title: Plant Reactome: a resource for plant pathways and comparative analysis.
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.
authors: 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
authors: Sushma
authors: S
authors: Naithani
authors: 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
authors: Justin
authors: J
authors: Preece
authors: Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA.
authors: Peter
authors: P
authors: D'Eustachio
authors: 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
authors: Parul
authors: P
authors: Gupta
authors: 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
authors: Vindhya
authors: V
authors: Amarasinghe
authors: 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
authors: Palitha D
authors: PD
authors: Dharmawardhana
authors: Ontario Institute of Cancer Research, Toronto, ON M5G 0A3, Canada.|Oregon Health & Science University, Portland, OR 97239, USA.
authors: Guanming
authors: G
authors: Wu
authors: European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK.
authors: Antonio
authors: A
authors: Fabregat
authors: 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
authors: Justin L
authors: JL
authors: Elser
authors: Ontario Institute of Cancer Research, Toronto, ON M5G 0A3, Canada.
authors: Joel
authors: J
authors: Weiser
authors: European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK.
authors: Maria
authors: 0000-0003-2034-601X
authors: M
authors: Keays
authors: European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK.
authors: Alfonso Munoz-Pomer
authors: AM
authors: Fuentes
authors: European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK.
authors: Robert
authors: R
authors: Petryszak
authors: Ontario Institute of Cancer Research, Toronto, ON M5G 0A3, Canada.
authors: Lincoln D
authors: LD
authors: Stein
authors: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.|United States Department of Agriculture - Agriculture Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA.
authors: Doreen
authors: D
authors: Ware
authors: 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA jaiswalp@science.oregonstate.edu.
authors: Pankaj
authors: P
authors: Jaiswal
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods; D053858:Metabolic Networks and Pathways; D010944:Plants / Q000235:genetics* / Q000378:metabolism*; D057386:Search Engine; D015398:Signal Transduction; D049490:Systems Biology / Q000379:methods; D014584:User-Computer Interface; D064878:Web Browser