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FF:10003-101A7

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Name:SABiosciences XpressRef Mouse Universal Total RNA, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs10611
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuewhole body
dev stageUNDEFINED
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companySABiosciences
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberA705103
catalog numberCat:GA-005
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005255
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10611 CAGE DRX008924 DRR009798
Accession ID Mm9

Library idBAMCTSS
CNhs10611 DRZ001223 DRZ002606
Accession ID Mm10

Library idBAMCTSS
CNhs10611 DRZ012573 DRZ013956
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

CNhs10611

MCL coexpression id Coexpression dpi cluster scores median value
0 0.153
1 0.0571
10 0.0571
100 0
1000 0.744
1001 0.11
1002 --0.0334
1003 0.131
1004 0
1005 0.131
1006 0.596
1007 --0.145
1008 1.177
1009 0.0974
101 --0.0481
1010 0
1011 0.206
1012 0
1013 0.22
1014 --0.0874
1015 --0.193
1016 --0.272
1017 0
1018 0.194
1019 0.297
102 0
1020 0
1021 0
1022 0.741
1023 0
1024 0.144
1025 0.236
1026 0.194
1027 0
1028 0
1029 --0.0685
103 0.123
1030 0.108
1031 --0.3
1032 0.174
1033 --0.0737
1034 0.269
1035 0
1036 --0.367
1037 0.108
1038 --0.11
1039 0.502
104 0
1040 --0.158
1041 0.451



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: CNhs10611

Jaspar motif P-value
MA0002.2 0.0556
MA0003.1 0.00892
MA0004.1 0.852
MA0006.1 0.279
MA0007.1 0.523
MA0009.1 0.162
MA0014.1 0.866
MA0017.1 2.24196e-10
MA0018.2 0.978
MA0019.1 0.903
MA0024.1 0.0125
MA0025.1 0.00948
MA0027.1 0.532
MA0028.1 0.0337
MA0029.1 0.446
MA0030.1 0.0262
MA0031.1 0.0268
MA0035.2 5.46371e-4
MA0038.1 0.901
MA0039.2 0.121
MA0040.1 0.0885
MA0041.1 0.264
MA0042.1 0.565
MA0043.1 0.378
MA0046.1 1.99647e-57
MA0047.2 6.87632e-4
MA0048.1 0.332
MA0050.1 0.344
MA0051.1 0.911
MA0052.1 4.35728e-7
MA0055.1 0.382
MA0057.1 0.255
MA0058.1 0.728
MA0059.1 0.795
MA0060.1 0.533
MA0061.1 0.806
MA0062.2 1.50984e-4
MA0065.2 2.17268e-10
MA0066.1 0.0906
MA0067.1 0.353
MA0068.1 0.683
MA0069.1 0.461
MA0070.1 0.966
MA0071.1 0.0398
MA0072.1 0.268
MA0073.1 0.848
MA0074.1 0.564
MA0076.1 0.00812
MA0077.1 0.832
MA0078.1 0.0537
MA0079.2 0.572
MA0080.2 0.165
MA0081.1 0.103
MA0083.1 0.217
MA0084.1 0.735
MA0087.1 0.922
MA0088.1 0.398
MA0090.1 0.112
MA0091.1 0.83
MA0092.1 0.338
MA0093.1 0.742
MA0099.2 0.509
MA0100.1 0.0415
MA0101.1 0.296
MA0102.2 0.955
MA0103.1 0.0203
MA0104.2 0.96
MA0105.1 0.157
MA0106.1 0.863
MA0107.1 0.228
MA0108.2 8.75735e-18
MA0111.1 0.413
MA0112.2 3.11231e-6
MA0113.1 0.393
MA0114.1 3.83557e-10
MA0115.1 6.07712e-7
MA0116.1 0.0351
MA0117.1 0.883
MA0119.1 0.0557
MA0122.1 0.636
MA0124.1 0.488
MA0125.1 0.433
MA0131.1 0.429
MA0135.1 0.624
MA0136.1 0.0191
MA0137.2 0.334
MA0138.2 1.7811e-4
MA0139.1 0.153
MA0140.1 0.0411
MA0141.1 2.92985e-4
MA0142.1 0.525
MA0143.1 0.0883
MA0144.1 0.638
MA0145.1 0.0186
MA0146.1 0.121
MA0147.1 0.871
MA0148.1 0.00108
MA0149.1 0.182
MA0150.1 0.0598
MA0152.1 0.138
MA0153.1 1.08698e-33
MA0154.1 0.0101
MA0155.1 0.206
MA0156.1 0.00361
MA0157.1 0.13
MA0159.1 0.00464
MA0160.1 1.75553e-5
MA0162.1 0.117
MA0163.1 0.001
MA0164.1 0.746
MA0258.1 1.009e-4
MA0259.1 0.304



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: CNhs10611

Novel motif P-value
1 0.177
10 0.534
100 0.724
101 0.138
102 0.797
103 0.27
104 0.368
105 0.475
106 0.0836
107 0.147
108 0.989
109 0.0937
11 0.128
110 0.228
111 0.255
112 0.0753
113 0.598
114 0.08
115 0.628
116 0.0657
117 0.76
118 0.708
119 0.0623
12 0.599
120 0.611
121 0.0711
122 0.447
123 0.743
124 0.78
125 0.741
126 0.437
127 0.865
128 0.167
129 0.681
13 0.14
130 0.639
131 0.217
132 0.588
133 0.556
134 0.916
135 0.507
136 0.211
137 0.784
138 0.989
139 0.0577
14 0.314
140 0.966
141 0.43
142 0.991
143 0.926
144 0.847
145 0.276
146 0.16
147 0.874
148 0.96
149 0.268
15 0.318
150 0.448
151 0.303
152 0.12
153 0.596
154 0.647
155 0.873
156 1.16178e-4
157 0.607
158 0.351
159 0.476
160 0.405
161 0.717
162 0.441
163 0.842
164 0.606
165 0.199
166 0.477
167 0.303
168 0.239
169 0.00211
17 0.129
18 0.98
19 0.0768
2 0.34
20 0.547
21 0.66
22 0.147
23 0.153
24 0.0518
25 0.427
26 0.308
27 0.53
28 0.389
29 0.521
3 0.213
30 0.32
31 0.27
32 0.0213
33 0.64
34 0.302
35 0.527
36 0.436
37 0.133
38 0.41
39 0.388
4 0.601
40 0.0997
41 0.0295
42 0.512
43 0.206
44 0.0191
45 0.248
46 0.234
47 0.148
48 0.186
49 0.27
5 0.481
50 0.624
51 0.553
52 0.2
53 0.662
54 0.401
55 0.951
56 0.495
57 0.975
58 0.237
59 0.0169
6 0.663
60 0.15
61 0.853
62 0.115
63 0.105
64 0.437
65 0.22
66 0.604
67 0.589
68 0.478
69 0.514
7 0.271
70 0.0449
71 0.205
72 0.273
73 0.178
74 0.409
75 0.251
76 0.369
77 0.0615
78 0.558
79 0.366
8 0.018
80 0.265
81 0.435
82 0.045
83 0.232
84 0.104
85 0.0185
86 0.31
87 0.0196
88 0.36
89 0.0467
9 0.541
90 0.401
91 0.249
92 0.283
93 0.689
94 0.855
95 0.211
96 0.404
97 0.121
98 0.421
99 0.101



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: CNhs10611


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
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