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FF:11413-118E9: 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 17:07, 29 March 2012


Name:Endothelial Cells - Artery, donor3
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 stage53 years old adult
sexmale
age53
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 number1596
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-0.11
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-lymphoma0.15
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: CNhs12023

Jaspar motifP-value
MA0002.20.189
MA0003.10.378
MA0004.10.312
MA0006.10.0516
MA0007.10.0471
MA0009.10.292
MA0014.10.994
MA0017.10.682
MA0018.22.88203e-4
MA0019.10.0404
MA0024.10.224
MA0025.10.948
MA0027.10.943
MA0028.10.643
MA0029.10.493
MA0030.10.181
MA0031.10.114
MA0035.20.00179
MA0038.10.152
MA0039.20.254
MA0040.10.46
MA0041.10.203
MA0042.10.719
MA0043.11.00519e-5
MA0046.10.645
MA0047.20.267
MA0048.10.0225
MA0050.10.0148
MA0051.10.696
MA0052.10.564
MA0055.11.43533e-4
MA0057.10.292
MA0058.10.308
MA0059.10.135
MA0060.18.92255e-4
MA0061.10.21
MA0062.20.381
MA0065.20.832
MA0066.10.811
MA0067.10.0966
MA0068.10.939
MA0069.10.0782
MA0070.10.996
MA0071.10.761
MA0072.10.518
MA0073.10.266
MA0074.10.778
MA0076.10.28
MA0077.12.36816e-6
MA0078.10.062
MA0079.20.327
MA0080.22.63279e-4
MA0081.10.0856
MA0083.10.173
MA0084.10.316
MA0087.10.194
MA0088.10.153
MA0090.10.214
MA0091.10.723
MA0092.10.706
MA0093.10.317
MA0099.22.79238e-14
MA0100.10.3
MA0101.10.681
MA0102.25.67965e-5
MA0103.10.0311
MA0104.20.871
MA0105.10.415
MA0106.10.00645
MA0107.10.615
MA0108.20.00719
MA0111.10.364
MA0112.20.637
MA0113.10.197
MA0114.10.339
MA0115.10.787
MA0116.10.916
MA0117.10.298
MA0119.10.0146
MA0122.10.056
MA0124.10.568
MA0125.10.458
MA0131.10.638
MA0135.10.274
MA0136.10.0068
MA0137.20.372
MA0138.20.896
MA0139.10.376
MA0140.10.0033
MA0141.10.0535
MA0142.10.443
MA0143.10.559
MA0144.10.331
MA0145.10.165
MA0146.10.751
MA0147.10.552
MA0148.10.128
MA0149.10.0187
MA0150.10.0519
MA0152.10.374
MA0153.10.539
MA0154.10.813
MA0155.10.122
MA0156.11.00275e-4
MA0157.10.431
MA0159.10.91
MA0160.10.485
MA0162.10.0998
MA0163.10.336
MA0164.10.658
MA0258.10.684
MA0259.10.89



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: CNhs12023

Novel motifP-value
10.864
100.512
1000.517
1010.0239
1020.716
1030.63
1040.686
1050.754
1060.319
1070.00579
1080.549
1090.0826
110.21
1100.016
1110.817
1120.699
1130.0805
1140.964
1150.683
1160.468
1170.502
1180.201
1190.972
120.342
1200.028
1210.251
1220.751
1230.00866
1240.0322
1250.676
1260.682
1270.882
1280.385
1290.735
130.167
1300.217
1310.484
1320.533
1330.274
1340.401
1350.364
1360.00972
1370.104
1380.999
1390.671
140.472
1400.82
1410.926
1420.863
1430.174
1440.11
1450.151
1460.131
1470.486
1480.0462
1490.109
150.935
1500.0428
1510.996
1520.0233
1530.0312
1540.82
1550.467
1560.417
1570.185
1580.0373
1590.669
161
1600.0622
1610.447
1620.775
1630.902
1640.662
1650.0683
1660.214
1670.115
1680.46
1690.128
170.364
180.56
190.253
20.84
200.481
210.617
220.417
230.695
240.442
250.452
260.428
270.794
280.0735
290.575
30.786
300.874
310.766
320.509
330.248
340.226
350.253
360.0997
370.508
380.29
390.584
40.929
400.00449
410.207
420.835
430.426
440.79
450.262
460.948
470.362
480.0743
490.21
50.458
500.61
510.87
520.242
530.443
540.688
550.154
560.835
570.47
580.0544
590.168
60.268
600.381
610.957
620.25
630.403
640.809
650.892
660.0864
670.717
680.219
690.532
70.753
700.24
710.683
720.362
731.45882e-4
740.232
750.424
760.771
770.156
780.595
790.188
80.0378
800.919
810.256
820.175
830.655
840.414
850.196
860.918
870.00149
880.937
890.757
90.516
900.0666
910.602
920.496
930.836
940.19
950.0176
960.583
970.782
980.492
990.00676



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: CNhs12023


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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