Plant Reactome

Plant Reactome provides a curated pathway knowledgebase for visualization, interpretation, and comparative analysis of plant metabolic, transport, transcriptional, hormone signaling, and developmental pathways using Oryza sativa as the reference species.

Key Features:

• Reference species and comparative analysis: Uses Oryza sativa as the manually curated reference and projects pathway knowledge to 82 additional plant species via gene-orthology projection within the Reactome data model and framework.
• Extensive curated pathway collection: Hosts 298 reference pathways covering metabolic, transport, transcriptional networks, hormone signaling, and developmental processes.
• Omics and interaction data integration: Supports integration of omics datasets (e.g., gene-expression) and overlay of curated or experimental gene–gene interaction data onto existing pathways to extend and refine pathway models.
• Pathway visualization and interpretation: Provides visualization and interpretation of pathways to facilitate analysis of plant biological processes across species.

Scientific Applications:

• Pathway analysis: Enables detailed interpretation of metabolic, signaling, and developmental pathway activity in plant systems.
• Comparative genomics: Supports cross-species comparison of pathways to infer conserved and divergent mechanisms among plants.
• Functional genomics: Facilitates integration of gene-expression and interaction data for functional inference and hypothesis generation.
• Crop improvement research: Assists identification of pathway targets relevant to crop yield, resistance, and sustainability studies.
• Evolutionary and developmental studies: Aids identification of conserved mechanisms in plant development and stress responses across species.

Methodology:

Manual curation of pathways using Oryza sativa as the reference, gene-orthology projection to 82 species, implementation within the Reactome data model and framework, and support for overlaying omics and gene–gene interaction data onto pathways.