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Nucleic Acids Research 2006 34(Database Issue):D68-D73; doi:10.1093/nar/gkj075
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Nucleic Acids Research, 2006, Vol. 34, Database issue D68-D73
© The Author 2006. 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}oxfordjournals.org

Article

cisRED: a database system for genome-scale computational discovery of regulatory elements

G. Robertson*, M. Bilenky, K. Lin, A. He, W. Yuen, M. Dagpinar, R. Varhol, K. Teague, O. L. Griffith, X. Zhang, Y. Pan, M. Hassel, M. C. Sleumer, W. Pan, E. D. Pleasance, M. Chuang, H. Hao, Y. Y. Li, N. Robertson, C. Fjell, B. Li, S. B. Montgomery, T. Astakhova, J. Zhou1, J. Sander1, A. S. Siddiqui and S. J. M. Jones

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency Vancouver, BC, Canada 1Department of Computing Science, University of Alberta Edmonton, AB, Canada

*To whom correspondence should be addressed. Tel: +1 604 675 8170; Fax: +1 604 876 3561; Email: grobertson{at}bcgsc.ca

Received August 15, 2005. Revised October 8, 2005. Accepted October 8, 2005.

We describe cisRED, a database for conserved regulatory elements that are identified and ranked by a genome-scale computational system (www.cisred.org). The database and high-throughput predictive pipeline are designed to address diverse target genomes in the context of rapidly evolving data resources and tools. Motifs are predicted in promoter regions using multiple discovery methods applied to sequence sets that include corresponding sequence regions from vertebrates. We estimate motif significance by applying discovery and post-processing methods to randomized sequence sets that are adaptively derived from target sequence sets, retain motifs with p-values below a threshold and identify groups of similar motifs and co-occurring motif patterns. The database offers information on atomic motifs, motif groups and patterns. It is web-accessible, and can be queried directly, downloaded or installed locally.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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