Tim Ting Chen, Ph.D.

Department of Biological Sciences, Computer Science, and Mathematics

University of Southern California

Abstract

Understanding protein-protein interactions is one of the most important

challenges in the post-genomic era. Behind protein-protein interactions there are

protein domains physically interacting with one another to perform functions of

proteins.Yeast 2-hybrid screens have generated more than 6000 interactions between

proteins of the yeast Saccharomyces cerevisiae. This allows us to study the

large-scale conserved patterns of interactions between protein domains. We use

evolutionarily conserved domains defined in a protein-domain database called Pfam, and

apply the Maximum Likelihood Estimation method to infer interacting domains that are

consistent with the observed protein-protein interactions. Using these interacting

domains, we predict statistically significant novel yeast protein-protein interactions,

among which many proteins have either unknown function or no observed interactions

with other proteins. Our results can also be applied to predict protein-protein

interactions of other species.