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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 (http://rsat.scmbb.ulb.ac.be/rsat/).
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Submitted on : Wednesday, October 11, 2006 - 7:51:24 AM
Last modification on : Tuesday, September 28, 2021 - 5:20:19 PM
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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, Oxford University Press (OUP), 2005, 21, pp.3490-3500. ⟨lirmm-00105316⟩

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