functional equivalency inferred from “authoritative sources” in networks of homologous proteins从u201c权威u201d功能相等的同源蛋白质的网络.pdfVIP

Functional Equivalency Inferred from ‘‘Authoritative Sources’’ in Networks of Homologous Proteins Shreedhar Natarajan1¤, Eric Jakobsson1,2,3* 1 Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, Illinois, United States of America, 2 National Center for Supercomputing Applications, University of Illinois, Urbana-Champaign, Illinois, United States of America, 3 Department of Molecular and Integrative Physiology, University of Illinois, Urbana- Champaign, Illinois, United States of America Abstract A one-on-one mapping of protein functionality across different species is a critical component of comparative analysis. This paper presents a heuristic algorithm for discovering the Most Likely Functional Counterparts (MoLFunCs) of a protein, based on simple concepts from network theory. A key feature of our algorithm is utilization of the user’s knowledge to assign high confidence to selected functional identification. We show use of the algorithm to retrieve functional equivalents for 7 membrane proteins, from an exploration of almost 40 genomes form multiple online resources. We verify the functional equivalency of our dataset through a series of tests that include sequence, structure and function comparisons. Comparison is made to the OMA methodology, which also identifies one-on-one mapping between proteins from different species. Based on that comparison, we believe that incorporation of user’s knowledge as a key aspect of the technique adds value to purely statistical formal methods. Citation: Natarajan S, Jakobsson E (2009) Functional Equivalency Inferred from ‘‘Authoritative Sources’’ in Networks of Homologous Proteins. PLoS ONE 4(6): e5898. doi:10.1371/journal.pone.0005898 Editor: Olaf Sporns, Indiana University, United States of America Received July 9, 2008; Accepted April 29, 2009; Published June 12, 2009 C