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.
The AthaMap database generates a map of cis-regulatory elements for the Arabidopsis thaliana genome. AthaMap contains more than 7.4 x 10(6) 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 x 10(5) 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.
Steffens
Nils Ole
NO
Institut für Genetik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany.
Galuschka
Claudia
C
Schindler
Martin
M
Bülow
Lorenz
L
Hehl
Reinhard
R
D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D030561:Databases, Nucleic Acid; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D020407:Internet; D020218:Response Elements; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
D029681:Arabidopsis Proteins; D014157:Transcription Factors