Revisiting the Yeast Cell Cycle Problem with the Improved TriGen Algorithm

Abstract

Analyzing microarray data represents a computational challenge due to the characteristics of these data. Clustering techniques are widely applied to create groups of genes that exhibit a similar behavior under the conditions tested. Biclustering emerges as an improvement of classical clustering since it relaxes the constraints for grouping allowing genes to be evaluated only under a subset of the conditions and not under all of them. However, this technique is not appropriate for the analysis of temporal microarray data in which the genes are evaluated under certain conditions at several time points. On a previous work we presented the TriGen algorithm, a genetic algorithm that finds triclusters of gene expression that take into account the experimental conditions and the time points simultaneously, and was applied to the yeast (Saccharomyces Cerevisiae) cell cycle problem. In this article we present some improvements on the genetic algorithm and we also present the results of applying the improved TriGen algorithm to the yeast cell cycle problem, where the goal is to identify all genes whose expression levels are regulated by the cell cycle.