TitlePathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study.
Publication TypeJournal Article
Year of Publication2017
AuthorsNaithani, S, Jaiswal, P
JournalMethods in molecular biology (Clifton, N.J.)
Date Published2017
KeywordsComputational Biology, Databases, Gene Regulatory Networks, Genetic, Genome, Genomics, Metabolic Networks and Pathways, plant, Plants, Search Engine, Signal Transduction, Software, Species Specificity, Web Browser

The species-specific plant Pathway Genome Databases (PGDBs) based on the BioCyc platform provide a conceptual model of the cellular metabolic network of an organism. Such frameworks allow analysis of the genome-scale expression data to understand changes in the overall metabolisms of an organism (or organs, tissues, and cells) in response to various extrinsic (e.g. developmental and differentiation) and/or extrinsic signals (e.g. pathogens and abiotic stresses) from the surrounding environment. Using FragariaCyc, a pathway database for the diploid strawberry Fragaria vesca, we show (1) the basic navigation across a PGDB; (2) a case study of pathway comparison across plant species; and (3) an example of RNA-Seq data analysis using Omics Viewer tool. The protocols described here generally apply to other Pathway Tools-based PGDBs.