title: A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences.
abstract: Predicting functional amino acid residues in silico is important for comparative genomics. In this paper, we focus on the issue of how to statistically identify cluster-specific amino acid residues that are related to the functional divergence after gene duplication. We approach this problem using a framework based on site-specific shift of amino acid property (type-II functional divergence), as opposed to site-specific shift of evolutionary rate (type-I functional divergence). An efficient statistical procedure is implemented to facilitate the development of phylogenomic database for cluster-specific residues of large-scale protein families. Our method has the following features: 1) statistical testing of the type-II functional divergence and 2) the site-specific Bayesian profile to measure how amino acid residues contribute to type-II (cluster-specific) functional divergence. Consequently, one may obtain the posterior probability for "functional" cluster-specific residues. Case studies are presented and indicate that radical cluster-specific residues are responsible for most of inferred type-II functional divergence, whereas conserved cluster-specific residues appear less than even those imperfect radical cluster-specific residues to this type of functional divergence.
authors.affiliation: Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, USA. xgu@iastate.edu
authors.forename: Xun
authors.initials: X
authors.lastname: Gu
mesh_terms: D000595:Amino Acid Sequence; D001499:Bayes Theorem; D001699:Biometry; D020169:Caspases / Q000235:genetics; D019143:Evolution, Molecular; D044385:GTP-Binding Protein alpha Subunits / Q000235:genetics; D020440:Gene Duplication; D023281:Genomics / Q000706:statistics & numerical data; D016013:Likelihood Functions; D008957:Models, Genetic; D005810:Multigene Family; D010802:Phylogeny; D011451:Prostaglandin-Endoperoxide Synthases / Q000235:genetics; D011506:Proteins / Q000235:genetics*; D016415:Sequence Alignment / Q000706:statistics & numerical data
chemical_list: D044385:GTP-Binding Protein alpha Subunits; D011506:Proteins; D011451:Prostaglandin-Endoperoxide Synthases; D020169:Caspases