Plant Reactome: a knowledgebase and resource for comparative pathway analysis

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).

Comparative Transcriptomics of Rice Genotypes with Contrasting Responses to Nitrogen Stress Reveals Genes Influencing Nitrogen Uptake through the Regulation of Root Architecture

“…Gene ontology enrichment of the DEGs was performed to determine the biological significance with respect to the biological processes, molecular functions, and cellular localization of their proteins using a singular enrichment analysis (SEA) with agriGO v2 [ 78 ]. In addition, plant pathway analyses were performed using Plant Reactome ( ) to determine the involvement of DEGs in plant pathways or processes [ 79 ].…”

Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily

“…Based on the analysis of gene structure, transcription profile, and extensive literature review, we propose the gene nomenclature and gene description for the 144 members of the rice SDRLK family (see Table S1 ). We will integrate this information in the Plant Reactome knowledgebase ( Naithani et al, 2020 ) that also exchanges information with other public resources such as UniProt and the RAP database.…”

Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks

“…Currently, pathway mapping of comparative multi-omics data hardly considers pathway compartmentalization, despite the fact that topological differences are evident between global and compartment-specific metabolic networks [193] . Fortunately, such information has increasingly become available during the last decade due to the construction of pathway databases containing tissue-, cell-, and cellular compartment-specific information [20] , [21] .…”

“…For the construction of a metabolic network, information can be readily gathered from pathway databases ( Fig. 1 A), such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) [16] , [17] , [18] , BioCyc [19] , the Plant Reactome database [20] , [21] and the Gramene database [22] , yet these databases might be incomplete or insufficiently detailed. When attempting to complete the metabolic network of a particular species, gaps representing unknown reactions have to be filled in, which demands an exhaustive search for all gene–protein–reaction associations by concatenating gene–protein and protein–reaction information from different databases.…”