Resources for Comparative Genomics and Pathway Analysis for Grapevine

The cellular-level pathway networks for grapevine, such as VitisCyc, or the Plant Reactome can provide a framework for analysis and visualization of the large-scale expression data sets and aid grape researchers in understanding the metabolic composition of the grape berry and how it is influenced by genetic diversity or in response to various environmental factors. VitisCyc (http://pathways.cgrb.oregonstate.edu) is a curated cellular metabolic network based on the BioCyc platform. The Plant Reactome database (http://plantreactome.gramene.org), a pathway portal of Gramene database, is based on the Reactome Data model that hosts signaling, transport, developmental pathways in addition to the metabolic pathways for 66 plants including grapevine based on orthology to Oryza sativa. The utility of these resources in Omics data analysis will be illustrated using publicly available gene expression data sets available for grapevine in the EMBL-EBI plant gene Expression Atlas (https://www.ebi.ac.uk/gxa/plant/experiments). Furthermore, users can analyse the gene expression in relation to genetic diversity by uploading this data on the Gramene Ensembl Genome Browser. The VitisCyc is partially supported by Oregon State University funds to SN and the Gramene database is supported by NSF (award #: NSF IOS-1127112). The Plant Reactome portal of Gramene is being developed in collaboration with the Human Reactome (award #: NIH: P41 HG003751 and U54 GM114833, ENFIN LSHG-CT-2005-518254, Ontario Research Fund, and EBI Industry Programme).