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FF:11341-117F9: 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 17:04, 29 March 2012


Name:Endothelial Cells - Artery, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueartery
dev stage26 years old adult
sexmale
age26
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 number2463
catalog numberCA300-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-0.0581
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-lymphoma0.158
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: CNhs11977

Jaspar motifP-value
MA0002.20.014
MA0003.10.449
MA0004.10.854
MA0006.10.0212
MA0007.10.0872
MA0009.10.801
MA0014.10.607
MA0017.10.33
MA0018.25.33733e-6
MA0019.10.0135
MA0024.10.753
MA0025.10.402
MA0027.10.808
MA0028.10.179
MA0029.10.747
MA0030.10.101
MA0031.10.0725
MA0035.20.0946
MA0038.10.494
MA0039.20.643
MA0040.10.293
MA0041.10.309
MA0042.10.849
MA0043.16.10315e-8
MA0046.10.352
MA0047.20.5
MA0048.10.0259
MA0050.10.016
MA0051.10.319
MA0052.10.00925
MA0055.10.0686
MA0057.10.304
MA0058.10.826
MA0059.10.0953
MA0060.10.507
MA0061.10.2
MA0062.20.0419
MA0065.20.22
MA0066.10.465
MA0067.10.025
MA0068.10.821
MA0069.10.198
MA0070.10.905
MA0071.10.355
MA0072.10.706
MA0073.10.34
MA0074.10.206
MA0076.10.0016
MA0077.14.10471e-6
MA0078.10.0107
MA0079.20.236
MA0080.20.818
MA0081.10.42
MA0083.10.351
MA0084.10.056
MA0087.10.155
MA0088.10.327
MA0090.10.714
MA0091.10.613
MA0092.10.97
MA0093.10.894
MA0099.20.379
MA0100.10.328
MA0101.10.221
MA0102.29.79626e-6
MA0103.10.425
MA0104.20.463
MA0105.10.659
MA0106.10.00955
MA0107.10.286
MA0108.20.443
MA0111.10.811
MA0112.20.702
MA0113.10.361
MA0114.10.513
MA0115.10.797
MA0116.10.116
MA0117.10.22
MA0119.10.0867
MA0122.10.497
MA0124.10.669
MA0125.10.596
MA0131.10.471
MA0135.10.667
MA0136.10.902
MA0137.20.02
MA0138.20.634
MA0139.10.107
MA0140.10.493
MA0141.10.016
MA0142.10.924
MA0143.10.807
MA0144.10.824
MA0145.10.269
MA0146.10.449
MA0147.10.885
MA0148.10.129
MA0149.10.03
MA0150.10.402
MA0152.10.468
MA0153.10.0504
MA0154.10.617
MA0155.10.147
MA0156.10.748
MA0157.10.254
MA0159.10.257
MA0160.10.951
MA0162.10.135
MA0163.10.679
MA0164.10.428
MA0258.10.986
MA0259.10.681



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: CNhs11977

Novel motifP-value
10.831
100.881
1000.753
1010.1
1020.6
1030.299
1040.992
1050.137
1060.0741
1070.0188
1080.18
1090.175
110.203
1100.0405
1110.411
1120.646
1130.429
1140.341
1150.481
1160.0806
1170.632
1180.382
1190.66
120.819
1200.00104
1210.995
1220.43
1230.0143
1240.0374
1250.386
1260.492
1270.923
1280.99
1290.367
130.318
1300.752
1310.253
1320.185
1330.45
1340.0985
1350.561
1360.00902
1370.114
1380.819
1390.759
140.433
1400.35
1410.537
1420.627
1430.187
1440.396
1450.297
1460.956
1470.0832
1480.96
1490.0846
150.864
1500.0587
1510.587
1520.0207
1530.0201
1540.436
1550.885
1560.233
1570.557
1580.0396
1590.595
160.364
1600.06
1610.424
1620.729
1630.91
1640.0711
1650.326
1660.191
1670.149
1680.368
1690.0902
170.244
180.767
190.163
20.535
200.562
210.388
220.348
230.865
240.76
250.458
260.824
270.486
280.135
290.185
30.976
300.684
310.876
320.418
330.762
340.359
350.597
360.364
370.187
380.457
390.353
40.473
400.134
410.202
420.743
430.872
440.0707
450.508
460.393
470.261
480.142
490.278
50.472
500.831
510.555
520.608
530.195
540.854
550.33
560.856
570.986
580.161
590.0162
60.161
601
610.651
620.825
630.563
640.97
650.642
660.568
670.275
680.437
690.086
70.858
700.697
710.977
720.587
735.32496e-4
740.726
750.222
760.795
770.0394
780.292
790.0129
80.0178
800.693
810.573
820.857
830.118
840.0973
850.84
860.995
870.0252
880.59
890.584
90.656
900.705
910.517
920.853
930.162
940.593
950.0249
960.861
970.832
980.766
990.0154



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: CNhs11977


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)
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)
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)
0004572 (arterial system)
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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