title: Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study.
abstract: 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.
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331-2902, USA. naithans@science.oregonstate.edu.
authors.forename: Sushma
authors.initials: S
authors.lastname: Naithani
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331-2902, USA.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Jaiswal
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D053858:Metabolic Networks and Pathways; D010944:Plants / Q000235:genetics* / Q000378:metabolism*; D057386:Search Engine; D015398:Signal Transduction; D012984:Software; D013045:Species Specificity; D064878:Web Browser
keywords: BioCyc databases; FragariaCyc; Gene expression analysis; OMICs viewer; PGDBs; Plant metabolic networks; Plant pathways