title: Phylogenetic portrait of the Saccharomyces cerevisiae functional genome.
abstract: The genome of budding yeast (Saccharomyces cerevisiae) contains approximately 5800 protein-encoding genes, the majority of which are associated with some known biological function. Yet the extent of amino acid sequence conservation of these genes over all phyla has only been partially examined. Here we provide a more comprehensive overview and visualization of the conservation of yeast genes and a means for browsing and exploring the data in detail, down to the individual yeast gene, at http://yeast-phylogroups.princeton.edu. We used data from the OrthoMCL database, which has defined orthologs from approximately 150 completely sequenced genomes, including diverse representatives of the archeal, bacterial, and eukaryotic domains. By clustering genes based on similar patterns of conservation, we organized and visualized all the protein-encoding genes in yeast as a single heat map. Most genes fall into one of eight major clusters, called "phylogroups." Gene ontology analysis of the phylogroups revealed that they were associated with specific, distinct trends in gene function, generalizations likely to be of interest to a wide range of biologists.
authors.affiliation: The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA. pgibney@princeton.edu
authors.forename: Patrick A
authors.initials: PA
authors.lastname: Gibney
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Hickman
authors.forename: Patrick H
authors.initials: PH
authors.lastname: Bradley
authors.forename: John C
authors.initials: JC
authors.lastname: Matese
authors.forename: David
authors.initials: D
authors.lastname: Botstein
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D030541:Databases, Genetic; D016681:Genome, Fungal; D010802:Phylogeny; D012441:Saccharomyces cerevisiae / Q000145:classification / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics
chemical_list: D029701:Saccharomyces cerevisiae Proteins
keywords: evolution; genome; orthology; phylogeny; yeast