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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 Jacques van Helden 1 
2 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : Motivation: In yeast, methionine and phosphate metabolism are regulated by the complexes Met4p/Met28p/Cbf1p and Pho4p, respect- ively. 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 para- meters 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 (
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Submitted on : Wednesday, October 11, 2006 - 7:51:24 AM
Last modification on : Tuesday, September 6, 2022 - 4:56:05 PM
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  • HAL Id : lirmm-00105316, version 1



Didier Gonze, Sylvie Pinloche, Olivier Gascuel, Jacques van Helden. Discrimination of Yeast Genes Involved in Methionine and Phosphate Metabolism on the Basis of Upstream Motifs. Bioinformatics, 2005, 21, pp.3490-3500. ⟨lirmm-00105316⟩



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