Personal tools

FF:10349-105D7

From FANTOM5_SSTAR

Revision as of 07:35, 17 October 2013 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:visual cortex - wildtype, neonate N15, donor5
Species:Mouse (Mus musculus)
Library ID:CNhs13820
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueVisual cortex
dev stagepostnatal day 15
sexmale
ageP15
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  DRS008998
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13820 CAGE DRX009135 DRR010009
Accession ID Mm9

Library idBAMCTSS
CNhs13820 DRZ001434 DRZ002817
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs13820

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.823
10 0
100 0.0307
1000 0.0287
1001 0.0534
1002 --0.0804
1003 0.468
1004 0.0689
1005 0.0894
1006 0.565
1007 --0.193
1008 0
1009 --0.193
101 --0.104
1010 0
1011 0.89
1012 0.51
1013 0.109
1014 0.0689
1015 --0.053
1016 --0.031
1017 0
1018 0
1019 0
102 0
1020 0.835
1021 0
1022 --0.0704
1023 0
1024 --0.0113
1025 0
1026 0
1027 0.345
1028 0
1029 0.0444
103 --0.0788
1030 0
1031 --0.547
1032 0.115
1033 0.105
1034 0
1035 0
1036 --0.111
1037 0
1038 0.0388
1039 0.0887
104 0
1040 --0.39
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: CNhs13820

Jaspar motif P-value
MA0002.2 0.00343
MA0003.1 0.216
MA0004.1 0.55
MA0006.1 0.105
MA0007.1 0.482
MA0009.1 0.64
MA0014.1 0.621
MA0017.1 5.22257e-7
MA0018.2 0.0189
MA0019.1 0.076
MA0024.1 0.0679
MA0025.1 0.884
MA0027.1 0.0626
MA0028.1 0.0429
MA0029.1 0.779
MA0030.1 0.22
MA0031.1 0.0112
MA0035.2 0.0139
MA0038.1 0.599
MA0039.2 0.00286
MA0040.1 0.0415
MA0041.1 0.543
MA0042.1 0.667
MA0043.1 0.607
MA0046.1 7.46245e-11
MA0047.2 4.17909e-4
MA0048.1 0.166
MA0050.1 0.00109
MA0051.1 0.00925
MA0052.1 0.443
MA0055.1 0.0352
MA0057.1 0.375
MA0058.1 0.339
MA0059.1 0.346
MA0060.1 0.0503
MA0061.1 0.0572
MA0062.2 1.71301e-4
MA0065.2 3.36869e-7
MA0066.1 0.0811
MA0067.1 0.533
MA0068.1 0.59
MA0069.1 0.0752
MA0070.1 0.758
MA0071.1 0.0436
MA0072.1 0.155
MA0073.1 0.836
MA0074.1 0.134
MA0076.1 0.0842
MA0077.1 0.949
MA0078.1 0.719
MA0079.2 0.997
MA0080.2 3.51128e-10
MA0081.1 0.156
MA0083.1 0.00771
MA0084.1 0.836
MA0087.1 0.429
MA0088.1 0.263
MA0090.1 0.0469
MA0091.1 0.301
MA0092.1 0.339
MA0093.1 0.554
MA0099.2 9.70758e-5
MA0100.1 0.285
MA0101.1 0.0363
MA0102.2 0.384
MA0103.1 0.19
MA0104.2 0.948
MA0105.1 0.0608
MA0106.1 0.0938
MA0107.1 0.0604
MA0108.2 8.90945e-4
MA0111.1 0.799
MA0112.2 0.00108
MA0113.1 0.221
MA0114.1 1.65753e-6
MA0115.1 6.38924e-5
MA0116.1 0.116
MA0117.1 0.834
MA0119.1 0.114
MA0122.1 0.812
MA0124.1 0.85
MA0125.1 0.501
MA0131.1 0.93
MA0135.1 0.129
MA0136.1 8.6103e-10
MA0137.2 0.223
MA0138.2 0.00718
MA0139.1 0.452
MA0140.1 4.94393e-4
MA0141.1 0.0012
MA0142.1 0.372
MA0143.1 0.514
MA0144.1 0.097
MA0145.1 0.0512
MA0146.1 0.0119
MA0147.1 0.982
MA0148.1 9.16556e-4
MA0149.1 0.351
MA0150.1 0.0684
MA0152.1 0.397
MA0153.1 2.80728e-11
MA0154.1 0.0358
MA0155.1 0.298
MA0156.1 1.09515e-10
MA0157.1 0.0425
MA0159.1 0.00246
MA0160.1 0.00123
MA0162.1 0.183
MA0163.1 0.00363
MA0164.1 0.659
MA0258.1 0.0359
MA0259.1 0.694



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: CNhs13820

Novel motif P-value
1 0.363
10 0.137
100 0.53
101 0.74
102 0.943
103 0.0991
104 0.957
105 0.436
106 0.079
107 0.152
108 0.565
109 0.00372
11 0.102
110 0.0662
111 0.479
112 0.0125
113 0.519
114 0.468
115 0.761
116 0.391
117 0.00746
118 0.516
119 0.0874
12 0.605
120 0.887
121 0.0472
122 0.783
123 0.0145
124 0.129
125 0.858
126 0.0329
127 0.576
128 0.0595
129 0.37
13 1.10358e-7
130 0.0695
131 0.245
132 0.569
133 0.259
134 0.127
135 0.589
136 0.00752
137 0.549
138 0.859
139 0.708
14 0.647
140 0.694
141 0.737
142 0.833
143 0.515
144 0.58
145 0.00116
146 0.126
147 0.0974
148 0.711
149 0.279
15 0.182
150 0.0528
151 0.663
152 0.0979
153 0.996
154 0.743
155 0.415
156 6.98886e-32
157 0.264
158 0.135
159 0.754
160 0.302
161 0.0526
162 0.718
163 0.67
164 0.133
165 0.185
166 0.642
167 0.236
168 0.389
169 0.00375
17 0.0738
18 0.995
19 0.0634
2 0.766
20 0.165
21 0.31
22 0.0693
23 0.297
24 0.00632
25 0.785
26 4.31847e-6
27 0.745
28 0.612
29 0.0627
3 0.0652
30 0.838
31 0.826
32 0.771
33 0.2
34 0.468
35 0.63
36 0.594
37 0.0201
38 0.177
39 0.354
4 0.155
40 0.123
41 0.417
42 0.208
43 0.137
44 0.541
45 0.466
46 0.263
47 0.423
48 0.329
49 0.32
5 0.518
50 0.197
51 0.682
52 0.172
53 0.87
54 0.887
55 0.979
56 0.45
57 0.814
58 0.301
59 0.0874
6 0.961
60 0.0267
61 0.0606
62 0.237
63 0.117
64 0.615
65 0.151
66 0.563
67 0.715
68 0.321
69 0.214
7 0.0129
70 0.336
71 0.0182
72 0.349
73 0.0305
74 0.682
75 0.0627
76 0.989
77 0.252
78 0.00175
79 0.606
8 0.287
80 0.867
81 0.897
82 0.285
83 0.0458
84 0.579
85 0.152
86 0.165
87 0.00584
88 0.501
89 0.711
9 0.315
90 0.636
91 0.44
92 0.497
93 0.531
94 0.872
95 0.0237
96 0.452
97 0.932
98 0.254
99 0.499



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: CNhs13820


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)

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)