Functional modularity in a large-scale mammalian molecular interaction network

The Ingenuity/spl trade/ Pathways Knowledge Base (IPKB) contains over one million findings manually curated from the scientific literature. Highly-structured content from the IPKB forms the basis for a large-scale molecular network of direct interactions observed between mammalian orthologs, which is used in Ingenuity's Pathway Analysis (IPA) system. In this study we explore the relationship between this global network and known functional annotations of genes. In particular we show that (a) subnetworks formed by genes annotated with the same functional category have significantly more edges than equivalent random subnetworks, and (b) highly-interconnected subnetworks are significantly enriched in genes with specific functional annotations.