Nuclc. Acids. Res. OUP
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH ARTICLES TABLE OF CONTENTS
Compilation Paper
Categories List
Alphabetical List
Search Summary Papers

PlantCARE

http://sphinx.rug.ac.be:8080/PlantCARE/

Lescot, M.3, Dehais, P.1, Moreau, Y.3, Van de Peer, Y.1, Rouze, P.2, Rombauts, S.1

1Vakgroep Moleculaire Genetica & Departement Plantengenetica, Vlaams Interuniversitair Instituut voor Biotechnologie (VIB), Universiteit Gent, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
2Laboratoire AssociÈ de l'Institut National de la Recherche Agronomique (France), Universiteit Gent, B-9000 Gent, Belgium
3ESAT*SISTA/COSIC, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Leuven Belgium

Contact   strom@gengenp.rug.ac.be


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 417 cis-acting regulatory elements, of which 150 are from monocotyledonous species, 263 from dicotyledonous species and 4 from other higher plants (such as conifers). In total, these describe about 160 individual promoters from higher plant genes. The database 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://sphinx.rug.ac.be:8080/PlantCARE/

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.

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).

REFERENCES

  1. Wingender,E., Chen,X., Hehl,R., Karas,H., Liebich,I., Matys,V., Meinhardt,T., Pr¸þ,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., RouzÈ,P. and Moreau,Y. (2001). A Gibbs Sampling method to detect over-represented motifs in upstream regions of co-expressed genes. Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB), ACM Press, New York., MontrÈal, Canada, pp. 296-302.
  3. Thijs, G., Lescot, M., Rombauts, S., Marchal, K., De Moor, B., Moreau, Y. And RouzÈ, P. (2001) A higher order background model improves the detection by Gibbs sampling of potential promoter regulatory elements in DNA sequences. Bioinformatics, in press.

Category   Gene Identification and Structure

Go to the abstract in the NAR 2002 Database Issue.

 

Compilation Paper
Categories List
Alphabetical List
Search Summary Papers