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FF:1392-42F2

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Name:cortex, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11107
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
tissuecortex
dev stage30 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  SAMD00004720
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11107 CAGE DRX008948 DRR009822
Accession ID Mm9

Library idBAMCTSS
CNhs11107 DRZ001247 DRZ002630
Accession ID Mm10

Library idBAMCTSS
CNhs11107 DRZ012597 DRZ013980
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 sample
Ranked 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 sample
Ranked 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

CNhs11107

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.828
10 0
100 0
1000 0
1001 0.0729
1002 -0.0956
1003 0.16
1004 0
1005 0.114
1006 0.696
1007 0.0595
1008 0
1009 -0.179
101 -0.0521
1010 0
1011 0.879
1012 0.512
1013 0.152
1014 0
1015 -0.0015
1016 -0.2
1017 0
1018 0
1019 0
102 0
1020 0
1021 -0.0229
1022 -0.0251
1023 0
1024 0
1025 0
1026 0
1027 0.306
1028 0
1029 0.0704
103 -0.0788
1030 0
1031 -0.441
1032 0.129
1033 -0.0647
1034 0
1035 0
1036 -0.249
1037 0
1038 0.00542
1039 0.0996
104 0
1040 -0.318
1041 0



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs11107
Jaspar motif P-value
MA0002.2 0.00325
MA0003.1 0.28
MA0004.1 0.572
MA0006.1 0.135
MA0007.1 0.359
MA0009.1 0.95
MA0014.1 0.691
MA0017.1 7.55596e-7
MA0018.2 0.00908
MA0019.1 0.25
MA0024.1 0.0506
MA0025.1 0.015
MA0027.1 0.0563
MA0028.1 0.0897
MA0029.1 0.922
MA0030.1 0.773
MA0031.1 0.185
MA0035.2 0.0127
MA0038.1 0.552
MA0039.2 0.0209
MA0040.1 0.0876
MA0041.1 0.765
MA0042.1 0.414
MA0043.1 0.149
MA0046.1 4.35054e-11
MA0047.2 3.0384e-4
MA0048.1 0.0571
MA0050.1 1.61357e-4
MA0051.1 0.0127
MA0052.1 0.672
MA0055.1 0.0162
MA0057.1 0.507
MA0058.1 0.448
MA0059.1 0.169
MA0060.1 0.488
MA0061.1 0.0371
MA0062.2 0.00267
MA0065.2 1.31542e-6
MA0066.1 0.0203
MA0067.1 0.511
MA0068.1 0.333
MA0069.1 0.0534
MA0070.1 0.511
MA0071.1 0.0283
MA0072.1 0.331
MA0073.1 0.726
MA0074.1 0.104
MA0076.1 0.219
MA0077.1 0.716
MA0078.1 0.66
MA0079.2 0.453
MA0080.2 5.42935e-10
MA0081.1 0.223
MA0083.1 0.00763
MA0084.1 0.741
MA0087.1 0.665
MA0088.1 0.315
MA0090.1 0.197
MA0091.1 0.182
MA0092.1 0.305
MA0093.1 0.6
MA0099.2 0.00745
MA0100.1 0.337
MA0101.1 0.0223
MA0102.2 0.386
MA0103.1 0.217
MA0104.2 0.901
MA0105.1 0.0117
MA0106.1 0.0693
MA0107.1 0.0421
MA0108.2 3.64563e-4
MA0111.1 0.887
MA0112.2 7.78892e-4
MA0113.1 0.297
MA0114.1 6.94097e-6
MA0115.1 3.38497e-5
MA0116.1 0.0685
MA0117.1 0.891
MA0119.1 0.112
MA0122.1 0.897
MA0124.1 0.544
MA0125.1 0.0304
MA0131.1 0.828
MA0135.1 0.794
MA0136.1 3.76654e-11
MA0137.2 0.122
MA0138.2 0.00167
MA0139.1 0.475
MA0140.1 4.02241e-4
MA0141.1 4.74423e-4
MA0142.1 0.438
MA0143.1 0.683
MA0144.1 0.0992
MA0145.1 0.12
MA0146.1 0.02
MA0147.1 0.774
MA0148.1 2.14096e-4
MA0149.1 0.154
MA0150.1 0.184
MA0152.1 0.16
MA0153.1 1.1127e-11
MA0154.1 0.0481
MA0155.1 0.347
MA0156.1 8.91241e-8
MA0157.1 0.07
MA0159.1 0.00151
MA0160.1 0.00324
MA0162.1 0.151
MA0163.1 0.00108
MA0164.1 0.876
MA0258.1 0.0192
MA0259.1 0.969



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs11107
Novel motif P-value
1 0.23
10 0.0575
100 0.408
101 0.849
102 0.883
103 0.0627
104 0.769
105 0.618
106 0.0497
107 0.159
108 0.725
109 0.00437
11 0.075
110 0.0443
111 0.113
112 0.0093
113 0.392
114 0.449
115 0.959
116 0.252
117 0.00402
118 0.493
119 0.29
12 0.942
120 0.983
121 0.427
122 0.798
123 0.00352
124 0.0426
125 0.309
126 0.0269
127 0.422
128 0.0477
129 0.298
13 2.07711e-7
130 0.0848
131 0.507
132 0.703
133 0.596
134 0.0983
135 0.421
136 0.038
137 0.711
138 0.858
139 0.246
14 0.94
140 0.071
141 0.525
142 0.814
143 0.416
144 0.674
145 2.64552e-4
146 0.316
147 0.247
148 0.368
149 0.468
15 0.226
150 0.0507
151 0.849
152 0.106
153 0.825
154 0.983
155 0.307
156 0.00225
157 0.353
158 0.207
159 0.605
160 0.162
161 0.0435
162 0.581
163 0.741
164 0.0689
165 0.0971
166 0.964
167 0.585
168 0.586
169 0.00365
17 0.0527
18 0.862
19 0.0691
2 0.874
20 0.0521
21 0.199
22 0.134
23 0.741
24 0.0322
25 0.777
26 5.7437e-7
27 0.604
28 0.687
29 0.0212
3 0.0455
30 0.933
31 0.986
32 0.503
33 0.194
34 0.594
35 0.805
36 0.297
37 0.0239
38 0.533
39 0.309
4 0.193
40 0.151
41 0.417
42 0.163
43 0.127
44 0.443
45 0.662
46 0.133
47 0.323
48 0.253
49 0.245
5 0.181
50 0.24
51 0.777
52 0.247
53 0.493
54 0.967
55 0.903
56 0.418
57 0.726
58 0.374
59 0.101
6 0.978
60 0.0388
61 0.0345
62 0.255
63 0.133
64 0.619
65 0.408
66 0.553
67 0.487
68 0.553
69 0.23
7 0.0207
70 0.121
71 0.00588
72 0.607
73 0.0332
74 0.928
75 0.049
76 0.568
77 0.34
78 0.00232
79 0.546
8 0.0627
80 0.568
81 0.858
82 0.229
83 0.066
84 0.792
85 0.176
86 0.196
87 0.0529
88 0.462
89 0.789
9 0.442
90 0.276
91 0.0984
92 0.24
93 0.114
94 0.895
95 0.0236
96 0.47
97 0.97
98 0.409
99 0.411



de novo motifs identified by HOMER in promoters active in this sample
Summary:The result of HOMER in this sample is shown.
Analyst:NA

library id: CNhs11107


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)
0001851 (cortex)
0005889 (zygote cortex)
0000479 (tissue)
0000064 (organ part)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000470 (cell part)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011469 (mouse cortex- neonate N30 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


FF:0000294 (mouse embryonic day 11 sample)