Predicting functional gene links from phylogenetic-statistical analyses of whole genomes.

ABSTRACT: An important element of the developing field of proteomics is to understand protein-protein interactions and other functional links amongst genes. Across-species correlation methods for detecting functional links work on the premise that functionally linked proteins will tend to show a common pattern of presence and absence across a range of genomes. We describe a maximum likelihood statistical model for predicting functional gene linkages. The method detects independent instances of the correlated gain or loss of pairs of proteins on phylogenetic trees, reducing the high rates of false positives observed in conventional across-species methods that do not explicitly incorporate a phylogeny. We show, in a dataset of 10,551 protein pairs, that the phylogenetic method improves by up to 35% on

SUBMITTER: Barker D 

PROVIDER: S-EPMC1183509 | biostudies-literature | 2005 Jun

REPOSITORIES: biostudies-literature