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FF:10240-104A6

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Name:visual cortex - wildtype
Species:Mouse (Mus musculus)
Library ID:CNhs13036
Sample type:tissues
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueVisual cortex
dev stagepostnatal day 30
sexmale
ageP30
cell typemixed
cell lineN/A
companyN/A
collaborationMichela Fagiolini/Alka Saxena/Piero Carninci
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberN/A
catalog numberN/A
sample typeVisual cortex tissue
extraction protocol (Details)Total RNA Trizol Qiagen minElute

Accession numbers
MethodSample accession id
CAGE  SAMD00005545
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13036 CAGE DRX009138 DRR010012
Accession ID Mm9

Library idBAMCTSS
CNhs13036 DRZ001437 DRZ002820
Accession ID Mm10

Library idBAMCTSS
CNhs13036 DRZ012787 DRZ014170
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs13036

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.817
10 0
100 0
1000 0
1001 -0.0275
1002 -0.116
1003 0.146
1004 0
1005 0
1006 0.611
1007 -0.145
1008 0
1009 -0.15
101 -0.0855
1010 0
1011 0.926
1012 0.224
1013 0.304
1014 0.139
1015 -0.0136
1016 -0.293
1017 0
1018 0
1019 0
102 0
1020 0.568
1021 0
1022 -0.0704
1023 0
1024 0.0845
1025 0
1026 0
1027 0.521
1028 0
1029 0.0472
103 -0.0861
1030 0
1031 -0.489
1032 0.0404
1033 0
1034 0
1035 0
1036 -0.183
1037 0
1038 0.0728
1039 0.0167
104 0
1040 -0.466
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: CNhs13036
Jaspar motif P-value
MA0002.2 0.0132
MA0003.1 0.273
MA0004.1 0.562
MA0006.1 0.0891
MA0007.1 0.332
MA0009.1 0.794
MA0014.1 0.633
MA0017.1 5.96451e-7
MA0018.2 0.00378
MA0019.1 0.152
MA0024.1 0.0146
MA0025.1 0.179
MA0027.1 0.0416
MA0028.1 0.0457
MA0029.1 0.573
MA0030.1 0.307
MA0031.1 0.0193
MA0035.2 0.0348
MA0038.1 0.789
MA0039.2 0.00276
MA0040.1 0.0518
MA0041.1 0.453
MA0042.1 0.534
MA0043.1 0.41
MA0046.1 2.29168e-10
MA0047.2 2.86369e-4
MA0048.1 0.062
MA0050.1 6.00889e-5
MA0051.1 0.00208
MA0052.1 0.751
MA0055.1 0.0169
MA0057.1 0.552
MA0058.1 0.402
MA0059.1 0.321
MA0060.1 0.0201
MA0061.1 0.0331
MA0062.2 1.12357e-4
MA0065.2 3.88928e-6
MA0066.1 0.0853
MA0067.1 0.488
MA0068.1 0.336
MA0069.1 0.0886
MA0070.1 0.718
MA0071.1 0.0419
MA0072.1 0.291
MA0073.1 0.94
MA0074.1 0.132
MA0076.1 0.0807
MA0077.1 0.698
MA0078.1 0.999
MA0079.2 0.894
MA0080.2 1.45221e-10
MA0081.1 0.172
MA0083.1 0.00237
MA0084.1 0.488
MA0087.1 0.446
MA0088.1 0.324
MA0090.1 0.172
MA0091.1 0.331
MA0092.1 0.28
MA0093.1 0.581
MA0099.2 0.00175
MA0100.1 0.331
MA0101.1 0.00783
MA0102.2 0.284
MA0103.1 0.355
MA0104.2 0.881
MA0105.1 0.0576
MA0106.1 0.0687
MA0107.1 0.0186
MA0108.2 4.42869e-5
MA0111.1 0.859
MA0112.2 0.00206
MA0113.1 0.148
MA0114.1 6.02031e-6
MA0115.1 3.60278e-4
MA0116.1 0.171
MA0117.1 0.806
MA0119.1 0.114
MA0122.1 0.808
MA0124.1 0.884
MA0125.1 0.246
MA0131.1 0.778
MA0135.1 0.178
MA0136.1 3.22146e-12
MA0137.2 0.145
MA0138.2 0.00201
MA0139.1 0.578
MA0140.1 0.00246
MA0141.1 0.00204
MA0142.1 0.26
MA0143.1 0.879
MA0144.1 0.049
MA0145.1 0.0891
MA0146.1 0.0112
MA0147.1 0.959
MA0148.1 2.4784e-4
MA0149.1 0.302
MA0150.1 0.222
MA0152.1 0.826
MA0153.1 3.68464e-9
MA0154.1 0.0656
MA0155.1 0.403
MA0156.1 1.20027e-11
MA0157.1 0.0382
MA0159.1 0.00659
MA0160.1 0.00242
MA0162.1 0.191
MA0163.1 0.00419
MA0164.1 0.827
MA0258.1 0.0556
MA0259.1 0.757



