Personal tools

FF:10242-104A8

From FANTOM5_SSTAR

Jump to: navigation, search


Name:visual cortex - wildtype
Species:Mouse (Mus musculus)
Library ID:CNhs13038
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  SAMD00004869
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13038 CAGE DRX009140 DRR010014
Accession ID Mm9

Library idBAMCTSS
CNhs13038 DRZ001439 DRZ002822
Accession ID Mm10

Library idBAMCTSS
CNhs13038 DRZ012789 DRZ014172
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

CNhs13038

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.838
10 0
100 0
1000 0
1001 0.0345
1002 -0.116
1003 0.397
1004 0
1005 0
1006 0.62
1007 -0.246
1008 0
1009 -0.0938
101 -0.0304
1010 0
1011 0.938
1012 0.373
1013 0.186
1014 -0.0874
1015 -0.112
1016 -0.23
1017 0
1018 0
1019 0
102 0
1020 0.449
1021 0
1022 -0.0704
1023 0
1024 -0.0269
1025 -0.0194
1026 0
1027 0.388
1028 0
1029 0.273
103 -0.0848
1030 0
1031 -0.661
1032 0.196
1033 -0.0013
1034 0
1035 0
1036 -0.292
1037 0
1038 0.0919
1039 0.00256
104 0
1040 -0.139
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: CNhs13038
Jaspar motif P-value
MA0002.2 0.0187
MA0003.1 0.253
MA0004.1 0.573
MA0006.1 0.0852
MA0007.1 0.471
MA0009.1 0.984
MA0014.1 0.693
MA0017.1 9.53978e-7
MA0018.2 0.00112
MA0019.1 0.129
MA0024.1 0.0276
MA0025.1 0.0107
MA0027.1 0.0348
MA0028.1 0.0656
MA0029.1 0.814
MA0030.1 0.345
MA0031.1 0.024
MA0035.2 0.0129
MA0038.1 0.887
MA0039.2 0.00256
MA0040.1 0.0374
MA0041.1 0.336
MA0042.1 0.404
MA0043.1 0.139
MA0046.1 1.32877e-10
MA0047.2 3.48871e-4
MA0048.1 0.0488
MA0050.1 6.60438e-6
MA0051.1 0.00135
MA0052.1 0.966
MA0055.1 0.00731
MA0057.1 0.501
MA0058.1 0.327
MA0059.1 0.257
MA0060.1 0.0209
MA0061.1 0.0416
MA0062.2 4.24129e-4
MA0065.2 2.83918e-6
MA0066.1 0.0701
MA0067.1 0.288
MA0068.1 0.223
MA0069.1 0.138
MA0070.1 0.659
MA0071.1 0.0261
MA0072.1 0.0848
MA0073.1 0.839
MA0074.1 0.131
MA0076.1 0.136
MA0077.1 0.94
MA0078.1 0.978
MA0079.2 0.916
MA0080.2 1.31596e-10
MA0081.1 0.196
MA0083.1 0.00876
MA0084.1 0.229
MA0087.1 0.679
MA0088.1 0.27
MA0090.1 0.14
MA0091.1 0.231
MA0092.1 0.32
MA0093.1 0.588
MA0099.2 0.00565
MA0100.1 0.422
MA0101.1 0.0114
MA0102.2 0.208
MA0103.1 0.4
MA0104.2 0.913
MA0105.1 0.0582
MA0106.1 0.0449
MA0107.1 0.0232
MA0108.2 3.75612e-5
MA0111.1 0.669
MA0112.2 0.00231
MA0113.1 0.258
MA0114.1 2.64155e-6
MA0115.1 5.29622e-4
MA0116.1 0.132
MA0117.1 0.637
MA0119.1 0.0842
MA0122.1 0.678
MA0124.1 0.841
MA0125.1 0.319
MA0131.1 0.695
MA0135.1 0.23
MA0136.1 5.42514e-13
MA0137.2 0.305
MA0138.2 0.00278
MA0139.1 0.626
MA0140.1 0.00125
MA0141.1 0.00147
MA0142.1 0.356
MA0143.1 0.548
MA0144.1 0.119
MA0145.1 0.0903
MA0146.1 0.0112
MA0147.1 0.926
MA0148.1 1.59235e-4
MA0149.1 0.31
MA0150.1 0.319
MA0152.1 0.634
MA0153.1 5.34461e-10
MA0154.1 0.0543
MA0155.1 0.349
MA0156.1 5.55586e-11
MA0157.1 0.0542
MA0159.1 0.00625
MA0160.1 0.0042
MA0162.1 0.174
MA0163.1 0.00444
MA0164.1 0.965
MA0258.1 0.0417
MA0259.1 0.837



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: CNhs13038
Novel motif P-value
1 0.396
10 0.102
100 0.488
101 0.557
102 0.879
103 0.095
104 0.992
105 0.53
106 0.0664
107 0.142
108 0.439
109 0.00237
11 0.1
110 0.0615
111 0.57
112 0.0241
113 0.359
114 0.653
115 0.852
116 0.25
117 0.00477
118 0.556
119 0.308
12 0.761
120 0.741
121 0.194
122 0.876
123 8.76756e-4
124 0.014
125 0.342
126 0.0368
127 0.519
128 0.0611
129 0.402
13 8.33679e-9
130 0.0537
131 0.623
132 0.584
133 0.31
134 0.0758
135 0.483
136 0.00626
137 0.565
138 0.725
139 0.404
14 0.841
140 0.251
141 0.956
142 0.704
143 0.515
144 0.569
145 9.04384e-5
146 0.165
147 0.0908
148 0.391
149 0.506
15 0.267
150 0.0353
151 0.832
152 0.0701
153 0.947
154 0.885
155 0.411
156 0.0196
157 0.171
158 0.284
159 0.451
160 0.321
161 0.089
162 0.473
163 0.821
164 0.193
165 0.129
166 0.497
167 0.194
168 0.622
169 0.00566
17 0.0802
18 0.87
19 0.0526
2 0.841
20 0.0367
21 0.224
22 0.0923
23 0.755
24 0.00797
25 0.948
26 1.06538e-6
27 0.403
28 0.7
29 0.044
3 0.0523
30 0.959
31 0.82
32 0.779
33 0.241
34 0.391
35 0.497
36 0.601
37 0.0207
38 0.423
39 0.21
4 0.178
40 0.115
41 0.598
42 0.165
43 0.14
44 0.93
45 0.534
46 0.254
47 0.594
48 0.361
49 0.364
5 0.353
50 0.141
51 0.759
52 0.181
53 0.541
54 0.951
55 0.955
56 0.475
57 0.918
58 0.436
59 0.105
6 0.961
60 0.0385
61 0.0335
62 0.351
63 0.123
64 0.679
65 0.438
66 0.52
67 0.827
68 0.253
69 0.234
7 0.0181
70 0.372
71 0.0142
72 0.517
73 0.021
74 0.764
75 0.0529
76 0.845
77 0.278
78 0.00263
79 0.554
8 0.166
80 0.678
81 0.699
82 0.412
83 0.0251
84 0.861
85 0.173
86 0.215
87 0.0151
88 0.673
89 0.899
9 0.353
90 0.582
91 0.154
92 0.52
93 0.497
94 0.887
95 0.0162
96 0.605
97 0.836
98 0.342
99 0.475



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: CNhs13038


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)