Plant Reactome: a knowledgebase and resource for comparative pathway analysis

Authors: NAITHANI, S. - Oregon State University; GUPTA, P. - Oregon State University; PREECE, J. - Oregon State University; D'EUSTACHIO, P. - New York University School Of Medicine; ELSER, J. - Oregon State University; GARG, P. - Oregon State University; DIKEMAN, D. - Oregon State University; KIFF, J. - Oregon State University; COOK, J. - Ontario Cancer Institute; OLSON, A. - Cold Spring Harbor Laboratory; WEI, S. - Cold Spring Harbor Laboratory; TELLO-RUIZ, M. - Cold Spring Harbor Laboratory; MUNDO, A. - European Bioinformatics Institute; MUNOZ-POMER, A. - European Bioinformatics Institute; MOHAMMED, S. - European Bioinformatics Institute; CHENG, T. - National Center For Biotechnology Information (NCBI); BOLTON, E. - National Center For Biotechnology Information (NCBI); PAPATHEODOROU, I. - European Bioinformatics Institute; STEIN, L. - Ontario Cancer Institute; Ware, Doreen; JAISWAL, P. - Oregon State University

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/14/2019
Publication Date: 1/8/2020
Citation: Naithani, S., Gupta, P., Preece, J., D'Eustachio, P., Elser, J.L., Garg, P., Dikeman, D.A., Kiff, J., Cook, J., Olson, A., Wei, S., Tello-Ruiz, M.K., Mundo, A.F., Munoz-Pomer, A., Mohammed, S., Cheng, T., Bolton, E., Papatheodorou, I., Stein, L., Ware, D., Jaiswal, P. 2020. Plant Reactome: a knowledgebase and resource for comparative pathway analysis. Nucleic Acids Research. 48(D1):D1093-D1103. https://doi.org/10.1093/nar/gkz996.
DOI: https://doi.org/10.1093/nar/gkz996

Interpretive Summary: A pathway is a series of chemical reactions that are important in the maintenance of a stable environment for a living organism. This article describes a new computational resource, Plant Reactome, that allows users to visualize and analyze plant pathways and gene expression data, in a holistic and comparative manner. This resource includes 222 manually curated rice pathways and computational projections to 62 other model crops and economically important plant species like Arabidopsis, maize, and sorghum. Users can visualize, upload and analyze their own transcript expression, as well as curated baseline expression of pathway-associated genes provided by the Expression Atlas project. Together with the genome data hosted at the Gramene website, the pathway data in Plant Reactome serve as a reference resource for comparative analyses for the broad scientific community, and supports basic and translational research, which ultimately impact societal issues, such as food security, energy production, and climate change.

Technical Abstract: Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another 82 plant species via gene-orthology projection using the Reactome data model and framework. It currently hosts 298 reference pathways, including metabolic and transport pathways, transcriptional networks, hormone signaling pathways, and plant developmental processes. In addition to browsing plant pathways, users can upload and analyze their omics data, such as the gene-expression data, and overlay curated or experimental gene-gene interaction data to extend pathway knowledge. The curation team actively engages researchers and students on gene and pathway curation by offering workshops and online tutorials. The Plant Reactome supports, implements and collaborates with the wider community to make data and tools related to genes, genomes, and pathways Findable, Accessible, Interoperable and Re-usable (FAIR).