In this article, we apply a different and systematic approach towards uncovering the genetic basis of complex diseases – one based on the analysis of sets of genes whose protein products collaborate in specific functions. This may be thought of as in-between a candidate gene study and a GWAS. For the purposes of this paper, we define a functional gene set as one whose protein products are involved in a closely coordinated biological function. While network approaches are common in the analysis of expression arrays, we are aware of only three prior steps in this direction in linkage or association studies in relation to complex disease 10–12. These papers have used methods devised for continuous gene expression data and adapted them to discrete genotype data. By contrast our approach is grounded in the methodology of statistical genetics extended in a natural manner to gene networks.
