Bioinformatics Advance Access originally published online on February 5, 2004
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Bioinformatics 20(7) © Oxford University Press 2004; all rights reserved.
Predicting rules on organization of cis-regulatory elements, taking the order of elements into account
1 INTEC Web and Genome Informatics Corp., 1-3-3 Shinsuna, Koto-ku, Tokyo 136-8637, Japan and 2 Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan
Received on March 12, 2003; revised on October 30, 2003; accepted on November 20, 2003
Advance Access Publication February 5, 2004
Motivation: In eukaryotes, rules regarding organization of cis-regulatory elements are complex. They sometimes govern multiple kinds of elements and positional restrictions on elements.
Results: We propose a method for detecting rules, by which the order of elements is restricted. The order restriction is expressed as element patterns. We extract all the element patterns that occur in promoter regions of at least the specified number of genes. Then, we find significant patterns based on the expression similarity of genes with promoter regions containing each of the extracted patterns. When we applied our method to Saccharomyces cerevisiae, we detected significant patterns overlooked by previous methods, thus demonstrating the utility of our method for analyses of eukaryotic gene regulation. We also suggest that several types of element organization exist: (i) those in which only the order of elements is important, (ii) order and distance both are important and (iii) only the combination of elements is important.
Availability: The program for extracting element patterns is available upon request.
Supplementary information: http://elpa.hgc.jp/ElementPatterns
Contact: tt{at}k.u-tokyo.ac.jp
* To whom correspondence should be addressed.
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