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FF:10001-101A3

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Name:Clontech Mouse Universal Reference Total RNA, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs10609
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
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number8092682
catalog numberCat:636657
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005443
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10609 CAGE DRX008920 DRR009794
Accession ID Mm9

Library idBAMCTSS
CNhs10609 DRZ001219 DRZ002602
Accession ID Mm10

Library idBAMCTSS
CNhs10609 DRZ012569 DRZ013952
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
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Relative expression to median (log10)


Transcription factors with enriched expression in this sample
Ranked 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 sample
Ranked 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

CNhs10609

MCL coexpression id Coexpression dpi cluster scores median value
0 0.715
1 0.323
10 0
100 0
1000 0.0652
1001 0.0244
1002 -0.0343
1003 -0.00177
1004 0.236
1005 0.0354
1006 0.259
1007 0.0894
1008 0
1009 0.168
101 -0.0613
1010 0.0354
1011 0.692
1012 0.0682
1013 0.0807
1014 -0.0851
1015 0.122
1016 -0.0769
1017 0
1018 0.0682
1019 0.0354
102 0
1020 0
1021 0
1022 0.217
1023 0
1024 0.233
1025 0.373
1026 0.581
1027 0.131
1028 0.0354
1029 -0.0307
103 0.00251
1030 0
1031 -0.0963
1032 0.053
1033 0.0322
1034 0.125
1035 0.247
1036 -0.238
1037 0
1038 0.0329
1039 0.179
104 0
1040 0.082
1041 0.225



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs10609
Jaspar motif P-value
MA0002.2 0.26
MA0003.1 0.159
MA0004.1 0.81
MA0006.1 0.0516
MA0007.1 0.746
MA0009.1 0.309
MA0014.1 0.913
MA0017.1 0.592
MA0018.2 2.88425e-14
MA0019.1 0.0969
MA0024.1 0.346
MA0025.1 0.00866
MA0027.1 0.0693
MA0028.1 0.0117
MA0029.1 0.672
MA0030.1 0.374
MA0031.1 0.913
MA0035.2 0.00266
MA0038.1 0.375
MA0039.2 0.468
MA0040.1 0.279
MA0041.1 0.0618
MA0042.1 0.353
MA0043.1 0.00211
MA0046.1 0.00346
MA0047.2 0.265
MA0048.1 0.835
MA0050.1 0.0197
MA0051.1 0.967
MA0052.1 0.0616
MA0055.1 0.0454
MA0057.1 0.364
MA0058.1 0.897
MA0059.1 0.478
MA0060.1 6.26947e-5
MA0061.1 2.34811e-4
MA0062.2 1.0206e-5
MA0065.2 0.523
MA0066.1 0.411
MA0067.1 0.411
MA0068.1 0.222
MA0069.1 0.197
MA0070.1 0.97
MA0071.1 0.755
MA0072.1 0.27
MA0073.1 0.942
MA0074.1 0.547
MA0076.1 0.0668
MA0077.1 5.72116e-5
MA0078.1 8.26167e-10
MA0079.2 0.686
MA0080.2 1.44718e-5
MA0081.1 0.00323
MA0083.1 0.387
MA0084.1 0.554
MA0087.1 0.0301
MA0088.1 0.402
MA0090.1 0.143
MA0091.1 0.994
MA0092.1 0.0993
MA0093.1 0.941
MA0099.2 0.134
MA0100.1 2.94888e-22
MA0101.1 0.00555
MA0102.2 0.495
MA0103.1 0.166
MA0104.2 4.70328e-4
MA0105.1 2.07987e-7
MA0106.1 1.70295e-4
MA0107.1 0.00145
MA0108.2 0.821
MA0111.1 0.0386
MA0112.2 0.0726
MA0113.1 0.611
MA0114.1 0.301
MA0115.1 0.917
MA0116.1 0.0201
MA0117.1 0.95
MA0119.1 0.341
MA0122.1 0.666
MA0124.1 0.619
MA0125.1 0.453
MA0131.1 0.492
MA0135.1 0.793
MA0136.1 2.5896e-5
MA0137.2 0.101
MA0138.2 0.37
MA0139.1 0.432
MA0140.1 3.39424e-7
MA0141.1 0.335
MA0142.1 0.498
MA0143.1 3.38138e-4
MA0144.1 0.227
MA0145.1 0.18
MA0146.1 0.0203
MA0147.1 0.00513
MA0148.1 0.133
MA0149.1 0.491
MA0150.1 0.659
MA0152.1 0.0808
MA0153.1 0.151
MA0154.1 0.0539
MA0155.1 0.244
MA0156.1 1.22068e-6
MA0157.1 0.381
MA0159.1 0.543
MA0160.1 0.0011
MA0162.1 0.582
MA0163.1 0.363
MA0164.1 0.726
MA0258.1 0.499
MA0259.1 0.16



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs10609
Novel motif P-value
1 0.915
10 0.389
100 0.308
101 0.3
102 0.353
103 0.547
104 0.899
105 0.929
106 0.00252
107 0.0468
108 0.449
109 0.947
11 0.656
110 0.689
111 0.862
112 0.497
113 0.856
114 0.395
115 0.904
116 0.917
117 0.514
118 0.551
119 0.667
12 0.867
120 0.657
121 0.0271
122 0.615
123 0.371
124 0.855
125 0.735
126 0.924
127 0.202
128 0.0167
129 0.444
13 0.00371
130 0.934
131 0.824
132 0.683
133 0.423
134 0.969
135 0.1
136 0.00394
137 0.385
138 0.989
139 0.333
14 0.649
140 0.064
141 0.142
142 0.727
143 0.529
144 0.27
145 0.834
146 0.199
147 0.368
148 0.298
149 0.389
15 0.671
150 0.803
151 0.372
152 0.521
153 0.806
154 0.315
155 0.462
156 1.84924e-5
157 0.987
158 1.38689e-5
159 0.0548
160 0.0135
161 0.23
162 0.48
163 0.733
164 0.49
165 0.477
166 0.471
167 0.639
168 0.791
169 0.543
17 0.49
18 0.473
19 0.426
2 0.074
20 0.275
21 0.531
22 0.949
23 0.499
24 0.0694
25 0.438
26 0.0485
27 0.0435
28 0.459
29 0.848
3 0.322
30 0.825
31 0.414
32 0.737
33 0.618
34 0.225
35 0.665
36 0.335
37 0.0688
38 0.73
39 0.497
4 0.992
40 0.0822
41 5.29361e-4
42 0.497
43 0.29
44 0.767
45 0.734
46 0.312
47 0.0627
48 0.245
49 0.815
5 0.347
50 0.578
51 0.656
52 0.662
53 0.983
54 0.489
55 0.807
56 0.157
57 0.48
58 0.402
59 0.5
6 0.756
60 0.347
61 0.345
62 0.6
63 0.578
64 0.691
65 0.527
66 0.152
67 0.257
68 0.785
69 0.425
7 0.442
70 0.814
71 0.00348
72 0.329
73 0.243
74 0.786
75 0.17
76 0.4
77 0.748
78 2.14088e-6
79 0.963
8 0.016
80 0.533
81 0.301
82 0.916
83 0.658
84 0.682
85 0.891
86 0.287
87 0.00114
88 0.282
89 0.874
9 0.971
90 0.629
91 0.52
92 0.518
93 0.683
94 0.418
95 0.9
96 0.774
97 0.154
98 0.956
99 0.912



de novo motifs identified by HOMER in promoters active in this sample
Summary:The result of HOMER in this sample is shown.
Analyst:NA

library id: CNhs10609


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)

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