Bioinformatics Vol. 18 no. 1 2002
Pages 160-166
© 2002 Oxford University Press
Machine learning of functional class from phenotype data
Department of Computer Science, University of Wales, Aberystwyth SY23 3DB, UK
Received on April 13, 2001
; revised on August 21, 2001
; accepted on August 21, 2001
Motivation: Mutant phenotype growth experiments are an important novel source of functional genomics data which have received little attention in bioinformatics. We applied supervised machine learning to the problem of using phenotype data to predict the functional class of Open Reading Frames (ORFs) in Saccaromyces cerevisiae. Three sources of data were used: TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces (TRIPLES), European Functional Analysis Network (EUROFAN) and Munich Information Center for Protein Sequences (MIPS). The analysis of the data presented a number of challenges to machine learning: multi-class labels, a large number of sparsely populated classes, the need to learn a set of accurate rules (not a complete classification), and a very large amount of missing values. We modified the algorithm C4.5 to deal with these problems.
Results: Rules were learnt which are accurate and biologically
meaningful. The rules predict function of 83 ORFs of unknown
function at an estimated accuracy of 
80%.
Availability: The data and complete results are available at http://users.aber.ac.uk/ajc99/phenotype/.
Contact: ajc99{at}aber.ac.uk
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