PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences

TLDR

PlantCARE is a database cataloguing plant cis‑acting regulatory elements, enhancers, and repressors. The database stores regulatory elements as positional matrices and consensus sequences, links to EMBL, TRANSFAC, and MEDLINE, and includes literature‑derived and in silico‑predicted transcription sites with confidence scores, functional annotations, and promoter positions, and allows automatic submission of new elements for curation. New search tools enable users to query cis‑acting elements in sequences and link to a clustering and motif‑search method for exploring co‑expressed gene clusters. The PlantCARE database is accessible online at http://sphinx.rug.ac.be:8080/PlantCARE/.

Abstract

PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequencesand 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/.