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FF:693-20I5

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Name:skin, neonate N06
Species:Mouse (Mus musculus)
Library ID:CNhs11097
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 stage6 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  SAMD00005816
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11097 CAGE DRX009080 DRR009954
Accession ID Mm9

Library idBAMCTSS
CNhs11097 DRZ001379 DRZ002762
Accession ID Mm10

Library idBAMCTSS
CNhs11097 DRZ012729 DRZ014112
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

CNhs11097

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0922
1001 0
1002 0.049
1003 0.148
1004 0
1005 0
1006 --0.033
1007 0.0725
1008 0
1009 0.219
101 0.0515
1010 0
1011 --0.0324
1012 0
1013 --0.0663
1014 0.00563
1015 --0.0612
1016 --0.0346
1017 0
1018 0.626
1019 0
102 0
1020 0
1021 0
1022 0.0728
1023 0
1024 0.133
1025 --0.0122
1026 0
1027 0
1028 0
1029 0.0586
103 0.507
1030 0
1031 0.128
1032 --0.0533
1033 --0.0262
1034 0.049
1035 0
1036 --0.00147
1037 0
1038 --0.00712
1039 --0.131
104 0
1040 0.126
1041 0.498



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: CNhs11097

Jaspar motif P-value
MA0002.2 0.931
MA0003.1 0.481
MA0004.1 0.805
MA0006.1 0.0517
MA0007.1 0.683
MA0009.1 0.0311
MA0014.1 0.295
MA0017.1 2.49169e-6
MA0018.2 0.0266
MA0019.1 0.0588
MA0024.1 0.54
MA0025.1 0.677
MA0027.1 0.884
MA0028.1 1.93207e-4
MA0029.1 0.429
MA0030.1 0.411
MA0031.1 0.523
MA0035.2 0.00147
MA0038.1 0.248
MA0039.2 7.87253e-4
MA0040.1 0.0264
MA0041.1 0.188
MA0042.1 0.715
MA0043.1 0.298
MA0046.1 6.54956e-18
MA0047.2 0.194
MA0048.1 0.121
MA0050.1 0.0076
MA0051.1 0.0658
MA0052.1 0.00542
MA0055.1 9.46352e-4
MA0057.1 0.117
MA0058.1 0.51
MA0059.1 0.394
MA0060.1 0.89
MA0061.1 0.144
MA0062.2 5.4432e-7
MA0065.2 0.107
MA0066.1 0.465
MA0067.1 0.752
MA0068.1 0.484
MA0069.1 0.867
MA0070.1 0.753
MA0071.1 0.0578
MA0072.1 0.962
MA0073.1 0.607
MA0074.1 0.19
MA0076.1 2.7022e-4
MA0077.1 0.576
MA0078.1 0.123
MA0079.2 0.0317
MA0080.2 2.22316e-6
MA0081.1 0.00136
MA0083.1 0.113
MA0084.1 0.631
MA0087.1 0.707
MA0088.1 0.666
MA0090.1 0.00444
MA0091.1 0.555
MA0092.1 0.0801
MA0093.1 0.706
MA0099.2 3.33529e-15
MA0100.1 0.0629
MA0101.1 0.365
MA0102.2 0.225
MA0103.1 0.00177
MA0104.2 0.153
MA0105.1 0.207
MA0106.1 0.0136
MA0107.1 0.43
MA0108.2 4.63043e-51
MA0111.1 0.96
MA0112.2 0.612
MA0113.1 0.0173
MA0114.1 1.87416e-5
MA0115.1 1.78274e-4
MA0116.1 0.646
MA0117.1 0.513
MA0119.1 0.593
MA0122.1 0.522
MA0124.1 0.523
MA0125.1 6.38918e-5
MA0131.1 0.482
MA0135.1 0.0675
MA0136.1 1.07484e-6
MA0137.2 0.254
MA0138.2 0.827
MA0139.1 0.364
MA0140.1 0.00105
MA0141.1 1.7393e-4
MA0142.1 0.542
MA0143.1 0.316
MA0144.1 0.786
MA0145.1 0.0525
MA0146.1 0.275
MA0147.1 0.0982
MA0148.1 0.235
MA0149.1 0.308
MA0150.1 0.833
MA0152.1 0.533
MA0153.1 3.63679e-12
MA0154.1 0.467
MA0155.1 0.794
MA0156.1 3.88507e-6
MA0157.1 0.0485
MA0159.1 0.0538
MA0160.1 0.00384
MA0162.1 0.568
MA0163.1 0.551
MA0164.1 0.226
MA0258.1 0.396
MA0259.1 0.254



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: CNhs11097

Novel motif P-value
1 0.846
10 0.964
100 0.681
101 0.653
102 0.286
103 0.443
104 0.0494
105 0.539
106 0.0181
107 0.0222
108 0.511
109 0.97
11 0.97
110 0.919
111 0.485
112 0.659
113 0.916
114 0.641
115 0.268
116 0.719
117 0.55
118 0.102
119 0.835
12 0.792
120 0.924
121 0.733
122 0.864
123 0.991
124 0.357
125 0.872
126 0.688
127 0.969
128 0.0716
129 0.89
13 0.0285
130 0.578
131 0.21
132 0.963
133 0.432
134 0.673
135 0.108
136 0.137
137 0.473
138 0.156
139 0.322
14 0.43
140 0.125
141 0.846
142 0.452
143 0.574
144 0.615
145 0.205
146 0.649
147 0.133
148 0.243
149 0.476
15 0.101
150 0.237
151 0.711
152 0.0114
153 0.733
154 0.478
155 0.968
156 3.76453e-4
157 0.0391
158 0.223
159 0.0327
160 0.236
161 0.356
162 0.846
163 0.737
164 0.574
165 0.347
166 0.369
167 0.0159
168 0.533
169 0.0549
17 0.0404
18 0.306
19 0.333
2 0.0419
20 0.117
21 0.412
22 0.463
23 0.0627
24 0.723
25 0.253
26 0.00238
27 0.842
28 0.948
29 0.353
3 0.793
30 0.0273
31 0.279
32 0.701
33 0.896
34 0.769
35 0.0186
36 0.0437
37 0.576
38 0.997
39 0.0347
4 0.916
40 0.596
41 0.71
42 0.653
43 0.935
44 0.444
45 0.357
46 0.521
47 0.858
48 0.95
49 0.409
5 0.341
50 0.603
51 0.861
52 0.0661
53 0.214
54 0.536
55 0.279
56 0.889
57 0.47
58 0.888
59 0.378
6 0.478
60 0.0602
61 0.513
62 0.776
63 0.591
64 0.501
65 0.782
66 0.671
67 0.6
68 0.045
69 0.0618
7 0.507
70 0.435
71 0.513
72 0.775
73 0.101
74 0.823
75 0.509
76 0.00315
77 0.0594
78 0.0152
79 0.826
8 0.46
80 0.17
81 0.432
82 0.837
83 0.379
84 0.674
85 0.0797
86 0.127
87 0.0333
88 0.735
89 0.368
9 0.403
90 0.857
91 0.799
92 0.781
93 0.548
94 0.369
95 0.351
96 0.819
97 0.0655
98 0.881
99 0.107



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: CNhs11097


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)
0000312 (mouse neonate N6 sample)
0011406 (mouse skin- neonate N06 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)