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Bioinformatics Advance Access published online on July 5, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti558
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received January 16, 2005
Revised June 15, 2005
Accepted June 27, 2005

Article

Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs

Didier Gonze 1*, Sylvie Pinloche 2, Olivier Gascuel 2, and Jacques van Helden 3

1 Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles, CP 263, Campus Plaine, Bvd du Triomphe, B-1050 Bruxelles, Belgium; Unité de Chronobiologie Théorique, CP 231, Campus Plaine, Bvd du Triomphe, B-1050 Bruxelles, Belgium
2 Projet Méthodes et Algorithmes pour la Bioinformatique, LIRMM-CNRS, 161 rue Ada, 34392, Montpellier, France
3 Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles, CP 263, Campus Plaine, Bvd du Triomphe, B-1050 Bruxelles, Belgium

* To whom correspondence should be addressed.
Didier Gonze, E-mail: dgonze{at}scmbb.ulb.ac.be


  Abstract

Motivation: In yeast, methionine and phosphate metabolism are regulated by the complexes Met4p/Met28p/Cbf1p and Pho4p respectively. The binding sites for these factors share a common core CACGTG. We evaluate our capability to discriminate phosphate- and methionine-responding genes on the basis of putative regulatory elements, despite the similarity between Met4p/Met28p/Cbf1p and Pho4p consensus.

Results: We scanned upstream regions of methionine, phosphate and control genes with position-specific weight matrices for Pho4p, Met4p/Met28p/Cbf1p, and Met31p/Met32p, and applied discriminant analysis to classify genes according to matrix matching scores. This analysis showed that matrix scores provided a good discrimination between phosphate, methionine and control genes. The optimal parameters have then been used to predict phosphate and methionine regulation at a genome scale. Genome-scale analysis predicts 37 genes as methionine-regulated, and 40 as phosphate-regulated. We compare the predictive results with high throughput data and discuss the difference.

Availability: The programs for sequence retrieval and analysis, as well as the complete data and results, are available on the web site Regulatory Sequence Analysis Tools (http://rsat.scmbb.ulb.ac.be/rsat/) (van Helden et al., 2000; van Helden, 2003).


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[Abstract] [Full Text] [PDF]


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