Metabolic and Regulatory Networks for Cereals

Gramene is an open-source, curated comparative plant genomics database (www.gramene.org). In order to represent the metabolomes of cereal crops and thereby support their analysis and comparison, we develop and curate pathway databases for cereal species. The Gramene portal includes pathways for rice (RiceCyc), sorghum (SorghumCyc), maize (MaizeCyc, developed in collaboration with MaizeGDB; maizecyc.maizegdb.org) and Brachypodium (BrachyCyc). The portal also mirrors other crop and model species-specific pathway databases and reference pathway databases MetaCyc and PlantCyc. Having all the individual pathway databases at one site facilitates inter- and intra-specific comparisons between pathways and associated genes, and searches for patterns of coexpression. The integrated Omics Viewer tool allows users to overlay and visualize transcriptomic, proteomic, and metabolomic datasets with expressed values on pathway maps in a cellular overview in real time. Moving beyond the MetaCyc based pathway databases, Gramene in collaboration with the Reactome project (www.reactome.org) is in the process of developing metabolic and regulatory networks for rice and Arabidopsis on the Reactome platform, which would integrate plant-specific regulatory, signaling and metabolic pathways from multiple sources. Funded by USDA ARS 1907-21000-030, 3625-21000-051, NIH P41 HG003751 and NSF IOS-0703908