  BACKGROUND: Transcriptional regulation is a key mechanism in the functioning
of the cell, and is mostly effected through transcription factors binding to
specific recognition motifs located upstream of the coding region of the
regulated gene. The computational identification of such motifs is made easier
by the fact that they often appear several times in the upstream region of the
regulated genes, so that the number of occurrences of relevant motifs is often
significantly larger than expected by pure chance. RESULTS: To exploit this
fact, we construct sets of genes characterized by the statistical
overrepresentation of a certain motif in their upstream regions. Then we study
the functional characterization of these sets by analyzing their annotation to
Gene Ontology terms. For the sets showing a statistically significant specific
functional characterization, we conjecture that the upstream motif
characterizing the set is a binding site for a transcription factor involved in
the regulation of the genes in the set. CONCLUSIONS: The method we propose is
able to identify many known binding sites in S. cerevisiae and new candidate
targets of regulation by known transcription factors. Its application to less
well studied organisms is likely to be valuable in the exploration of their
regulatory interaction network.
