Likelihood-Based Approach to Gene Set Enrichment Analysis with a Finite Mixture Model

Stat Biosci. 2014 May 1;6(1):38-54. doi: 10.1007/s12561-012-9076-3.

Abstract

In this paper, we study a parametric modeling approach to gene set enrichment analysis. Existing methods have largely relied on nonparametric approaches employing, e.g., categorization, permutation or resampling-based significance analysis methods. These methods have proven useful yet might not be powerful. By formulating the enrichment analysis into a model comparison problem, we adopt the likelihood ratio-based testing approach to assess significance of enrichment. Through simulation studies and application to gene expression data, we will illustrate the competitive performance of the proposed method.

Keywords: EM; Finite mixture model; Gene set enrichment analysis.