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FF:10238-104A4

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Name:visual cortex - wildtype
Species:Mouse (Mus musculus)
Library ID:CNhs13034
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  SAMD00005503
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13034 CAGE DRX009136 DRR010010
Accession ID Mm9

Library idBAMCTSS
CNhs13034 DRZ001435 DRZ002818
Accession ID Mm10

Library idBAMCTSS
CNhs13034 DRZ012785 DRZ014168
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

CNhs13034

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.813
10 0
100 0
1000 --0.0355
1001 --0.0595
1002 --0.116
1003 0.289
1004 0
1005 0
1006 0.74
1007 --0.231
1008 0
1009 --0.19
101 --0.0876
1010 0
1011 0.995
1012 0.375
1013 0.158
1014 --0.0874
1015 --0.192
1016 --0.379
1017 0
1018 0
1019 0
102 0
1020 0.618
1021 0
1022 0
1023 0
1024 --0.14
1025 --0.0611
1026 0
1027 0.396
1028 0
1029 0.128
103 --0.0848
1030 0
1031 --0.684
1032 0.195
1033 0
1034 0
1035 0
1036 --0.183
1037 0
1038 0.0022
1039 0.0697
104 0
1040 --0.279
1041 0



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: CNhs13034

Jaspar motif P-value
MA0002.2 0.0112
MA0003.1 0.314
MA0004.1 0.567
MA0006.1 0.0988
MA0007.1 0.388
MA0009.1 0.923
MA0014.1 0.691
MA0017.1 5.12468e-7
MA0018.2 0.003
MA0019.1 0.161
MA0024.1 0.0321
MA0025.1 0.0108
MA0027.1 0.137
MA0028.1 0.0735
MA0029.1 0.805
MA0030.1 0.532
MA0031.1 0.0534
MA0035.2 0.00852
MA0038.1 0.925
MA0039.2 0.00378
MA0040.1 0.075
MA0041.1 0.115
MA0042.1 0.282
MA0043.1 0.121
MA0046.1 9.71351e-9
MA0047.2 2.20919e-4
MA0048.1 0.0454
MA0050.1 1.10185e-5
MA0051.1 0.00363
MA0052.1 0.403
MA0055.1 0.00969
MA0057.1 0.45
MA0058.1 0.434
MA0059.1 0.323
MA0060.1 0.0574
MA0061.1 0.0364
MA0062.2 0.00105
MA0065.2 2.96916e-6
MA0066.1 0.0584
MA0067.1 0.465
MA0068.1 0.253
MA0069.1 0.0426
MA0070.1 0.929
MA0071.1 0.0887
MA0072.1 0.354
MA0073.1 0.851
MA0074.1 0.156
MA0076.1 0.155
MA0077.1 0.538
MA0078.1 0.91
MA0079.2 0.977
MA0080.2 1.33197e-10
MA0081.1 0.212
MA0083.1 0.00304
MA0084.1 0.892
MA0087.1 0.311
MA0088.1 0.298
MA0090.1 0.221
MA0091.1 0.21
MA0092.1 0.29
MA0093.1 0.578
MA0099.2 0.00454
MA0100.1 0.42
MA0101.1 0.0137
MA0102.2 0.27
MA0103.1 0.411
MA0104.2 0.864
MA0105.1 0.036
MA0106.1 0.0535
MA0107.1 0.023
MA0108.2 1.04482e-4
MA0111.1 0.66
MA0112.2 9.75766e-4
MA0113.1 0.207
MA0114.1 4.35608e-6
MA0115.1 1.57509e-4
MA0116.1 0.13
MA0117.1 0.764
MA0119.1 0.114
MA0122.1 0.426
MA0124.1 0.798
MA0125.1 0.444
MA0131.1 0.707
MA0135.1 0.455
MA0136.1 1.15175e-11
MA0137.2 0.192
MA0138.2 0.00278
MA0139.1 0.53
MA0140.1 4.81602e-4
MA0141.1 0.00263
MA0142.1 0.385
MA0143.1 0.642
MA0144.1 0.127
MA0145.1 0.0883
MA0146.1 0.00993
MA0147.1 0.887
MA0148.1 1.50989e-4
MA0149.1 0.42
MA0150.1 0.281
MA0152.1 0.562
MA0153.1 3.29286e-9
MA0154.1 0.049
MA0155.1 0.342
MA0156.1 7.55339e-10
MA0157.1 0.0347
MA0159.1 0.0134
MA0160.1 0.00697
MA0162.1 0.197
MA0163.1 0.00645
MA0164.1 0.988
MA0258.1 0.0328
MA0259.1 0.816



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: CNhs13034

Novel motif P-value
1 0.36
10 0.0946
100 0.418
101 0.579
102 0.889
103 0.164
104 0.791
105 0.682
106 0.0518
107 0.141
108 0.381
109 0.00276
11 0.0988
110 0.0461
111 0.403
112 0.00603
113 0.337
114 0.615
115 0.934
116 0.293
117 0.00459
118 0.517
119 0.306
12 0.83
120 0.785
121 0.158
122 0.992
123 0.00211
124 0.0187
125 0.662
126 0.0626
127 0.422
128 0.0332
129 0.231
13 9.79521e-9
130 0.0603
131 0.529
132 0.55
133 0.5
134 0.056
135 0.307
136 0.0427
137 0.539
138 0.649
139 0.994
14 0.944
140 0.217
141 0.929
142 0.894
143 0.699
144 0.568
145 5.03722e-5
146 0.186
147 0.113
148 0.403
149 0.467
15 0.261
150 0.0367
151 0.822
152 0.067
153 0.96
154 0.94
155 0.431
156 0.00218
157 0.134
158 0.124
159 0.907
160 0.237
161 0.12
162 0.574
163 0.921
164 0.127
165 0.227
166 0.464
167 0.367
168 0.438
169 0.00336
17 0.0591
18 0.816
19 0.0558
2 0.923
20 0.0446
21 0.273
22 0.0843
23 0.671
24 0.0165
25 0.993
26 1.96553e-6
27 0.458
28 0.655
29 0.0305
3 0.0509
30 0.933
31 0.854
32 0.888
33 0.28
34 0.493
35 0.523
36 0.522
37 0.0186
38 0.438
39 0.188
4 0.16
40 0.188
41 0.741
42 0.171
43 0.135
44 0.738
45 0.567
46 0.227
47 0.5
48 0.358
49 0.313
5 0.308
50 0.136
51 0.817
52 0.156
53 0.603
54 0.95
55 0.955
56 0.512
57 0.813
58 0.367
59 0.124
6 0.966
60 0.0362
61 0.0379
62 0.324
63 0.113
64 0.624
65 0.449
66 0.476
67 0.643
68 0.192
69 0.142
7 0.0175
70 0.485
71 0.0132
72 0.675
73 0.025
74 0.895
75 0.0593
76 0.702
77 0.373
78 0.00227
79 0.417
8 0.167
80 0.712
81 0.719
82 0.485
83 0.0597
84 0.97
85 0.235
86 0.199
87 0.0549
88 0.572
89 0.959
9 0.35
90 0.415
91 0.208
92 0.604
93 0.284
94 0.932
95 0.0192
96 0.5
97 0.932
98 0.367
99 0.563



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: CNhs13034


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)