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|library_id=CNhs11297
|library_id=CNhs11297
|library_id_phase_based=2:CNhs11297
|library_id_phase_based=2:CNhs11297
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%252c%2520donor1.CNhs11297.11299-117B3.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%252c%2520donor1.CNhs11297.11299-117B3.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%252c%2520donor1.CNhs11297.11299-117B3.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%252c%2520donor1.CNhs11297.11299-117B3.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%252c%2520donor1.CNhs11297.11299-117B3.mm9.nobarcode.rdna.fa.gz
|name=Mouse Aortic Smooth Muscle cells, donor1
|name=Mouse Aortic Smooth Muscle cells, donor1
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 15:25, 17 May 2017


Name:Mouse Aortic Smooth Muscle cells, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs11297
Sample type:primary cells
Genomic View: UCSC
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

CAGE 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
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11297

00
10
100
1000
10000.00112
10010.0559
10020.633
10030.0979
10040
10050
1006-0.214
1007-0.00561
10080
10090.702
1010.0513
10100
1011-0.264
10120
10130.252
1014-0.0851
10150.0802
10160.153
10170
10180
10190
1020
10200
10210
1022-0.0761
10230
1024-0.117
10250
10260
1027-0.048
10280.634
10290.0199
1030.266
10300
10310.377
10320.0402
10330.0606
10340
10350
10360.0563
10370
10380.0889
1039-0.0737
1040
10400.585
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



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: CNhs11297

Jaspar motifP-value
MA0002.20.555
MA0003.10.685
MA0004.10.00299
MA0006.10.786
MA0007.10.354
MA0009.10.0513
MA0014.10.0512
MA0017.10.00277
MA0018.20.898
MA0019.10.707
MA0024.10.0262
MA0025.10.0549
MA0027.10.138
MA0028.19.8713e-5
MA0029.10.699
MA0030.10.608
MA0031.10.281
MA0035.21.47799e-5
MA0038.10.0438
MA0039.20.67
MA0040.10.209
MA0041.10.354
MA0042.10.405
MA0043.10.746
MA0046.12.99033e-9
MA0047.20.00195
MA0048.14.10366e-4
MA0050.10.393
MA0051.10.698
MA0052.10.00468
MA0055.11.16674e-4
MA0057.10.546
MA0058.11.02113e-5
MA0059.10.0771
MA0060.15.02851e-7
MA0061.10.515
MA0062.28.7272e-5
MA0065.20.0211
MA0066.10.587
MA0067.10.522
MA0068.10.0211
MA0069.10.841
MA0070.10.878
MA0071.10.642
MA0072.10.921
MA0073.10.594
MA0074.10.822
MA0076.14.85851e-4
MA0077.10.283
MA0078.10.852
MA0079.20.114
MA0080.28.2785e-4
MA0081.10.506
MA0083.10.0164
MA0084.10.611
MA0087.10.561
MA0088.10.0847
MA0090.10.0244
MA0091.10.586
MA0092.10.416
MA0093.10.00206
MA0099.24.19667e-7
MA0100.10.273
MA0101.10.136
MA0102.20.454
MA0103.12.9454e-7
MA0104.20.415
MA0105.10.647
MA0106.11.6617e-5
MA0107.10.336
MA0108.21.33902e-5
MA0111.10.314
MA0112.20.34
MA0113.10.748
MA0114.10.00127
MA0115.10.321
MA0116.10.835
MA0117.10.411
MA0119.10.996
MA0122.10.705
MA0124.10.602
MA0125.10.129
MA0131.10.473
MA0135.10.0355
MA0136.10.241
MA0137.20.00516
MA0138.22.13263e-4
MA0139.10.813
MA0140.18.22728e-4
MA0141.10.429
MA0142.10.0208
MA0143.10.986
MA0144.10.0656
MA0145.10.339
MA0146.10.0066
MA0147.10.784
MA0148.10.00619
MA0149.10.607
MA0150.10.0102
MA0152.10.451
MA0153.11.83336e-6
MA0154.10.916
MA0155.10.357
MA0156.10.822
MA0157.10.487
MA0159.10.662
MA0160.10.262
MA0162.10.316
MA0163.10.132
MA0164.10.761
MA0258.10.895
MA0259.10.31



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: CNhs11297

Novel motifP-value
10.898
100.242
1000.666
1010.141
1020.523
1030.761
1040.548
1050.834
1060.66
1070.401
1080.726
1090.0768
110.363
1100.0867
1110.259
1120.674
1130.242
1140.296
1150.483
1160.278
1170.0468
1180.881
1190.599
120.135
1200.428
1210.26
1220.517
1230.225
1240.456
1250.759
1260.949
1270.307
1280.236
1290.861
130.281
1300.971
1310.989
1320.542
1330.0177
1340.758
1350.0323
1360.333
1370.7
1380.857
1390.0599
140.69
1400.0729
1410.523
1420.246
1430.745
1440.62
1450.648
1460.305
1470.949
1480.591
1490.845
150.503
1500.0898
1510.617
1520.156
1530.819
1540.54
1550.799
1560.00355
1570.967
1580.324
1590.0361
1600.195
1610.6
1620.667
1630.815
1640.0729
1650.384
1660.728
1670.542
1680.154
1690.0417
170.989
180.87
190.551
20.31
200.0705
210.339
220.298
230.894
240.632
250.415
260.0667
270.111
280.947
290.109
30.303
300.221
310.434
320.504
330.764
340.311
350.141
360.328
370.0805
380.715
390.346
40.0999
400.0669
410.997
420.737
430.849
440.74
450.427
460.922
470.608
480.846
490.355
50.453
500.337
510.69
520.695
530.655
540.554
550.463
560.862
570.598
580.539
590.805
60.764
600.951
610.593
620.97
630.965
640.889
650.558
660.635
670.619
680.116
690.0823
70.688
700.0194
710.504
720.732
730.0219
740.441
750.071
760.0215
770.888
780.269
790.803
80.283
800.00375
810.993
820.299
830.298
840.175
850.86
860.369
870.0796
880.763
890.184
90.742
900.273
910.452
920.679
930.293
940.659
950.2
960.498
970.0962
980.0235
990.652



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: CNhs11297


FANTOM5 (FF) ontology

Direct parent terms


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)
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)<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
CL:0000355 (multi-potent skeletal muscle stem cell)
CL:0000222 (mesodermal cell)
CL:0000514 (smooth muscle myoblast)

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