plant-reactome

is a Data Source.

Plant Reactome is a freely-accessible, open-source pathway knowledgebase for comparative pathway analysis and systems biology in plants. It provides manually curated pathways in rice with gene-orthology based projections across 138 additional plant species.

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Domains

pathways, systems biology

License

CC BY 3.0

Homepage

plant-reactome

Repository

GitHub

Infores ID

Unknown

FAIRsharing ID

Unknown

Product Summary

Products

From this Resource
ID Name URL Category Format Description
plant-reactome.portal Plant Reactome Web Portal plantreactome.gramene.org GraphicalInterface http Web portal for browsing, searching, a...
plant-reactome.api Plant Reactome REST API ContentService ProgrammingInterface http RESTful Content Service API for progr...
plant-reactome.biopax Plant Reactome BioPAX3 Data biopax3.zip (112.5 MB) Product biopax BioPAX3 format pathway data downloads...
plant-reactome.sbgn ⚠ Plant Reactome SBGN Diagrams current Product sbgnml SBGN format pathway diagrams and path...
plant-reactome.svg Plant Reactome SVG Diagrams diagrams.svg.tgz (1.6 GB) Product svg Scalable Vector Graphics (SVG) format...
plant-reactome.png Plant Reactome PNG Diagrams diagrams.png.tgz (531.5 MB) Product png PNG raster image format pathway diagr...
plant-reactome.mappings Plant Reactome Identifier Mappings gene_ids_by_pathway_and_species.tab (23.3 MB) MappingProduct tsv Tab-delimited identifier mapping file...

Details

Plant Reactome

Overview

Plant Reactome is a freely-accessible, open-source pathway knowledgebase developed by the Gramene project. It provides researchers with intuitive bioinformatics tools for visualization, interpretation, and analysis of plant pathway knowledge to support basic research, genome analysis, modeling, systems biology, and education.

The database uses Oryza sativa (rice) as the primary reference organism for manual pathway curation, with curated pathways extended via gene-orthology projection to 138 additional plant species, creating a comprehensive resource for comparative plant pathway analysis.

Data Content and Scale

Plant Reactome houses a comprehensive collection of pathway knowledge across 139 plant species:

Reference Pathways (Rice)

  • 351 Reference Pathways - Manually curated for rice
  • 2,098 Reactions - Detailed biochemical reactions
  • 2,233 Gene Products - Proteins and gene products
  • 1,320 Small Molecules - Metabolites and chemical entities

Total Coverage Across All Species

  • Over 38,000 Pathways - Including orthology-based projections
  • Over 118,000 Reactions - Across all projected species
  • Over 263,000 Gene Products - Total unique proteins/genes
  • 138 Projected Species - Beyond the primary reference

Pathway Categories

The database encompasses a diverse range of biological processes:

  • Metabolic and Transport Pathways - Energy metabolism, nutrient transport, biosynthesis
  • Hormone Signaling Pathways - Auxin, gibberellin, ethylene, jasmonate, salicylate signaling
  • Genetic Regulation - Developmental processes and transcriptional networks
  • Cell Cycle Pathways - Cell division and cycle control
  • Plant Defense and Stress Response - Biotic and abiotic stress responses
  • Developmental Processes - Organ differentiation and morphogenesis
  • Signaling Cascades - Multi-level regulatory networks

Species Coverage

Plant Reactome covers diverse plant organisms spanning multiple taxonomic groups:

Model Organisms

  • Arabidopsis thaliana (3702) - Well-characterized flowering plant
  • Oryza sativa (4530) - Rice (primary reference)
  • Zea mays (4577) - Maize/Corn
  • Hordeum vulgare (4513) - Barley
  • Sorghum bicolor (4558) - Sorghum

Legumes and Pulses

  • Glycine max (3847) - Soybean
  • Medicago truncatula (3880) - Medicago

Fruits and Vegetables

  • Solanum lycopersicum (4081) - Tomato
  • Solanum tuberosum (4113) - Potato
  • Musa acuminata (4641) - Banana

Trees and Perennials

  • Populus trichocarpa (3694) - Poplar

Non-Seed Plants

  • Physcomitrella patens (3218) - Moss (non-vascular)
  • Selaginella moellendorffii (88036) - Lycophyte (vascular non-seed)

Photosynthetic Protists

  • Chlamydomonas reinhardtii (3055) - Green algae
  • Cyanidioschyzon merolae (2763) - Red algae

Additional Species

Additional species coverage extends through orthology-based projections to include relatives of the species listed above, totaling 138 species beyond the primary reference.

Data Access and Formats

Plant Reactome provides multiple access modes and standardized data formats for integration and analysis:

Web Interface

  • Interactive pathway browser and search functionality
  • Pathway visualization tools with subcellular localization
  • Comparative pathway views across species
  • Expression data integration and analysis
  • Embeddable pathway diagram widgets

REST API

  • JSON-formatted responses
  • Programmatic access to pathways, reactions, and entities
  • Hierarchical querying capabilities

Data Downloads

  • BioPAX3 - Standard pathway exchange format
  • SBGN - Systems Biology Graphical Notation for visualizations; no standalone SBGN archive was listed in the current download directory during this curation pass
  • SVG/PNG - Pathway diagrams in vector and raster formats
  • TSV and text mapping files - Identifier mappings and analysis files

Data Integration

  • Gene identifiers linked to Gramene-Ensembl Plants
  • Protein cross-references to UniProt
  • Small molecule/metabolite references to ChEBI and PubChem

Key Features

Pathway Analysis Tools

  • Gene Expression Summary Analysis (GSA) - Identify differentially expressed pathways
  • Pathway Enrichment Analysis - Statistical analysis of OMICS data
  • Comparative Pathway Analysis - Cross-species pathway comparison

OMICS Data Integration

  • Transcriptomics baseline expression visualization
  • Support for high-throughput gene expression data analysis
  • Proteomics data integration capabilities

Data Accessibility

  • Multiple query modes and search functionality
  • Hierarchical pathway organization
  • Cross-species navigation and comparison

Use Cases

Plant Reactome serves diverse research and educational applications:

  • Plant Systems Biology - Understanding regulatory networks and systems-level biology
  • Functional Genomics - Annotation and characterization of gene function
  • Genome Analysis - Integration of genomic data with pathway knowledge
  • Comparative Genomics - Understanding functional evolution across plant species
  • Agricultural Research - Crop improvement and trait optimization
  • Environmental Stress Biology - Plant responses to drought, temperature, pathogens
  • Developmental Biology - Understanding plant growth and morphogenesis
  • Education - Teaching plant biology and systems biology concepts

Citation and Usage

Plant Reactome data is freely available under the Creative Commons Attribution 3.0 Unported (CC BY 3.0) license, with external annotations and datasets remaining under their source-provider licenses unless otherwise specified. Users are encouraged to cite the appropriate Plant Reactome publication(s) when using data from this resource in research or educational materials.

Community and Support

Plant Reactome is maintained by the Gramene project and welcomes community feedback on:

  • Database content and data quality
  • Website functionality and user experience
  • Documentation and tutorials
  • Feature requests and suggestions

Support and information are available through the Plant Reactome website and the broader Gramene community.

Is this information incorrect or incomplete? Request an update.

Created: December 17, 2025 | Last modified: June 02, 2026