Gramene's Plant Pathways Databases & Analysis of User-Defined Expression Data Sets

Pathway databases – when integrated with the wide array of high-throughput expression data sets – can help in advancing the knowledge of cellular metabolism of an organism and how it is affected in response to developmental and environmental signals.  Gramene (http://www.gramene.org/pathway) hosts ten plant pathways databases: the Gramene-developed RiceCyc (Oryza sativa japonica), SorghumCyc (Sorghum bicolor), MaizeCyc (Zea mays) and BrachyCyc (Brachypodium distachyon), and the mirrored databases AraCyc (Arabidopsis thaliana), MedicCyc (Medicago truncatula), PoplarCyc (Populus trichocarpa), CoffeaCyc (Coffea canephora), LycoCyc (Solanum lycopersicum) and PotatoCyc (Solanum tuberosum). These BioCyc based Plant Pathways databases support search for metabolites, genes, enzymes etc. Users can make cross-species comparisons of metabolic pathways and can also upload and analyse datasets of their choce. We will demonstrate, the utilities and anlytical functions of plant pathway databases using publically available expression data.