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FF:11263-116G3: 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 17:20, 29 March 2012


Name:Endothelial Cells - Aortic, donor1
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 stage28 years old adult
sexfemale
age28
cell typeblood vessel endothelial cell
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1151
catalog numberCA304-R10a
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-penis0.361
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-0.00281
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs12495

Jaspar motifP-value
MA0002.20.714
MA0003.10.35
MA0004.10.494
MA0006.10.198
MA0007.10.0161
MA0009.10.364
MA0014.10.511
MA0017.10.0173
MA0018.27.78285e-6
MA0019.10.696
MA0024.10.44
MA0025.10.0705
MA0027.10.73
MA0028.10.335
MA0029.10.841
MA0030.10.607
MA0031.10.152
MA0035.20.00821
MA0038.10.414
MA0039.20.228
MA0040.10.33
MA0041.10.229
MA0042.10.524
MA0043.12.71198e-8
MA0046.10.38
MA0047.20.516
MA0048.10.716
MA0050.12.75888e-4
MA0051.10.237
MA0052.10.519
MA0055.10.0576
MA0057.10.174
MA0058.10.548
MA0059.10.16
MA0060.10.127
MA0061.10.458
MA0062.20.0251
MA0065.20.298
MA0066.10.5
MA0067.10.032
MA0068.10.676
MA0069.10.206
MA0070.10.572
MA0071.10.581
MA0072.10.906
MA0073.10.632
MA0074.10.753
MA0076.10.0219
MA0077.10.00127
MA0078.10.0177
MA0079.20.97
MA0080.20.0314
MA0081.10.0821
MA0083.10.11
MA0084.10.503
MA0087.10.573
MA0088.10.494
MA0090.10.185
MA0091.10.276
MA0092.10.227
MA0093.10.515
MA0099.26.53654e-14
MA0100.10.282
MA0101.10.683
MA0102.27.963e-4
MA0103.10.238
MA0104.20.647
MA0105.10.81
MA0106.10.00168
MA0107.10.581
MA0108.20.00304
MA0111.10.729
MA0112.20.269
MA0113.10.23
MA0114.10.59
MA0115.10.702
MA0116.10.66
MA0117.10.323
MA0119.10.00967
MA0122.10.152
MA0124.10.681
MA0125.10.966
MA0131.10.601
MA0135.10.332
MA0136.10.0368
MA0137.20.068
MA0138.20.812
MA0139.10.277
MA0140.10.016
MA0141.10.0455
MA0142.10.0729
MA0143.10.748
MA0144.10.788
MA0145.10.213
MA0146.10.962
MA0147.10.698
MA0148.10.18
MA0149.10.0282
MA0150.10.00535
MA0152.10.961
MA0153.10.738
MA0154.10.651
MA0155.10.0592
MA0156.10.139
MA0157.10.568
MA0159.10.417
MA0160.10.183
MA0162.10.0526
MA0163.10.461
MA0164.10.99
MA0258.10.402
MA0259.10.974



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: CNhs12495

Novel motifP-value
10.433
100.738
1000.624
1010.176
1020.532
1030.641
1040.825
1050.882
1060.122
1070.0322
1080.51
1090.019
110.0414
1100.0143
1110.456
1120.833
1130.533
1140.218
1150.13
1160.686
1170.953
1180.83
1190.131
120.353
1200.0228
1210.934
1220.678
1230.0404
1240.377
1250.323
1260.941
1270.172
1280.526
1290.0489
130.312
1300.587
1310.961
1320.84
1330.99
1340.789
1350.19
1360.65
1370.211
1380.48
1390.553
140.795
1400.563
1410.479
1420.769
1430.0117
1440.597
1450.144
1460.266
1470.0222
1480.619
1490.0496
150.311
1500.293
1510.689
1520.0365
1530.438
1540.86
1550.274
1560.717
1570.214
1580.603
1590.701
160.494
1600.0073
1610.815
1620.54
1630.6
1640.853
1650.892
1660.709
1670.286
1680.0783
1690.0555
170.185
180.471
190.0886
20.591
200.892
210.515
220.145
230.161
240.387
250.647
260.563
270.219
280.104
290.688
30.711
300.364
310.719
320.54
330.122
340.206
350.641
360.112
370.312
380.164
390.412
40.427
400.0122
410.12
420.459
430.276
440.747
450.24
460.136
470.286
480.0556
490.395
50.659
500.672
510.621
520.788
530.547
540.857
550.931
560.531
570.128
580.426
590.211
60.344
600.538
610.596
620.951
630.226
640.494
650.138
660.134
670.762
680.0323
690.565
70.646
700.597
710.819
720.353
730.00496
740.531
750.611
760.433
770.211
780.46
790.572
80.00934
800.303
810.706
820.661
830.768
840.0663
850.346
860.79
870.152
880.55
890.205
90.209
900.12
910.497
920.405
930.49
940.966
950.118
960.143
970.681
980.179
990.00773



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: CNhs12495


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)
0000066 (epithelial cell)
0000071 (blood vessel endothelial cell)
0000076 (squamous epithelial cell)
0000115 (endothelial cell)
0000213 (lining cell)
0000215 (barrier cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002078 (meso-epithelial cell)
0002139 (endothelial cell of vascular tree)
0002321 (embryonic cell)
0002371 (somatic cell)
0002544 (aortic endothelial cell)
0002546 (embryonic blood vessel endothelial progenitor cell)
1000413 (endothelial cell of artery)

UBERON: Anatomy
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000487 (simple squamous epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000947 (aorta)
0001009 (circulatory system)
0001062 (anatomical entity)
0001637 (artery)
0001917 (endothelium of artery)
0001981 (blood vessel)
0001986 (endothelium)
0002049 (vasculature)
0002050 (embryonic structure)
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)
0004638 (blood vessel endothelium)
0004700 (arterial system endothelium)
0004852 (cardiovascular system endothelium)
0004872 (splanchnic layer of lateral plate mesoderm)
0005423 (developing anatomical structure)
0006914 (squamous epithelium)
0006965 (vascular cord)
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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