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FF:11484-119D8

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Name:Mouse Aortic Smooth Muscle cells - differentiated, biol_rep1
Species:Mouse (Mus musculus)
Library ID:CNhs11055
Sample type:primary cells
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companyCell Applications
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.16

Accession numbers
MethodSample accession id
CAGE  SAMD00005370
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11055 CAGE DRX008803 DRR009675
Accession ID Mm9

Library idBAMCTSS
CNhs11055 DRZ001100 DRZ002485
Accession ID Mm10

Library idBAMCTSS
CNhs11055 DRZ012450 DRZ013835
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

CNhs11055

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0515
1001 -0.0136
1002 0.472
1003 0.259
1004 0
1005 0.0126
1006 -0.143
1007 -0.172
1008 0
1009 0.716
101 0.0536
1010 0
1011 -0.0627
1012 0
1013 0.294
1014 -0.0874
1015 -0.0478
1016 0.23
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 -0.0126
1023 0
1024 -0.21
1025 0
1026 0
1027 -0.048
1028 0.878
1029 -0.0501
103 0.119
1030 0
1031 0.264
1032 0.295
1033 0.0515
1034 0
1035 0
1036 0.0572
1037 0
1038 0.22
1039 -0.0193
104 0
1040 0.828
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: CNhs11055
Jaspar motif P-value
MA0002.2 0.986
MA0003.1 0.388
MA0004.1 0.00198
MA0006.1 0.72
MA0007.1 0.299
MA0009.1 0.214
MA0014.1 0.105
MA0017.1 0.00101
MA0018.2 0.114
MA0019.1 1
MA0024.1 0.00313
MA0025.1 0.803
MA0027.1 0.159
MA0028.1 0.00123
MA0029.1 0.477
MA0030.1 0.329
MA0031.1 0.331
MA0035.2 3.05314e-5
MA0038.1 0.635
MA0039.2 0.373
MA0040.1 0.363
MA0041.1 0.58
MA0042.1 0.364
MA0043.1 0.735
MA0046.1 2.9703e-8
MA0047.2 0.00692
MA0048.1 0.00499
MA0050.1 1.39084e-4
MA0051.1 0.00375
MA0052.1 6.60329e-4
MA0055.1 0.00342
MA0057.1 0.714
MA0058.1 1.90164e-4
MA0059.1 0.2
MA0060.1 3.98068e-7
MA0061.1 0.0654
MA0062.2 0.01
MA0065.2 0.0886
MA0066.1 0.746
MA0067.1 0.995
MA0068.1 0.0136
MA0069.1 0.967
MA0070.1 0.64
MA0071.1 0.599
MA0072.1 0.559
MA0073.1 0.649
MA0074.1 0.699
MA0076.1 0.0227
MA0077.1 0.131
MA0078.1 0.91
MA0079.2 0.318
MA0080.2 0.00272
MA0081.1 0.597
MA0083.1 0.0886
MA0084.1 0.874
MA0087.1 0.753
MA0088.1 0.0112
MA0090.1 3.69655e-4
MA0091.1 0.724
MA0092.1 0.288
MA0093.1 0.0032
MA0099.2 2.34015e-5
MA0100.1 0.365
MA0101.1 0.0145
MA0102.2 0.851
MA0103.1 1.29214e-7
MA0104.2 0.678
MA0105.1 0.492
MA0106.1 1.49719e-8
MA0107.1 0.0786
MA0108.2 3.60711e-6
MA0111.1 0.296
MA0112.2 0.202
MA0113.1 0.693
MA0114.1 7.3699e-4
MA0115.1 0.0504
MA0116.1 0.733
MA0117.1 0.661
MA0119.1 0.152
MA0122.1 0.706
MA0124.1 0.951
MA0125.1 0.0589
MA0131.1 0.776
MA0135.1 0.0799
MA0136.1 0.0532
MA0137.2 0.021
MA0138.2 0.00475
MA0139.1 0.252
MA0140.1 5.094e-4
MA0141.1 0.255
MA0142.1 0.0631
MA0143.1 0.608
MA0144.1 0.0574
MA0145.1 0.106
MA0146.1 0.0123
MA0147.1 0.996
MA0148.1 0.0223
MA0149.1 0.889
MA0150.1 0.0116
MA0152.1 0.0206
MA0153.1 1.96829e-6
MA0154.1 0.905
MA0155.1 0.616
MA0156.1 0.503
MA0157.1 0.157
MA0159.1 0.578
MA0160.1 0.033
MA0162.1 0.256
MA0163.1 0.0635
MA0164.1 0.852
MA0258.1 0.608
MA0259.1 0.357



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: CNhs11055
Novel motif P-value
1 0.669
10 0.159
100 0.518
101 0.209
102 0.162
103 0.894
104 0.843
105 0.774
106 0.975
107 0.735
108 0.908
109 0.0119
11 0.247
110 0.0222
111 0.19
112 0.383
113 0.175
114 0.0728
115 0.865
116 0.308
117 0.227
118 0.948
119 0.541
12 0.4
120 0.539
121 0.312
122 0.588
123 0.289
124 0.796
125 0.67
126 0.336
127 0.256
128 0.407
129 0.72
13 0.0424
130 0.963
131 0.236
132 0.55
133 0.0203
134 0.832
135 0.218
136 0.206
137 0.608
138 0.931
139 0.0618
14 0.903
140 0.082
141 0.729
142 0.129
143 0.652
144 0.322
145 0.814
146 0.856
147 0.932
148 0.434
149 0.165
15 0.935
150 0.049
151 0.787
152 0.109
153 0.446
154 0.836
155 0.447
156 0.00155
157 0.572
158 0.0248
159 0.0172
160 0.337
161 0.473
162 0.604
163 0.897
164 0.0402
165 0.463
166 0.865
167 0.489
168 0.313
169 0.0118
17 0.728
18 0.604
19 0.188
2 0.884
20 0.433
21 0.283
22 0.0974
23 0.997
24 0.564
25 0.564
26 0.0673
27 0.311
28 0.921
29 0.221
3 0.182
30 0.214
31 0.441
32 0.224
33 0.832
34 0.296
35 0.0969
36 0.458
37 0.0342
38 0.929
39 0.301
4 0.171
40 0.0732
41 0.867
42 0.459
43 0.398
44 0.76
45 0.832
46 0.928
47 0.578
48 0.77
49 0.445
5 0.746
50 0.38
51 0.652
52 0.886
53 0.906
54 0.315
55 0.964
56 0.88
57 0.716
58 0.237
59 0.767
6 0.77
60 0.453
61 0.631
62 0.666
63 0.801
64 0.644
65 0.75
66 0.442
67 0.728
68 0.0397
69 0.0541
7 0.864
70 0.0596
71 0.227
72 0.907
73 0.0099
74 0.921
75 0.102
76 0.104
77 0.755
78 0.0697
79 0.423
8 0.252
80 0.00324
81 0.344
82 0.16
83 0.271
84 0.34
85 0.186
86 0.283
87 0.00422
88 0.72
89 0.207
9 0.766
90 0.255
91 0.346
92 0.636
93 0.329
94 0.451
95 0.00639
96 0.295
97 0.146
98 0.027
99 0.646



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: CNhs11055


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)