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Background  The analysis of gene expression using DNA microarrays provides genome wide profiles of the genes controlled by the presence or absence of a specific transcription factor. However, the question arises of whether a change in the level of transcription of a specific gene is caused by the transcription factor acting directly at the promoter of the gene or through regulation of other transcription factors working at the promoter.    Results  To address this problem we have devised a computational method that combines microarray expression and site preference data. We have tested this approach by identifying functional targets of the  a 1- α 2 complex, which represses haploid-specific genes in the yeast  Saccharomyces cerevisiae . Our analysis identified many known or suspected haploid-specific genes that are direct targets of the  a 1- α 2 complex, as well as a number of previously uncharacterized targets. We were also able to identify a number of haploid-specific genes which do not appear to be direct targets of the  a 1- α 2 complex, as well as  a 1- α 2 target sites that do not repress transcription of nearby genes. Our method has a much lower false positive rate when compared to some of the conventional bioinformatic approaches.    Conclusions  These findings show advantages of combining these two forms of data to investigate the mechanism of co-regulation of specific sets of genes.

Combined analysis of expression data and transcription factor binding sites in the yeast genome