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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.<\/jats:p><jats:p>Availability: freely available at http:\/\/pathvar.embl.de<\/jats:p><jats:p>Contact: \u00a0enrico.glaab@uni.lu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr656","type":"journal-article","created":{"date-parts":[[2011,11,29]],"date-time":"2011-11-29T04:16:10Z","timestamp":1322540170000},"page":"446-447","source":"Crossref","is-referenced-by-count":10,"title":["PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data"],"prefix":"10.1093","volume":"28","author":[{"given":"Enrico","family":"Glaab","sequence":"first","affiliation":[{"name":"1 Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg and 2Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, Germany"},{"name":"1 Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg and 2Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, Germany"}]},{"given":"Reinhard","family":"Schneider","sequence":"additional","affiliation":[{"name":"1 Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg and 2Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, Germany"},{"name":"1 Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg and 2Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2011,11,28]]},"reference":[{"key":"2023012512170374700_B1","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1093\/nar\/29.1.37","article-title":"The InterPro database, an integrated documentation resource for protein families, domains and functional sites","volume":"29","author":"Apweiler","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023012512170374700_B2","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. 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