Atherosclerosis is a complex disease that gene and environment interaction influences the progression of atherosclerotic lesion development. Our laboratory used mice lacking both the low density lipoprotein (LDL) receptor and Apobec1 genes (LDLR-/-Apobec1-/-, designated LDb) to investigate gene-gene interaction and the influence of an environmental factor (high-fat diet) on gene networks. LDb mice (males and females) at 5 months of age were fed a chow or high fat diet for 3-month. The mice on a chow diet had elevated plasma cholesterol and triglyceride levels and developed atherosclerosis. Feeding a high-fat diet accelerated the development of lesions >1.5-fold. We performed microarray analysis of the expression of 12442 murine genes in the livers of these animals, which identified 54 genes in males and 77 genes in females were significantly perturbed by the high-fat diet. Moreover, most of these genes (>70%) were upregulated. The results suggested that glycolysis, fat transport, and steroid hormone biosynthesis pathways were upregulated, probably to compensate for the high fat intake. Furthermore, a batch of stress-responsive genes was upregulated. The study also shows a dynamic cellular communication network including T cells, neutrophils, and monocytes/macrophages, which related to inflammatory and immune/complement responses. Importantly, this study discovered that many genes involved in calcium signaling and bone formation were up regulated. Alizarin Red S staining was used to detect calcium deposits in the region of atherosclerotic lesions. Real-time quantitative RT-PCR and Western blot analyses provided verification of the gene expression levels. In conclusion, this study demonstrated the global differential gene expression profiles, which are influenced by feeding a high fat diet to LDb mice. The results of the study provide new insights into the significance of calcification in atherogenesis.