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FF:10243-104A9

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Name:visual cortex - wildtype
Species:Mouse (Mus musculus)
Library ID:CNhs13039
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 60-70
sexmale
ageP60-70
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  SAMD00004914
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13039 CAGE DRX009141 DRR010015
Accession ID Mm9

Library idBAMCTSS
CNhs13039 DRZ001440 DRZ002823
Accession ID Mm10

Library idBAMCTSS
CNhs13039 DRZ012790 DRZ014173
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

CNhs13039

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.834
10 0
100 0
1000 --0.0355
1001 0.0737
1002 --0.0873
1003 0.399
1004 0
1005 0
1006 0.668
1007 --0.174
1008 0
1009 --0.19
101 --0.104
1010 0
1011 0.884
1012 0.487
1013 0.092
1014 0
1015 --0.205
1016 --0.37
1017 0
1018 0
1019 0
102 0
1020 0.487
1021 0
1022 --0.0464
1023 0
1024 0
1025 0
1026 0
1027 0.261
1028 0
1029 0.126
103 --0.0848
1030 0
1031 --0.528
1032 0.125
1033 0
1034 0
1035 0
1036 --0.183
1037 0
1038 0.0983
1039 0.0942
104 0
1040 --0.134
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: CNhs13039

Jaspar motif P-value
MA0002.2 0.0239
MA0003.1 0.239
MA0004.1 0.614
MA0006.1 0.0955
MA0007.1 0.365
MA0009.1 0.824
MA0014.1 0.614
MA0017.1 6.06206e-7
MA0018.2 0.00207
MA0019.1 0.084
MA0024.1 0.0184
MA0025.1 0.0288
MA0027.1 0.0711
MA0028.1 0.0316
MA0029.1 0.8
MA0030.1 0.422
MA0031.1 0.0273
MA0035.2 0.0156
MA0038.1 0.454
MA0039.2 0.00224
MA0040.1 0.0475
MA0041.1 0.438
MA0042.1 0.416
MA0043.1 0.132
MA0046.1 9.4658e-11
MA0047.2 3.35562e-4
MA0048.1 0.0718
MA0050.1 5.64718e-6
MA0051.1 4.69052e-4
MA0052.1 0.676
MA0055.1 0.00975
MA0057.1 0.495
MA0058.1 0.38
MA0059.1 0.283
MA0060.1 0.00427
MA0061.1 0.0409
MA0062.2 1.28257e-4
MA0065.2 3.87464e-6
MA0066.1 0.0879
MA0067.1 0.394
MA0068.1 0.166
MA0069.1 0.0976
MA0070.1 0.957
MA0071.1 0.0621
MA0072.1 0.149
MA0073.1 0.81
MA0074.1 0.185
MA0076.1 0.0694
MA0077.1 0.928
MA0078.1 0.967
MA0079.2 0.924
MA0080.2 2.64054e-10
MA0081.1 0.175
MA0083.1 0.00186
MA0084.1 0.347
MA0087.1 0.682
MA0088.1 0.223
MA0090.1 0.174
MA0091.1 0.444
MA0092.1 0.285
MA0093.1 0.639
MA0099.2 0.00505
MA0100.1 0.313
MA0101.1 0.0104
MA0102.2 0.358
MA0103.1 0.458
MA0104.2 0.924
MA0105.1 0.0479
MA0106.1 0.0541
MA0107.1 0.0195
MA0108.2 6.18179e-6
MA0111.1 0.592
MA0112.2 0.00162
MA0113.1 0.129
MA0114.1 4.24064e-6
MA0115.1 4.38193e-4
MA0116.1 0.177
MA0117.1 0.751
MA0119.1 0.0808
MA0122.1 0.789
MA0124.1 0.89
MA0125.1 0.46
MA0131.1 0.669
MA0135.1 0.0966
MA0136.1 1.09683e-12
MA0137.2 0.128
MA0138.2 0.00883
MA0139.1 0.573
MA0140.1 0.00163
MA0141.1 0.00255
MA0142.1 0.379
MA0143.1 0.406
MA0144.1 0.11
MA0145.1 0.0975
MA0146.1 0.0108
MA0147.1 0.952
MA0148.1 2.75743e-4
MA0149.1 0.23
MA0150.1 0.177
MA0152.1 0.452
MA0153.1 5.12675e-10
MA0154.1 0.0765
MA0155.1 0.301
MA0156.1 7.41177e-12
MA0157.1 0.0288
MA0159.1 0.00858
MA0160.1 0.00535
MA0162.1 0.189
MA0163.1 0.00608
MA0164.1 0.841
MA0258.1 0.0547
MA0259.1 0.856



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: CNhs13039

Novel motif P-value
1 0.386
10 0.0881
100 0.483
101 0.467
102 0.978
103 0.0839
104 0.969
105 0.603
106 0.0677
107 0.258
108 0.351
109 0.00251
11 0.103
110 0.051
111 0.369
112 0.00969
113 0.399
114 0.748
115 0.922
116 0.245
117 0.00431
118 0.55
119 0.22
12 0.821
120 0.739
121 0.159
122 0.99
123 3.99086e-4
124 0.0289
125 0.528
126 0.0385
127 0.602
128 0.0747
129 0.306
13 5.06591e-9
130 0.0423
131 0.423
132 0.532
133 0.31
134 0.0645
135 0.298
136 0.0144
137 0.483
138 0.703
139 0.955
14 0.941
140 0.379
141 0.862
142 0.655
143 0.566
144 0.557
145 7.99265e-5
146 0.126
147 0.0755
148 0.56
149 0.537
15 0.293
150 0.0463
151 0.785
152 0.0681
153 0.989
154 0.852
155 0.331
156 0.127
157 0.192
158 0.351
159 0.354
160 0.242
161 0.107
162 0.623
163 0.907
164 0.145
165 0.0503
166 0.644
167 0.168
168 0.676
169 0.00476
17 0.074
18 0.7
19 0.0641
2 0.894
20 0.0443
21 0.258
22 0.0854
23 0.814
24 0.00747
25 0.906
26 2.27727e-7
27 0.446
28 0.631
29 0.0416
3 0.0516
30 0.979
31 0.754
32 0.793
33 0.232
34 0.493
35 0.42
36 0.419
37 0.0194
38 0.525
39 0.225
4 0.352
40 0.104
41 0.551
42 0.19
43 0.149
44 0.771
45 0.576
46 0.271
47 0.489
48 0.339
49 0.393
5 0.28
50 0.146
51 0.754
52 0.159
53 0.599
54 0.936
55 0.971
56 0.494
57 0.877
58 0.431
59 0.152
6 0.999
60 0.0309
61 0.0318
62 0.353
63 0.121
64 0.708
65 0.48
66 0.451
67 0.953
68 0.196
69 0.251
7 0.0143
70 0.45
71 0.00754
72 0.587
73 0.023
74 0.866
75 0.0558
76 0.844
77 0.38
78 0.00115
79 0.657
8 0.173
80 0.776
81 0.66
82 0.368
83 0.0472
84 0.967
85 0.21
86 0.204
87 0.0118
88 0.591
89 0.968
9 0.377
90 0.553
91 0.184
92 0.527
93 0.311
94 0.941
95 0.0173
96 0.633
97 0.921
98 0.608
99 0.417



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: CNhs13039


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)
0007023 (adult 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)
0000998 (adult tissue sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000315 (mouse neonate N60-70 sample)
0011270 (mouse visual cortex from wildtype- neonate N60-70 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)