CMF: a combinatorial tool to find composite motifs

Abstract. Controlling the differential expression of many thousands genes at any given time is a fundamental task of metazoan organisms and this complex orchestration is controlled by the so-called regulatory genome encoding complex regulatory networks. Cis-Regulatory Modules are fundamental units of such networks. To detect Cis-Regulatory Mod-ules “in-silico ” a key step is the discovery of recurrent clusters of DNA binding sites for sets of cooperating Transcription Factors. Composite motif is the term often adopted to refer to these clusters of sites. In this paper we describe CMF, a new efficient combinatorial method for the problem of detecting composite motifs, given in input a description of the binding affinities for a set of transcription factors. Testing with known benchmark data, we attain statistically significant better perfor-mance against nine state-of-the-art competing methods.