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|sample_ethnicity=
|sample_ethnicity=
|rna_rin=
|rna_rin=
|rna_od260/230=1.53000
|rna_od260/230=1.53
|rna_od260/280=2.05000
|rna_od260/280=2.05
|sample_cell_type=
|sample_cell_type=
|sample_cell_line=
|sample_cell_line=
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|rna_sample_type=
|rna_sample_type=
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.17
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.17
|rna_weight_ug=0.31000
|rna_weight_ug=0.31
|rna_concentration=14.00000
|rna_concentration=14
|sample_note=
|sample_note=
|profile_hcage=CNhs11056,LSID722,release008,COMPLETED
|profile_hcage=CNhs11056,LSID722,release008,COMPLETED

Revision as of 17:48, 27 February 2012


Name:Mouse Aortic Smooth Muscle cells - differentiated, biol_rep2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs11056

00
10
100
1000
10000.0419
10010.00318
10020.356
10030.243
10040
10050
1006-0.143
1007-0.129
10080
10090.758
1010.024
10100
1011-0.0656
10120
10130.286
1014-0.051
10150.0124
10160.218
10170
10180
10190
1020
10200
10210
1022-0.0704
10230
1024-0.129
10250
10260
1027-0.048
10280.818
1029-0.135
1030.0842
10300
10310.215
10320.306
10330
10340
10350
1036-0.0446
10370
10380.213
1039-0.0124
1040
10400.776
10410



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11056

Jaspar motifP-value
MA0002.20.924
MA0003.10.445
MA0004.10.00353
MA0006.10.706
MA0007.10.397
MA0009.10.137
MA0014.10.0862
MA0017.15.99092e-4
MA0018.20.384
MA0019.10.816
MA0024.10.0101
MA0025.10.522
MA0027.10.297
MA0028.19.35158e-4
MA0029.10.485
MA0030.10.321
MA0031.10.348
MA0035.22.00761e-5
MA0038.10.484
MA0039.20.295
MA0040.10.426
MA0041.10.845
MA0042.10.445
MA0043.10.499
MA0046.12.88563e-8
MA0047.20.00796
MA0048.10.00194
MA0050.16.09535e-5
MA0051.10.00111
MA0052.10.00164
MA0055.10.00174
MA0057.10.744
MA0058.11.10511e-4
MA0059.10.344
MA0060.18.47853e-7
MA0061.10.0845
MA0062.20.00584
MA0065.20.0398
MA0066.10.836
MA0067.10.696
MA0068.10.0247
MA0069.10.933
MA0070.10.892
MA0071.10.504
MA0072.10.717
MA0073.10.624
MA0074.10.75
MA0076.10.0106
MA0077.10.188
MA0078.10.828
MA0079.20.0543
MA0080.20.00232
MA0081.10.736
MA0083.10.00309
MA0084.10.797
MA0087.10.785
MA0088.10.0325
MA0090.10.00127
MA0091.10.549
MA0092.10.481
MA0093.10.0031
MA0099.21.04817e-5
MA0100.10.425
MA0101.10.011
MA0102.20.593
MA0103.11.37638e-7
MA0104.20.778
MA0105.10.976
MA0106.11.96814e-7
MA0107.10.0465
MA0108.26.15564e-6
MA0111.10.284
MA0112.20.401
MA0113.10.775
MA0114.13.04246e-4
MA0115.10.0869
MA0116.10.836
MA0117.10.579
MA0119.10.287
MA0122.10.681
MA0124.10.883
MA0125.10.196
MA0131.10.626
MA0135.10.289
MA0136.10.0899
MA0137.20.00964
MA0138.20.00811
MA0139.10.426
MA0140.11.20103e-4
MA0141.10.194
MA0142.10.0222
MA0143.10.727
MA0144.10.037
MA0145.10.144
MA0146.10.00542
MA0147.10.753
MA0148.10.0327
MA0149.10.906
MA0150.10.00883
MA0152.10.0309
MA0153.14.00583e-6
MA0154.10.858
MA0155.10.673
MA0156.10.706
MA0157.10.206
MA0159.10.366
MA0160.10.0336
MA0162.10.322
MA0163.10.118
MA0164.10.839
MA0258.10.415
MA0259.10.448



FANTOM5 phase1 novel unique motifs<b>Summary:</b>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 in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11056

Novel motifP-value
10.868
100.308
1000.446
1010.191
1020.262
1030.73
1040.882
1050.911
1060.747
1070.735
1080.761
1090.0436
110.334
1100.0549
1110.182
1120.505
1130.102
1140.17
1150.986
1160.309
1170.19
1180.985
1190.521
120.419
1200.626
1210.431
1220.757
1230.342
1240.573
1250.778
1260.495
1270.367
1280.227
1290.703
130.108
1300.826
1310.195
1320.674
1330.0124
1340.896
1350.0816
1360.0749
1370.625
1380.992
1390.0793
140.867
1400.0978
1410.559
1420.1
1430.766
1440.261
1450.904
1460.581
1470.914
1480.414
1490.289
150.891
1500.0572
1510.69
1520.0675
1530.598
1540.818
1550.666
1560.0305
1570.591
1580.0453
1590.0295
1600.186
1610.47
1620.666
1630.999
1640.0422
1650.466
1660.827
1670.333
1680.27
1690.0203
170.85
180.716
190.286
20.907
200.24
210.536
220.11
230.997
240.594
250.361
260.106
270.275
280.988
290.283
30.297
300.231
310.467
320.278
330.906
340.324
350.0715
360.242
370.0452
380.911
390.258
40.189
400.0351
410.772
420.581
430.566
440.758
450.978
460.811
470.525
480.748
490.285
50.679
500.277
510.665
520.776
530.812
540.389
550.859
560.949
570.961
580.177
590.956
60.745
600.56
610.697
620.422
630.789
640.663
650.699
660.512
670.842
680.0464
690.0767
70.915
700.11
710.55
720.713
730.00858
740.845
750.131
760.111
770.779
780.128
790.421
80.222
800.00691
810.477
820.288
830.244
840.417
850.267
860.356
870.00342
880.772
890.222
90.818
900.293
910.375
920.72
930.298
940.249
950.0236
960.3
970.111
980.026
990.868



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs11056


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000056 (myoblast)
0000183 (contractile cell)
0000187 (muscle cell)
0000192 (smooth muscle cell)
0000211 (electrically active cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000355 (multi-potent skeletal muscle stem cell)
0000359 (vascular associated smooth muscle cell)
0000393 (electrically responsive cell)
0000514 (smooth muscle myoblast)
0000548 (animal cell)
0000680 (muscle precursor cell)
0000723 (somatic stem cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002539 (aortic smooth muscle cell)

UBERON: Anatomy
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000119 (cell layer)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000947 (aorta)
0001009 (circulatory system)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001135 (smooth muscle tissue)
0001637 (artery)
0001981 (blood vessel)
0002036 (striated muscle tissue)
0002049 (vasculature)
0002050 (embryonic structure)
0002111 (artery smooth muscle tissue)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003081 (lateral plate mesoderm)
0003082 (myotome)
0003104 (mesenchyme)
0003509 (arterial blood vessel)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004178 (aorta smooth muscle tissue)
0004237 (blood vessel smooth muscle)
0004290 (dermomyotome)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004571 (systemic arterial system)
0004572 (arterial system)
0004573 (systemic artery)
0004695 (arterial system smooth muscle)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006965 (vascular cord)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)
0009142 (entire embryonic mesenchyme)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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