Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

BarleyBase – Putting Large-Scale Plant Expression Profiling Data Into A Functional Genomics Context

Lishuang Shen¹ , Jian Gong¹ , Rico A Caldo² , Dan Nettleton³ , Dianne Cook^1,3 , Roger P. Wise^2,4 , Julie A. Dickerson¹

¹  Virtual Reality Applications Center, Iowa State University, Ames, Iowa 50011, USA

²  Department of Plant Pathology and Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, IA 50011-1020, USA

³  Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA

⁴  Corn Insects and Crop Genetics Research, USDA-ARS, Iowa State University, Ames, IA 50011-1020, USA

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 (~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. PlantGDB, Gramene, and GrainGenes, where users can perform sequence alignment and function prediction using BarleyBase microarray sequences. BarleyBase is funded by USDA-NRI grant no. 2002-35300-12619.