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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005460
 
|DRA_sample_Accession=CAGE@SAMD00005460
|accession_numbers=CAGE;DRX009134;DRR010008;DRZ001433;DRZ002816
+
|accession_numbers=CAGE;DRX009134;DRR010008;DRZ001433;DRZ002816;DRZ012783;DRZ014166
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0002021,UBERON:0000411,UBERON:0000956,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0002619,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002780,UBERON:0002020,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203,UBERON:0001950
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0002021,UBERON:0000411,UBERON:0000956,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0002619,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002780,UBERON:0002020,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203,UBERON:0001950
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_cell_lineage_facet=

Latest revision as of 10:12, 10 August 2017


Name:visual cortex - wildtype
Species:Mouse (Mus musculus)
Library ID:CNhs13033
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 15
sexmale
ageP15
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  SAMD00005460
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13033 CAGE DRX009134 DRR010008
Accession ID Mm9

Library idBAMCTSS
CNhs13033 DRZ001433 DRZ002816
Accession ID Mm10

Library idBAMCTSS
CNhs13033 DRZ012783 DRZ014166
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

CNhs13033

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.809
10 0
100 0
1000 0.0342
1001 --0.00595
1002 --0.0468
1003 0.44
1004 0
1005 0
1006 0.666
1007 --0.259
1008 0
1009 --0.177
101 --0.0768
1010 0
1011 0.842
1012 0.587
1013 0.0876
1014 0
1015 --0.113
1016 --0.134
1017 0
1018 0
1019 0
102 0
1020 0.434
1021 0
1022 --0.0704
1023 0
1024 --0.0899
1025 0
1026 0
1027 0.197
1028 0
1029 0.252
103 --0.0848
1030 0
1031 --0.403
1032 0.144
1033 0
1034 0
1035 0
1036 --0.183
1037 0
1038 --0.0391
1039 0.0123
104 0
1040 --0.484
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: CNhs13033

Jaspar motif P-value
MA0002.2 0.0264
MA0003.1 0.246
MA0004.1 0.528
MA0006.1 0.0956
MA0007.1 0.305
MA0009.1 0.879
MA0014.1 0.605
MA0017.1 1.89415e-7
MA0018.2 0.00771
MA0019.1 0.109
MA0024.1 0.0336
MA0025.1 0.375
MA0027.1 0.0448
MA0028.1 0.0275
MA0029.1 0.539
MA0030.1 0.37
MA0031.1 0.0161
MA0035.2 0.0102
MA0038.1 0.714
MA0039.2 0.00224
MA0040.1 0.0605
MA0041.1 0.393
MA0042.1 0.587
MA0043.1 0.763
MA0046.1 3.86586e-10
MA0047.2 2.53641e-4
MA0048.1 0.0568
MA0050.1 1.40012e-5
MA0051.1 7.68255e-4
MA0052.1 0.997
MA0055.1 0.00837
MA0057.1 0.471
MA0058.1 0.305
MA0059.1 0.295
MA0060.1 0.0617
MA0061.1 0.0557
MA0062.2 3.3502e-5
MA0065.2 1.4145e-6
MA0066.1 0.163
MA0067.1 0.601
MA0068.1 0.22
MA0069.1 0.145
MA0070.1 0.977
MA0071.1 0.0404
MA0072.1 0.109
MA0073.1 0.826
MA0074.1 0.104
MA0076.1 0.0443
MA0077.1 0.77
MA0078.1 0.974
MA0079.2 0.823
MA0080.2 2.01646e-10
MA0081.1 0.234
MA0083.1 0.00221
MA0084.1 0.614
MA0087.1 0.572
MA0088.1 0.331
MA0090.1 0.14
MA0091.1 0.338
MA0092.1 0.298
MA0093.1 0.514
MA0099.2 3.67271e-4
MA0100.1 0.378
MA0101.1 0.0167
MA0102.2 0.214
MA0103.1 0.271
MA0104.2 0.886
MA0105.1 0.0916
MA0106.1 0.0792
MA0107.1 0.0431
MA0108.2 1.54453e-4
MA0111.1 0.766
MA0112.2 0.00104
MA0113.1 0.169
MA0114.1 3.14022e-6
MA0115.1 2.83795e-4
MA0116.1 0.163
MA0117.1 0.738
MA0119.1 0.115
MA0122.1 0.511
MA0124.1 0.962
MA0125.1 0.267
MA0131.1 0.808
MA0135.1 0.148
MA0136.1 1.38507e-11
MA0137.2 0.0615
MA0138.2 0.00328
MA0139.1 0.391
MA0140.1 0.0017
MA0141.1 5.7324e-4
MA0142.1 0.227
MA0143.1 0.789
MA0144.1 0.0404
MA0145.1 0.0693
MA0146.1 0.00912
MA0147.1 0.934
MA0148.1 5.68554e-4
MA0149.1 0.5
MA0150.1 0.118
MA0152.1 0.954
MA0153.1 4.45823e-10
MA0154.1 0.061
MA0155.1 0.331
MA0156.1 2.24336e-11
MA0157.1 0.0229
MA0159.1 0.0048
MA0160.1 0.00366
MA0162.1 0.181
MA0163.1 0.00392
MA0164.1 0.772
MA0258.1 0.0473
MA0259.1 0.758



