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We present a new computational method for discovering cis- regulatory elements which circumvents the need to cluster genes based on their expression profiles. Based on a model in which upstream motifs contribute additively to the expression level of a gene, it requires a single genome-wide set of expression ratios and the upstream sequence for each gene, and outputs statistically significant motifs. Analysis of publicly available expression data for Sac charomyes cerevisiae reveals several new putative regulatory elements, some of which plausibly control the early, transient induction of genes during sporulation. Known motifs generally have high statistical significance.
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Bussemaker et al. (2001) studied this question.