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FF:11485-119D9

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Name:Mouse Aortic Smooth Muscle cells - differentiated, biol_rep2
Species:Mouse (Mus musculus)
Library ID:CNhs11056
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-v1.17

Accession numbers
MethodSample accession id
CAGE  SAMD00005597
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11056 CAGE DRX008804 DRR009676
Accession ID Mm9

Library idBAMCTSS
CNhs11056 DRZ001101 DRZ002486
Accession ID Mm10

Library idBAMCTSS
CNhs11056 DRZ012451 DRZ013836
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 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

CNhs11056

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0419
1001 0.00318
1002 0.356
1003 0.243
1004 0
1005 0
1006 --0.143
1007 --0.129
1008 0
1009 0.758
101 0.024
1010 0
1011 --0.0656
1012 0
1013 0.286
1014 --0.051
1015 0.0124
1016 0.218
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 --0.0704
1023 0
1024 --0.129
1025 0
1026 0
1027 --0.048
1028 0.818
1029 --0.135
103 0.0842
1030 0
1031 0.215
1032 0.306
1033 0
1034 0
1035 0
1036 --0.0446
1037 0
1038 0.213
1039 --0.0124
104 0
1040 0.776
1041 0



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: CNhs11056

Jaspar motif P-value
MA0002.2 0.924
MA0003.1 0.445
MA0004.1 0.00353
MA0006.1 0.706
MA0007.1 0.397
MA0009.1 0.137
MA0014.1 0.0862
MA0017.1 5.99092e-4
MA0018.2 0.384
MA0019.1 0.816
MA0024.1 0.0101
MA0025.1 0.522
MA0027.1 0.297
MA0028.1 9.35158e-4
MA0029.1 0.485
MA0030.1 0.321
MA0031.1 0.348
MA0035.2 2.00761e-5
MA0038.1 0.484
MA0039.2 0.295
MA0040.1 0.426
MA0041.1 0.845
MA0042.1 0.445
MA0043.1 0.499
MA0046.1 2.88563e-8
MA0047.2 0.00796
MA0048.1 0.00194
MA0050.1 6.09535e-5
MA0051.1 0.00111
MA0052.1 0.00164
MA0055.1 0.00174
MA0057.1 0.744
MA0058.1 1.10511e-4
MA0059.1 0.344
MA0060.1 8.47853e-7
MA0061.1 0.0845
MA0062.2 0.00584
MA0065.2 0.0398
MA0066.1 0.836
MA0067.1 0.696
MA0068.1 0.0247
MA0069.1 0.933
MA0070.1 0.892
MA0071.1 0.504
MA0072.1 0.717
MA0073.1 0.624
MA0074.1 0.75
MA0076.1 0.0106
MA0077.1 0.188
MA0078.1 0.828
MA0079.2 0.0543
MA0080.2 0.00232
MA0081.1 0.736
MA0083.1 0.00309
MA0084.1 0.797
MA0087.1 0.785
MA0088.1 0.0325
MA0090.1 0.00127
MA0091.1 0.549
MA0092.1 0.481
MA0093.1 0.0031
MA0099.2 1.04817e-5
MA0100.1 0.425
MA0101.1 0.011
MA0102.2 0.593
MA0103.1 1.37638e-7
MA0104.2 0.778
MA0105.1 0.976
MA0106.1 1.96814e-7
MA0107.1 0.0465
MA0108.2 6.15564e-6
MA0111.1 0.284
MA0112.2 0.401
MA0113.1 0.775
MA0114.1 3.04246e-4
MA0115.1 0.0869
MA0116.1 0.836
MA0117.1 0.579
MA0119.1 0.287
MA0122.1 0.681
MA0124.1 0.883
MA0125.1 0.196
MA0131.1 0.626
MA0135.1 0.289
MA0136.1 0.0899
MA0137.2 0.00964
MA0138.2 0.00811
MA0139.1 0.426
MA0140.1 1.20103e-4
MA0141.1 0.194
MA0142.1 0.0222
MA0143.1 0.727
MA0144.1 0.037
MA0145.1 0.144
MA0146.1 0.00542
MA0147.1 0.753
MA0148.1 0.0327
MA0149.1 0.906
MA0150.1 0.00883
MA0152.1 0.0309
MA0153.1 4.00583e-6
MA0154.1 0.858
MA0155.1 0.673
MA0156.1 0.706
MA0157.1 0.206
MA0159.1 0.366
MA0160.1 0.0336
MA0162.1 0.322
MA0163.1 0.118
MA0164.1 0.839
MA0258.1 0.415
MA0259.1 0.448



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: CNhs11056

Novel motif P-value
1 0.868
10 0.308
100 0.446
101 0.191
102 0.262
103 0.73
104 0.882
105 0.911
106 0.747
107 0.735
108 0.761
109 0.0436
11 0.334
110 0.0549
111 0.182
112 0.505
113 0.102
114 0.17
115 0.986
116 0.309
117 0.19
118 0.985
119 0.521
12 0.419
120 0.626
121 0.431
122 0.757
123 0.342
124 0.573
125 0.778
126 0.495
127 0.367
128 0.227
129 0.703
13 0.108
130 0.826
131 0.195
132 0.674
133 0.0124
134 0.896
135 0.0816
136 0.0749
137 0.625
138 0.992
139 0.0793
14 0.867
140 0.0978
141 0.559
142 0.1
143 0.766
144 0.261
145 0.904
146 0.581
147 0.914
148 0.414
149 0.289
15 0.891
150 0.0572
151 0.69
152 0.0675
153 0.598
154 0.818
155 0.666
156 0.0305
157 0.591
158 0.0453
159 0.0295
160 0.186
161 0.47
162 0.666
163 0.999
164 0.0422
165 0.466
166 0.827
167 0.333
168 0.27
169 0.0203
17 0.85
18 0.716
19 0.286
2 0.907
20 0.24
21 0.536
22 0.11
23 0.997
24 0.594
25 0.361
26 0.106
27 0.275
28 0.988
29 0.283
3 0.297
30 0.231
31 0.467
32 0.278
33 0.906
34 0.324
35 0.0715
36 0.242
37 0.0452
38 0.911
39 0.258
4 0.189
40 0.0351
41 0.772
42 0.581
43 0.566
44 0.758
45 0.978
46 0.811
47 0.525
48 0.748
49 0.285
5 0.679
50 0.277
51 0.665
52 0.776
53 0.812
54 0.389
55 0.859
56 0.949
57 0.961
58 0.177
59 0.956
6 0.745
60 0.56
61 0.697
62 0.422
63 0.789
64 0.663
65 0.699
66 0.512
67 0.842
68 0.0464
69 0.0767
7 0.915
70 0.11
71 0.55
72 0.713
73 0.00858
74 0.845
75 0.131
76 0.111
77 0.779
78 0.128
79 0.421
8 0.222
80 0.00691
81 0.477
82 0.288
83 0.244
84 0.417
85 0.267
86 0.356
87 0.00342
88 0.772
89 0.222
9 0.818
90 0.293
91 0.375
92 0.72
93 0.298
94 0.249
95 0.0236
96 0.3
97 0.111
98 0.026
99 0.868



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: CNhs11056


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), 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)