@article{55,
  keywords = {Computational Biology, Databases, Genetic, Gene Regulatory Networks, Genome, Plant, Genomics, Metabolic Networks and Pathways, Plants, Search Engine, Signal Transduction, Software, Species Specificity, Web Browser},
  author = {Sushma Naithani and Pankaj Jaiswal},
  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.},
  year = {2017},
  journal = {Methods in molecular biology (Clifton, N.J.)},
  volume = {1533},
  pages = {241-256},
  month = {2017},
  issn = {1940-6029},
  url = {https://doi.org/10.1007/978-1-4939-6658-5_14},
  doi = {10.1007/978-1-4939-6658-5_14},
  language = {eng},
}