1. Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study.

Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study.

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.)
Volume1533
Pagination241-256
Date Published2017
ISSN1940-6029
KeywordsComputational Biology, Databases, Gene Regulatory Networks, Genetic, Genome, Genomics, Metabolic Networks and Pathways, plant, Plants, Search Engine, Signal Transduction, Software, Species Specificity, Web Browser
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.
URLhttps://doi.org/10.1007/978-1-4939-6658-5_14
DOI10.1007/978-1-4939-6658-5_14