TY - JOUR
KW - Computational Biology
KW - Databases, Genetic
KW - Genomics
KW - Metabolic Networks and Pathways
KW - Plants
KW - Search Engine
KW - Signal Transduction
KW - Systems Biology
KW - User-Computer Interface
KW - Web Browser
AU - Sushma Naithani
AU - Justin Preece
AU - Peter D'Eustachio
AU - Parul Gupta
AU - Vindhya Amarasinghe
AU - Palitha Dharmawardhana
AU - Guanming Wu
AU - Antonio Fabregat
AU - Justin Elser
AU - Joel Weiser
AU - Maria Keays
AU - Alfonso Fuentes
AU - Robert Petryszak
AU - Lincoln Stein
AU - Doreen Ware
AU - Pankaj Jaiswal
AB - Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX.
BT - Nucleic acids research
C1 - http://www.ncbi.nlm.nih.gov/pubmed/27799469?dopt=Abstract
DA - 2017 Jan 04
DO - 10.1093/nar/gkw932
IS - D1
J2 - Nucleic Acids Res.
LA - eng
N2 - Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX.
PY - 2018
SP - D1029
EP - D1039
T2 - Nucleic acids research
TI - Plant Reactome: a resource for plant pathways and comparative analysis.
UR - https://doi.org/10.1093/nar/gkw932
VL - 45
SN - 1362-4962
ER -