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

Methods Mol Biol. 2017;1533:241-256. doi: 10.1007/978-1-4939-6658-5_14.

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.

Keywords: BioCyc databases; FragariaCyc; Gene expression analysis; OMICs viewer; PGDBs; Plant metabolic networks; Plant pathways.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computational Biology / methods*
  • Databases, Genetic*
  • Gene Regulatory Networks
  • Genome, Plant*
  • Genomics* / methods
  • Metabolic Networks and Pathways
  • Plants / genetics*
  • Plants / metabolism*
  • Search Engine
  • Signal Transduction
  • Software*
  • Species Specificity
  • Web Browser