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Learning pathway-based decision rules to classify microarray cancer samples

Glaab, Enrico; Garibaldi, Jonathan M.; Krasnogor, Natalio

Authors

Enrico Glaab

Jonathan M. Garibaldi

Natalio Krasnogor



Abstract

Despite recent advances in DNA chip technology current microarray gene expression studies are still affected by high noise levels, small sample sizes and large numbers of uninformative genes. Combining microarray data with cellular pathway data by using new integrative analysis methods could help to alleviate some of these problems and provide new biological insights.
We present a method for learning simple decision rules for class prediction from pairwise comparisons of cellular pathways in terms of gene set expression levels representing the up- and down-regulation of pathway members. The procedure generates compact and comprehensible sets of rules, describing changes in the relative ranks of
gene expression levels in pairs of pathways across different biological conditions. Results for two large-scale microarray studies, containing samples from prostate cancer and B-cell lymphoma patients, show that the method provides robust and accurate rule sets and new insights on differentially regulated pathway pairs. However, the main benefit of these predictive models in comparison to other classification methods like support vector machines lies not in the attained accuracy levels but in the ease of interpretation and the insights they provide on the relative regulation of cellular pathways in the biological conditions under consideration.

Citation

Glaab, E., Garibaldi, J. M., & Krasnogor, N. (2010). Learning pathway-based decision rules to classify microarray cancer samples

Conference Name 25th German Conference on Bioinformatics 2010
End Date Sep 22, 2010
Publication Date Sep 1, 2010
Deposit Date Jul 31, 2012
Publicly Available Date Jul 31, 2012
Peer Reviewed Peer Reviewed
Public URL http://eprints.nottingham.ac.uk/id/eprint/1424
Publisher URL http://www.gi.de/service/publikationen/lni/gi-edition-proceedings-2010/gi-edition-lecture-notes-in-informatics-lni-p-173.html
Additional Information First published in: Schomberg, Dietmar, & Grote, Andreas, eds, German Conference on Bioinformatics 2010 : September 20-22, 2010, Technische Universität Carolo Wilhelmina zu Braunschweig, Germany. Bonn : Gesellschaft für Informatik, 2010. (Lecture notes in informatics ; P-173). ISBN: 9783885792673, pp. 123-134.

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