Plant Pathways & Gene Expression Analysis in Gramene

The pathways section in the Gramene harbors species-specific metabolic pathway databases for rice (RiceCyc), maize (MaizeCyc), Bracypodium (BrachyCyc) and sorghum (SorghumCyc). These databases were constructed and curated by Gramene. We also mirror the reference databases; EcoCyc, MetaCyc and PlantCyc, in addition to pathway databases of Arabidopsis (AraCyc), tomato (LycoCyc), potato (PotatoCyc), coffee (CoffeaCyc), and Medicago (MedicCyc) developed by our collaborators.  Researchers can search for genes, proteins, enzymes, reactions, metabolites, biochemical, and metabolic and transport pathways in any of these databases and compare two or more species. Furthermore, Omics-viewer tool in the pathway databases allows users to upload and analyze their high-throughput expression data (from microarray, proteomics, metabolomics etc.) and generate cellular overview of pathways. The plant genome browser allows users to view and search genome information from the chromosome to a base-pair level. It also allows researchers to upload and analyze their data such as those from transcriptome assembly, gene expression and SNP analysis.  In the hands-on session, we will use publicly available RNA-Seq gene expression and SNP data to illustrate utility of these tools. Researchers are welcome to bring their own datasets for practice.