Personal tools

Difference between revisions of "FF:10236-104A2"

From FANTOM5_SSTAR

Jump to: navigation, search
 
(One intermediate revision by the same user not shown)
Line 1: Line 1:
 
{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005835
 
|DRA_sample_Accession=CAGE@SAMD00005835
|accession_numbers=CAGE;DRX009133;DRR010007;DRZ001432;DRZ002815
+
|accession_numbers=CAGE;DRX009133;DRR010007;DRZ001432;DRZ002815;DRZ012782;DRZ014165
 
|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=
Line 49: Line 49:
 
|microRNAs=
 
|microRNAs=
 
|microRNAs_nn=
 
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;10236
+
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;10236
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;10236
+
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;10236
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N15%252c%2520donor2.CNhs13032.10236-104A2.mm10.nobarcode.bam
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N15%252c%2520donor2.CNhs13032.10236-104A2.mm10.nobarcode.bam
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N15%252c%2520donor2.CNhs13032.10236-104A2.mm10.nobarcode.ctss.bed.gz
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N15%252c%2520donor2.CNhs13032.10236-104A2.mm10.nobarcode.ctss.bed.gz

Latest revision as of 10:12, 10 August 2017


Name:visual cortex - wildtype
Species:Mouse (Mus musculus)
Library ID:CNhs13032
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  SAMD00005835
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13032 CAGE DRX009133 DRR010007
Accession ID Mm9

Library idBAMCTSS
CNhs13032 DRZ001432 DRZ002815
Accession ID Mm10

Library idBAMCTSS
CNhs13032 DRZ012782 DRZ014165
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

CNhs13032

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.815
10 0
100 0
1000 0.0919
1001 --0.00227
1002 --0.0941
1003 0.409
1004 0
1005 0
1006 0.603
1007 --0.164
1008 0
1009 --0.19
101 --0.0675
1010 0
1011 0.941
1012 0.651
1013 0.119
1014 0
1015 0.0837
1016 --0.0769
1017 0
1018 0
1019 0
102 0
1020 0.454
1021 0
1022 --0.124
1023 0
1024 --0.0899
1025 --0.0611
1026 0
1027 0.519
1028 0
1029 0.107
103 --0.0848
1030 0
1031 --0.627
1032 0.107
1033 0.137
1034 0
1035 0
1036 --0.183
1037 0
1038 --0.0774
1039 --0.02
104 0
1040 --0.457
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: CNhs13032

Jaspar motif P-value
MA0002.2 0.0281
MA0003.1 0.282
MA0004.1 0.515
MA0006.1 0.105
MA0007.1 0.432
MA0009.1 0.878
MA0014.1 0.526
MA0017.1 1.59959e-7
MA0018.2 0.00938
MA0019.1 0.132
MA0024.1 0.0292
MA0025.1 0.439
MA0027.1 0.104
MA0028.1 0.0295
MA0029.1 0.548
MA0030.1 0.427
MA0031.1 0.00547
MA0035.2 0.0151
MA0038.1 0.803
MA0039.2 0.00253
MA0040.1 0.0705
MA0041.1 0.264
MA0042.1 0.504
MA0043.1 0.668
MA0046.1 1.32485e-9
MA0047.2 2.93056e-4
MA0048.1 0.0526
MA0050.1 2.92095e-6
MA0051.1 1.35642e-4
MA0052.1 0.796
MA0055.1 0.00973
MA0057.1 0.491
MA0058.1 0.327
MA0059.1 0.254
MA0060.1 0.0377
MA0061.1 0.0657
MA0062.2 8.11293e-5
MA0065.2 7.78532e-7
MA0066.1 0.106
MA0067.1 0.61
MA0068.1 0.173
MA0069.1 0.124
MA0070.1 0.97
MA0071.1 0.0446
MA0072.1 0.115
MA0073.1 0.824
MA0074.1 0.164
MA0076.1 0.0617
MA0077.1 0.782
MA0078.1 0.958
MA0079.2 0.91
MA0080.2 1.31688e-10
MA0081.1 0.177
MA0083.1 7.4769e-4
MA0084.1 0.628
MA0087.1 0.711
MA0088.1 0.303
MA0090.1 0.14
MA0091.1 0.245
MA0092.1 0.265
MA0093.1 0.529
MA0099.2 6.06593e-4
MA0100.1 0.354
MA0101.1 0.0226
MA0102.2 0.17
MA0103.1 0.258
MA0104.2 0.936
MA0105.1 0.0951
MA0106.1 0.0809
MA0107.1 0.0512
MA0108.2 7.21059e-5
MA0111.1 0.693
MA0112.2 9.7593e-4
MA0113.1 0.244
MA0114.1 1.56758e-6
MA0115.1 1.54161e-4
MA0116.1 0.152
MA0117.1 0.785
MA0119.1 0.0981
MA0122.1 0.633
MA0124.1 0.947
MA0125.1 0.19
MA0131.1 0.76
MA0135.1 0.276
MA0136.1 7.48477e-12
MA0137.2 0.0877
MA0138.2 0.00476
MA0139.1 0.432
MA0140.1 0.00149
MA0141.1 0.00118
MA0142.1 0.301
MA0143.1 0.783
MA0144.1 0.0501
MA0145.1 0.0726
MA0146.1 0.00922
MA0147.1 0.988
MA0148.1 4.11275e-4
MA0149.1 0.33
MA0150.1 0.141
MA0152.1 0.83
MA0153.1 4.37855e-10
MA0154.1 0.0501
MA0155.1 0.313
MA0156.1 5.24508e-11
MA0157.1 0.00695
MA0159.1 0.00401
MA0160.1 0.00195
MA0162.1 0.182
MA0163.1 0.00473
MA0164.1 0.873
MA0258.1 0.0296
MA0259.1 0.827



