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

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W397-402. doi: 10.1093/nar/gki395.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis Proteins / metabolism
  • Base Sequence
  • Binding Sites
  • Conserved Sequence
  • Databases, Nucleic Acid*
  • Gene Expression Regulation, Plant*
  • Genome, Plant
  • Genomics / methods*
  • Internet
  • Response Elements*
  • Software*
  • Transcription Factors / metabolism*

Substances

  • Arabidopsis Proteins
  • Transcription Factors