Plant Reactome: A Resource for Comparative Analysis of Plant Pathways

The Plant Reactome database (http://plantreactome.gramene.org/) developed collaboratively by Gramene and the human Reactome project hosts metabolic, genetic and signaling pathways for several model and crop plant species. The pathway data model organizes gene products, small molecules and macromolecular interactions into reactions and pathways in the context of their subcellular location to build a systems-level framework of a eukaryotic cell. The Plant Reactome features Oryza sativa (rice) as a reference species built by importing RiceCyc metabolic network, adding highly conserved pathways (e.g., cell cycle, DNA replication, transcription, translation, etc.) from human Reactome, and curating new metabolic, signaling and genetic pathways. The Plant Reactome database now contains ~240 rice reference pathways and orthology-based pathway projections for 66 plant species of agricultural crops and evolutionary importance. Plant Reactome allows users to i) compare pathways across various plant species; ii) query and visualize curated baseline and differential expression data available in the EMBL-EBI’s Expression Atlas in the context of pathways in the Plant Reactome; and iii) analyze genome-scale expression data and conduct pathway enrichment analysis to identify pathways likely to be modulated in response to environmental stresses and experimental treatments. Plant Reactome data links to external sources, such as Gramene, Phytozome, UniProt, PIR, ChEBI, PubChem, PubMed, and GO, etc. Users can access/download our data in various formats from our web site and via APIs. The presentation will discuss tools for pathway analysis and homologous pathway comparison, curation of reference pathways, and phylogeny based analyses of projected pathway annotations. The Gramene database project is supported by an NSF award (IOS-1127112). Intellectual and infrastructure support for the Plant Reactome is provided by the Human Reactome award (NIH: P41 HG003751 and U54 GM114833, ENFIN LSHG-CT-2005-518254, Ontario Research Fund, and EBI Industry Programme).