Plant & Animal Genomes XVIII Conference

January 9-13, 2010
Town & Country Convention Center
San Diego, CA

Metabolic Pathway Networks For Cereal Plants In The Gramene Database

Palitha Dharmawardhana¹ , Liya Ren² , Jim Thomason² , Doreen Ware^2,3 , Pankaj Jaiswal¹

¹  Oregon State University, Department. of Botany and Plant Pathology, 2082 Cordley Hall, Corvallis, OR, 97331-2902, USA

²  Cold Spring Harbor Laboratory Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY, 11724, USA

³  USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY, 14853, USA

The Gramene database (www.gramene.org), a comprehensive comparative plant genomics platform developes and curates RiceCyc and SorghumCyc pathway databases for cereal plants. RiceCyc with 342 known and/or predicted metabolic pathways for Oryza sativa japonica cv. Nipponbare has undergone several rounds of data quality enhancement and manual curation whereas SorghumCyc with 328 pathways for Sorghum bicolor Strain BTX623 is in its initial computational build. The plant metabolic pathways module within Gramene mirrors several other species specific pathways such as Arabidopsis, Medicago, Tomato, Potato and Coffee as well as MetaCyc reference database allowing the user to extract interspecific comparison between pathways and associated genes. The user is also able to download lists of genes associated with each pathway. The database comes with the Omics Viewer data visualization tool. This tool allows users to overlay microarray, transcriptomic, proteomic, and metabolomic datasets with expressed values on pathway maps. The overlaid views allow to visualize the pathways and reactions that are up/down regulated in an experiment or a set of experiments. We have also built an Omics Validator tool to validate user provided expression data files by mapping probe IDs from various microarray platforms to their respective gene IDs..