- Article -
| In Silico Biology 6, 0023 (2006); ©2006, Bioinformation Systems e.V. |
AthaMap: from in silico data to real transcription factor binding sites
Lorenz Bülow, Nils Ole Steffens, Claudia Galuschka, Martin Schindler1 and Reinhard Hehl*
Institut für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany
1 present address: Software Systems Engineering, Technische Universität Braunschweig,
Mühlenpfordtstr. 23, 38106 Braunschweig, Germany
* Corresponding author
Email: R.Hehl@tu-braunschweig.de
Edited by E. Wingender; received January 10, 2006; revised March 23 & April 07, 2006; accepted April 09, 2006; published April 21, 2006
Abstract
AthaMap generates a map for cis-regulatory sequences for the whole Arabidopsis thaliana genome. AthaMap was initially developed by matrix-based detection of putative transcription factor binding sites (TFBS) mostly determined from random binding site selection experiments. Now, also experimentally verified TFBS have been included for 48 different Arabidopsis thaliana transcription factors (TF). Based on these sequences, 89,416 very similar putative TFBS were determined within the genome of A. thaliana and annotated to AthaMap. Matrix- and single sequence-based binding sites can be included in colocalization analysis for the identification of combinatorial cis-regulatory elements. As an example, putative target genes of the WRKY18 transcription factor that is involved in plant-pathogen interaction were determined. New functions of AthaMap include descriptions for all annotated Arabidopsis thaliana genes and direct links to TAIR, TIGR and MIPS. Transcription factors used in the binding site determination are linked to TAIR and TRANSFAC® databases. AthaMap is freely available at http://www.athamap.de.
Keywords: Arabidopsis thaliana, database, gene expression, plant, pathogen, transcription factor