Plant Reactome: A Resource for Comparative Plant Pathway Analysis

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 Reactome data model organizes gene products, small molecules and macromolecular interactions into reactions and pathways in context of their subcellular location to build a systems-level framework of an eukaryotic cell. The Plant Reactome features Oryza sativa (rice) as a reference species that was built by importing RiceCyc metabolic network; adding highly conserved projected 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 238 rice reference pathways and orthology-based pathway projections for 33 plant species. 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 context of pathways listed 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 gene loci pages in the genome section of the Gramene and to external sources like, UniProt, PIR, ChEBI, PubChem, PubMed, and GO.  Users can access/download our data in various formats from our web site and via APIs. The presentation will discuss tools for pathway enrichment analysis and homologue pathway comparison, development of the Plant Reactome portal, curation of reference rice 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, ENFIN LSHG-CT-2005-518254, Ontario Research Fund, and EBI Industry Programme).