An improved map of conserved regulatory sites for Saccharomyces cerevisiae

Background: The regulatory map of a genome consists of the binding sites for proteins that determine the transcription of nearby genes. An initial regulatory map for S. cerevisiae was recently published using six motif discovery programs to analyze genome-wide chromatin immunoprecipitation data for 203 transcription factors. The programs were used to identify sequence motifs that were likely to correspond to the DNA-binding specificity of the immunoprecipitated proteins. We report improved versions of two conservation-based motif discovery algorithms, PhyloCon and Converge. Using these programs, we create a refined regulatory map for S. cerevisiae by reanalyzing the same chromatin immunoprecipitation data. Results: Applying the same conservative criteria that were applied in the original study, we find that PhyloCon and Converge each separately discover more known specificities than the combination of all six programs in the previous study. Combining the results of PhyloCon and Conver...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Kenzie D. MacIsaac, Ting Wang, D. Benjamin Gordon, David K. Gifford, Gary D. Stormo, Ernest Fraenkel
• Keywords: BMCBI 2006, Chromatin Immunoprecipitation Data, Motif Discovery, Regulatory Map