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: CNhs13033

Novel motif P-value
1 0.352
10 0.123
100 0.476
101 0.52
102 0.821
103 0.198
104 0.949
105 0.55
106 0.0478
107 0.16
108 0.492
109 0.00232
11 0.104
110 0.0699
111 0.451
112 0.0191
113 0.308
114 0.602
115 0.794
116 0.336
117 0.00675
118 0.526
119 0.189
12 0.579
120 0.912
121 0.144
122 0.949
123 0.00125
124 0.0342
125 0.978
126 0.0431
127 0.684
128 0.052
129 0.432
13 6.9781e-9
130 0.0337
131 0.447
132 0.51
133 0.366
134 0.0842
135 0.234
136 0.0014
137 0.547
138 0.694
139 0.988
14 0.755
140 0.283
141 0.659
142 0.935
143 0.581
144 0.666
145 6.91146e-4
146 0.255
147 0.107
148 0.759
149 0.567
15 0.289
150 0.0352
151 0.748
152 0.0632
153 0.721
154 0.911
155 0.5
156 1.20876e-14
157 0.27
158 0.375
159 0.216
160 0.343
161 0.0669
162 0.602
163 0.787
164 0.098
165 0.21
166 0.656
167 0.217
168 0.578
169 0.00369
17 0.0506
18 0.821
19 0.0628
2 0.975
20 0.0588
21 0.231
22 0.0783
23 0.648
24 0.0131
25 0.958
26 8.84069e-7
27 0.59
28 0.639
29 0.0487
3 0.0525
30 0.927
31 0.767
32 0.873
33 0.187
34 0.473
35 0.497
36 0.617
37 0.0155
38 0.332
39 0.224
4 0.214
40 0.105
41 0.61
42 0.198
43 0.121
44 0.899
45 0.541
46 0.246
47 0.527
48 0.432
49 0.324
5 0.458
50 0.149
51 0.723
52 0.168
53 0.654
54 0.918
55 0.858
56 0.452
57 0.848
58 0.412
59 0.132
6 0.981
60 0.0263
61 0.0421
62 0.367
63 0.123
64 0.674
65 0.263
66 0.494
67 0.822
68 0.275
69 0.309
7 0.0195
70 0.458
71 0.0102
72 0.518
73 0.0164
74 0.571
75 0.0646
76 0.693
77 0.345
78 0.00316
79 0.661
8 0.22
80 0.971
81 0.553
82 0.413
83 0.03
84 0.827
85 0.248
86 0.162
87 0.00253
88 0.453
89 0.945
9 0.354
90 0.525
91 0.406
92 0.547
93 0.658
94 0.776
95 0.0166
96 0.572
97 0.932
98 0.534
99 0.411



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: CNhs13033


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)
0000316 (mouse neonate N15 sample)
0011268 (mouse visual cortex from wildtype- neonate N15 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)