Dataset Information

PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data.

ABSTRACT:

Summary

Finding significant differences between the expression levels of genes or proteins across diverse biological conditions is one of the primary goals in the analysis of functional genomics data. However, existing methods for identifying differentially expressed genes or sets of genes by comparing measures of the average expression across predefined sample groups do not detect differential variance in the expression levels across genes in cellular pathways. Since corresponding pathway deregulations occur frequently in microarray gene or protein expression data, we present a new dedicated web application, PathVar, to analyze these data sources. The software ranks pathway-representing gene/protein sets in terms of the differences of the variance in the within-pathway expression levels across different biological conditions. Apart from identifying new pathway deregulation patterns, the tool exploits these patterns by combining different machine learning methods to find clusters of similar samples and build sample classification models.

Availability

freely available at http://pathvar.embl.de

Contact

enrico.glaab@uni.lu

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Glaab E

PROVIDER: S-EPMC3268235 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature

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Publications

PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data.

Glaab Enrico E Schneider Reinhard R

Bioinformatics (Oxford, England) 20111128 3

<h4>Summary</h4>Finding significant differences between the expression levels of genes or proteins across diverse biological conditions is one of the primary goals in the analysis of functional genomics data. However, existing methods for identifying differentially expressed genes or sets of genes by comparing measures of the average expression across predefined sample groups do not detect differential variance in the expression levels across genes in cellular pathways. Since corresponding pathw ...[more]

PMID: 22123829

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Dataset Information

PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data.

Summary

Availability

Contact

Supplementary information

Publications

PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data.

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