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


BACKGROUND
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/).


BACKGROUND
jvanheld@scmbb.ulb.ac.be


BACKGROUND
The complete datasets and results are available at http://rsat.scmbb.ulb.ac.be/rsat/data/published_data/Gonze_MET_PHO/
Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles, CP 263, Campus Plaine, Blvd du Triomphe, B-1050 Bruxelles, Belgium.
Didier
D
Gonze
Sylvie
S
Pinloche
Olivier
O
Gascuel
Jacques
J
van Helden
D000465:Algorithms; D000595:Amino Acid Sequence; D016002:Discriminant Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000502:physiology*; D008715:Methionine / Q000737:chemistry / Q000378:metabolism*; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D010710:Phosphates / Q000737:chemistry / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D020539:Sequence Analysis, Protein / Q000379:methods*
D010710:Phosphates; D029701:Saccharomyces cerevisiae Proteins; D008715:Methionine