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Bioinformatics Advance Access originally published online on April 26, 2007
Bioinformatics 2007 23(12):1503-1510; doi:10.1093/bioinformatics/btm141
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Identifying the biologically relevant gene categories based on gene expression and biological data: an example on prostate cancer

D. Huang * and Tommy W. S. Chow

Department of Electrical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR

*To whom correspondence should be addressed.


  Abstract

Motivation: Most gene-expression based studies aim to identify genes with the capability of distinguishing different phenotypes. Although analysis at the genomic level is important, results of the molecular/cellular level are essential for understanding biological mechanisms. To deliver molecular/cellular-level results, a two-stage scheme is widely employed. This scheme just evaluates biological processes/molecular activities individually, totally overlooking the relationship between processes/activities. This treatment conflicts with the fact that most biological processes/molecular activities do not work alone. In order to deliver improved results, this shortcoming should be addressed.

Results: We design a selection model from a novel perspective to directly detect important gene functional categories (each category represents a cellular process or a molecular activity). More importantly, the correlations between gene categories are considered. Contributed by this capability, the proposed method shows its advantages over others.

Availability: the source code in Matlab is accessible via http://www.ee.cityu.edu.hk/~twschow/category_selection/category_selection.htm

Contact: ifkorf{at}ucdavis.edu

Supplementary information: http://www.ee.cityu.edu.hk/~twschow/category_selection/category_selection.htm

Associate Editor: Alfonso Valencia

Received on July 10, 2006; revised on April 2, 2007; accepted on April 6, 2007

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