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FF:11340-117F8: 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 16:47, 29 March 2012


Name:Endothelial Cells - Aortic, donor2
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 stage56 years old adult
sexfemale
age56
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 number1508
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-0.0713
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
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: CNhs11375

Jaspar motifP-value
MA0002.20.466
MA0003.10.359
MA0004.10.692
MA0006.10.0678
MA0007.10.0246
MA0009.10.475
MA0014.10.86
MA0017.10.238
MA0018.24.32923e-6
MA0019.10.425
MA0024.10.488
MA0025.10.555
MA0027.10.961
MA0028.10.011
MA0029.10.392
MA0030.10.503
MA0031.10.459
MA0035.20.00178
MA0038.10.815
MA0039.20.195
MA0040.10.251
MA0041.10.0732
MA0042.10.65
MA0043.12.98206e-8
MA0046.10.352
MA0047.20.399
MA0048.10.47
MA0050.13.42663e-4
MA0051.10.0348
MA0052.10.999
MA0055.10.104
MA0057.10.0945
MA0058.10.237
MA0059.10.942
MA0060.10.348
MA0061.10.275
MA0062.20.00199
MA0065.20.506
MA0066.10.88
MA0067.10.00637
MA0068.10.894
MA0069.10.265
MA0070.10.996
MA0071.10.374
MA0072.10.261
MA0073.10.395
MA0074.10.899
MA0076.18.34533e-5
MA0077.19.99611e-6
MA0078.10.015
MA0079.20.248
MA0080.23.8535e-4
MA0081.10.118
MA0083.10.221
MA0084.10.613
MA0087.10.264
MA0088.10.627
MA0090.10.132
MA0091.10.284
MA0092.10.318
MA0093.10.536
MA0099.24.41357e-12
MA0100.10.329
MA0101.10.505
MA0102.26.16765e-5
MA0103.10.553
MA0104.20.105
MA0105.10.729
MA0106.16.27341e-4
MA0107.10.71
MA0108.20.905
MA0111.10.673
MA0112.20.498
MA0113.10.263
MA0114.10.843
MA0115.10.543
MA0116.10.784
MA0117.10.287
MA0119.10.00227
MA0122.10.069
MA0124.10.159
MA0125.10.952
MA0131.10.436
MA0135.10.755
MA0136.10.0146
MA0137.20.0263
MA0138.20.984
MA0139.10.435
MA0140.10.00442
MA0141.10.0536
MA0142.10.388
MA0143.10.858
MA0144.10.927
MA0145.10.0543
MA0146.10.317
MA0147.10.434
MA0148.10.0447
MA0149.10.0186
MA0150.10.131
MA0152.10.597
MA0153.10.379
MA0154.10.633
MA0155.10.0217
MA0156.10.0342
MA0157.10.674
MA0159.10.517
MA0160.10.419
MA0162.10.0905
MA0163.10.495
MA0164.10.598
MA0258.10.568
MA0259.10.281



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: CNhs11375

Novel motifP-value
10.503
100.226
1000.946
1010.537
1020.82
1030.695
1040.889
1050.633
1060.0356
1070.00135
1080.605
1090.144
110.118
1100.0315
1110.0812
1120.672
1130.708
1140.136
1150.822
1160.908
1170.804
1180.521
1190.38
120.629
1200.102
1210.665
1220.781
1230.501
1240.494
1250.856
1260.64
1270.991
1280.331
1290.378
130.86
1300.876
1310.599
1320.297
1330.419
1340.575
1350.262
1360.33
1370.252
1380.739
1390.874
140.987
1400.847
1410.444
1420.411
1430.128
1440.482
1450.0333
1460.285
1470.157
1480.404
1490.0174
150.656
1500.184
1510.405
1520.0159
1530.265
1540.618
1550.676
1560.0699
1570.705
1580.173
1590.608
160.832
1600.0118
1610.268
1620.511
1630.875
1640.638
1650.426
1660.489
1670.0302
1680.263
1690.0513
170.119
180.8
190.114
20.459
200.926
210.954
220.216
230.0613
240.446
250.504
260.732
270.454
280.161
290.539
30.665
300.793
310.949
320.609
330.354
340.114
350.329
360.262
370.505
380.106
390.199
40.606
400.00484
410.0501
420.365
430.575
440.635
450.213
460.207
470.371
480.047
490.732
50.726
500.587
510.574
520.477
530.878
540.489
550.78
560.492
570.213
580.423
590.173
60.28
600.538
610.707
620.983
630.135
640.525
650.0992
660.102
670.639
680.221
690.226
70.677
700.878
710.925
720.757
730.00455
740.478
750.47
760.362
770.119
780.67
790.73
80.0375
800.274
810.506
820.94
830.546
840.242
850.977
860.771
870.312
880.986
890.505
90.191
900.733
910.306
920.301
930.952
940.815
950.312
960.271
970.505
980.189
990.00223



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: CNhs11375


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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