Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/15/2005
Publication Date: 1/15/2005
Citation: Shen, L., Gong, J., Caldo, R.A., Nettleton, D., Cook, D., Wise, R.P., Dickerson, J.A. 2005. BarleyBase - Putting large-scale plant expression profiling data into a functional genomics context. Plant and Animal Genome XIII Conference Proceedings. P878.
Technical Abstract: BarleyBase, www.BarleyBase.org, is an online database for plant microarrays with integrated tools for data visualization and statistical analysis. Enhancements in 2004 include features tuned for biologist users, including new data flow design, web-interface, analysis tools, a wider range of microarray platforms, and enhanced annotations. BarleyBase houses raw and normalized expression data (approximately 1000 hybridizations) from the Affymetrix Barley1 GeneChip, as well as the Arabidopsis ATH1 and AG genome arrays. In the near future, BarleyBase will evolve and expand to Plant Expression Database (PlexDB) by supporting the emerging Affymetrix 61K wheat, maize, soybean, and rice arrays, with added support for spotted 20k rice and 58k maize long-oligo microarrays. BarleyBase contains a broad set of query, retrieval, and display options at all data levels, ranging from experiments to hybridizations to probe sets down to individual probes. Users can perform cross-platform and cross-experiment queries on probe sets based on expression profiles and/or on known biological information. Integrated links to PlantGDB, Gramene, and GrainGenes allow users to perform sequence alignment and function prediction using BarleyBase microarray sequences. BarleyBase is funded by USDA-NRI grant no. 2002-35300-12619.