Discovering Gene–Gene and Gene–Environment Causal Interactions Using Bioinformatics Approaches

The exponential growth of molecular biology data led to an intense focus on the study of interactions among DNA, RNA, protein biosynthesis, and environment. Using advanced genomics revolution tools, large datasets generated by the gene expression profiling experiments and next generation sequences technologies enable us to link molecular states and environmental effects to physiological states through the reverse engineering of gene–gene and gene–environment interaction networks that sense DNA and environmental perturbations. This will ultimately let us understand variations in physiological states associated with disease. In this chapter we review different mathematical and statistical bioinformatics approaches to discover and model gene–gene and gene–environment causal interactions. We also present new additional modeling methods in probabilistic networks to incorporate various interventions to perturb the system.