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FF:10241-104A7

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Name:visual cortex - wildtype
Species:Mouse (Mus musculus)
Library ID:CNhs13037
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  SAMD00005563
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13037 CAGE DRX009139 DRR010013
Accession ID Mm9

Library idBAMCTSS
CNhs13037 DRZ001438 DRZ002821
Accession ID Mm10

Library idBAMCTSS
CNhs13037 DRZ012788 DRZ014171
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

CNhs13037

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.836
10 0
100 0
1000 0
1001 0.0395
1002 -0.0639
1003 0.287
1004 0
1005 0
1006 0.598
1007 -0.101
1008 0
1009 -0.19
101 -0.0853
1010 0
1011 0.864
1012 0.279
1013 0.169
1014 -0.0874
1015 -0.0569
1016 -0.126
1017 0
1018 0
1019 0
102 0
1020 0.447
1021 0
1022 -0.0704
1023 0
1024 -0.0899
1025 0
1026 0
1027 0.33
1028 0
1029 0.164
103 -0.0829
1030 0
1031 -0.54
1032 0.188
1033 -0.00214
1034 0
1035 0
1036 -0.183
1037 0
1038 0.0222
1039 0.025
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: CNhs13037
Jaspar motif P-value
MA0002.2 0.0138
MA0003.1 0.251
MA0004.1 0.51
MA0006.1 0.0859
MA0007.1 0.472
MA0009.1 0.783
MA0014.1 0.687
MA0017.1 7.82949e-7
MA0018.2 0.00273
MA0019.1 0.0938
MA0024.1 0.0223
MA0025.1 0.0225
MA0027.1 0.0673
MA0028.1 0.0592
MA0029.1 0.933
MA0030.1 0.401
MA0031.1 0.0326
MA0035.2 0.0202
MA0038.1 0.727
MA0039.2 0.00242
MA0040.1 0.0568
MA0041.1 0.354
MA0042.1 0.496
MA0043.1 0.303
MA0046.1 8.07743e-11
MA0047.2 7.48377e-4
MA0048.1 0.0546
MA0050.1 2.7057e-5
MA0051.1 6.47204e-4
MA0052.1 0.945
MA0055.1 0.00718
MA0057.1 0.469
MA0058.1 0.302
MA0059.1 0.263
MA0060.1 0.029
MA0061.1 0.0453
MA0062.2 3.05115e-4
MA0065.2 1.75335e-6
MA0066.1 0.104
MA0067.1 0.495
MA0068.1 0.248
MA0069.1 0.0608
MA0070.1 0.921
MA0071.1 0.0555
MA0072.1 0.199
MA0073.1 0.785
MA0074.1 0.123
MA0076.1 0.113
MA0077.1 0.858
MA0078.1 0.969
MA0079.2 0.966
MA0080.2 2.90366e-10
MA0081.1 0.238
MA0083.1 0.00597
MA0084.1 0.475
MA0087.1 0.558
MA0088.1 0.32
MA0090.1 0.223
MA0091.1 0.295
MA0092.1 0.241
MA0093.1 0.51
MA0099.2 0.00263
MA0100.1 0.401
MA0101.1 0.00952
MA0102.2 0.175
MA0103.1 0.403
MA0104.2 0.889
MA0105.1 0.0601
MA0106.1 0.0521
MA0107.1 0.0234
MA0108.2 6.07477e-6
MA0111.1 0.748
MA0112.2 0.00201
MA0113.1 0.26
MA0114.1 2.27965e-6
MA0115.1 3.39321e-4
MA0116.1 0.179
MA0117.1 0.79
MA0119.1 0.164
MA0122.1 0.595
MA0124.1 0.859
MA0125.1 0.253
MA0131.1 0.723
MA0135.1 0.23
MA0136.1 1.82808e-12
MA0137.2 0.194
MA0138.2 9.50974e-4
MA0139.1 0.493
MA0140.1 0.00144
MA0141.1 0.00328
MA0142.1 0.388
MA0143.1 0.509
MA0144.1 0.0866
MA0145.1 0.0824
MA0146.1 0.00924
MA0147.1 0.882
MA0148.1 2.67634e-4
MA0149.1 0.301
MA0150.1 0.198
MA0152.1 0.987
MA0153.1 2.19889e-12
MA0154.1 0.0813
MA0155.1 0.36
MA0156.1 1.08325e-10
MA0157.1 0.037
MA0159.1 0.00897
MA0160.1 0.00469
MA0162.1 0.184
MA0163.1 0.00541
MA0164.1 0.735
MA0258.1 0.0479
MA0259.1 0.773



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: CNhs13037
Novel motif P-value
1 0.303
10 0.0994
100 0.447
101 0.521
102 0.922
103 0.153
104 0.901
105 0.59
106 0.0574
107 0.19
108 0.476
109 0.00257
11 0.104
110 0.0622
111 0.523
112 0.0138
113 0.37
114 0.843
115 0.814
116 0.35
117 0.00491
118 0.548
119 0.216
12 0.751
120 0.753
121 0.16
122 0.958
123 9.70657e-4
124 0.043
125 0.736
126 0.0449
127 0.483
128 0.0483
129 0.364
13 4.25523e-9
130 0.0305
131 0.502
132 0.433
133 0.192
134 0.0757
135 0.399
136 0.00704
137 0.498
138 0.533
139 0.489
14 0.881
140 0.37
141 0.861
142 0.886
143 0.556
144 0.648
145 1.33291e-4
146 0.184
147 0.113
148 0.464
149 0.504
15 0.251
150 0.0519
151 0.827
152 0.0664
153 0.773
154 0.909
155 0.42
156 1.33485e-6
157 0.195
158 0.232
159 0.4
160 0.285
161 0.0846
162 0.5
163 0.983
164 0.107
165 0.118
166 0.661
167 0.195
168 0.577
169 0.00502
17 0.0705
18 0.858
19 0.0564
2 0.855
20 0.051
21 0.153
22 0.0879
23 0.702
24 0.0141
25 0.881
26 1.62361e-6
27 0.452
28 0.639
29 0.0387
3 0.0558
30 0.996
31 0.821
32 0.79
33 0.232
34 0.432
35 0.482
36 0.578
37 0.018
38 0.41
39 0.26
4 0.155
40 0.116
41 0.586
42 0.187
43 0.138
44 0.844
45 0.528
46 0.232
47 0.558
48 0.365
49 0.381
5 0.43
50 0.155
51 0.816
52 0.174
53 0.642
54 0.92
55 0.811
56 0.493
57 0.86
58 0.398
59 0.134
6 0.928
60 0.0397
61 0.0344
62 0.345
63 0.129
64 0.651
65 0.39
66 0.476
67 0.765
68 0.53
69 0.127
7 0.0154
70 0.383
71 0.0124
72 0.522
73 0.0177
74 0.969
75 0.0542
76 0.756
77 0.368
78 0.00262
79 0.35
8 0.151
80 0.758
81 0.834
82 0.427
83 0.0185
84 0.982
85 0.231
86 0.194
87 0.0165
88 0.559
89 0.976
9 0.363
90 0.456
91 0.146
92 0.423
93 0.371
94 0.87
95 0.0126
96 0.47
97 0.838
98 0.364
99 0.51



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: CNhs13037


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)