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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #273652

Title: Metabolic and regulatory networks in gramene

item DHARMAWARDHANA, PALITHA - Oregon State University
item MONACO, MARCELA - Cold Spring Harbor Laboratory
item AMARASINGHE, VINDHYA - Oregon State University
item PREECE, JUSTIN - Oregon State University
item WU, GUANMING - Ontario Cancer Institute
item D'EUSTACHIO, PETER - 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: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 9/9/2011
Publication Date: 11/30/2011
Citation: Dharmawardhana, P., Monaco, M., Amarasinghe, V., Preece, J., Wu, G., D'Eustachio, P., 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 in gramene. Meeting Abstract. Paper No. 2.

Interpretive Summary:

Technical Abstract: Gramene is an open-source, curated, comparative plant genomics database ( In order to understand the metabolome of cereal crops, we develop and curate pathway databases for cereal species, including pathways for rice (RiceCyc), sorghum (SorghumCyc), maize (MaizeCyc), and Brachypodium (BrachyCyc). Gramene also mirrors several other crop and model species-specific pathway databases, such as Arabidopsis (AraCyc), Medicago (MedicCyc), tomato (LycoCyc), potato (PotatoCyc), poplar (PoplarCyc), and coffee (CoffeeCyc), as well as the reference pathway databases MetaCyc and PlantCyc. Aggregating these individual pathway data sets allows the user to extract inter- and intra-specific comparisons between pathways and associated genes, and also makes it possible to look 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. We are also 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. As part of that effort, we are focusing on developing a regulatory network for abiotic stress. We envision the integrated database to house a comprehensive collection of plant metabolic and regulatory networks for use by the plant research community.