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Nucleic Acids Research Advance Access published online on October 8, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn709
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© 2008 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, integrating transcriptional and post-transcriptional data

Lorenz Bülow1, Stefan Engelmann2, Martin Schindler2 and Reinhard Hehl1,*

1Institut für Genetik,Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig and 2Software Systems Engineering Institute, Technische Universität Braunschweig, Mühlenpfordtstr. 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 1, 2008. Revised September 29, 2008. Accepted September 29, 2008.

The AthaMap database generates a map of predicted transcription factor binding sites (TFBS) for the whole Arabidopsis thaliana genome. AthaMap has now been extended to include data on post-transcriptional regulation. A total of 403 173 genomic positions of small RNAs have been mapped in the A. thaliana genome. These identify 5772 putative post-transcriptionally regulated target genes. AthaMap tools have been modified to improve the identification of common TFBS in co-regulated genes by subtracting post-transcriptionally regulated genes from such analyses. Furthermore, AthaMap was updated to the TAIR7 genome annotation, a graphic display of gene analysis results was implemented, and the TFBS data content was increased. AthaMap is freely available at http://www.athamap.de/.


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