Abstract: Computational analysis is essential to transform the masses of microarray data into a mechanistic understanding of cancer. Here we presented a method for finding cancer gene functional modules from microarray data and applied it to colon cancer. Comparison colon cancer gene modules with normal gene modules show that these cancer genes involved in the biological processes including:regulation of cell cycle, cell proliferation, signal transduction, and anti-apoptosis. Functional changes were accompanied with module changes The effectiveness and feasibility of the method is proved by the results.