A combined algorithm for genome-wide prediction of protein function

• Published in: Nature (London) Vol. 402; no. 6757; pp. 83 - 86
• Main Authors: Eisenberg, David, Marcotte, Edward M, Pellegrini, Matteo, Thompson, Michael J, Yeates, Todd O
• Format: Journal Article
• Language: English
• Published: London Nature Publishing 04-11-1999; Nature Publishing Group
• Subjects: Algorithms; Biological and medical sciences; Classical genetics, quantitative genetics, hybrids; Colorectal Neoplasms - etiology; DNA-Binding Proteins; Evolution, Molecular; Fundamental and applied biological sciences. Psychology; Fungal Proteins - classification; Fungal Proteins - genetics; Fungal Proteins - physiology; Genetics of eukaryotes. Biological and molecular evolution; Genomics; Humans; Methods, theories and miscellaneous; Peptide Termination Factors; Phylogeny; Prions - classification; Prions - physiology; Proteins; RNA, Messenger - biosynthesis; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Yeast; Yeasts; Yeast; Cell function; Nucleotide sequence; Prediction; Homology; Molecular interaction; Algorithm; Protein; Fungi; Statistical method; Gene; Database; Ascomycetes; Genome; Saccharomyces cerevisiae; Thallophyta
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/47048

The availability of over 20 fully sequenced genomes has driven the development
of new methods to find protein function and interactions. Here we group proteins
by correlated evolution, correlated messenger RNA expression
patterns and patterns of domain fusion to determine
functional relationships among the 6,217 proteins of the yeast Saccharomyces
cerevisiae. Using these methods, we discover over 93,000 pairwise links
between functionally related yeast proteins. Links between characterized and
uncharacterized proteins allow a general function to be assigned to more than
half of the 2,557 previously uncharacterized yeast proteins. Examples of functional
links are given for a protein family of previously unknown function, a protein
whose human homologues are implicated in colon cancer and the yeast prion
Sup35.