Resources for Comparative Pathway Analysis for Grapevine

Cellular-level pathway networks for grapevine such as VitisCyc and Plant Reactome can provide a framework for the analysis and visualization of 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 and 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 provided by Gramene, hosts signaling, transport, developmental and metabolic pathways for 66 plant species, including Vitis vinifera, 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 for grapevine in the EMBL-EBI plant gene Expression Atlas (https://www.ebi.ac.uk/gxa/plant/experiments). Users can further analyze gene expression in relation to genetic diversity by uploading this data on the Gramene Ensembl Genome Browser. Support for VitisCyc is provided in part by Oregon State University. Gramene is supported by the NSF (Award # IOS-1127112). The Plant Reactome portal 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).