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

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  • 12082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.

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Summary
This summary is machine-generated.

Plant Reactome is a comprehensive plant pathway database offering bioinformatics tools for pathway analysis and visualization. It supports research, genome annotation, and education across 62 plant species.

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Area of Science:

  • Plant biology
  • Bioinformatics
  • Systems biology

Background:

  • Plant Reactome is a free, open-source pathway database portal from the Gramene project.
  • It provides bioinformatics tools for pathway knowledge visualization, analysis, and interpretation.
  • The database supports various research areas including genome annotation, systems biology, and education.

Purpose of the Study:

  • To present the Plant Reactome database and its functionalities.
  • To detail the manual curation process for plant pathways, focusing on Oryza sativa (rice).
  • To describe the projection of curated pathways to other plant species using gene homology.

Main Methods:

  • Manual curation of molecular pathway details for Oryza sativa based on literature.
  • Development of bioinformatics tools for pathway visualization and analysis.
  • Projection of pathways to 62 other plant species using gene homology.
  • Integration of curated data with Expression Atlas and provision of API access.

Main Results:

  • Currently contains 222 rice pathways, 1025 reactions, 1173 proteins, 907 small molecules, and 256 references.
  • Pathways have been projected for 62 model, crop, and evolutionarily significant plant species.
  • Includes tools for searching, browsing, visualizing gene expression, and analyzing Omics datasets.

Conclusions:

  • Plant Reactome serves as a valuable resource for plant biology research, systems biology, and education.
  • The database facilitates in-depth analysis of plant metabolic, transport, genetic, developmental, and signaling pathways.
  • Provides accessible data through APIs and standard formats like SBML and BioPAX.