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FF:662-22H3

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Name:skin, neonate N03
Species:Mouse (Mus musculus)
Library ID:CNhs11215
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 stage3 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  SAMD00004789
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11215 CAGE DRX009079 DRR009953
Accession ID Mm9

Library idBAMCTSS
CNhs11215 DRZ001378 DRZ002761
Accession ID Mm10

Library idBAMCTSS
CNhs11215 DRZ012728 DRZ014111
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

CNhs11215

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0804
1001 0.0374
1002 --0.0566
1003 0.121
1004 0
1005 0
1006 0.0495
1007 0.0759
1008 0
1009 0.21
101 0.111
1010 0
1011 0.0254
1012 0
1013 --0.058
1014 0.0836
1015 --0.0122
1016 0.0979
1017 0
1018 0.467
1019 0
102 0
1020 0
1021 0.0254
1022 0.153
1023 0
1024 0.0984
1025 0
1026 0
1027 0.0113
1028 0
1029 --0.0267
103 0.389
1030 0
1031 0.245
1032 --0.0495
1033 0
1034 0.0495
1035 0.0254
1036 0.051
1037 0
1038 0.0376
1039 --0.0756
104 0
1040 0.14
1041 0.733



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: CNhs11215

Jaspar motif P-value
MA0002.2 0.123
MA0003.1 0.446
MA0004.1 0.496
MA0006.1 0.101
MA0007.1 0.303
MA0009.1 0.164
MA0014.1 0.725
MA0017.1 2.1883e-9
MA0018.2 0.239
MA0019.1 0.175
MA0024.1 0.161
MA0025.1 0.9
MA0027.1 0.995
MA0028.1 0.00487
MA0029.1 0.335
MA0030.1 0.321
MA0031.1 0.956
MA0035.2 5.15306e-4
MA0038.1 0.00233
MA0039.2 0.00412
MA0040.1 0.244
MA0041.1 0.287
MA0042.1 0.602
MA0043.1 0.493
MA0046.1 1.88659e-21
MA0047.2 0.0487
MA0048.1 0.438
MA0050.1 0.0181
MA0051.1 0.138
MA0052.1 1.22503e-9
MA0055.1 0.0449
MA0057.1 0.312
MA0058.1 0.262
MA0059.1 0.013
MA0060.1 0.00292
MA0061.1 0.0559
MA0062.2 9.58976e-5
MA0065.2 0.0246
MA0066.1 0.182
MA0067.1 0.909
MA0068.1 0.353
MA0069.1 0.81
MA0070.1 0.597
MA0071.1 0.00188
MA0072.1 0.615
MA0073.1 0.871
MA0074.1 0.0795
MA0076.1 0.0134
MA0077.1 0.56
MA0078.1 0.0316
MA0079.2 0.0326
MA0080.2 7.35174e-7
MA0081.1 0.00665
MA0083.1 0.00417
MA0084.1 0.88
MA0087.1 0.466
MA0088.1 0.647
MA0090.1 0.0157
MA0091.1 0.171
MA0092.1 0.269
MA0093.1 0.504
MA0099.2 2.3907e-10
MA0100.1 0.0469
MA0101.1 0.712
MA0102.2 0.111
MA0103.1 0.788
MA0104.2 0.049
MA0105.1 0.00457
MA0106.1 0.066
MA0107.1 0.913
MA0108.2 6.78402e-37
MA0111.1 0.393
MA0112.2 0.187
MA0113.1 0.136
MA0114.1 5.08266e-7
MA0115.1 7.43795e-5
MA0116.1 0.0179
MA0117.1 0.647
MA0119.1 0.776
MA0122.1 0.436
MA0124.1 0.404
MA0125.1 8.73086e-4
MA0131.1 0.827
MA0135.1 0.0149
MA0136.1 9.9065e-8
MA0137.2 0.414
MA0138.2 0.246
MA0139.1 0.014
MA0140.1 3.87348e-4
MA0141.1 2.6763e-8
MA0142.1 0.211
MA0143.1 0.0973
MA0144.1 0.973
MA0145.1 0.275
MA0146.1 0.352
MA0147.1 0.0166
MA0148.1 0.0378
MA0149.1 0.348
MA0150.1 0.392
MA0152.1 0.105
MA0153.1 4.97641e-13
MA0154.1 0.268
MA0155.1 0.664
MA0156.1 2.22717e-4
MA0157.1 0.346
MA0159.1 0.00462
MA0160.1 1.51697e-4
MA0162.1 0.485
MA0163.1 0.00929
MA0164.1 0.137
MA0258.1 0.0257
MA0259.1 0.343



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: CNhs11215

Novel motif P-value
1 0.235
10 0.356
100 0.975
101 0.93
102 0.818
103 0.0437
104 0.176
105 0.381
106 0.526
107 0.156
108 0.943
109 0.286
11 0.256
110 0.429
111 0.118
112 0.106
113 0.947
114 0.233
115 0.131
116 0.637
117 0.129
118 0.0177
119 0.374
12 0.497
120 0.485
121 0.446
122 0.645
123 0.726
124 0.159
125 0.533
126 0.754
127 0.352
128 0.751
129 0.433
13 0.172
130 0.666
131 0.277
132 0.569
133 0.35
134 0.806
135 0.215
136 0.204
137 0.465
138 0.394
139 0.0612
14 0.706
140 0.388
141 0.386
142 0.948
143 0.179
144 0.93
145 0.889
146 0.816
147 0.194
148 0.0936
149 0.462
15 0.0131
150 0.526
151 0.393
152 0.0195
153 0.675
154 0.609
155 0.434
156 0.345
157 0.00324
158 0.132
159 0.0794
160 0.711
161 0.2
162 0.587
163 0.764
164 0.199
165 0.273
166 0.183
167 0.00789
168 0.322
169 0.148
17 0.494
18 0.0978
19 0.763
2 0.197
20 0.141
21 0.99
22 0.869
23 0.371
24 0.971
25 0.224
26 0.0545
27 0.435
28 0.81
29 0.0583
3 0.158
30 0.0373
31 0.209
32 0.504
33 0.346
34 0.646
35 2.56414e-4
36 0.00992
37 0.769
38 0.586
39 0.272
4 0.615
40 0.223
41 0.473
42 0.694
43 0.269
44 0.0806
45 0.332
46 0.739
47 0.381
48 0.515
49 0.0414
5 0.151
50 0.571
51 0.781
52 0.139
53 0.287
54 0.885
55 0.745
56 0.719
57 0.776
58 0.833
59 0.758
6 0.977
60 0.29
61 0.998
62 0.363
63 0.921
64 0.184
65 0.329
66 0.871
67 0.985
68 0.0169
69 0.591
7 0.674
70 0.0854
71 0.527
72 0.648
73 0.499
74 0.823
75 0.0384
76 0.0012
77 0.427
78 0.0754
79 0.516
8 0.0744
80 0.22
81 0.29
82 0.271
83 0.251
84 0.61
85 0.912
86 0.232
87 0.0439
88 0.757
89 0.0963
9 0.528
90 0.186
91 0.484
92 0.394
93 0.674
94 0.673
95 0.72
96 0.622
97 0.0663
98 0.276
99 0.399



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: CNhs11215


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)
0000311 (mouse neonate N3 sample)
0011400 (mouse skin- neonate N03 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)