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|repeat_enrich_byfamily=0.146130584095924,0,0,0,0,0,0.118978214046109,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.219920079889023,0,0,0,0,0,0,0,0,0,0,0,0,0.411813430771597,-0.413759002288101,0,0,0,0,0,-0.13699083047786,0.105846527510721,0.159208774116547,-0.572397935706229,-0.0168759865998161,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0.039114937140418,0.144663790035931,0.527852360872609,0,0.0530820501022021,-0.310650657339386,0.417906242853869,-0.140687683267293,0,0,0.0343321647030315,-0.0355972074602148,0.144663790035931,0,0.0221313252912246,0.162839766198232,0.408045960402211,-0.0788315948399074,0,0,0,0,0,0,0.16172838040778,0.0277939780230736,0.120619503910173,0,0,0,0.339623005182409,0
 
|rna_box=124
 
|rna_box=124
 
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|rna_catalog_number=

Revision as of 01:50, 24 September 2012


Name:neurospheres - sympathetic neuron derived, biol_rep3
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companyNA
collaborationHideki Enomoto (RIKEN CDB)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numbersym3
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
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

CNhs13083

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.0786
10 0
100 0
1000 --0.0355
1001 --0.0749
1002 --0.115
1003 0.032
1004 0
1005 --0.123
1006 0.107
1007 --0.0872
1008 0
1009 0.0874
101 --0.00897
1010 0
1011 0.00247
1012 0
1013 --0.072
1014 --0.0851
1015 0.18
1016 0.297
1017 0
1018 0
1019 0
102 0
1020 0.253
1021 0
1022 --0.124
1023 0
1024 --0.0899
1025 --0.0161
1026 0.0198
1027 0.487
1028 0
1029 --0.0989
103 --0.0659
1030 0
1031 0.538
1032 0.018
1033 0.145
1034 0
1035 0
1036 --0.0624
1037 0
1038 0.0617
1039 --0.191
104 0
1040 0.244
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: CNhs13083

Jaspar motif P-value
MA0002.2 3.66323e-5
MA0003.1 0.0319
MA0004.1 0.991
MA0006.1 0.432
MA0007.1 0.462
MA0009.1 0.0363
MA0014.1 0.816
MA0017.1 4.03421e-5
MA0018.2 8.96482e-4
MA0019.1 0.591
MA0024.1 0.0567
MA0025.1 0.839
MA0027.1 0.424
MA0028.1 0.832
MA0029.1 0.258
MA0030.1 0.817
MA0031.1 0.453
MA0035.2 0.00164
MA0038.1 0.0617
MA0039.2 0.447
MA0040.1 0.608
MA0041.1 0.157
MA0042.1 0.498
MA0043.1 0.0136
MA0046.1 2.96645e-12
MA0047.2 0.00786
MA0048.1 0.481
MA0050.1 0.00524
MA0051.1 0.0376
MA0052.1 0.00506
MA0055.1 0.405
MA0057.1 0.273
MA0058.1 0.689
MA0059.1 0.205
MA0060.1 1.05038e-4
MA0061.1 0.0452
MA0062.2 0.775
MA0065.2 1.75186e-5
MA0066.1 0.146
MA0067.1 0.362
MA0068.1 0.424
MA0069.1 0.376
MA0070.1 0.00314
MA0071.1 0.271
MA0072.1 0.272
MA0073.1 0.865
MA0074.1 0.442
MA0076.1 0.529
MA0077.1 0.042
MA0078.1 0.353
MA0079.2 0.306
MA0080.2 5.16925e-9
MA0081.1 0.613
MA0083.1 0.919
MA0084.1 0.845
MA0087.1 0.663
MA0088.1 0.667
MA0090.1 0.668
MA0091.1 0.757
MA0092.1 0.903
MA0093.1 0.928
MA0099.2 0.915
MA0100.1 0.742
MA0101.1 0.249
MA0102.2 0.85
MA0103.1 8.83727e-4
MA0104.2 0.744
MA0105.1 1.8065e-4
MA0106.1 0.198
MA0107.1 0.116
MA0108.2 0.00315
MA0111.1 0.567
MA0112.2 4.29685e-6
MA0113.1 0.195
MA0114.1 8.29929e-5
MA0115.1 0.0311
MA0116.1 8.38088e-4
MA0117.1 0.783
MA0119.1 0.178
MA0122.1 0.911
MA0124.1 1
MA0125.1 0.0466
MA0131.1 0.589
MA0135.1 0.249
MA0136.1 7.36297e-6
MA0137.2 0.689
MA0138.2 0.519
MA0139.1 0.079
MA0140.1 5.29e-5
MA0141.1 0.00327
MA0142.1 0.132
MA0143.1 0.127
MA0144.1 0.371
MA0145.1 0.0998
MA0146.1 0.434
MA0147.1 0.488
MA0148.1 0.00601
MA0149.1 0.932
MA0150.1 0.14
MA0152.1 0.632
MA0153.1 3.53354e-11
MA0154.1 0.00294
MA0155.1 0.383
MA0156.1 0.00355
MA0157.1 0.167
MA0159.1 0.0839
MA0160.1 0.0531
MA0162.1 0.207
MA0163.1 6.25396e-4
MA0164.1 0.878
MA0258.1 0.00384
MA0259.1 0.968



