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Nucleic Acids Research 2005 33(Web Server Issue):W427-W431; doi:10.1093/nar/gki467
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets

Matti Kankainen1 and Liisa Holm1,2,*

1Institute of Biotechnology, University of Helsinki PO Box 56 (Viikinkaari 5), FIN-00014, Helsinki, Finland 2Department of Biosciences, Division of Genetics, University of Helsinki PO Box 56 (Viikinkaari 5), FIN-00014, Helsinki, Finland

*To whom correspondence should be addressed. Tel: +358 9 19159115; Fax: +358 9 19159079; Email: liisa.holm{at}helsinki.fi

Received February 15, 2005. Revised March 18, 2005. Accepted April 13, 2005.

Functionally associated genes tend to be co-expressed, which indicates that they could also be co-regulated. Since co-regulation is usually governed by transcription factors via their specific binding elements, putative regulators can be identified from promoter sets of (co-expressed) genes by screening for over-represented nucleotide patterns. Here, we present a program, POCO, which discovers such over-represented patterns from either one or two promoter sets. Typical microarray experiments yield up- and down-regulated gene sets that may represent, for example, distinct defense pathways. Assuming that a functional transcription factor cannot simultaneously both up- and down-regulate the gene sets, its binding element should respectively be over- and under-represented in the corresponding promoter sets. This idea is implemented in POCO, which tests the hypothesis that the distributions of a pattern differ among three sets of promoters: up-regulated, down-regulated and randomly-chosen. In the program, pattern discovery is based on explicit enumeration of all possible patterns on the alphabet (A, C, G, T and N). The mean occurrences and SDs of the patterns are estimated using bootstrapping and their significance is assessed using ANOVA F-statistics, Tukey's honestly significantly difference test and P-values. The program is freely available at http://ekhidna.biocenter.helsinki.fi/poco.


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