Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/10/2004
Publication Date: 1/10/2004
Citation: Tang, X., Gong, J., Xin, J., Lishuang, S., Turner, S., Caldo, R., Nettleton, D., Wise, R.P., Dickerson, J. 2004. BarleyBase - An expression profiling database for cereal genomics. Plant and Animal Genome XII Conference. p. 944. Interpretive Summary:
Technical Abstract: BarleyBase, a MIAME-compliant, MySQL relational database, serves as a public repository for raw and normalized expression data from the Affymetrix Barley1- and ATH1-121501-GeneChip probe arrays, presently the only two available Affymetrix high-density arrays from plants. Funded by the USDA-IFAFS program and released in June 2003, the Barley1 GeneChip was developed by an international consortium of barley researchers and serves as a model platform for abiotic and biotic stress studies. BarleyBase features a web-based experiment submission tool, BarleyExpress, which allows users to manage their experiment descriptions, array design and expression analysis information, either individually or as a group. The BarleyBase web interface contains a broad set of query and display options for probe sets. Users can query microarray elements by expression profile, sequence similarity, biological context of annotation, and pathway or gene family information. Probe set queries are integrated with analysis tools such as hierarchical clustering, k-means partitioning, and multi-dimensional scaling (MDS) analyses. BarleyBase provides query and visualization options for raw probe-level intensity data, as well as batch downloads for further analysis. Interconnecting links with PlantGDB and Gramene allow BarleyBase users to perform EST alignments and gene prediction using Barley1 exemplar sequences or cross-species comparison at the genome level, respectively. BarleyBase is funded by USDA-NRI grant no. 2002-35300-12619.