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Coexpression cluster:C2639: Difference between revisions

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|tf_chipseq_enrich=EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240534204095483!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195082549671452!GATA2#2624;3:9.5586988001655:0.00181815161835744:0.0109029591679853!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.00074400985540264
|tf_chipseq_enrich=EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240534204095483!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195082549671452!GATA2#2624;3:9.5586988001655:0.00181815161835744:0.0109029591679853!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.00074400985540264
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}}
}}

Revision as of 15:37, 26 November 2012


Full id: C2639_Smooth_large_Endothelial_Aortic_osteosarcoma_Preadipocyte_Renal



Phase1 CAGE Peaks

Hg19::chr22:21134295..21134309,+p@chr22:21134295..21134309
+
Hg19::chr22:21138297..21138307,+p@chr22:21138297..21138307
+
Hg19::chr22:21138313..21138336,+p@chr22:21138313..21138336
+
Hg19::chr22:21138343..21138378,+p@chr22:21138343..21138378
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>


Cell Type
Ontology termp-valuen
vascular associated smooth muscle cell5.89e-2832
mesodermal cell3.61e-23121
blood vessel endothelial cell1.60e-2118
embryonic blood vessel endothelial progenitor cell1.60e-2118
smooth muscle cell1.60e-2043
smooth muscle myoblast1.60e-2043
endothelial cell of vascular tree4.36e-1924
muscle cell1.76e-1855
muscle precursor cell4.33e-1758
myoblast4.33e-1758
multi-potent skeletal muscle stem cell4.33e-1758
contractile cell1.17e-1659
electrically responsive cell7.67e-1661
electrically active cell7.67e-1661
endothelial cell of artery2.01e-139
endothelial cell1.19e-1236
aortic smooth muscle cell2.29e-1210
embryonic cell3.19e-12250
vein endothelial cell1.59e-116
cardiocyte1.86e-0916
non-terminally differentiated cell3.49e-09106
meso-epithelial cell4.03e-0945
lining cell1.00e-0858
barrier cell1.00e-0858
smooth muscle cell of the umbilical artery1.70e-084
somatic cell3.39e-08588
aortic endothelial cell3.46e-086
smooth muscle cell of the coronary artery4.46e-073
smooth muscle cell of the subclavian artery8.29e-075
Uber Anatomy
Ontology termp-valuen
artery3.47e-4942
arterial blood vessel3.47e-4942
arterial system3.47e-4942
epithelial tube open at both ends3.49e-4859
blood vessel3.49e-4859
blood vasculature3.49e-4859
vascular cord3.49e-4859
vessel6.02e-4468
splanchnic layer of lateral plate mesoderm8.97e-4383
epithelial tube3.10e-37117
systemic artery5.85e-3733
systemic arterial system5.85e-3733
vasculature1.91e-3678
vascular system1.91e-3678
cardiovascular system1.42e-31109
circulatory system2.67e-30112
unilaminar epithelium1.82e-23148
blood vessel endothelium1.60e-2118
endothelium1.60e-2118
cardiovascular system endothelium1.60e-2118
aorta4.66e-2021
aortic system4.66e-2021
tube1.53e-18192
simple squamous epithelium8.86e-1722
anatomical conduit1.13e-15240
skeletal muscle tissue1.87e-1562
striated muscle tissue1.87e-1562
myotome1.87e-1562
muscle tissue1.02e-1464
musculature1.02e-1464
musculature of body1.02e-1464
squamous epithelium3.12e-1425
somite1.21e-1371
presomitic mesoderm1.21e-1371
presumptive segmental plate1.21e-1371
dermomyotome1.21e-1371
trunk paraxial mesoderm1.21e-1371
lateral plate mesoderm1.58e-13203
endothelial tube2.01e-139
arterial system endothelium2.01e-139
endothelium of artery2.01e-139
paraxial mesoderm2.43e-1372
presumptive paraxial mesoderm2.43e-1372
dense mesenchyme tissue4.80e-1373
epithelial vesicle8.16e-1378
blood vessel smooth muscle2.29e-1210
arterial system smooth muscle2.29e-1210
artery smooth muscle tissue2.29e-1210
aorta smooth muscle tissue2.29e-1210
trunk mesenchyme1.77e-11122
multilaminar epithelium1.90e-1183
mesoderm1.12e-10315
mesoderm-derived structure1.12e-10315
presumptive mesoderm1.12e-10315
cell layer1.48e-10309
epithelium2.75e-10306
umbilical blood vessel6.19e-109
smooth muscle tissue2.36e-0915
umbilical artery1.70e-084
anatomical cluster6.87e-08373
mesenchyme1.48e-07160
entire embryonic mesenchyme1.48e-07160
vein2.36e-079
venous blood vessel2.36e-079
venous system2.36e-079
coronary artery4.46e-073
heart7.91e-0724
primitive heart tube7.91e-0724
primary heart field7.91e-0724
anterior lateral plate mesoderm7.91e-0724
heart tube7.91e-0724

Disease
Ontology termp-valuen


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
EBF1#187936.679850134926750.005184294118278910.0240534204095483
FOS#235348.99795530889440.0001525147711168630.00195082549671452
GATA2#262439.55869880016550.001818151618357440.0109029591679853
JUN#3725412.51282919233634.07770316866756e-050.00074400985540264



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.