Overview of the study design and method.

Abstract

(A) The gene expression datasets used in this study. Stimulated monocyte gene expression profiles from Fairfax et al. [12] in four conditions: response to lipopolysaccharide at 24 hours (LPS24) and at 2 hours (LPS2), interferon-γ (IFN-γ), and naive (left panel). Peripheral blood monocytes (MP) and macrophages (MC) from the Cardiogenics Consortium (right panel). (B) Overview of the SDA approach. An illustration of decomposition of gene expression datasets to yield component vectors for relative contribution of each individual, gene and condition. The individual scores matrices are then used as phenotypes with SNP genotypes in order to identify genetic variation correlated with the components (top). The stimulation or cell-activity scores matrix is used to identify the contribution of each condition for the components (middle). The gene scores matrix is used to identify the contribution of each gene within the components (bottom).</p