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FF:11207-116A1: 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 16:33, 29 March 2012


Name:Endothelial Cells - Aortic, donor0
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 stageNA
sexNA
ageNA
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 numberNA
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-penis-0.168
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-lymphoma0.157
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: CNhs10837

Jaspar motifP-value
MA0002.20.172
MA0003.10.606
MA0004.10.389
MA0006.10.0472
MA0007.10.0852
MA0009.10.462
MA0014.10.751
MA0017.10.895
MA0018.20.00766
MA0019.10.238
MA0024.10.0484
MA0025.10.679
MA0027.10.594
MA0028.10.146
MA0029.10.46
MA0030.10.811
MA0031.10.911
MA0035.20.00386
MA0038.10.0101
MA0039.20.0356
MA0040.10.301
MA0041.10.134
MA0042.10.565
MA0043.16.30138e-4
MA0046.10.605
MA0047.20.223
MA0048.10.0306
MA0050.10.0915
MA0051.10.95
MA0052.10.635
MA0055.14.35004e-4
MA0057.10.368
MA0058.10.478
MA0059.10.515
MA0060.13.19207e-5
MA0061.10.0138
MA0062.20.174
MA0065.20.658
MA0066.10.526
MA0067.10.33
MA0068.10.402
MA0069.10.178
MA0070.10.967
MA0071.10.997
MA0072.10.544
MA0073.10.178
MA0074.10.375
MA0076.10.929
MA0077.11.10068e-6
MA0078.10.0365
MA0079.20.324
MA0080.27.28666e-6
MA0081.10.0763
MA0083.10.124
MA0084.10.188
MA0087.10.0897
MA0088.10.0928
MA0090.10.42
MA0091.10.772
MA0092.10.335
MA0093.10.361
MA0099.27.77459e-22
MA0100.10.821
MA0101.10.99
MA0102.20.00272
MA0103.10.00118
MA0104.20.472
MA0105.10.0346
MA0106.10.00192
MA0107.10.636
MA0108.20.173
MA0111.10.193
MA0112.20.253
MA0113.10.264
MA0114.10.299
MA0115.10.772
MA0116.10.151
MA0117.10.653
MA0119.10.0437
MA0122.10.0376
MA0124.10.43
MA0125.10.575
MA0131.10.385
MA0135.10.859
MA0136.13.41583e-5
MA0137.20.769
MA0138.20.261
MA0139.10.381
MA0140.12.90656e-4
MA0141.10.323
MA0142.10.572
MA0143.10.719
MA0144.10.244
MA0145.10.119
MA0146.10.835
MA0147.10.905
MA0148.10.0645
MA0149.10.0144
MA0150.15.29734e-4
MA0152.10.78
MA0153.10.204
MA0154.10.181
MA0155.10.39
MA0156.11.40585e-8
MA0157.10.717
MA0159.10.721
MA0160.10.603
MA0162.10.13
MA0163.10.0309
MA0164.10.786
MA0258.10.277
MA0259.10.887



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: CNhs10837

Novel motifP-value
10.724
100.679
1000.692
1010.0941
1020.871
1030.661
1040.908
1050.95
1060.932
1070.182
1080.972
1090.201
110.501
1100.0279
1110.859
1120.522
1130.131
1140.796
1150.189
1160.588
1170.568
1180.981
1190.644
120.268
1200.132
1210.323
1220.452
1230.0247
1240.0518
1250.429
1260.519
1270.803
1280.358
1290.487
130.257
1300.179
1310.91
1320.938
1330.401
1340.94
1350.239
1360.0517
1370.348
1380.815
1390.215
140.365
1400.856
1410.475
1420.71
1430.314
1440.403
1450.226
1460.169
1470.541
1480.0169
1490.271
150.887
1500.178
1510.732
1520.0285
1530.238
1540.857
1550.191
1560.0728
1570.0172
1580.106
1590.427
160.679
1600.216
1610.0821
1620.334
1630.499
1640.783
1650.599
1660.52
1670.173
1680.219
1690.282
170.507
180.758
190.405
20.682
200.244
210.492
220.62
230.583
240.334
250.296
260.574
270.427
280.21
290.819
30.551
300.905
310.38
320.0622
330.146
340.186
350.0367
360.0748
370.457
380.341
390.52
40.719
400.011
410.136
420.738
430.292
440.0893
450.364
460.985
470.486
480.102
490.359
50.789
500.507
510.434
520.244
530.463
540.964
550.184
560.936
570.334
580.0365
590.976
60.159
600.285
610.964
620.16
630.558
640.757
650.893
660.014
670.845
680.325
690.955
70.543
700.0495
710.688
720.225
733.55325e-4
740.108
750.417
760.879
770.681
780.637
790.561
80.162
800.295
810.217
820.107
830.444
840.892
850.0291
860.756
870.0265
880.884
890.899
90.499
900.333
910.705
920.34
930.991
940.253
950.153
960.746
970.423
980.908
990.0395



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: CNhs10837


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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