Databases and Web-Tools for Gene Expression Analysis in Arabidopsis thaliana

The number of internet resources for gene expression analysis in Arabidopsis thaliana has increased tremendously during the last years. These resources permit the database-assisted identification of putative cis-regulatory DNA sequences, their binding proteins, and the determination of common cis-regulatory motifs in coregulated genes. Also, genes targeted by inhibitory RNA can be identified with databases and webservers. DNA-binding proteins may be predicted by the type of cis-regulatory motif. Further questions of combinatorial control based on the interaction of DNA-binding proteins and the colocalization of cis-regulatory motifs can be addressed. The databaseassisted spatial and temporal expression analysis of DNA-binding proteins and their target genes may help to further refine experimental approaches. Signal transduction pathways upstream of regulated genes are beginning to be accessible in databases. This review focuses on the use of the AthaMap and PathoPlant databases for gene expression regulation analysis and discusses similar and complementary online databases and webtools. Online databases are helpful for the development of working hypothesis and for designing subsequent experiments.

Keywords: Bioinformatics, databases, gene expression, plants, transcription, post-transcriptional regulation, web-server.