Bridging Phylogeny and Taxonomy with Protein-protein Interaction Networks

Abstract

The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has not been large-scale research on how individual PPI networks reflect on the species relationships. In this study we aim to increase our understanding of the tree of life and taxonomy by gleaming information from the PPI networks. We successful created (1) a predictor of network statistics based on known traits of existing species in the phylogeny, and (2) a taxonomic classifier of organism using the known protein network statistics, whether experimentally determined or predicted de novo. With the knowledge of protein interactions at its core, our two models effectively connects two field with widely diverging methodologies - the phylogeny and taxonomy of species.