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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #268903

Title: Metabolic and regulatory networks for cereals

item DHARMAWARDHANA, PALITHA - Oregon State University
item MONACO, MARCELA - Cold Spring Harbor Laboratory
item AMARASINGHE, VINDHYA - Cold Spring Harbor Laboratory
item PREECE, JUSTIN - Cold Spring Harbor Laboratory
item D'EUSTACHIO, PETER - New York University School Of Medicine
item REN, LIYA - Cold Spring Harbor Laboratory
item THOMASON, JIM - Cold Spring Harbor Laboratory
item Sen, Taner
item GARDINER, JACK - Iowa State University
item Harper, Elisabeth
item Schaeffer, Mary
item Lawrence, Carolyn
item Ware, Doreen
item JAISWAL, PANKAJ - Oregon State University

Submitted to: American Society of Plant Biologists Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 5/27/2011
Publication Date: 8/6/2011
Citation: Dharmawardhana, P., Monaco, M., Amarasinghe, V., Preece, J., D'Eustachio, P., Ren, L., Thomason, J., Sen, T.Z., Gardiner, J.M., Harper, E.C., Schaeffer, M.L., Lawrence, C.J., Ware, D., Jaiswal, P. 2011. Metabolic and regulatory networks for cereals. American Society of Plant Biologists Annual Meeting, August 6-10, 2011, Minneapolis, MN. Available:

Interpretive Summary:

Technical Abstract: Gramene is an open-source, curated comparative plant genomics database ( 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) and sorghum (SorghumCyc), updated twice a year, and recently released pathways for maize [MaizeCyc, developed in collaboration with the Maize Genetic and Genomic Database (MaizeGDB);] and Brachypodium (BrachyCyc). The portal also mirrors other crop and model species-specific pathway databases and reference pathway databases MetaCyc and PlantCyc. Comparative analysis feasible through this collaboration among PMN, SGN, MetaCyc and Gramene will be discussed. 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. Compounds and reactions have cross-reference links to resource libraries like KEGG, CAS, LIGAND, ChEBI, and PubChem. Moving beyond the MetaCyc based pathway databases, Gramene is developing a Plant Reactome, a plant centric version of the human Reactome (an all-inclusive human-centric pathway database; to integrate regulatory and signaling pathways with metabolic ones and to house all of these expanded plant pathway networks. We will present our progress in developing a rice (Oryza sativa) Reactome as a test case.