Microarrays allow researchers to simultaneously monitor the expression of thousands of genes. Independent of the platform and analysis methods used, the result of a microarray experiment is a list of differentially expressed genes. Presenting a unified analysis of the field, this book explores the tools available to better understand the underlying biological phenomena of differentially expressed genes. It focuses on two major analytic approaches: 1) ontological profiling and 2) gene interaction networks and known pathways. The author presents the fundamentals and tools for each approach.