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Nucleic Acids Research 2005 33(Web Server Issue):W397-W402; doi:10.1093/nar/gki395
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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

AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana

Nils Ole Steffens, Claudia Galuschka, Martin Schindler, Lorenz Bülow and Reinhard Hehl*

Institut für Genetik, Technische Universität Braunschweig Spielmannstraße 7, D-38106 Braunschweig, Germany

*To whom correspondence should be addressed. Tel: +49 531 391 5772; Fax: +49 531 391 5765; Email: R.Hehl{at}tu-braunschweig.de

Received February 14, 2005. Revised March 11, 2005. Accepted March 11, 2005.

The AthaMap database generates a map of cis-regulatory elements for the Arabidopsis thaliana genome. AthaMap contains more than 7.4 x 106 putative binding sites for 36 transcription factors (TFs) from 16 different TF families. A newly implemented functionality allows the display of subsets of higher conserved transcription factor binding sites (TFBSs). Furthermore, a web tool was developed that permits a user-defined search for co-localizing cis-regulatory elements. The user can specify individually the level of conservation for each TFBS and a spacer range between them. This web tool was employed for the identification of co-localizing sites of known interacting TFs and TFs containing two DNA-binding domains. More than 1.8 x 105 combinatorial elements were annotated in the AthaMap database. These elements can also be used to identify more complex co-localizing elements consisting of up to four TFBSs. The AthaMap database and the connected web tools are a valuable resource for the analysis and the prediction of gene expression regulation at http://www.athamap.de.

Present address: Martin Schindler, Software Systems Engineering, Technische Universität, Braunschweig, Mühlenpfordtstraße 23, D-38106 Braunschweig, Germany


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