Bioinformatics Advance Access published online on October 28, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti094
Bioinformatics © Oxford University Press 2004; all rights reserved
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1 Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan; Computational Biology Research Center, The National Institute of Advanced Industrial Science and Technology, Aomi Frontier Building 2-43 Aomi, 17F, Koto-ku, Tokyo 135-0064, Japan
* To whom correspondence should be addressed.
Motivation: The relations between the promoter sequences and their strengths were extensively studied in the 1980s. Although these studies uncovered strong sequence-strength correlations, the cost of their elaborate experimental methods have been too high to be applied to a large number of promoters. On the other hand, a recent increase in the microarray data allows us to compare thousands of gene expressions with their DNA sequences. Results: We studied the relations between the promoter sequences and their strengths using the E. coli microarray data. We modeled those relations using a simple weight matrix, which was optimized with a novel support vector regression method. It was observed that several nonconsensus bases in the "-35’ and "-10" regions of promoter sequences act positively on the promoter strength and that certain consensus bases have a minor effect on the strength. We analyzed outliers for which the observed gene expressions deviate from the promoter strength predictions, and identified several genes with enhanced expressions due to multiple promoters and genes under strong regulation by transcription factors. Our method is applicable to other prokaryotes for which both the promoter sequences and the microarray data are available.
Revised October 10, 2004
Accepted October 10, 2004
Article
Extracting relations between promoter sequences and their strengths from microarray data
2 Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
3 Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan; Computational Biology Research Center, The National Institute of Advanced Industrial Science and Technology, Aomi Frontier Building 2-43 Aomi, 17F, Koto-ku, Tokyo 135-0064, Japan; Department of Computational Biology, Faculty of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
Hisanori Kiryu, E-mail: hisano-k{at}is.aist-nara.ac.jp
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