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FF:650-25G4

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Name:skin, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11124
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 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  SAMD00004964
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11124 CAGE DRX009078 DRR009952
Accession ID Mm9

Library idBAMCTSS
CNhs11124 DRZ001377 DRZ002760
Accession ID Mm10

Library idBAMCTSS
CNhs11124 DRZ012727 DRZ014110
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

CNhs11124

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.065
1001 0.0975
1002 --0.012
1003 0.152
1004 0
1005 0
1006 0.172
1007 0.0614
1008 0
1009 0.104
101 0.0718
1010 0
1011 0.0307
1012 0.0145
1013 0.0224
1014 0.267
1015 --0.0724
1016 0.092
1017 0
1018 0.554
1019 0
102 0
1020 0
1021 0
1022 0.198
1023 0
1024 0.222
1025 0
1026 0.0356
1027 0.065
1028 0
1029 0.0568
103 0.554
1030 0
1031 0.412
1032 --0.131
1033 --0.0752
1034 0.065
1035 0.065
1036 0.0742
1037 0
1038 0.0251
1039 --0.11
104 0
1040 0.288
1041 0.328



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: CNhs11124

Jaspar motif P-value
MA0002.2 0.00618
MA0003.1 0.553
MA0004.1 0.284
MA0006.1 0.0849
MA0007.1 0.845
MA0009.1 0.155
MA0014.1 0.682
MA0017.1 1.53909e-10
MA0018.2 0.00602
MA0019.1 0.258
MA0024.1 0.131
MA0025.1 0.936
MA0027.1 0.905
MA0028.1 4.41834e-8
MA0029.1 0.657
MA0030.1 0.145
MA0031.1 0.0468
MA0035.2 9.42179e-4
MA0038.1 0.457
MA0039.2 0.0526
MA0040.1 0.891
MA0041.1 0.248
MA0042.1 0.524
MA0043.1 0.245
MA0046.1 4.30148e-26
MA0047.2 0.277
MA0048.1 0.113
MA0050.1 0.198
MA0051.1 0.0625
MA0052.1 9.97678e-11
MA0055.1 0.0052
MA0057.1 0.391
MA0058.1 0.0774
MA0059.1 0.00405
MA0060.1 0.00132
MA0061.1 0.197
MA0062.2 2.30598e-10
MA0065.2 0.00441
MA0066.1 0.333
MA0067.1 0.532
MA0068.1 0.0851
MA0069.1 0.725
MA0070.1 0.553
MA0071.1 0.00463
MA0072.1 0.179
MA0073.1 0.902
MA0074.1 0.327
MA0076.1 1.38178e-7
MA0077.1 0.392
MA0078.1 0.0144
MA0079.2 0.0296
MA0080.2 2.46915e-5
MA0081.1 0.00391
MA0083.1 0.0056
MA0084.1 0.801
MA0087.1 0.112
MA0088.1 0.193
MA0090.1 0.0187
MA0091.1 0.818
MA0092.1 0.201
MA0093.1 0.208
MA0099.2 1.16458e-10
MA0100.1 0.014
MA0101.1 0.3
MA0102.2 0.423
MA0103.1 0.962
MA0104.2 0.0159
MA0105.1 0.0665
MA0106.1 0.137
MA0107.1 0.669
MA0108.2 1.81878e-14
MA0111.1 0.998
MA0112.2 0.701
MA0113.1 0.431
MA0114.1 2.5707e-10
MA0115.1 1.35561e-4
MA0116.1 0.0961
MA0117.1 0.529
MA0119.1 0.531
MA0122.1 0.543
MA0124.1 0.149
MA0125.1 0.0979
MA0131.1 0.797
MA0135.1 0.459
MA0136.1 7.30687e-10
MA0137.2 0.0924
MA0138.2 0.957
MA0139.1 0.0321
MA0140.1 0.00197
MA0141.1 1.33052e-7
MA0142.1 0.173
MA0143.1 0.0906
MA0144.1 0.564
MA0145.1 0.339
MA0146.1 0.657
MA0147.1 0.00632
MA0148.1 0.217
MA0149.1 0.14
MA0150.1 0.266
MA0152.1 0.014
MA0153.1 1.73122e-15
MA0154.1 0.599
MA0155.1 0.58
MA0156.1 1.07147e-6
MA0157.1 0.00272
MA0159.1 0.0242
MA0160.1 5.00719e-6
MA0162.1 0.508
MA0163.1 0.203
MA0164.1 0.283
MA0258.1 0.463
MA0259.1 0.156



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: CNhs11124

Novel motif P-value
1 0.24
10 0.434
100 0.7
101 0.771
102 0.633
103 0.142
104 0.805
105 0.349
106 0.0258
107 0.00342
108 0.925
109 0.135
11 0.226
110 0.612
111 0.0859
112 0.412
113 0.677
114 0.736
115 0.455
116 0.408
117 0.111
118 0.0638
119 0.481
12 0.242
120 0.286
121 0.286
122 0.417
123 0.794
124 0.238
125 0.504
126 0.732
127 0.716
128 0.125
129 0.245
13 0.139
130 0.726
131 0.344
132 0.987
133 0.141
134 0.96
135 0.446
136 0.6
137 0.451
138 0.506
139 0.372
14 0.461
140 0.203
141 0.619
142 0.589
143 0.152
144 0.232
145 0.405
146 0.381
147 0.162
148 0.2
149 0.907
15 0.0246
150 0.404
151 0.838
152 0.0194
153 0.898
154 0.249
155 0.533
156 0.0215
157 0.00245
158 0.114
159 0.348
160 0.347
161 0.125
162 0.664
163 0.751
164 0.461
165 0.518
166 0.213
167 0.0107
168 0.82
169 0.144
17 0.233
18 0.21
19 0.451
2 0.101
20 0.214
21 0.94
22 0.524
23 0.255
24 0.959
25 0.125
26 0.0676
27 0.701
28 0.889
29 0.0289
3 0.171
30 0.1
31 0.536
32 0.807
33 0.644
34 0.636
35 0.00408
36 0.0151
37 0.707
38 0.353
39 0.157
4 0.981
40 0.0442
41 0.285
42 0.678
43 0.906
44 0.0232
45 0.249
46 0.737
47 0.275
48 0.307
49 0.42
5 0.511
50 0.303
51 0.973
52 0.0633
53 0.269
54 0.655
55 0.82
56 0.687
57 0.617
58 0.855
59 0.782
6 0.766
60 0.082
61 0.875
62 0.479
63 0.544
64 0.19
65 0.416
66 0.0949
67 0.778
68 0.058
69 0.258
7 0.763
70 0.217
71 0.654
72 0.395
73 0.47
74 0.97
75 0.0755
76 0.0249
77 0.444
78 0.0505
79 0.533
8 0.137
80 0.114
81 0.587
82 0.766
83 0.303
84 0.377
85 0.399
86 0.107
87 0.607
88 0.882
89 0.266
9 0.396
90 0.398
91 0.873
92 0.783
93 0.515
94 0.442
95 0.445
96 0.714
97 0.194
98 0.46
99 0.224



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: CNhs11124


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)
0000304 (mouse neonate N0 sample)
0011397 (mouse skin- 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:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)