Personal tools

FF:10008-101B6

From FANTOM5_SSTAR

Jump to: navigation, search


Name:Universal RNA - Mouse Normal Tissues Biochain, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs10613
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainBalb/C
tissuewhole body
dev stage6-8 weeks old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB307206
catalog numberCat:R4334566-1
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004898
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10613 CAGE DRX008925 DRR009799
Accession ID Mm9

Library idBAMCTSS
CNhs10613 DRZ001224 DRZ002607
Accession ID Mm10

Library idBAMCTSS
CNhs10613 DRZ012574 DRZ013957
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

CNhs10613

MCL coexpression id Coexpression dpi cluster scores median value
0 0.196
1 0.047
10 0
100 0
1000 0.163
1001 --0.0121
1002 --0.0475
1003 0.00475
1004 0
1005 0.261
1006 0.252
1007 --0.0772
1008 1.686
1009 0.0312
101 --0.0509
1010 0
1011 0.0975
1012 0
1013 0.349
1014 --0.0851
1015 --0.237
1016 --0.251
1017 0
1018 0.227
1019 0.047
102 0
1020 0
1021 --0.00173
1022 0.439
1023 0
1024 0.0834
1025 0.246
1026 0.255
1027 0.0141
1028 0
1029 --0.0678
103 --0.03
1030 0.047
1031 --0.325
1032 0.174
1033 0.0141
1034 0.395
1035 0.047
1036 --0.272
1037 0.128
1038 --0.0576
1039 0.423
104 0.047
1040 --0.126
1041 0.353



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: CNhs10613

Jaspar motif P-value
MA0002.2 0.0871
MA0003.1 0.0227
MA0004.1 0.817
MA0006.1 0.255
MA0007.1 0.0366
MA0009.1 0.264
MA0014.1 0.617
MA0017.1 2.23801e-19
MA0018.2 0.819
MA0019.1 0.941
MA0024.1 0.0065
MA0025.1 0.0225
MA0027.1 0.186
MA0028.1 0.0665
MA0029.1 0.577
MA0030.1 0.035
MA0031.1 0.0166
MA0035.2 0.0282
MA0038.1 0.594
MA0039.2 0.087
MA0040.1 0.0943
MA0041.1 0.291
MA0042.1 0.719
MA0043.1 0.371
MA0046.1 1.05311e-86
MA0047.2 2.05608e-4
MA0048.1 0.902
MA0050.1 0.495
MA0051.1 0.162
MA0052.1 0.363
MA0055.1 0.94
MA0057.1 0.367
MA0058.1 0.964
MA0059.1 0.448
MA0060.1 0.327
MA0061.1 0.923
MA0062.2 0.00122
MA0065.2 3.06091e-16
MA0066.1 0.104
MA0067.1 0.413
MA0068.1 0.81
MA0069.1 0.499
MA0070.1 0.857
MA0071.1 0.0476
MA0072.1 0.563
MA0073.1 0.965
MA0074.1 0.373
MA0076.1 0.0183
MA0077.1 0.937
MA0078.1 0.0499
MA0079.2 0.261
MA0080.2 0.771
MA0081.1 0.0469
MA0083.1 0.737
MA0084.1 0.73
MA0087.1 0.948
MA0088.1 0.638
MA0090.1 0.176
MA0091.1 0.84
MA0092.1 0.334
MA0093.1 0.959
MA0099.2 0.84
MA0100.1 5.62472e-4
MA0101.1 0.292
MA0102.2 0.841
MA0103.1 0.00259
MA0104.2 0.714
MA0105.1 0.232
MA0106.1 0.948
MA0107.1 0.173
MA0108.2 9.36828e-5
MA0111.1 0.412
MA0112.2 2.3113e-6
MA0113.1 0.123
MA0114.1 4.07977e-19
MA0115.1 2.63916e-12
MA0116.1 0.102
MA0117.1 0.782
MA0119.1 0.0234
MA0122.1 0.998
MA0124.1 0.332
MA0125.1 0.195
MA0131.1 0.555
MA0135.1 0.7
MA0136.1 0.174
MA0137.2 0.7
MA0138.2 0.0153
MA0139.1 0.274
MA0140.1 0.413
MA0141.1 8.21654e-5
MA0142.1 0.805
MA0143.1 0.127
MA0144.1 0.5
MA0145.1 0.0251
MA0146.1 0.0411
MA0147.1 0.71
MA0148.1 1.01109e-4
MA0149.1 0.168
MA0150.1 0.125
MA0152.1 0.689
MA0153.1 4.56784e-52
MA0154.1 0.0365
MA0155.1 0.388
MA0156.1 0.0557
MA0157.1 0.0683
MA0159.1 0.00336
MA0160.1 9.37665e-6
MA0162.1 0.195
MA0163.1 0.00111
MA0164.1 0.629
MA0258.1 1.17331e-4
MA0259.1 0.588



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: CNhs10613

Novel motif P-value
1 0.148
10 0.367
100 0.541
101 0.304
102 0.598
103 0.163
104 0.345
105 0.608
106 0.0365
107 0.0696
108 0.769
109 0.0937
11 0.112
110 0.149
111 0.143
112 0.0194
113 0.638
114 0.0265
115 0.523
116 0.159
117 0.381
118 0.436
119 0.126
12 0.756
120 0.588
121 0.0966
122 0.461
123 0.636
124 0.974
125 0.902
126 0.225
127 0.794
128 0.0775
129 0.701
13 0.0263
130 0.908
131 0.409
132 0.362
133 0.447
134 0.93
135 0.372
136 0.143
137 0.949
138 0.855
139 0.0513
14 0.549
140 0.962
141 0.747
142 0.908
143 0.837
144 0.929
145 0.0897
146 0.204
147 0.477
148 0.982
149 0.47
15 0.172
150 0.232
151 0.322
152 0.0902
153 0.856
154 0.811
155 0.823
156 7.11735e-11
157 0.564
158 0.243
159 0.334
160 0.472
161 0.383
162 0.248
163 0.93
164 0.369
165 0.617
166 0.516
167 0.993
168 0.539
169 6.68224e-4
17 0.071
18 0.866
19 0.0566
2 0.52
20 0.978
21 0.651
22 0.146
23 0.26
24 0.0563
25 0.424
26 0.0772
27 0.699
28 0.333
29 0.332
3 0.179
30 0.474
31 0.363
32 0.0385
33 0.447
34 0.47
35 0.322
36 0.18
37 0.128
38 0.69
39 0.332
4 0.829
40 0.0802
41 0.0195
42 0.518
43 0.151
44 0.0708
45 0.297
46 0.191
47 0.14
48 0.137
49 0.164
5 0.266
50 0.67
51 0.536
52 0.159
53 0.99
54 0.496
55 0.764
56 0.6
57 0.944
58 0.204
59 0.0835
6 0.897
60 0.102
61 0.642
62 0.0971
63 0.11
64 0.476
65 0.441
66 0.795
67 0.164
68 0.189
69 0.981
7 0.198
70 0.0464
71 0.162
72 0.36
73 0.16
74 0.323
75 0.107
76 0.707
77 0.108
78 0.525
79 0.728
8 0.00662
80 0.491
81 0.829
82 0.0408
83 0.209
84 0.183
85 0.0257
86 0.22
87 0.0152
88 0.643
89 0.117
9 0.702
90 0.236
91 0.217
92 0.177
93 0.923
94 0.901
95 0.21
96 0.484
97 0.0779
98 0.337
99 0.0921



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: CNhs10613


FANTOM5 (FF) ontology


Direct parent terms

has_quality relathionship
PATO:0000461

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
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000343 (control treatment 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

NA