PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.
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 and MEDLINE databases are provided when available. Data about the transcription sites are extracted mainly from the literature, supplemented with an increasing number of in silico predicted data. Apart from a general description for specific transcription factor sites, levels of confidence for the experimental evidence, functional information and the position on the promoter are given as well. 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 and motif search method to investigate clusters of co-expressed genes. New regulatory elements can be sent automatically and will be added to the database after curation. The PlantCARE relational database is available via the World Wide Web at http://sphinx.rug.ac.be:8080/PlantCARE/.
Lescot
Magali
M
Vakgroep Moleculaire Genetica, Departement Plantengenetica, Vlaams Interuniversitair Instituut voor Biotechnologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium.
Déhais
Patrice
P
Thijs
Gert
G
Marchal
Kathleen
K
Moreau
Yves
Y
Van de Peer
Yves
Y
Rouzé
Pierre
P
Rombauts
Stephane
S
D016384:Consensus Sequence; D030561:Databases, Nucleic Acid; D004742:Enhancer Elements, Genetic; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D016247:Information Storage and Retrieval; D020407:Internet; D005810:Multigene Family; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D018511:Systems Integration; D014158:Transcription, Genetic