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Nucleic Acids Research 2005 33(Web Server Issue):W403-W407; doi:10.1093/nar/gki466
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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

Identifying synonymous regulatory elements in vertebrate genomes

Ivan Ovcharenko* and Marcelo A. Nobrega1

Energy, Environment, Biology, and Institutional Computing, Lawrence Livermore National Laboratory Livermore, CA 94550, USA 1Genomics Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720, USA

*To whom correspondence should be addressed. Tel: +1 925 422 5035; Fax: +1 925 422 2099; Email: ovcharenko1{at}llnl.gov

Received March 2, 2005. Revised March 23, 2005. Accepted April 13, 2005.

Synonymous gene regulation, defined by regulatory elements driving shared temporal and/or spatial aspects of gene expression, is most probably predicated on genomic elements that contain similar modules of certain transcription factor binding sites (TFBS). We have developed a method to scan vertebrate genomes for evolutionary conserved modules of TFBS in a predefined configuration, and created a tool, named SynoR that identifies synonymous regulatory elements (SREs) in vertebrate genomes. SynoR performs de novo identification of SREs utilizing known patterns of TFBS in active regulatory elements (REs) as seeds for genome scans. Layers of multiple-species conservation allow the use of differential phylogenetic sequence conservation filters in search of SREs and the results are displayed such as to provide an extensive annotation of the genes containing the detected REs. Gene Ontology categories are utilized to further functionally classify the identified genes, and integrated GNF Expression Atlas 2 data allow the cataloging of tissue-specificities of the predicted SREs. SynoR is publicly available at http://synor.dcode.org.


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