Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive as

Background: A widely-used approach for discovering functional and physical interactions among proteins involves phylogenetic profile comparisons (PPCs). Here, proteins with similar profiles are inferred to be functionally related under the assumption that proteins involved in the same metabolic pathway or cellular system are likely to have been coinherited during evolution. Results: Our experimentation with E. coli and yeast proteins with 16 different carefully composed reference sets of genomes revealed that the phyletic patterns of proteins in prokaryotes alone could be adequate enough to make reasonably accurate functional linkage predictions. A slight improvement in performance is observed on adding few eukaryotes into the reference set, but a noticeable drop-off in performance is observed with increased number of eukaryotes. Inclusion of most parasitic, pathogenic or vertebrate genomes and multiple strains of the same species into the reference set do not necessarily contribute t...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Raja Jothi, Teresa M. Przytycka, L. Aravind
• Keywords: Accurate Functional Linkage, BMCBI 2007, Genomes, Proteins