Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases

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, researchers from Oregon State University 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.


(a) Plant Metabolic Pathways homepage showing a list of Pathway/Genome Databases (PGDBs ) hosted on the Pathway-Tool platform. Users can get a quick “Summary” of an individual database (b), and “Browse” pathways in a specific database, such as FragariaCyc (c). FragariaCyc, VitisCyc, and EucalyptusCyc were developed and curated in our laboratory. The PGDBs of four monocot species, RiceCyc, SorghumCyc, MaizeCyc, and BrachyCyc, were developed by the NSF-funded Gramene database project. The three reference PGDBs (EcoCyc, MetaCyc, and PlantCyc), and PGDBs for five dicot species (AraCyc, MedicCyc, PoplarCyc, PotatoCyc, and CoffeaCyc) developed by various laboratories are publicly available and are mirrored here for the convenience of the users interested in comparative studies

Availability – Plant Metabolic Pathways is available at:

Registry of BioCyc Pathway/Genome Databases at:

Naithani S, Jaiswal P. (2017) Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study. Methods Mol Biol 1533:241-256. [abstract]

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