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FF:11264-116G4: 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 - Artery, donor1
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 stage51 years old adult
sexfemale
age51
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 number1851
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-0.0318
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-0.0782
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: CNhs12496

Jaspar motifP-value
MA0002.20.45
MA0003.10.332
MA0004.10.93
MA0006.10.0444
MA0007.10.0379
MA0009.10.34
MA0014.10.816
MA0017.10.235
MA0018.24.9676e-5
MA0019.10.0332
MA0024.10.00311
MA0025.10.287
MA0027.10.931
MA0028.10.0514
MA0029.10.265
MA0030.10.506
MA0031.10.267
MA0035.20.00474
MA0038.10.429
MA0039.20.367
MA0040.10.279
MA0041.10.199
MA0042.10.593
MA0043.15.95052e-7
MA0046.10.622
MA0047.20.0275
MA0048.10.342
MA0050.10.034
MA0051.10.842
MA0052.10.195
MA0055.10.0379
MA0057.10.132
MA0058.10.868
MA0059.10.76
MA0060.10.37
MA0061.10.954
MA0062.20.0351
MA0065.20.585
MA0066.10.658
MA0067.10.0278
MA0068.10.8
MA0069.10.104
MA0070.10.702
MA0071.10.212
MA0072.10.568
MA0073.10.399
MA0074.10.26
MA0076.15.17806e-4
MA0077.13.23815e-6
MA0078.10.0562
MA0079.20.216
MA0080.20.0315
MA0081.10.434
MA0083.10.176
MA0084.10.643
MA0087.10.568
MA0088.10.686
MA0090.10.196
MA0091.10.401
MA0092.10.778
MA0093.10.961
MA0099.21.3098e-7
MA0100.10.0774
MA0101.10.762
MA0102.26.46064e-5
MA0103.10.673
MA0104.20.122
MA0105.10.9
MA0106.10.0244
MA0107.10.357
MA0108.20.259
MA0111.10.4
MA0112.20.9
MA0113.10.201
MA0114.10.355
MA0115.10.277
MA0116.10.508
MA0117.10.253
MA0119.10.0918
MA0122.10.263
MA0124.10.883
MA0125.10.643
MA0131.10.322
MA0135.10.309
MA0136.10.101
MA0137.20.0581
MA0138.20.936
MA0139.10.504
MA0140.10.0335
MA0141.10.0157
MA0142.10.326
MA0143.10.444
MA0144.10.555
MA0145.10.203
MA0146.10.498
MA0147.10.296
MA0148.10.0254
MA0149.10.0978
MA0150.10.451
MA0152.10.809
MA0153.10.102
MA0154.10.318
MA0155.10.0361
MA0156.10.13
MA0157.10.344
MA0159.10.402
MA0160.10.142
MA0162.10.0394
MA0163.10.541
MA0164.10.739
MA0258.10.961
MA0259.10.193



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: CNhs12496

Novel motifP-value
10.902
100.204
1000.951
1010.112
1020.73
1030.58
1040.671
1050.898
1060.246
1070.0479
1080.303
1090.33
110.257
1100.0708
1110.74
1120.467
1130.372
1140.511
1150.698
1160.285
1170.772
1180.339
1190.777
120.573
1200.00172
1210.609
1220.681
1230.00461
1240.126
1250.915
1260.713
1270.439
1280.435
1290.398
130.886
1300.889
1310.532
1320.137
1330.905
1340.548
1350.305
1360.413
1370.106
1380.572
1390.562
140.914
1400.711
1410.915
1420.762
1430.105
1440.727
1450.197
1460.399
1470.0626
1480.442
1490.0124
150.964
1500.184
1510.804
1520.0194
1530.0626
1540.337
1550.564
1560.301
1570.871
1580.107
1590.843
160.471
1600.034
1610.273
1620.883
1630.725
1640.366
1650.121
1660.518
1670.132
1680.336
1690.0688
170.261
180.839
190.283
20.27
200.559
210.851
220.247
230.252
240.731
250.378
260.803
270.226
280.182
290.854
30.841
300.672
310.65
320.48
330.361
340.0755
350.444
360.248
370.299
380.183
390.508
40.969
400.00508
410.0806
420.913
430.795
440.774
450.234
460.496
470.588
480.138
490.734
50.878
500.744
510.616
520.698
530.325
540.525
550.714
560.76
570.561
580.191
590.0624
60.21
600.868
610.837
620.672
630.396
640.68
650.119
660.605
670.409
680.0552
690.23
70.972
700.677
710.689
720.102
730.00241
740.348
750.546
760.409
770.0382
780.815
790.0138
80.0276
800.237
810.597
820.744
830.415
840.465
850.819
860.655
870.111
880.8
890.145
90.327
900.117
910.363
920.507
930.841
940.965
950.0419
960.35
970.552
980.372
990.0135



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: CNhs12496


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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