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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis.

Parul Gupta¹, Justin Elser¹, Elizabeth Hooks¹

¹Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.

Nucleic Acids Research

|November 21, 2023

Summary

Plant Reactome is a comprehensive plant pathway knowledgebase offering curated pathways for rice and projections for 129 species. This resource enables analysis and visualization of omics data within plant pathways, promoting data interoperability.

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Area of Science:

Plant biology
Bioinformatics
Systems biology

Background:

Plant Reactome is a freely accessible knowledgebase for plant pathways.
It includes curated pathways for rice (Oryza sativa) and projections for 129 additional plant species.
The knowledgebase covers metabolic, transport, signaling, and regulatory pathways.

Purpose of the Study:

To present Plant Reactome as a comprehensive resource for plant pathway information.
To highlight its utility as a dynamic data discovery platform.
To emphasize its commitment to data interoperability and FAIR data principles.

Main Methods:

Curating reference pathways for rice (Oryza sativa).
Generating gene-orthology-based pathway projections for 129 plant species.
Integrating omics data (gene expression, proteome, metabolome) for analysis and visualization.

Main Results:

Plant Reactome currently houses 339 reference pathways.
It encompasses a wide taxonomic diversity, from single-cell photoautotrophs to higher plants.
The platform allows users to analyze and visualize omics data within the context of plant pathways.

Conclusions:

Plant Reactome serves as a valuable, dynamic resource for plant science research.
It facilitates the exploration of complex biological processes in plants.
The knowledgebase supports data interoperability and adheres to FAIR data principles.