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Plant Reactome: a resource for plant pathways and comparative analysis.

TitlePlant Reactome: a resource for plant pathways and comparative analysis.
Publication TypeJournal Article
Year of Publication2018
AuthorsNaithani, S, Preece J, D'Eustachio P, Gupta P, Amarasinghe V, Dharmawardhana PD, Wu G, Fabregat A, Elser JL, Weiser J, Keays M, Munoz-Pomer Fuentes A, Petryszak R, Stein LD, Ware D, Jaiswal P
JournalNucleic acids research
Volume45
IssueD1
PaginationD1029-D1039
Date Published2017 Jan 04
ISSN1362-4962
KeywordsComputational Biology, Databases, Genetic, Genomics, Metabolic Networks and Pathways, Plants, Search Engine, Signal Transduction, Systems Biology, User-Computer Interface, Web Browser
Abstract

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.

URLhttps://doi.org/10.1093/nar/gkw932
DOI10.1093/nar/gkw932
Alternate JournalNucleic Acids Res.
Refereed DesignationRefereed