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FF:11344-117G3: 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 - Vein, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuevein
dev stageinfant
sexmale
ageNeonatal
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 number1643
catalog numberCA200-R10n
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-0.17
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-lymphoma0.0166
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: CNhs11377

Jaspar motifP-value
MA0002.20.547
MA0003.10.127
MA0004.10.333
MA0006.10.156
MA0007.10.0124
MA0009.10.969
MA0014.10.992
MA0017.10.105
MA0018.20.00418
MA0019.10.0795
MA0024.10.213
MA0025.10.481
MA0027.10.954
MA0028.10.102
MA0029.10.319
MA0030.10.914
MA0031.10.34
MA0035.29.86183e-4
MA0038.10.284
MA0039.20.677
MA0040.10.406
MA0041.10.287
MA0042.10.663
MA0043.17.45945e-5
MA0046.10.174
MA0047.20.245
MA0048.10.481
MA0050.18.26333e-5
MA0051.10.0216
MA0052.10.235
MA0055.10.0737
MA0057.10.364
MA0058.10.321
MA0059.10.0462
MA0060.10.00204
MA0061.10.606
MA0062.20.0457
MA0065.20.174
MA0066.10.871
MA0067.10.19
MA0068.10.0494
MA0069.10.417
MA0070.10.426
MA0071.10.331
MA0072.10.481
MA0073.10.19
MA0074.10.811
MA0076.10.00418
MA0077.17.9121e-6
MA0078.10.00482
MA0079.20.839
MA0080.21.97242e-4
MA0081.10.0586
MA0083.10.0344
MA0084.10.312
MA0087.10.24
MA0088.10.25
MA0090.10.375
MA0091.10.717
MA0092.10.542
MA0093.10.309
MA0099.21.98138e-20
MA0100.10.214
MA0101.10.855
MA0102.26.31832e-4
MA0103.10.378
MA0104.20.488
MA0105.10.819
MA0106.10.00297
MA0107.10.811
MA0108.25.42254e-5
MA0111.10.811
MA0112.20.16
MA0113.10.17
MA0114.10.643
MA0115.10.436
MA0116.10.279
MA0117.10.536
MA0119.10.0931
MA0122.10.185
MA0124.10.236
MA0125.10.577
MA0131.10.332
MA0135.10.325
MA0136.10.0322
MA0137.20.182
MA0138.20.649
MA0139.10.222
MA0140.11.50826e-4
MA0141.10.0476
MA0142.10.193
MA0143.10.418
MA0144.10.911
MA0145.10.0556
MA0146.10.68
MA0147.10.157
MA0148.10.0965
MA0149.10.0429
MA0150.10.00557
MA0152.10.568
MA0153.10.329
MA0154.10.22
MA0155.10.0404
MA0156.10.0343
MA0157.10.816
MA0159.10.452
MA0160.10.141
MA0162.10.0571
MA0163.10.215
MA0164.10.396
MA0258.10.453
MA0259.10.985



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: CNhs11377

Novel motifP-value
10.5
100.265
1000.929
1010.368
1020.728
1030.967
1040.747
1050.465
1060.0558
1070.0721
1080.83
1090.171
110.0791
1100.0327
1110.538
1120.913
1130.317
1140.258
1150.613
1160.679
1170.51
1180.721
1190.356
120.0653
1200.00551
1210.641
1220.283
1230.104
1240.915
1250.575
1260.533
1270.484
1280.551
1290.106
130.305
1300.302
1310.394
1320.822
1330.356
1340.761
1350.0303
1360.359
1370.232
1380.696
1390.458
140.884
1400.248
1410.132
1420.659
1430.0314
1440.41
1450.0308
1460.0496
1470.15
1480.246
1490.0499
150.253
1500.125
1510.824
1520.0756
1530.536
1540.418
1550.919
1560.0505
1570.473
1580.551
1590.698
160.861
1600.0297
1610.634
1620.632
1630.571
1640.739
1650.724
1660.144
1670.0519
1680.996
1690.0394
170.144
180.325
190.239
20.701
200.978
210.67
220.285
230.111
240.211
250.72
260.394
270.384
280.278
290.95
30.755
300.474
310.752
320.468
330.283
340.0725
350.604
360.0653
370.357
380.261
390.556
40.375
400.0066
410.0309
420.385
430.449
440.299
450.193
460.082
470.359
480.0578
490.623
50.684
500.878
510.697
520.951
530.815
540.993
550.694
560.814
570.326
580.362
590.0654
60.344
600.526
610.853
620.815
630.411
640.45
650.182
660.0434
670.779
680.0676
690.374
70.184
700.921
710.601
720.913
730.00958
740.277
750.491
760.482
770.309
780.755
790.946
80.02
800.0987
810.516
820.831
830.652
840.136
850.351
860.697
870.134
880.656
890.285
90.082
900.478
910.163
920.55
930.548
940.988
950.277
960.209
970.47
980.147
990.0257



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: CNhs11377


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)
0002543 (vein endothelial cell)
0002546 (embryonic blood vessel endothelial progenitor cell)

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)
0001009 (circulatory system)
0001062 (anatomical entity)
0001638 (vein)
0001981 (blood vessel)
0001986 (endothelium)
0002049 (vasculature)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003914 (epithelial tube)
0003920 (venous blood vessel)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004582 (venous system)
0004638 (blood vessel 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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