Plant Reactome: Metabolic and Regulatory Networks for Plants

Gramene, in collaboration with the Reactome project (www.reactome.org), has developed a new platform for the comparative analysis of plant metabolic and regulatory networks. Here we present the first public version of the Plant Reactome, initially featuring rice as a reference species. Future releases will include Arabidopsis and maize pathways. To date, the Gramene database portal (www.gramene.org) has presented MetaCyc-based pathway databases for rice, sorghum, maize and Brachypodium, along with mirrors of similar databases for other species-specific reference genomes, such as AraCyc. The Plant Reactome will strengthen and extend MetaCyc based capabilities in pathway analysis. In addition to browsing and searching pathways, reactions, compounds and gene products, this new database and accompanying web application provide tools for pathway overrepresentation analysis, inter-species comparison and overlaying of expression and gene-gene interaction data. Pathways, reactions and gene entries in the Plant Reactome provide external links to Uniprot, PIR, ChEBI, PubChem, PubMed and the Gene Ontology (GO). To construct the Plant Reactome, we converted RiceCyc data to conform to the Reactome data structure. This initial conversion was followed by the addition of a small set of signaling and regulatory pathways based on gene orthology and known projections of curated Human Reactome pathways. The computational projections were enhanced with a substantial manual curation effort to improve biological relevance and a  customized web application was implemented to host the data. We expect the Plant Reactome to become a primary investigative source for plant pathways, network analysis and community curation.