01693nas a2200313   4500000000100000000000100001008004100002260000900043653002600052653002300078653002900101653001800130653001300148653003600161653001100197653001800208653002400226653001300250653002400263653001600287100002000303700001900323245010900342856004900451300001200500490000900512520084400521022001401365       2017                            d  c201710aComputational Biology10aDatabases, Genetic10aGene Regulatory Networks10aGenome, Plant10aGenomics10aMetabolic Networks and Pathways10aPlants10aSearch Engine10aSignal Transduction10aSoftware10aSpecies Specificity10aWeb Browser1 aSushma Naithani1 aPankaj Jaiswal00aPathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study.  uhttps://doi.org/10.1007/978-1-4939-6658-5_14  a241-2560 v15333 aThe 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.  a1940-6029