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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;46
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;46
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;46
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;46
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/aorta%252c%2520adult.CNhs10498.46-23H1.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/aorta%252c%2520adult.CNhs10498.46-23H1.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/aorta%252c%2520adult.CNhs10498.46-23H1.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/aorta%252c%2520adult.CNhs10498.46-23H1.mm10.nobarcode.ctss.bed.gz

Revision as of 18:43, 4 August 2017


Name:aorta, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10498
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueaorta
dev stageadult
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005242
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10498 CAGE DRX008935 DRR009809
Accession ID Mm9

Library idBAMCTSS
CNhs10498 DRZ001234 DRZ002617
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

CNhs10498

00
10
100
1000
10000.217
10010.171
10020.197
10030.112
10040
10050
10060.202
1007-0.169
10080
10090.444
101-0.0128
10100
10110.049
10120
1013-0.00452
1014-0.0874
1015-0.268
1016-0.105
10170
10180
10190
1020
10200
10210
10220.849
10230
10240.432
10250.0374
10260
10270
10280
10290.0114
103-0.00232
10300.0587
1031-0.0192
10320.116
10330.0169
10340
10350.156
1036-0.302
10370
10380.036
10390.426
1040
10400.43
10411.361



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: CNhs10498

Jaspar motifP-value
MA0002.20.0479
MA0003.10.217
MA0004.10.679
MA0006.10.182
MA0007.10.282
MA0009.10.784
MA0014.10.132
MA0017.10.0674
MA0018.20.339
MA0019.10.161
MA0024.18.52595e-9
MA0025.11.96307e-7
MA0027.10.772
MA0028.10.0612
MA0029.10.706
MA0030.10.843
MA0031.10.165
MA0035.20.343
MA0038.10.596
MA0039.20.0052
MA0040.10.61
MA0041.10.178
MA0042.10.605
MA0043.10.64
MA0046.15.04885e-9
MA0047.20.781
MA0048.10.141
MA0050.15.52138e-12
MA0051.11.47363e-9
MA0052.15.03028e-8
MA0055.10.307
MA0057.10.678
MA0058.10.526
MA0059.10.0344
MA0060.12.97078e-6
MA0061.10.337
MA0062.20.0441
MA0065.21.70722e-7
MA0066.10.944
MA0067.10.742
MA0068.10.14
MA0069.10.354
MA0070.10.85
MA0071.10.24
MA0072.10.635
MA0073.10.473
MA0074.10.61
MA0076.10.0894
MA0077.10.0941
MA0078.10.0077
MA0079.20.0209
MA0080.20.00377
MA0081.10.559
MA0083.14.13628e-9
MA0084.10.779
MA0087.10.562
MA0088.10.174
MA0090.10.112
MA0091.10.371
MA0092.10.573
MA0093.10.716
MA0099.20.541
MA0100.10.0217
MA0101.10.559
MA0102.24.67632e-4
MA0103.11.58905e-4
MA0104.20.107
MA0105.10.601
MA0106.10.724
MA0107.10.346
MA0108.20.908
MA0111.10.96
MA0112.20.00122
MA0113.10.296
MA0114.10.0122
MA0115.10.773
MA0116.10.986
MA0117.10.283
MA0119.10.469
MA0122.10.406
MA0124.10.491
MA0125.10.841
MA0131.10.56
MA0135.10.235
MA0136.10.188
MA0137.20.0931
MA0138.20.597
MA0139.10.376
MA0140.10.305
MA0141.10.00486
MA0142.10.0641
MA0143.10.149
MA0144.10.147
MA0145.10.0589
MA0146.10.0538
MA0147.10.12
MA0148.10.506
MA0149.10.959
MA0150.10.0732
MA0152.10.421
MA0153.12.23686e-8
MA0154.10.0096
MA0155.10.743
MA0156.10.02
MA0157.10.022
MA0159.10.184
MA0160.10.00218
MA0162.10.133
MA0163.10.611
MA0164.10.0789
MA0258.10.0726
MA0259.10.126



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: CNhs10498

Novel motifP-value
10.741
100.77
1000.637
1010.307
1020.246
1030.731
1040.965
1050.145
1060.121
1070.333
1080.586
1090.336
110.728
1100.387
1110.105
1120.343
1130.214
1140.14
1150.567
1160.555
1170.157
1180.411
1190.365
120.659
1200.0129
1210.0781
1220.895
1230.398
1240.752
1250.908
1260.666
1270.996
1280.167
1290.515
130.00132
1300.195
1310.543
1320.837
1330.326
1340.289
1350.319
1360.693
1370.808
1380.93
1390.965
140.413
1400.777
1410.453
1420.285
1430.492
1440.673
1450.989
1460.126
1470.994
1480.423
1490.00304
150.476
1500.553
1510.0553
1520.0369
1530.817
1540.774
1550.891
1560.134
1570.522
1580.985
1590.421
1600.163
1610.252
1620.449
1630.0564
1640.564
1650.0934
1660.035
1670.176
1680.364
1690.00953
170.252
180.271
190.0999
20.0525
200.259
210.284
220.0584
230.467
240.0326
250.558
260.951
270.891
280.793
290.383
30.981
300.854
310.876
320.407
330.441
340.305
350.23
360.524
370.0336
380.337
390.388
40.695
400.923
410.391
420.951
430.278
440.567
450.101
460.761
470.895
480.658
490.981
50.71
500.323
510.711
520.21
530.144
540.587
550.365
560.436
570.166
580.438
590.242
60.792
600.106
610.963
620.474
630.113
640.884
650.508
660.874
670.423
680.887
690.884
70.048
700.77
710.337
720.66
730.0275
740.0847
750.841
760.217
770.379
780.00758
790.718
80.619
800.0815
810.417
820.105
830.0929
840.0303
850.0742
860.237
870.431
880.966
890.667
90.191
900.354
910.243
920.354
930.195
940.194
950.195
960.222
970.168
980.346
990.635



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: CNhs10498


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
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)
0003509 (arterial blood vessel)
0007500 (epithelial tube open at both ends)
0001981 (blood vessel)
0002049 (vasculature)
0010317 (germ layer / neural crest derived structure)
0007798 (vascular system)
0004535 (cardiovascular system)
0004571 (systemic arterial system)
0010191 (aortic system)
0004572 (arterial system)
0004537 (blood vasculature)
0001009 (circulatory system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011359 (mouse aorta - adult 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
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0006965 (vascular cord)
UBERON:0010316 (germ layer / neural crest)

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