Abstract
Model organisms and human studies have led to increasing empirical evidence that interactions among genes contribute broadly to genetic variation of complex traits. In the presence of gene-by-gene interactions, the dimensionality of the feature space becomes extremely high relative to the sample size. This imposes a significant methodological challenge in identifying gene-by-gene interactions. In the present paper, through a Gaussian graphical model framework, we translate the problem of identifying gene-by-gene interactions associated with a binary trait D into an inference problem on the difference of two high-dimensional precision matrices, which summarize the conditional dependence network structures of the genes. We propose a procedure for testing the differential network globally that is particularly powerful against sparse alternatives. In addition, a multiple testing procedure with false discovery rate control is developed to infer the specific structure of the differential network. Theoretical justification is provided to ensure the validity of the proposed tests and optimality results are derived under sparsity assumptions. A simulation study demonstrates that the proposed tests maintain the desired error rates under the null and have good power under the alternative. The methods are applied to a breast cancer gene expression study.