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FF:11299-117B3

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Name:Mouse Aortic Smooth Muscle cells, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs11297
Sample type:primary cells
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samplessRNA samples)
Excluding candidate novel miRNAs(CAGE samplessRNA samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainBalb/c
tissueaorta
dev stageNA
sexunknown
ageU
cell typesmooth muscle cell
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004682
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11297 CAGE DRX008805 DRR009677
Accession ID Mm9

Library idBAMCTSS
CNhs11297 DRZ001102 DRZ002487
Accession ID Mm10

Library idBAMCTSS
CNhs11297 DRZ012452 DRZ013837
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00004682
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10002.CGATGT sRNA-Seq DRX037375 DRR041741
Accession ID Mm9

Library idBAMCTSS
SRhi10002.CGATGT DRZ007350


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

CNhs11297

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.00112
1001 0.0559
1002 0.633
1003 0.0979
1004 0
1005 0
1006 -0.214
1007 -0.00561
1008 0
1009 0.702
101 0.0513
1010 0
1011 -0.264
1012 0
1013 0.252
1014 -0.0851
1015 0.0802
1016 0.153
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 -0.0761
1023 0
1024 -0.117
1025 0
1026 0
1027 -0.048
1028 0.634
1029 0.0199
103 0.266
1030 0
1031 0.377
1032 0.0402
1033 0.0606
1034 0
1035 0
1036 0.0563
1037 0
1038 0.0889
1039 -0.0737
104 0
1040 0.585
1041 0



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: CNhs11297
Jaspar motif P-value
MA0002.2 0.555
MA0003.1 0.685
MA0004.1 0.00299
MA0006.1 0.786
MA0007.1 0.354
MA0009.1 0.0513
MA0014.1 0.0512
MA0017.1 0.00277
MA0018.2 0.898
MA0019.1 0.707
MA0024.1 0.0262
MA0025.1 0.0549
MA0027.1 0.138
MA0028.1 9.8713e-5
MA0029.1 0.699
MA0030.1 0.608
MA0031.1 0.281
MA0035.2 1.47799e-5
MA0038.1 0.0438
MA0039.2 0.67
MA0040.1 0.209
MA0041.1 0.354
MA0042.1 0.405
MA0043.1 0.746
MA0046.1 2.99033e-9
MA0047.2 0.00195
MA0048.1 4.10366e-4
MA0050.1 0.393
MA0051.1 0.698
MA0052.1 0.00468
MA0055.1 1.16674e-4
MA0057.1 0.546
MA0058.1 1.02113e-5
MA0059.1 0.0771
MA0060.1 5.02851e-7
MA0061.1 0.515
MA0062.2 8.7272e-5
MA0065.2 0.0211
MA0066.1 0.587
MA0067.1 0.522
MA0068.1 0.0211
MA0069.1 0.841
MA0070.1 0.878
MA0071.1 0.642
MA0072.1 0.921
MA0073.1 0.594
MA0074.1 0.822
MA0076.1 4.85851e-4
MA0077.1 0.283
MA0078.1 0.852
MA0079.2 0.114
MA0080.2 8.2785e-4
MA0081.1 0.506
MA0083.1 0.0164
MA0084.1 0.611
MA0087.1 0.561
MA0088.1 0.0847
MA0090.1 0.0244
MA0091.1 0.586
MA0092.1 0.416
MA0093.1 0.00206
MA0099.2 4.19667e-7
MA0100.1 0.273
MA0101.1 0.136
MA0102.2 0.454
MA0103.1 2.9454e-7
MA0104.2 0.415
MA0105.1 0.647
MA0106.1 1.6617e-5
MA0107.1 0.336
MA0108.2 1.33902e-5
MA0111.1 0.314
MA0112.2 0.34
MA0113.1 0.748
MA0114.1 0.00127
MA0115.1 0.321
MA0116.1 0.835
MA0117.1 0.411
MA0119.1 0.996
MA0122.1 0.705
MA0124.1 0.602
MA0125.1 0.129
MA0131.1 0.473
MA0135.1 0.0355
MA0136.1 0.241
MA0137.2 0.00516
MA0138.2 2.13263e-4
MA0139.1 0.813
MA0140.1 8.22728e-4
MA0141.1 0.429
MA0142.1 0.0208
MA0143.1 0.986
MA0144.1 0.0656
MA0145.1 0.339
MA0146.1 0.0066
MA0147.1 0.784
MA0148.1 0.00619
MA0149.1 0.607
MA0150.1 0.0102
MA0152.1 0.451
MA0153.1 1.83336e-6
MA0154.1 0.916
MA0155.1 0.357
MA0156.1 0.822
MA0157.1 0.487
MA0159.1 0.662
MA0160.1 0.262
MA0162.1 0.316
MA0163.1 0.132
MA0164.1 0.761
MA0258.1 0.895
MA0259.1 0.31



