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Nucleic Acids Research Advance Access first published online on December 5, 2006
This version published online on December 8, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl1006
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

AthaMap web tools for the analysis and identification of co-regulated genes

Claudia Galuschka, Martin Schindler1, Lorenz Bülow and Reinhard Hehl*

Institut für Genetik, Technische Universität Braunschweig, Spielmanstraße 7, D-38106 Braunschweig, Germany 1 Software Systems Engineering Institute, Technische Universität Braunschweig, Mühlenpfordtstraße 23 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 September 13, 2006. Revised November 2, 2006. Accepted November 2, 2006.

The AthaMap database generates a map of cis-regulatory elements for the whole Arabidopsis thaliana genome. This database has been extended by new tools to identify common cis-regulatory elements in specific regions of user-provided gene sets. A resulting table displays all cis-regulatory elements annotated in AthaMap including positional information relative to the respective gene. Further tables show overviews with the number of individual transcription factor binding sites (TFBS) present and TFBS common to the whole set of genes. Over represented cis-elements are easily identified. These features were used to detect specific enrichment of drought-responsive elements in cold-induced genes. For identification of co-regulated genes, the output table of the colocalization function was extended to show the closest genes and their relative distances to the colocalizing TFBS. Gene sets determined by this function can be used for a co-regulation analysis in microarray gene expression databases such as Genevestigator or PathoPlant. Additional improvements of AthaMap include display of the gene structure in the sequence window and a significant data increase. AthaMap is freely available at http://www.athamap.de/.


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