High throughput data sets from DNA, RNA and protein assays are abundant and will only become more prevalent in the near future. When combined with knowledge from decades of detailed genetic investigations linking individual genes to phenotypes, these data sets offer genome-wide insights into the functional relationship among genes. However, questions still arise regarding the feasibility of integrating these disparate data sets. Our goal is to demonstrate that by adopting a logic theoretic framework, the large and diverse data sets acquired from studies of a complex metazoan can be integrated to provide a meaningful gene interaction network and to draw new and unforeseen connections.