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United States Department of Agriculture

Agricultural Research Service

Research Project: THE MAIZE GENETICS AND GENOMICS DATABASE Title: Metabolic and regulatory networks for cereals

Authors
item Dharmawardhana, Palitha -
item Monaco, Marcela -
item Amarasinghe, Vindhya -
item Preece, Justin -
item D'Eustachio, Peter -
item Ren, Liya -
item Thomason, Jim -
item Sen, Taner
item Gardiner, Jack -
item Harper, Elisabeth
item Schaeffer, Mary
item Lawrence, Carolyn
item Ware, Doreen
item Jaiswal, Pankaj -

Submitted to: American Society of Plant Biologists Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: May 27, 2011
Publication Date: August 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: http://abstracts.aspb.org/pb2011/public/P21/P21021.html.

Technical Abstract: 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) 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); 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. 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; www.reactome.org) 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.

Last Modified: 11/21/2014