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FF:14332-155F3: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:22, 29 March 2012


Name:Fibroblast - Aortic Adventitial, donor2 (nuclear fraction)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueaorta
dev stage19 years old adult
sexfemale
age19
cell typefibroblast
cell lineNA
companyLonza
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
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


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

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0706
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.25
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0.87
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



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: CNhs12581

Jaspar motifP-value
MA0002.20.0369
MA0003.10.0236
MA0004.10.935
MA0006.10.491
MA0007.10.275
MA0009.10.0137
MA0014.10.727
MA0017.10.00134
MA0018.20.993
MA0019.10.569
MA0024.10.0113
MA0025.10.0551
MA0027.10.519
MA0028.12.97782e-4
MA0029.10.0211
MA0030.10.555
MA0031.10.523
MA0035.20.128
MA0038.10.577
MA0039.20.464
MA0040.10.314
MA0041.10.767
MA0042.10.486
MA0043.10.174
MA0046.10.0113
MA0047.20.564
MA0048.10.21
MA0050.10.635
MA0051.10.362
MA0052.10.709
MA0055.10.421
MA0057.10.249
MA0058.10.569
MA0059.10.731
MA0060.10.0284
MA0061.10.0596
MA0062.21.16408e-4
MA0065.28.02025e-5
MA0066.10.0624
MA0067.10.237
MA0068.10.283
MA0069.10.303
MA0070.10.578
MA0071.10.0343
MA0072.10.794
MA0073.10.845
MA0074.10.398
MA0076.13.30205e-5
MA0077.10.861
MA0078.10.752
MA0079.20.85
MA0080.25.371e-6
MA0081.10.361
MA0083.12.09484e-4
MA0084.10.135
MA0087.10.478
MA0088.10.894
MA0090.12.50448e-6
MA0091.10.541
MA0092.10.694
MA0093.10.714
MA0099.21.65961e-17
MA0100.10.791
MA0101.10.909
MA0102.20.147
MA0103.11.25754e-5
MA0104.20.568
MA0105.18.1811e-4
MA0106.10.982
MA0107.10.768
MA0108.20.275
MA0111.10.108
MA0112.20.00183
MA0113.10.556
MA0114.10.00989
MA0115.10.00367
MA0116.18.61873e-4
MA0117.10.493
MA0119.10.833
MA0122.10.64
MA0124.10.374
MA0125.10.34
MA0131.10.105
MA0135.10.0604
MA0136.10.0417
MA0137.20.0503
MA0138.27.45232e-4
MA0139.10.235
MA0140.10.56
MA0141.10.00282
MA0142.10.272
MA0143.10.997
MA0144.10.553
MA0145.10.283
MA0146.10.117
MA0147.10.696
MA0148.10.575
MA0149.10.618
MA0150.10.00245
MA0152.10.0997
MA0153.10.52
MA0154.10.00208
MA0155.10.183
MA0156.10.454
MA0157.10.559
MA0159.10.15
MA0160.10.0169
MA0162.10.547
MA0163.10.00816
MA0164.10.329
MA0258.10.00512
MA0259.10.692



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: CNhs12581

Novel motifP-value
10.135
100.365
1000.662
1010.702
1020.147
1030.231
1040.924
1050.186
1060.00623
1070.0498
1080.453
1090.296
110.178
1100.674
1110.101
1120.286
1130.438
1140.392
1150.0122
1160.889
1170.917
1180.706
1190.34
120.932
1200.315
1210.573
1220.115
1230.242
1240.054
1250.316
1260.145
1270.0317
1280.0364
1290.158
130.52
1300.719
1310.11
1320.573
1330.806
1340.785
1350.435
1360.994
1370.474
1380.242
1390.599
140.513
1400.679
1410.0355
1420.237
1430.12
1440.707
1450.492
1460.393
1470.322
1480.243
1490.43
150.0444
1500.713
1510.389
1520.379
1530.673
1540.88
1550.00287
1560.0643
1570.806
1580.168
1590.986
160.255
1600.00991
1610.231
1620.284
1630.179
1640.349
1650.636
1660.49
1670.558
1680.191
1690.0269
170.611
180.462
190.31
20.18
200.749
210.974
220.374
230.379
240.507
250.138
260.287
270.0761
280.961
290.826
30.658
300.67
310.497
320.388
330.745
340.262
350.497
360.178
370.846
380.222
390.962
40.081
400.0641
410.226
420.457
430.218
440.00749
450.372
460.136
470.246
480.368
490.0883
50.472
500.939
510.223
520.439
530.599
540.505
550.245
560.287
570.712
580.132
590.00666
60.156
600.0919
610.263
620.0278
630.332
640.0609
650.146
660.292
670.915
680.835
690.194
70.116
700.131
710.378
720.635
730.865
740.201
750.395
760.397
770.291
780.0609
790.931
80.0589
800.478
810.293
820.253
830.691
840.543
850.166
860.517
870.884
880.89
890.205
90.52
900.676
910.47
920.554
930.48
940.52
950.612
960.444
970.351
980.00263
990.913



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: CNhs12581


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002547 (fibroblast of the aortic adventitia)
1000306 (fibroblast of tunica adventitia of artery)

UBERON: Anatomy
0000025 (tube)
0000055 (vessel)
0000060 (anatomical wall)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000415 (artery wall)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000947 (aorta)
0001009 (circulatory system)
0001062 (anatomical entity)
0001637 (artery)
0001981 (blood vessel)
0002049 (vasculature)
0002050 (embryonic structure)
0002384 (connective tissue)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003509 (arterial blood vessel)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004571 (systemic arterial system)
0004572 (arterial system)
0004573 (systemic artery)
0004663 (aorta wall)
0004664 (aorta tunica adventitia)
0004872 (splanchnic layer of lateral plate mesoderm)
0004923 (organ component layer)
0005423 (developing anatomical structure)
0005734 (tunica adventitia of blood vessel)
0005742 (adventitia)
0006965 (vascular cord)
0007240 (tunica adventitia of artery)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)

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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