Identifying Fungal Regulatory Motif Patterns Using SCOPE, an Ensemble Learning Method Motif Finder

We reported previously on the development of SCOPE, an ensemble learning method motif finder. In this study, SCOPE was used to examine motif patterns for gene sets regulated by transcription factors MBF and SBF in Saccharomyces cerevisiae. Gene sets individually regulated by MBF or SBF and gene sets that could be regulated by either MBF or SBF clustered separately. This clustering was dependent on the presence of recognition motifs, their position distribution upstream of the gene start and binding site differences. Highly similar sequences were also identified for homologs of MBF-regulated S. cerevisiae genes in 11 other fungal species. SCOPE consistently identified a core motif, CGCG, but the neighboring bases slightly varied in different species, as did position preferences. Results indicate that the presence of a motif, its position with respect to a gene start and its context are important factors in gene regulation.