Nucleic Acids Research Advance Access published online on May 30, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm379
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MYBS: a comprehensive web server for mining transcription factor binding sites in yeast
1Institute of Information Science, 2Genomics Research Center, Academia Sinica, Taipei, 115 Taiwan, 3Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210 and 4Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
*To whom correspondence should be addressed. Tel: 886-2-27883799; Fax: 886-2-27824814; Email: hktsai{at}iis.sinica.edu.tw Correspondence may also be addressed to Wen-Hsiung Li. Tel: 1-773-702-3104; Email: wli{at}uchicago.edu
Received January 30, 2007. Revised April 12, 2007. Accepted April 30, 2007.
Correct interactions between transcription factors (TFs) and their binding sites (TFBSs) are of central importance to gene regulation. Recently developed chromatin-immunoprecipitation DNA chip (ChIP-chip) techniques and the phylogenetic footprinting method provide ways to identify TFBSs with high precision. In this study, we constructed a user-friendly interactive platform for dynamic binding site mapping using ChIP-chip data and phylogenetic footprinting as two filters. MYBS (Mining Yeast Binding Sites) is a comprehensive web server that integrates an array of both experimentally verified and predicted position weight matrixes (PWMs) from eleven databases, including 481 binding motif consensus sequences and 71 PWMs that correspond to 183 TFs. MYBS users can search within this platform for motif occurrences (possible binding sites) in the promoters of genes of interest via simple motif or gene queries in conjunction with the above two filters. In addition, MYBS enables users to visualize in parallel the potential regulators for a given set of genes, a feature useful for finding potential regulatory associations between TFs. MYBS also allows users to identify target gene sets of each TF pair, which could be used as a starting point for further explorations of TF combinatorial regulation. MYBS is available at http://cg1.iis.sinica.edu.tw/~mybs/.
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