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

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. © The Author 2007. Published by Oxford University Press. All rights reserved.