We demonstrate the strength of our methodology by analyzing genotype, gene expression, and downstream phenotype data from the F2 intercross generated from mouse strains C57BL/6 J and C3H/HeJ with apolipoprotein E as null on the background (BxH.ApoE-/-) [9,31] to identify network connections among genes and obesity related phenotypes. The gene discussed is APOE; the disease is Obesity.