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

• Published in: Nucleic acids research 2005-07, Vol.33 (suppl-2), p.W397-W402
• Main Authors: Steffens, Nils Ole, Galuschka, Claudia, Schindler, Martin, Bülow, Lorenz, Hehl, Reinhard
• Format: Article
• Language: English
• Subjects: Arabidopsis - genetics; Arabidopsis Proteins - metabolism; Arabidopsis thaliana; Base Sequence; Binding Sites; Conserved Sequence; Databases, Nucleic Acid; Gene Expression Regulation, Plant; Genome, Plant; Genomics - methods; Internet; Response Elements; Software; Transcription Factors - metabolism
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gki395

The AthaMap database generates a map of cis-regulatory elements for the Arabidopsis thaliana genome. AthaMap contains more than 7.4 × 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 × 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.