TY - JOUR
KW - Computational Biology
KW - Databases, Genetic
KW - Gene Regulatory Networks
KW - Genome, Plant
KW - Genomics
KW - Metabolic Networks and Pathways
KW - Plants
KW - Search Engine
KW - Signal Transduction
KW - Software
KW - Species Specificity
KW - Web Browser
AU - Sushma Naithani
AU - Pankaj Jaiswal
AB - 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.
BT - Methods in molecular biology (Clifton, N.J.)
C1 - http://www.ncbi.nlm.nih.gov/pubmed/27987175?dopt=Abstract
DA - 2017
DO - 10.1007/978-1-4939-6658-5_14
J2 - Methods Mol. Biol.
LA - eng
N2 - 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.
PY - 2017
SP - 241
EP - 256
T2 - Methods in molecular biology (Clifton, N.J.)
TI - Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study.
UR - https://doi.org/10.1007/978-1-4939-6658-5_14
VL - 1533
SN - 1940-6029
ER -