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Coexpression cluster:C4429: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4429_Adipocyte_Preadipocyte_neuroblastoma_Smooth_Fibroblast_Mesenchymal_mesenchymal
|full_id=C4429_Adipocyte_Preadipocyte_neuroblastoma_Smooth_Fibroblast_Mesenchymal_mesenchymal
|id=C4429
|id=C4429

Revision as of 17:30, 12 September 2012


Full id: C4429_Adipocyte_Preadipocyte_neuroblastoma_Smooth_Fibroblast_Mesenchymal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr4:80993800..80993850,-p5@ANTXR2
Hg19::chr4:80993855..80993906,-p3@ANTXR2
Hg19::chr4:80993925..80993962,-p4@ANTXR2


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>


Uber Anatomy
Ontology termp-valuen
splanchnic layer of lateral plate mesoderm1.63e-2184
blood vessel2.46e-1960
epithelial tube open at both ends2.46e-1960
blood vasculature2.46e-1960
vascular cord2.46e-1960
vasculature1.67e-1879
vascular system1.67e-1879
vessel3.21e-1869
artery5.60e-1642
arterial blood vessel5.60e-1642
arterial system5.60e-1642
cardiovascular system8.09e-16110
circulatory system1.02e-15113
epithelial tube6.91e-15118
muscle tissue1.49e-1363
musculature1.49e-1363
musculature of body1.49e-1363
musculoskeletal system3.95e-13167
multilaminar epithelium6.45e-1382
systemic artery7.21e-1333
systemic arterial system7.21e-1333
unilaminar epithelium7.69e-13138
somite7.77e-1383
paraxial mesoderm7.77e-1383
presomitic mesoderm7.77e-1383
presumptive segmental plate7.77e-1383
trunk paraxial mesoderm7.77e-1383
presumptive paraxial mesoderm7.77e-1383
skeletal muscle tissue8.19e-1361
striated muscle tissue8.19e-1361
myotome8.19e-1361
multi-cellular organism1.43e-12659
dermomyotome1.69e-1270
anatomical system2.59e-12625
anatomical group5.58e-12626
lateral plate mesoderm1.58e-11216
trunk mesenchyme5.50e-11143
mesoderm2.49e-09448
mesoderm-derived structure2.49e-09448
presumptive mesoderm2.49e-09448
aorta2.21e-0821
aortic system2.21e-0821
embryonic structure2.83e-08605
developing anatomical structure2.83e-08605
germ layer4.60e-08604
embryonic tissue4.60e-08604
presumptive structure4.60e-08604
epiblast (generic)4.60e-08604
embryo8.72e-08612
tissue6.46e-07787
trunk9.26e-07216
Disease
Ontology termp-valuen
ovarian cancer1.39e-0714


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
CTCF#1066435.360256373075030.0064925092527670.0280763187383435
ETS1#211339.728760922202340.001085840092584840.00764281260476262
HMGN3#932438.178547723350590.001827766942164210.0109011565114893
TRIM28#10155212.39368336350830.008368344129438470.0329356908552315
ZNF263#1012738.221841637010680.001799043925565870.010984527830586



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.