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FF:762-6C4

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Name:skin, neonate N10
Species:Mouse (Mus musculus)
Library ID:CNhs11108
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
tissueskin
dev stage10 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  SAMD00004754
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11108 CAGE DRX009081 DRR009955
Accession ID Mm9

Library idBAMCTSS
CNhs11108 DRZ001380 DRZ002763
Accession ID Mm10

Library idBAMCTSS
CNhs11108 DRZ012730 DRZ014113
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 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

CNhs11108

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0262
1001 --0.00258
1002 0.0544
1003 0.0635
1004 0
1005 --0.0389
1006 0
1007 0.11
1008 0
1009 0.108
101 0.0963
1010 0
1011 0.0383
1012 0
1013 0.0402
1014 0
1015 --0.0319
1016 --0.0547
1017 0
1018 0.818
1019 0
102 0
1020 0
1021 0
1022 0.066
1023 0
1024 0.189
1025 0
1026 0
1027 0
1028 0
1029 0.121
103 0.458
1030 0
1031 --0.0483
1032 --0.0097
1033 --0.00922
1034 0
1035 0
1036 --0.145
1037 0
1038 --0.0116
1039 --0.0661
104 0
1040 0.0446
1041 0.422



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: CNhs11108

Jaspar motif P-value
MA0002.2 0.718
MA0003.1 0.445
MA0004.1 0.988
MA0006.1 0.0417
MA0007.1 0.503
MA0009.1 0.0296
MA0014.1 0.224
MA0017.1 2.59372e-5
MA0018.2 0.127
MA0019.1 0.437
MA0024.1 0.216
MA0025.1 0.767
MA0027.1 0.506
MA0028.1 0.00141
MA0029.1 0.288
MA0030.1 0.155
MA0031.1 0.304
MA0035.2 0.00927
MA0038.1 0.342
MA0039.2 0.00108
MA0040.1 0.0058
MA0041.1 0.261
MA0042.1 0.748
MA0043.1 0.595
MA0046.1 1.49317e-11
MA0047.2 0.436
MA0048.1 0.0425
MA0050.1 2.77308e-4
MA0051.1 0.0386
MA0052.1 0.00414
MA0055.1 8.19366e-5
MA0057.1 0.122
MA0058.1 0.694
MA0059.1 0.332
MA0060.1 0.873
MA0061.1 0.0908
MA0062.2 2.64447e-5
MA0065.2 0.13
MA0066.1 0.438
MA0067.1 0.97
MA0068.1 0.484
MA0069.1 0.872
MA0070.1 0.986
MA0071.1 0.0879
MA0072.1 0.607
MA0073.1 0.339
MA0074.1 0.28
MA0076.1 0.00208
MA0077.1 0.49
MA0078.1 0.131
MA0079.2 0.0271
MA0080.2 2.57479e-4
MA0081.1 0.00687
MA0083.1 0.216
MA0084.1 0.486
MA0087.1 0.76
MA0088.1 0.389
MA0090.1 0.00843
MA0091.1 0.623
MA0092.1 0.302
MA0093.1 0.903
MA0099.2 6.4689e-19
MA0100.1 0.105
MA0101.1 0.253
MA0102.2 0.36
MA0103.1 3.03949e-4
MA0104.2 0.111
MA0105.1 0.0496
MA0106.1 0.0123
MA0107.1 0.284
MA0108.2 3.84437e-65
MA0111.1 0.932
MA0112.2 0.99
MA0113.1 0.0111
MA0114.1 1.1671e-4
MA0115.1 0.00117
MA0116.1 0.243
MA0117.1 0.801
MA0119.1 0.828
MA0122.1 0.533
MA0124.1 0.655
MA0125.1 3.40407e-5
MA0131.1 0.311
MA0135.1 0.0347
MA0136.1 2.4286e-5
MA0137.2 0.208
MA0138.2 0.941
MA0139.1 0.32
MA0140.1 0.0176
MA0141.1 3.80858e-4
MA0142.1 0.88
MA0143.1 0.238
MA0144.1 0.808
MA0145.1 0.0926
MA0146.1 0.226
MA0147.1 0.067
MA0148.1 0.357
MA0149.1 0.41
MA0150.1 0.635
MA0152.1 0.479
MA0153.1 2.73757e-8
MA0154.1 0.814
MA0155.1 0.543
MA0156.1 1.06888e-4
MA0157.1 0.0555
MA0159.1 0.15
MA0160.1 0.0141
MA0162.1 0.383
MA0163.1 0.245
MA0164.1 0.219
MA0258.1 0.272
MA0259.1 0.327



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: CNhs11108

Novel motif P-value
1 0.873
10 0.874
100 0.891
101 0.465
102 0.154
103 0.562
104 0.0674
105 0.754
106 0.0274
107 0.0152
108 0.355
109 0.535
11 0.783
110 0.732
111 0.748
112 0.746
113 0.759
114 0.585
115 0.206
116 0.773
117 0.647
118 0.111
119 0.624
12 0.921
120 0.837
121 0.956
122 0.966
123 0.949
124 0.399
125 0.557
126 0.559
127 0.498
128 0.159
129 0.717
13 0.107
130 0.877
131 0.229
132 0.868
133 0.559
134 0.764
135 0.0834
136 0.15
137 0.34
138 0.2
139 0.394
14 0.469
140 0.307
141 0.569
142 0.895
143 0.346
144 0.424
145 0.469
146 0.443
147 0.0604
148 0.153
149 0.591
15 0.174
150 0.12
151 0.908
152 0.00824
153 0.735
154 0.722
155 0.944
156 0.133
157 0.12
158 0.575
159 0.249
160 0.507
161 0.375
162 0.857
163 0.942
164 0.513
165 0.216
166 0.483
167 0.0194
168 0.601
169 0.104
17 0.0597
18 0.338
19 0.655
2 0.0322
20 0.0942
21 0.346
22 0.613
23 0.0787
24 0.748
25 0.267
26 0.00809
27 0.824
28 0.868
29 0.297
3 0.717
30 0.0338
31 0.301
32 0.641
33 0.808
34 0.958
35 0.0233
36 0.0248
37 0.679
38 0.921
39 0.168
4 0.728
40 0.564
41 0.794
42 0.619
43 0.741
44 0.497
45 0.381
46 0.505
47 0.841
48 0.975
49 0.389
5 0.416
50 0.815
51 0.871
52 0.0806
53 0.228
54 0.527
55 0.401
56 0.743
57 0.642
58 0.982
59 0.717
6 0.798
60 0.0737
61 0.502
62 0.826
63 0.68
64 0.359
65 0.946
66 0.821
67 0.487
68 0.146
69 0.236
7 0.747
70 0.184
71 0.552
72 0.733
73 0.145
74 0.925
75 0.395
76 0.0063
77 0.0606
78 0.0108
79 0.421
8 0.541
80 0.344
81 0.257
82 0.653
83 0.273
84 0.393
85 0.0902
86 0.18
87 0.0672
88 0.715
89 0.37
9 0.477
90 0.99
91 0.758
92 0.982
93 0.746
94 0.556
95 0.744
96 0.984
97 0.0576
98 0.804
99 0.166



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: CNhs11108


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)
0000014 (zone of skin)
0001003 (skin epidermis)
0002097 (skin of body)
0002199 (integument)
0007029 (surface)
0000483 (epithelium)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0003102 (surface structure)
0007376 (outer epithelium)
0010371 (ecto-epithelium)
0010317 (germ layer / neural crest derived structure)
0002416 (integumental system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000305 (mouse neonate N10 sample)
0011421 (mouse skin- neonate N10 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:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)