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: CNhs13032

Novel motif P-value
1 0.37
10 0.104
100 0.428
101 0.35
102 0.793
103 0.198
104 0.977
105 0.493
106 0.0501
107 0.0966
108 0.406
109 0.00303
11 0.0749
110 0.0536
111 0.35
112 0.0111
113 0.362
114 0.615
115 0.919
116 0.303
117 0.0067
118 0.579
119 0.136
12 0.714
120 0.885
121 0.135
122 0.812
123 3.91669e-4
124 0.0423
125 0.973
126 0.024
127 0.557
128 0.0535
129 0.332
13 4.64296e-9
130 0.0363
131 0.412
132 0.467
133 0.335
134 0.0652
135 0.137
136 0.00363
137 0.694
138 0.669
139 0.948
14 0.752
140 0.205
141 0.954
142 0.908
143 0.583
144 0.563
145 1.62379e-4
146 0.211
147 0.0829
148 0.509
149 0.577
15 0.289
150 0.0359
151 0.746
152 0.0745
153 0.928
154 0.84
155 0.425
156 1.28279e-10
157 0.253
158 0.231
159 0.376
160 0.354
161 0.0655
162 0.6
163 0.988
164 0.0966
165 0.129
166 0.511
167 0.321
168 0.651
169 0.00321
17 0.0661
18 0.834
19 0.0535
2 0.96
20 0.0509
21 0.192
22 0.075
23 0.596
24 0.0214
25 0.882
26 4.94484e-7
27 0.585
28 0.638
29 0.0502
3 0.0601
30 0.976
31 0.795
32 0.783
33 0.209
34 0.488
35 0.46
36 0.549
37 0.0182
38 0.328
39 0.208
4 0.246
40 0.112
41 0.585
42 0.232
43 0.13
44 0.886
45 0.542
46 0.27
47 0.418
48 0.344
49 0.326
5 0.422
50 0.166
51 0.773
52 0.192
53 0.599
54 0.969
55 0.732
56 0.497
57 0.812
58 0.443
59 0.119
6 0.969
60 0.028
61 0.029
62 0.336
63 0.109
64 0.643
65 0.27
66 0.407
67 0.912
68 0.39
69 0.239
7 0.0122
70 0.309
71 0.0121
72 0.527
73 0.0224
74 0.755
75 0.0738
76 0.771
77 0.362
78 0.00333
79 0.581
8 0.214
80 0.543
81 0.635
82 0.501
83 0.0327
84 0.892
85 0.269
86 0.181
87 0.00734
88 0.5
89 0.815
9 0.388
90 0.49
91 0.289
92 0.615
93 0.437
94 0.838
95 0.0179
96 0.673
97 0.918
98 0.47
99 0.485



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: CNhs13032


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)