In recent years,microarray technology has been widely applied in biological and clinical studies for simultaneous monitoring of gene expression in thousands of genes.Gene clustering analysis is found useful for discovering groups of correlated genes potentially co-regulated or associated to the disease or conditions under investigation.Many clustering methods including k-means,fuzzy c-means,and hierarchical clustering have been widely used in literatures.Yet no comprehensive comparative study has been performed to evaluate the effectiveness of these methods,specially,in yeast saccharomyces cerevislae.In this paper,these three gene clustering methods are compared.Classification accuracy and CPU time cost are employed for measuring performance of these algorithms.Our results show that hierarchical clustering outperforms k-means and fuzzy c-means clustering.The analysis provides deep insight to the complicated gene clustering problem of expression profile and serves as a practical guideline for routine microarray cluster analysis of gene expression.