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FF:10239-104A5

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Name:visual cortex - wildtype
Species:Mouse (Mus musculus)
Library ID:CNhs13035
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  SAMD00005946
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13035 CAGE DRX009137 DRR010011
Accession ID Mm9

Library idBAMCTSS
CNhs13035 DRZ001436 DRZ002819
Accession ID Mm10

Library idBAMCTSS
CNhs13035 DRZ012786 DRZ014169
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

CNhs13035

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.848
10 0
100 0
1000 0
1001 0
1002 -0.0941
1003 0.337
1004 0
1005 -0.0389
1006 0.677
1007 -0.228
1008 0
1009 -0.19
101 -0.111
1010 0
1011 1.06
1012 0.244
1013 0.127
1014 -0.0851
1015 -0.0585
1016 -0.337
1017 0
1018 0
1019 0
102 0
1020 0.604
1021 0
1022 -0.0704
1023 0
1024 -0.0899
1025 0
1026 0
1027 0.497
1028 0
1029 0.0615
103 -0.0848
1030 0
1031 -0.627
1032 0.0829
1033 0
1034 0
1035 0
1036 -0.183
1037 0
1038 -0.0337
1039 0.0616
104 0
1040 -0.216
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: CNhs13035
Jaspar motif P-value
MA0002.2 0.0133
MA0003.1 0.293
MA0004.1 0.564
MA0006.1 0.0941
MA0007.1 0.344
MA0009.1 0.667
MA0014.1 0.738
MA0017.1 4.56049e-7
MA0018.2 0.017
MA0019.1 0.172
MA0024.1 0.0163
MA0025.1 0.0797
MA0027.1 0.0707
MA0028.1 0.0415
MA0029.1 0.521
MA0030.1 0.501
MA0031.1 0.0256
MA0035.2 0.0181
MA0038.1 0.606
MA0039.2 0.00215
MA0040.1 0.073
MA0041.1 0.298
MA0042.1 0.437
MA0043.1 0.384
MA0046.1 2.79799e-10
MA0047.2 8.10748e-4
MA0048.1 0.0454
MA0050.1 9.27572e-6
MA0051.1 7.1989e-4
MA0052.1 0.856
MA0055.1 0.0106
MA0057.1 0.594
MA0058.1 0.388
MA0059.1 0.309
MA0060.1 0.0261
MA0061.1 0.0307
MA0062.2 1.4104e-4
MA0065.2 4.91823e-6
MA0066.1 0.15
MA0067.1 0.539
MA0068.1 0.199
MA0069.1 0.0462
MA0070.1 0.952
MA0071.1 0.0434
MA0072.1 0.243
MA0073.1 0.873
MA0074.1 0.132
MA0076.1 0.0774
MA0077.1 0.575
MA0078.1 0.926
MA0079.2 0.93
MA0080.2 1.27549e-10
MA0081.1 0.212
MA0083.1 3.4634e-4
MA0084.1 0.561
MA0087.1 0.54
MA0088.1 0.343
MA0090.1 0.131
MA0091.1 0.367
MA0092.1 0.254
MA0093.1 0.585
MA0099.2 0.00503
MA0100.1 0.338
MA0101.1 0.00712
MA0102.2 0.269
MA0103.1 0.388
MA0104.2 0.914
MA0105.1 0.0419
MA0106.1 0.0887
MA0107.1 0.0155
MA0108.2 1.21104e-5
MA0111.1 0.738
MA0112.2 0.00268
MA0113.1 0.255
MA0114.1 5.8289e-6
MA0115.1 7.7563e-4
MA0116.1 0.178
MA0117.1 0.788
MA0119.1 0.143
MA0122.1 0.765
MA0124.1 0.824
MA0125.1 0.27
MA0131.1 0.74
MA0135.1 0.318
MA0136.1 5.25452e-12
MA0137.2 0.169
MA0138.2 0.0015
MA0139.1 0.562
MA0140.1 8.18981e-4
MA0141.1 0.00325
MA0142.1 0.594
MA0143.1 0.493
MA0144.1 0.111
MA0145.1 0.0933
MA0146.1 0.0127
MA0147.1 0.966
MA0148.1 4.38299e-4
MA0149.1 0.376
MA0150.1 0.281
MA0152.1 0.898
MA0153.1 3.67898e-10
MA0154.1 0.0609
MA0155.1 0.309
MA0156.1 6.50832e-11
MA0157.1 0.0526
MA0159.1 0.0179
MA0160.1 0.00693
MA0162.1 0.199
MA0163.1 0.00724
MA0164.1 0.913
MA0258.1 0.0735
MA0259.1 0.735



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: CNhs13035
Novel motif P-value
1 0.403
10 0.084
100 0.52
101 0.442
102 0.935
103 0.278
104 0.909
105 0.536
106 0.0409
107 0.138
108 0.361
109 0.00211
11 0.0938
110 0.0558
111 0.485
112 0.0169
113 0.345
114 0.74
115 0.821
116 0.388
117 0.00508
118 0.687
119 0.191
12 0.864
120 0.846
121 0.0475
122 0.967
123 5.75021e-4
124 0.026
125 0.741
126 0.0474
127 0.661
128 0.066
129 0.442
13 6.10764e-9
130 0.0296
131 0.509
132 0.735
133 0.36
134 0.0482
135 0.529
136 0.00813
137 0.483
138 0.682
139 0.692
14 0.784
140 0.323
141 0.991
142 0.959
143 0.637
144 0.487
145 5.84465e-5
146 0.174
147 0.0992
148 0.533
149 0.342
15 0.33
150 0.0353
151 0.877
152 0.062
153 0.957
154 0.992
155 0.355
156 3.04106e-9
157 0.163
158 0.322
159 0.657
160 0.319
161 0.0708
162 0.611
163 0.738
164 0.0779
165 0.135
166 0.696
167 0.248
168 0.568
169 0.00411
17 0.0643
18 0.776
19 0.0684
2 0.846
20 0.0426
21 0.26
22 0.0761
23 0.675
24 0.00941
25 0.972
26 1.82929e-6
27 0.379
28 0.706
29 0.0277
3 0.0562
30 0.913
31 0.857
32 0.763
33 0.195
34 0.427
35 0.409
36 0.492
37 0.0175
38 0.353
39 0.203
4 0.178
40 0.126
41 0.517
42 0.197
43 0.148
44 0.966
45 0.557
46 0.232
47 0.574
48 0.319
49 0.349
5 0.446
50 0.152
51 0.786
52 0.172
53 0.57
54 0.973
55 0.992
56 0.466
57 0.978
58 0.399
59 0.135
6 0.87
60 0.0348
61 0.0437
62 0.285
63 0.135
64 0.696
65 0.304
66 0.494
67 0.957
68 0.396
69 0.218
7 0.0195
70 0.433
71 0.00775
72 0.404
73 0.0218
74 0.44
75 0.0543
76 0.744
77 0.417
78 0.00149
79 0.389
8 0.149
80 0.691
81 0.746
82 0.372
83 0.0317
84 0.792
85 0.268
86 0.212
87 0.0155
88 0.558
89 0.922
9 0.366
90 0.963
91 0.169
92 0.461
93 0.554
94 0.983
95 0.0169
96 0.594
97 0.829
98 0.476
99 0.53



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: CNhs13035


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)