PlantCARE

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Text from the NAR 2007 Database Issue (Database Summaries) by permission of Oxford University Press.

PlantCARE is NAR Database No. 41.

Contents

Database Description

PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular promoter sequences. Links to the EMBL, TRANSFAC (Wingender, E. et al.) and MEDLINE databases are provided where available. Data about the transcription sites are mainly extracted from the literature, added with an increasing number of in silico predicted data. Apart from a general description for specific transcription factor (TF) sites, levels of confidence for the experimental evidence, functional information and the position on the promoter are also given. New features have been implemented to search for plant cis-acting regulatory elements in a query sequence. Furthermore, links are now provided to a new clustering (De Smet, F. et al.) and motif search method to investigate clusters of co-expressed genes (Thijs, G. et al.). New regulatory elements can be sent automatically and added to the database after curation. At present, we have collected in total 668 cis-acting regulatory elements that can be queried on TF-site name, motif, function, species, cell type, gene, transcription factor, and literature references. These queries result in a listing of entries with links to other information within the database or beyond through accession numbers from other databases. The PlantCARE relational database is available via the WWW at the URL: http://intra.psb.ugent.be:8080/PlantCARE/index.html

Recent Developments

Upon submission of a promoter sequence by a user, a new implementation presents a dynamic HTML page with the PlantCARE TF-sites highlighted on the sequence. We also provide now the possibility for users to submit promoter data online. A new quality-based clustering method and a motif search algorithm called Motif sampler (Thijs,G. et al), both developed in the aim of identifying new regulatory elements in silico from transcriptome data have now been made available through the PlantCARE website. The PlantCARE database in partner in the european PlaNet http://mips.gsf.de/proj/planet/ project to share promoter data with the plant research community.

Acknowledgements

This research was supported by grants from IWT-STWW (980396), the GOA Mefisto-666, OSTC IUAP P4-02 and the Vlaams Interuniversitair Instituut voor Biotechnology (VIB - UG). The authors are in dept to M.Lescot for her contributions and wish to thank T Puissant, J.H.Christensen and L. De Veylder for sending data to the database.

References

  1. Wingender,E., Chen,X., Hehl,R., Karas,H., Liebich,I., Matys,V., Meinhardt,T., Prüß,M., Reuter,I. and Schacherer.F. (2000) TRANSFAC: an integrated system for gene expression regulation Nucleic Acids Res., 28, 316-319.
  2. Thijs,G., Marchal,K., Lescot,M., Rombauts,S., De Moor,B., Rouze,P., Moreau,Y. (2002) A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J Comput Biol., 9:447-64. Thijs,G., Lescot,M., Marchal,K., Rombauts,S., De Moor,B.,Moreau,Y. and Rouze, P. (2001) A higher order background model improves the detection by Gibbs sampling of potential promoter regulatory elements in DNA sequences. Bioinformatics., 17:1113-22.

Authors

Rombauts, S.1, Bonnet, E.1, Thijs, G.3, Marchal, K.3, Moreau, Y.3, Van de Peer, Y.1, Rouze, P.2

1Department Plant Systems Biology, Vakgroep Moleculaire Genetica, Vlaams Interuniversitair Instituut voor Biotechnologie (VIB), Universiteit Gent, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
2Laboratoire Associé de l'Institut National de la Recherche Agronomique (France), Universiteit Gent, B-9000 Gent, Belgium
3ESAT­SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium


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