AthaMap: From in silico Data to Real Transcription Factor Binding Sites

Article type: Research Article

Authors: Bülow, Lorenz | Steffens, Nils Ole | Galuschka, Claudia | Schindler, Martin | Hehl, Reinhard

Affiliations: Institut für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany

Note: [] Corresponding author. Tel.: +49 531 391 5772; Fax: +49 531 391 5765; E-mail: [email protected]

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

Journal: In Silico Biology, vol. 6, no. 3, pp. 243-252, 2006