Predicting gene function in Saccharomyces cerevisiae

Motivation: S.cerevisiae is one of the most important model organisms, and has has been the focus of over a century of study. In spite of these efforts, 40% of its open reading frames (ORFs) remain classified as having unknown function (MIPS: Munich Information Center for Protein Sequences). We wished to make predictions for the function of these ORFs using data mining, as we have previously successfully done for the genomes of M.tuberculosis and E.coli. Applying this approach to the larger and eukaryotic S.cerevisiae genome involves modifying the machine learning and data mining algorithms, as this is a larger organism with more data available, and a more challenging functional classification. Results: Novel extensions to the machine learning and data mining algorithms have been devised in order to deal with the challenges. Accurate rules have been learned and predictions have been made for many of the ORFs whose function is currently unknown. The rules are informative, agree with known biology and allow for scientific discovery. Availability: All predictions are freely available from http://www.genepredictions.org, all datasets used in this study are freely available from http://www.aber. ac.uk/compsci/Research/ bio/dss/yeastdata and software for relational data mining is available from http://www.aber.ac.uk/compsci/Research/bio/dss/polyfarm. © Oxford University Press 2003; all rights reserved.