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FF:716-20H2

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Name:liver, neonate N07
Species:Mouse (Mus musculus)
Library ID:CNhs11103
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 stage7 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  SAMD00005798
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11103 CAGE DRX009025 DRR009899
Accession ID Mm9

Library idBAMCTSS
CNhs11103 DRZ001324 DRZ002707
Accession ID Mm10

Library idBAMCTSS
CNhs11103 DRZ012674 DRZ014057
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

CNhs11103

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.175
1002 --0.0612
1003 --0.0892
1004 0
1005 0.203
1006 0.00427
1007 0.00843
1008 0
1009 0.022
101 --0.0174
1010 0
1011 --0.16
1012 0.137
1013 0.334
1014 0.122
1015 --0.263
1016 --0.223
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.393
1023 0
1024 0.137
1025 0.638
1026 0
1027 0
1028 0
1029 --0.0818
103 0
1030 0
1031 --0.00421
1032 --0.232
1033 0
1034 0.51
1035 0
1036 --0.054
1037 0
1038 --0.0389
1039 0.446
104 0
1040 --0.0865
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: CNhs11103

Jaspar motif P-value
MA0002.2 0.0402
MA0003.1 0.248
MA0004.1 0.95
MA0006.1 0.152
MA0007.1 0.637
MA0009.1 0.497
MA0014.1 0.539
MA0017.1 1.85065e-19
MA0018.2 1.65906e-6
MA0019.1 0.2
MA0024.1 0.168
MA0025.1 0.344
MA0027.1 0.889
MA0028.1 0.355
MA0029.1 0.149
MA0030.1 0.0024
MA0031.1 0.0102
MA0035.2 0.0192
MA0038.1 0.737
MA0039.2 0.378
MA0040.1 0.145
MA0041.1 0.504
MA0042.1 0.823
MA0043.1 0.0406
MA0046.1 5.18929e-75
MA0047.2 2.76294e-9
MA0048.1 0.366
MA0050.1 2.86326e-6
MA0051.1 3.17172e-5
MA0052.1 0.0166
MA0055.1 0.821
MA0057.1 0.84
MA0058.1 0.832
MA0059.1 0.483
MA0060.1 0.00728
MA0061.1 0.182
MA0062.2 0.166
MA0065.2 2.87921e-13
MA0066.1 0.0252
MA0067.1 0.0694
MA0068.1 0.606
MA0069.1 0.287
MA0070.1 0.419
MA0071.1 9.17655e-4
MA0072.1 0.00247
MA0073.1 0.757
MA0074.1 0.284
MA0076.1 0.109
MA0077.1 0.0211
MA0078.1 0.46
MA0079.2 0.5
MA0080.2 0.013
MA0081.1 0.73
MA0083.1 0.135
MA0084.1 0.432
MA0087.1 0.106
MA0088.1 0.664
MA0090.1 0.703
MA0091.1 0.916
MA0092.1 0.0518
MA0093.1 0.962
MA0099.2 0.383
MA0100.1 0.345
MA0101.1 0.663
MA0102.2 0.183
MA0103.1 0.403
MA0104.2 0.461
MA0105.1 0.0082
MA0106.1 0.0706
MA0107.1 0.626
MA0108.2 0.0166
MA0111.1 0.876
MA0112.2 1.48684e-5
MA0113.1 0.497
MA0114.1 6.06614e-19
MA0115.1 4.02358e-11
MA0116.1 0.0302
MA0117.1 0.808
MA0119.1 0.00177
MA0122.1 0.507
MA0124.1 0.661
MA0125.1 0.71
MA0131.1 0.693
MA0135.1 0.703
MA0136.1 0.736
MA0137.2 0.372
MA0138.2 0.815
MA0139.1 0.107
MA0140.1 0.00424
MA0141.1 3.99008e-4
MA0142.1 0.199
MA0143.1 0.11
MA0144.1 0.376
MA0145.1 0.116
MA0146.1 0.132
MA0147.1 0.518
MA0148.1 4.96153e-13
MA0149.1 0.162
MA0150.1 0.114
MA0152.1 0.413
MA0153.1 8.05743e-50
MA0154.1 0.019
MA0155.1 0.306
MA0156.1 0.779
MA0157.1 0.00349
MA0159.1 0.00252
MA0160.1 0.00175
MA0162.1 0.446
MA0163.1 9.34499e-5
MA0164.1 0.916
MA0258.1 0.0116
MA0259.1 0.329



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: CNhs11103

Novel motif P-value
1 0.185
10 0.226
100 0.759
101 0.899
102 0.0879
103 0.00696
104 0.479
105 0.932
106 0.0118
107 0.0158
108 0.71
109 0.0682
11 0.142
110 0.0816
111 0.152
112 0.00663
113 0.894
114 0.0678
115 0.455
116 0.911
117 0.125
118 0.186
119 0.148
12 0.55
120 0.604
121 0.456
122 0.818
123 0.23
124 0.133
125 0.455
126 0.227
127 0.83
128 0.0104
129 0.712
13 2.32836e-4
130 0.287
131 0.0486
132 0.604
133 0.369
134 0.873
135 0.363
136 0.433
137 0.451
138 0.354
139 0.97
14 0.475
140 0.0784
141 0.662
142 0.182
143 0.63
144 0.947
145 0.0298
146 0.23
147 0.479
148 0.771
149 0.314
15 0.137
150 0.141
151 0.467
152 0.113
153 0.127
154 0.691
155 0.537
156 0.201
157 0.426
158 0.215
159 0.391
160 0.0617
161 0.964
162 0.411
163 0.983
164 0.0733
165 0.548
166 0.264
167 0.456
168 0.591
169 0.00171
17 0.08
18 0.893
19 0.0201
2 0.425
20 0.714
21 0.47
22 0.106
23 0.202
24 0.261
25 0.996
26 8.62157e-4
27 0.504
28 0.511
29 0.42
3 0.0313
30 0.656
31 0.334
32 0.0493
33 0.176
34 0.699
35 0.914
36 0.0575
37 0.0877
38 0.322
39 0.241
4 0.681
40 0.132
41 0.612
42 0.177
43 0.056
44 0.143
45 0.589
46 0.0974
47 0.369
48 0.215
49 0.0686
5 0.101
50 0.406
51 0.251
52 0.125
53 0.917
54 0.386
55 0.517
56 0.354
57 0.989
58 0.364
59 0.0628
6 0.956
60 0.0764
61 0.221
62 0.164
63 0.0778
64 0.526
65 0.23
66 0.659
67 0.994
68 0.222
69 0.657
7 0.157
70 0.2
71 0.0634
72 0.633
73 0.187
74 0.396
75 0.0758
76 0.748
77 0.305
78 0.0172
79 0.89
8 0.0331
80 0.148
81 0.717
82 0.0884
83 0.721
84 0.862
85 0.0594
86 0.204
87 0.286
88 0.895
89 0.046
9 0.475
90 0.309
91 0.2
92 0.237
93 0.452
94 0.803
95 0.274
96 0.227
97 0.826
98 0.244
99 0.0424



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: CNhs11103


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)
0000313 (mouse neonate N7 sample)
0011409 (mouse liver- neonate N07 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)