Abstract: One of cancer related gene function research is the discovery of gene functional module.Here,a efficient clustering algorithm proposed to reveal the gene functional modules based on gene expression profiles. First,the betweenness algorithm was used to mine the cancer gene modules from the 158 feature genes extracted from the 20,000 colon cancer gene expression profiles.Second,the modularity function which was used to assess the performance of clustering algorithm was applied to the colon cancer gene modules and got 7 gene function modules.Finally,combining with GO database the biological process of these modules was classified.The results show that this algorithm is feasible and effective in gene function clustering.