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: CNhs11297
Novel motif P-value
1 0.898
10 0.242
100 0.666
101 0.141
102 0.523
103 0.761
104 0.548
105 0.834
106 0.66
107 0.401
108 0.726
109 0.0768
11 0.363
110 0.0867
111 0.259
112 0.674
113 0.242
114 0.296
115 0.483
116 0.278
117 0.0468
118 0.881
119 0.599
12 0.135
120 0.428
121 0.26
122 0.517
123 0.225
124 0.456
125 0.759
126 0.949
127 0.307
128 0.236
129 0.861
13 0.281
130 0.971
131 0.989
132 0.542
133 0.0177
134 0.758
135 0.0323
136 0.333
137 0.7
138 0.857
139 0.0599
14 0.69
140 0.0729
141 0.523
142 0.246
143 0.745
144 0.62
145 0.648
146 0.305
147 0.949
148 0.591
149 0.845
15 0.503
150 0.0898
151 0.617
152 0.156
153 0.819
154 0.54
155 0.799
156 0.00355
157 0.967
158 0.324
159 0.0361
160 0.195
161 0.6
162 0.667
163 0.815
164 0.0729
165 0.384
166 0.728
167 0.542
168 0.154
169 0.0417
17 0.989
18 0.87
19 0.551
2 0.31
20 0.0705
21 0.339
22 0.298
23 0.894
24 0.632
25 0.415
26 0.0667
27 0.111
28 0.947
29 0.109
3 0.303
30 0.221
31 0.434
32 0.504
33 0.764
34 0.311
35 0.141
36 0.328
37 0.0805
38 0.715
39 0.346
4 0.0999
40 0.0669
41 0.997
42 0.737
43 0.849
44 0.74
45 0.427
46 0.922
47 0.608
48 0.846
49 0.355
5 0.453
50 0.337
51 0.69
52 0.695
53 0.655
54 0.554
55 0.463
56 0.862
57 0.598
58 0.539
59 0.805
6 0.764
60 0.951
61 0.593
62 0.97
63 0.965
64 0.889
65 0.558
66 0.635
67 0.619
68 0.116
69 0.0823
7 0.688
70 0.0194
71 0.504
72 0.732
73 0.0219
74 0.441
75 0.071
76 0.0215
77 0.888
78 0.269
79 0.803
8 0.283
80 0.00375
81 0.993
82 0.299
83 0.298
84 0.175
85 0.86
86 0.369
87 0.0796
88 0.763
89 0.184
9 0.742
90 0.273
91 0.452
92 0.679
93 0.293
94 0.659
95 0.2
96 0.498
97 0.0962
98 0.0235
99 0.652



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: CNhs11297


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)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0000393 (electrically responsive cell)
0000183 (contractile cell)
0000187 (muscle cell)
0000192 (smooth muscle cell)
0000211 (electrically active cell)
0000255 (eukaryotic cell)
0000359 (vascular associated smooth muscle cell)
0002539 (aortic smooth muscle cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001135 (smooth muscle tissue)
0000947 (aorta)
0001637 (artery)
0000483 (epithelium)
0000479 (tissue)
0000055 (vessel)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0003914 (epithelial tube)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0004573 (systemic artery)
0002385 (muscle tissue)
0003509 (arterial blood vessel)
0007500 (epithelial tube open at both ends)
0001981 (blood vessel)
0004237 (blood vessel smooth muscle)
0004695 (arterial system smooth muscle)
0002049 (vasculature)
0010317 (germ layer / neural crest derived structure)
0002111 (artery smooth muscle tissue)
0007798 (vascular system)
0001015 (musculature)
0004178 (aorta smooth muscle tissue)
0002204 (musculoskeletal system)
0004535 (cardiovascular system)
0004571 (systemic arterial system)
0010191 (aortic system)
0000383 (musculature of body)
0004572 (arterial system)
0004537 (blood vasculature)
0001009 (circulatory system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000104 (mouse aortic smooth muscle cell 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:0000355 (multi-potent skeletal muscle stem cell)
CL:0000222 (mesodermal cell)
CL:0000514 (smooth muscle myoblast)