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: CNhs13083

Novel motif P-value
1 0.0674
10 0.0405
100 0.857
101 0.959
102 0.9
103 0.114
104 0.944
105 0.158
106 0.03
107 0.14
108 0.95
109 0.028
11 0.102
110 0.117
111 0.003
112 0.0176
113 0.537
114 0.0675
115 0.432
116 0.377
117 0.273
118 0.427
119 0.0363
12 0.483
120 0.462
121 0.249
122 0.404
123 0.357
124 0.425
125 0.865
126 0.494
127 0.28
128 0.0523
129 0.219
13 0.0152
130 0.918
131 0.846
132 0.515
133 0.952
134 0.529
135 0.767
136 0.844
137 0.431
138 0.908
139 0.182
14 0.54
140 0.0209
141 0.212
142 0.568
143 0.906
144 0.939
145 0.202
146 0.521
147 0.853
148 0.694
149 0.14
15 0.0866
150 0.414
151 0.426
152 0.158
153 0.898
154 0.811
155 0.941
156 4.64134e-9
157 0.081
158 0.537
159 0.112
160 0.097
161 0.338
162 0.938
163 0.619
164 0.0856
165 0.359
166 0.72
167 0.545
168 0.751
169 0.01
17 0.0536
18 0.677
19 0.172
2 0.645
20 0.516
21 0.341
22 0.276
23 0.304
24 0.135
25 0.357
26 0.0142
27 0.27
28 0.431
29 0.232
3 0.0747
30 0.758
31 0.682
32 0.0637
33 0.257
34 0.368
35 0.636
36 0.3
37 0.044
38 0.239
39 0.321
4 0.511
40 0.407
41 0.727
42 0.23
43 0.167
44 0.131
45 0.448
46 0.183
47 0.15
48 0.104
49 0.116
5 0.165
50 0.503
51 0.587
52 0.381
53 0.542
54 0.66
55 0.618
56 0.599
57 0.45
58 0.138
59 0.0389
6 0.552
60 0.0861
61 0.188
62 0.0432
63 0.0859
64 0.431
65 0.129
66 0.726
67 0.778
68 0.428
69 0.764
7 0.0474
70 0.007
71 0.0892
72 0.288
73 0.189
74 0.992
75 0.136
76 0.567
77 0.207
78 0.0878
79 0.123
8 0.0651
80 0.947
81 0.627
82 0.0215
83 0.149
84 0.669
85 0.0842
86 0.373
87 0.592
88 0.605
89 0.0804
9 0.444
90 0.346
91 0.255
92 0.139
93 0.581
94 0.383
95 0.113
96 0.403
97 0.71
98 0.144
99 0.211



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: CNhs13083


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0000107 (autonomic neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000013 (sympathetic nervous system)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0002410 (autonomic nervous system)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0000010 (peripheral nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0011144 (mouse neurospheres - sympathetic neuron derived 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

CL:0000133 (neurectodermal cell)
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)