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Bioinformatics Advance Access originally published online on July 5, 2005
Bioinformatics 2005 21(17):3490-3500; 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{at}oupjournals.org

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

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

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

*To whom correspondence should be addressed.

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. The 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 website on regulatory sequence analysis tools (http://rsat.scmbb.ulb.ac.be/rsat/).

Contact: jvanheld{at}scmbb.ulb.ac.be

Supplementary information: The complete datasets and results are available at http://rsat.scmbb.ulb.ac.be/rsat/data/published_data/Gonze_MET_PHO/

Received on January 16, 2005; revised on June 15, 2005; accepted on June 27, 2005

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[Abstract] [Full Text] [PDF]


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