Format

Send to

Choose Destination
Nucleic Acids Res. 2017 Jan 4;45(D1):D1029-D1039. doi: 10.1093/nar/gkw932. Epub 2016 Oct 30.

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

Author information

1
2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
2
Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA.
3
Ontario Institute of Cancer Research, Toronto, ON M5G 0A3, Canada.
4
Oregon Health & Science University, Portland, OR 97239, USA.
5
European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK.
6
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
7
United States Department of Agriculture - Agriculture Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA.
8
2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA jaiswalp@science.oregonstate.edu.

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.

PMID:
27799469
PMCID:
PMC5210633
DOI:
10.1093/nar/gkw932
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center