Personal tools

FF:11484-119D8: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 46: Line 46:
|library_id=CNhs11055
|library_id=CNhs11055
|library_id_phase_based=2:CNhs11055
|library_id_phase_based=2:CNhs11055
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%2520-%2520differentiated%252c%2520biol_rep1.CNhs11055.11484-119D8.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%2520-%2520differentiated%252c%2520biol_rep1.CNhs11055.11484-119D8.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%2520-%2520differentiated%252c%2520biol_rep1.CNhs11055.11484-119D8.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%2520-%2520differentiated%252c%2520biol_rep1.CNhs11055.11484-119D8.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%2520-%2520differentiated%252c%2520biol_rep1.CNhs11055.11484-119D8.mm9.nobarcode.rdna.fa.gz
|name=Mouse Aortic Smooth Muscle cells - differentiated, biol_rep1
|name=Mouse Aortic Smooth Muscle cells - differentiated, biol_rep1
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 16:00, 17 May 2017


Name:Mouse Aortic Smooth Muscle cells - differentiated, biol_rep1
Species:Mouse (Mus musculus)
Library ID:CNhs11055
Sample type:primary cells
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-v1.16

CAGE 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
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

CNhs11055

00
10
100
1000
10000.0515
1001-0.0136
10020.472
10030.259
10040
10050.0126
1006-0.143
1007-0.172
10080
10090.716
1010.0536
10100
1011-0.0627
10120
10130.294
1014-0.0874
1015-0.0478
10160.23
10170
10180
10190
1020
10200
10210
1022-0.0126
10230
1024-0.21
10250
10260
1027-0.048
10280.878
1029-0.0501
1030.119
10300
10310.264
10320.295
10330.0515
10340
10350
10360.0572
10370
10380.22
1039-0.0193
1040
10400.828
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: CNhs11055

Jaspar motifP-value
MA0002.20.986
MA0003.10.388
MA0004.10.00198
MA0006.10.72
MA0007.10.299
MA0009.10.214
MA0014.10.105
MA0017.10.00101
MA0018.20.114
MA0019.11
MA0024.10.00313
MA0025.10.803
MA0027.10.159
MA0028.10.00123
MA0029.10.477
MA0030.10.329
MA0031.10.331
MA0035.23.05314e-5
MA0038.10.635
MA0039.20.373
MA0040.10.363
MA0041.10.58
MA0042.10.364
MA0043.10.735
MA0046.12.9703e-8
MA0047.20.00692
MA0048.10.00499
MA0050.11.39084e-4
MA0051.10.00375
MA0052.16.60329e-4
MA0055.10.00342
MA0057.10.714
MA0058.11.90164e-4
MA0059.10.2
MA0060.13.98068e-7
MA0061.10.0654
MA0062.20.01
MA0065.20.0886
MA0066.10.746
MA0067.10.995
MA0068.10.0136
MA0069.10.967
MA0070.10.64
MA0071.10.599
MA0072.10.559
MA0073.10.649
MA0074.10.699
MA0076.10.0227
MA0077.10.131
MA0078.10.91
MA0079.20.318
MA0080.20.00272
MA0081.10.597
MA0083.10.0886
MA0084.10.874
MA0087.10.753
MA0088.10.0112
MA0090.13.69655e-4
MA0091.10.724
MA0092.10.288
MA0093.10.0032
MA0099.22.34015e-5
MA0100.10.365
MA0101.10.0145
MA0102.20.851
MA0103.11.29214e-7
MA0104.20.678
MA0105.10.492
MA0106.11.49719e-8
MA0107.10.0786
MA0108.23.60711e-6
MA0111.10.296
MA0112.20.202
MA0113.10.693
MA0114.17.3699e-4
MA0115.10.0504
MA0116.10.733
MA0117.10.661
MA0119.10.152
MA0122.10.706
MA0124.10.951
MA0125.10.0589
MA0131.10.776
MA0135.10.0799
MA0136.10.0532
MA0137.20.021
MA0138.20.00475
MA0139.10.252
MA0140.15.094e-4
MA0141.10.255
MA0142.10.0631
MA0143.10.608
MA0144.10.0574
MA0145.10.106
MA0146.10.0123
MA0147.10.996
MA0148.10.0223
MA0149.10.889
MA0150.10.0116
MA0152.10.0206
MA0153.11.96829e-6
MA0154.10.905
MA0155.10.616
MA0156.10.503
MA0157.10.157
MA0159.10.578
MA0160.10.033
MA0162.10.256
MA0163.10.0635
MA0164.10.852
MA0258.10.608
MA0259.10.357



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: CNhs11055

Novel motifP-value
10.669
100.159
1000.518
1010.209
1020.162
1030.894
1040.843
1050.774
1060.975
1070.735
1080.908
1090.0119
110.247
1100.0222
1110.19
1120.383
1130.175
1140.0728
1150.865
1160.308
1170.227
1180.948
1190.541
120.4
1200.539
1210.312
1220.588
1230.289
1240.796
1250.67
1260.336
1270.256
1280.407
1290.72
130.0424
1300.963
1310.236
1320.55
1330.0203
1340.832
1350.218
1360.206
1370.608
1380.931
1390.0618
140.903
1400.082
1410.729
1420.129
1430.652
1440.322
1450.814
1460.856
1470.932
1480.434
1490.165
150.935
1500.049
1510.787
1520.109
1530.446
1540.836
1550.447
1560.00155
1570.572
1580.0248
1590.0172
1600.337
1610.473
1620.604
1630.897
1640.0402
1650.463
1660.865
1670.489
1680.313
1690.0118
170.728
180.604
190.188
20.884
200.433
210.283
220.0974
230.997
240.564
250.564
260.0673
270.311
280.921
290.221
30.182
300.214
310.441
320.224
330.832
340.296
350.0969
360.458
370.0342
380.929
390.301
40.171
400.0732
410.867
420.459
430.398
440.76
450.832
460.928
470.578
480.77
490.445
50.746
500.38
510.652
520.886
530.906
540.315
550.964
560.88
570.716
580.237
590.767
60.77
600.453
610.631
620.666
630.801
640.644
650.75
660.442
670.728
680.0397
690.0541
70.864
700.0596
710.227
720.907
730.0099
740.921
750.102
760.104
770.755
780.0697
790.423
80.252
800.00324
810.344
820.16
830.271
840.34
850.186
860.283
870.00422
880.72
890.207
90.766
900.255
910.346
920.636
930.329
940.451
950.00639
960.295
970.146
980.027
990.646



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: CNhs11055


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)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11484-119D8&oldid=4334188"