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: CNhs13036
Novel motif P-value
1 0.434
10 0.115
100 0.406
101 0.554
102 0.935
103 0.183
104 0.872
105 0.616
106 0.0455
107 0.12
108 0.46
109 0.00251
11 0.103
110 0.0546
111 0.456
112 0.0134
113 0.366
114 0.689
115 0.896
116 0.28
117 0.00472
118 0.522
119 0.266
12 0.712
120 0.944
121 0.177
122 0.992
123 7.36134e-4
124 0.0354
125 0.877
126 0.025
127 0.444
128 0.0315
129 0.46
13 4.67443e-9
130 0.0296
131 0.36
132 0.556
133 0.401
134 0.119
135 0.294
136 0.00749
137 0.527
138 0.65
139 0.771
14 0.953
140 0.268
141 0.952
142 0.888
143 0.729
144 0.533
145 1.54892e-4
146 0.2
147 0.0972
148 0.515
149 0.58
15 0.358
150 0.0416
151 0.82
152 0.0662
153 0.863
154 0.937
155 0.283
156 4.71686e-10
157 0.209
158 0.23
159 0.882
160 0.249
161 0.0384
162 0.602
163 0.864
164 0.112
165 0.0866
166 0.547
167 0.243
168 0.744
169 0.00388
17 0.0675
18 0.806
19 0.0559
2 0.922
20 0.0629
21 0.287
22 0.0919
23 0.625
24 0.0199
25 0.952
26 4.58806e-7
27 0.475
28 0.671
29 0.0472
3 0.0681
30 0.887
31 0.915
32 0.845
33 0.257
34 0.405
35 0.455
36 0.594
37 0.021
38 0.311
39 0.213
4 0.177
40 0.133
41 0.684
42 0.175
43 0.138
44 0.808
45 0.559
46 0.266
47 0.527
48 0.348
49 0.394
5 0.462
50 0.145
51 0.758
52 0.163
53 0.603
54 0.97
55 0.973
56 0.514
57 0.894
58 0.471
59 0.127
6 0.957
60 0.0336
61 0.0341
62 0.392
63 0.134
64 0.69
65 0.266
66 0.489
67 0.976
68 0.245
69 0.219
7 0.014
70 0.458
71 0.0118
72 0.681
73 0.0237
74 0.952
75 0.0532
76 0.794
77 0.352
78 8.65183e-4
79 0.593
8 0.196
80 0.684
81 0.729
82 0.422
83 0.123
84 0.953
85 0.203
86 0.188
87 0.0275
88 0.486
89 0.922
9 0.346
90 0.625
91 0.33
92 0.64
93 0.819
94 0.811
95 0.0122
96 0.629
97 0.939
98 0.423
99 0.44



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: CNhs13036


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)
0000955 (brain)
0002021 (occipital lobe)
0000411 (visual cortex)
0000956 (cerebral cortex)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0001950 (neocortex)

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)
0011269 (mouse visual cortex from wildtype- 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


UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)