  DRS008890
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11220 CAGE DRX009027 DRR009901
Accession ID Mm9

Library idBAMCTSS
CNhs11220 DRZ001326 DRZ002709
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs11220

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0978
1001 0.0967
1002 --0.116
1003 0.0704
1004 0
1005 0
1006 --0.088
1007 --0.0636
1008 0
1009 0.0921
101 0.00512
1010 0
1011 --0.2
1012 0
1013 0.381
1014 --0.0851
1015 --0.382
1016 --0.282
1017 0
1018 0
1019 0
102 0
1020 0
1021 --0.0487
1022 0.556
1023 0
1024 0
1025 0.577
1026 0
1027 0
1028 0
1029 0.204
103 --0.0578
1030 0
1031 --0.00412
1032 --0.216
1033 --0.0665
1034 0.822
1035 0
1036 --0.217
1037 0
1038 --0.043
1039 0.717
104 0
1040 --0.139
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: CNhs11220

Jaspar motif P-value
MA0002.2 0.313
MA0003.1 0.517
MA0004.1 0.562
MA0006.1 0.216
MA0007.1 0.173
MA0009.1 0.43
MA0014.1 0.196
MA0017.1 5.60497e-27
MA0018.2 5.96061e-6
MA0019.1 0.597
MA0024.1 0.126
MA0025.1 0.0476
MA0027.1 0.88
MA0028.1 0.635
MA0029.1 0.347
MA0030.1 0.00153
MA0031.1 0.00555
MA0035.2 0.118
MA0038.1 0.718
MA0039.2 0.271
MA0040.1 0.332
MA0041.1 0.896
MA0042.1 0.992
MA0043.1 0.136
MA0046.1 4.14036e-95
MA0047.2 8.99945e-9
MA0048.1 0.237
MA0050.1 0.00212
MA0051.1 8.02751e-4
MA0052.1 0.0111
MA0055.1 0.171
MA0057.1 0.556
MA0058.1 0.387
MA0059.1 0.11
MA0060.1 0.156
MA0061.1 0.562
MA0062.2 0.996
MA0065.2 1.12927e-17
MA0066.1 0.0498
MA0067.1 0.071
MA0068.1 0.737
MA0069.1 0.208
MA0070.1 0.422
MA0071.1 3.05012e-5
MA0072.1 8.76728e-6
MA0073.1 0.744
MA0074.1 0.231
MA0076.1 0.744
MA0077.1 0.0365
MA0078.1 0.53
MA0079.2 0.345
MA0080.2 0.845
MA0081.1 0.837
MA0083.1 0.0202
MA0084.1 0.869
MA0087.1 0.211
MA0088.1 0.365
MA0090.1 0.724
MA0091.1 0.599
MA0092.1 0.135
MA0093.1 0.565
MA0099.2 0.492
MA0100.1 0.222
MA0101.1 0.715
MA0102.2 0.199
MA0103.1 0.194
MA0104.2 0.968
MA0105.1 0.172
MA0106.1 0.0292
MA0107.1 0.926
MA0108.2 7.02523e-4
MA0111.1 0.748
MA0112.2 6.35006e-6
MA0113.1 0.662
MA0114.1 1.89255e-27
MA0115.1 1.09815e-11
MA0116.1 0.183
MA0117.1 0.982
MA0119.1 0.00671
MA0122.1 0.302
MA0124.1 0.488
MA0125.1 0.512
MA0131.1 0.941
MA0135.1 0.488
MA0136.1 0.237
MA0137.2 0.179
MA0138.2 0.507
MA0139.1 0.175
MA0140.1 0.823
MA0141.1 5.85751e-7
MA0142.1 0.0529
MA0143.1 0.342
MA0144.1 0.45
MA0145.1 0.0834
MA0146.1 0.145
MA0147.1 0.934
MA0148.1 7.3925e-12
MA0149.1 0.0161
MA0150.1 0.00625
MA0152.1 0.46
MA0153.1 3.57731e-62
MA0154.1 0.171
MA0155.1 0.548
MA0156.1 0.683
MA0157.1 0.00251
MA0159.1 8.08258e-4
MA0160.1 2.74681e-5
MA0162.1 0.616
MA0163.1 0.00268
MA0164.1 0.792
MA0258.1 0.00421
MA0259.1 0.672



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: CNhs11220

Novel motif P-value
1 0.089
10 0.231
100 0.706
101 0.902
102 0.109
103 0.0114
104 0.798
105 0.646
106 0.0862
107 0.071
108 0.289
109 0.0391
11 0.104
110 0.0258
111 0.0723
112 0.004
113 0.922
114 0.0295
115 0.755
116 0.687
117 0.0727
118 0.277
119 0.119
12 0.636
120 0.245
121 0.606
122 0.335
123 0.164
124 0.67
125 0.393
126 0.178
127 0.627
128 0.0454
129 0.709
13 2.23115e-5
130 0.997
131 0.307
132 0.358
133 0.449
134 0.815
135 0.555
136 0.368
137 0.978
138 0.361
139 0.624
14 0.397
140 0.0306
141 0.665
142 0.122
143 0.829
144 0.638
145 0.0482
146 0.398
147 0.441
148 0.263
149 0.301
15 0.192
150 0.143
151 0.547
152 0.0887
153 0.233
154 0.83
155 0.6
156 0.378
157 0.657
158 0.993
159 0.726
160 0.151
161 0.985
162 0.335
163 0.482
164 0.0415
165 0.458
166 0.233
167 0.414
168 0.902
169 7.85895e-4
17 0.051
18 0.934
19 0.0163
2 0.862
20 0.43
21 0.305
22 0.137
23 0.309
24 0.316
25 0.708
26 0.00146
27 0.83
28 0.463
29 0.29
3 0.0632
30 0.89
31 0.383
32 0.208
33 0.314
34 0.873
35 0.683
36 0.0533
37 0.0668
38 0.199
39 0.297
4 0.917
40 0.116
41 0.517
42 0.379
43 0.0623
44 0.179
45 0.634
46 0.119
47 0.429
48 0.164
49 0.0449
5 0.136
50 0.641
51 0.323
52 0.372
53 0.621
54 0.507
55 0.586
56 0.428
57 0.996
58 0.286
59 0.304
6 0.667
60 0.163
61 0.256
62 0.133
63 0.11
64 0.682
65 0.161
66 0.779
67 0.889
68 0.141
69 0.828
7 0.138
70 0.105
71 0.0573
72 0.627
73 0.0797
74 0.792
75 0.0302
76 0.827
77 0.513
78 0.0177
79 0.856
8 0.0166
80 0.606
81 0.64
82 0.0521
83 0.529
84 0.144
85 0.0424
86 0.163
87 0.764
88 0.644
89 0.0562
9 0.816
90 0.0869
91 0.346
92 0.304
93 0.0733
94 0.686
95 0.282
96 0.2
97 0.419
98 0.585
99 0.117



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: CNhs11220


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)
0000308 (mouse neonate N20 sample)
0011429 (mouse liver- neonate N20 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)