Regulatory element detection using correlation with expression

We present here a new computational method for discovering cis-regulatory e lements that circumvents the need to cluster genes based on their expressio n profiles. Based on a model in which upstream motifs contribute additively to the log-expression level of a gene, this method requires a single genom e-wide set of expression ratios and the upstream sequence for each gene, an d outputs statistically significant motifs. Analysis of publicly available expression data for Saccharomyces cerevisiae reveals several new putative r egulatory elements, some of which plausibly control the early, transient in duction of genes during sporulation. Known motifs generally have high stati stical significance.