In this review, we discuss the detailed procedures for gene set analysis, along with parameter choices and the particular methodological challenges at each stage. In addition to providing a survey of recently developed tools, we also classify the analysis methods into larger categories and discuss their strengths and limitations. As many new methods are expected to be developed quickly due to the strong demand of initial and secondary (or advanced) analysis of numerous GWAS datasets, our goal is not to provide a comprehensive list of gene set analysis methods. Instead, we aim to provide readers with some of our insights so that they can assess and then use the most appropriate methods for their specific needs. In the last section, we outline several important areas for improving the analytical strategies in gene set analysis. Other recent reviews on gene set analysis of GWAS are Wang et al. (2010) [9] and Cantor et al. (2010) [7].
