Pathways

Plant Reactome: The Plant Reactome is a free, open-source, curated and peer reviewed pathway database for several crops and model plant species that uses framework of an eukaryotic cell model. Currently, we feature rice as a reference species and gene homology-based pathway projections to 62 plant species. The Plant Reactome allows users to upload and analyze large-scale expression data, and to compare pathways between a chosen species and the reference species O. sativa. It provides a Systems Biology Graphical Notation (SBGN)-based online user interface derived from the (Human) Reactome database model. Pathways, reactions and gene entries in Plant Reactome are cross-referenced to many bioinformatics databases, such as UniProt, ChEBI, PubChem, PubMed, Gramene and Plant Ensembl genomes and Gene Ontology (GO). Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education.

"Cyc" Pathways: Gramene hosts ten legacy plant pathways databases on the Pathway Tools platform: the Gramene-developed RiceCyc (Oryza sativa japonica), SorghumCyc (Sorghum bicolor), MaizeCyc (Zea mays) and BrachyCyc (Brachypodium distachyon), and mirrored databases AraCyc (Arabidopsis thaliana), MedicCyc (Medicago truncatula), PoplarCyc (Populus trichocarpa), CoffeaCyc (Coffea canephora), LycoCyc (Solanum lycopersicum) and PotatoCyc (Solanum tuberosum). Three reference databases, EcoCyc, MetaCyc and PlantCyc, are also available. These databases allow users to search or browse for genes, enzymes, metabolites, and metabolic pathways, to make cross-species comparisons, and to conduct analysis on their own data sets. These pathways were developed in previous funding cycle of Gramene and are not being actively curated.