title: AthaMap web tools for the analysis and identification of co-regulated genes.
abstract: The AthaMap database generates a map of cis-regulatory elements for the whole Arabidopsis thaliana genome. This database has been extended by new tools to identify common cis-regulatory elements in specific regions of user-provided gene sets. A resulting table displays all cis-regulatory elements annotated in AthaMap including positional information relative to the respective gene. Further tables show overviews with the number of individual transcription factor binding sites (TFBS) present and TFBS common to the whole set of genes. Over represented cis-elements are easily identified. These features were used to detect specific enrichment of drought-responsive elements in cold-induced genes. For identification of co-regulated genes, the output table of the colocalization function was extended to show the closest genes and their relative distances to the colocalizing TFBS. Gene sets determined by this function can be used for a co-regulation analysis in microarray gene expression databases such as Genevestigator or PathoPlant. Additional improvements of AthaMap include display of the gene structure in the sequence window and a significant data increase. AthaMap is freely available at http://www.athamap.de/.
authors.affiliation: Institut für Genetik, Technische Universität Braunschweig, Spielmanstrasse 7, D-38106 Braunschweig, Germany.
authors.forename: Claudia
authors.initials: C
authors.lastname: Galuschka
authors.forename: Martin
authors.initials: M
authors.lastname: Schindler
authors.forename: Lorenz
authors.initials: L
authors.lastname: Bülow
authors.forename: Reinhard
authors.initials: R
authors.lastname: Hehl
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001665:Binding Sites; D003080:Cold Temperature; D030561:Databases, Nucleic Acid; D003681:Dehydration; D018506:Gene Expression Regulation, Plant; D020407:Internet; D050436:Regulatory Elements, Transcriptional; D012984:Software; D014157:Transcription Factors / Q000378:metabolism; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors