Abstract
Gene set analysis has been widely used to gain insight from high-throughput expression studies. Although various tools and methods have been developed for gene set analysis, there is no consensus among researchers regarding best practice(s). Most often, evaluation studies have reported contradictory recommendations of which methods are superior. Therefore, an unbiased quantitative framework for evaluations of gene set analysis methods will be valuable. Such a framework requires gene expression datasets where enrichment status of gene sets is known a priori. In the absence of such gold standard datasets, artificial datasets are commonly used for evaluations of gene set analysis methods; however, they often rely on oversimplifying assumptions that make them biased in favor of or against a given method. In this paper, we propose a quantitative framework for evaluation of gene set analysis methods by synthesizing expression datasets using real data, without relying on oversimplifying or unrealistic assumptions, while preserving complex gene-gene correlations and retaining the distribution of expression values. The utility of the quantitative approach is shown by evaluating ten widely used gene set analysis methods. An implementation of the proposed method is publicly available. We suggest using Silver to evaluate existing and new gene set analysis methods. Evaluation using Silver provides a better understanding of current methods and can aid in the development of gene set analysis methods to achieve higher specificity without sacrificing sensitivity.