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Nucleic Acids Research 2005 33(Database Issue):D614-D618; doi:10.1093/nar/gki123
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Nucleic Acids Research, 2005, Vol. 33, Database issue D614-D618
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

BarleyBase—an expression profiling database for plant genomics

Lishuang Shen1, Jian Gong1, Rico A. Caldo2, Dan Nettleton3, Dianne Cook1,3, Roger P. Wise2,4 and Julie A. Dickerson1,*

1 Virtual Reality Applications Center, 2 Department of Plant Pathology, Center for Plant Responses to Environmental Stresses, 3 Department of Statistics and 4 Corn Insects and Crop Genetics Research, USDA-ARS, Iowa State University, Ames, IA 50011, USA

* To whom correspondence should be addressed. Tel: +1 515 294 7705; Fax: +1 515 294 8432; Email: julied{at}iastate.edu

Received August 12, 2004; Revised and Accepted October 21, 2004

BarleyBase (BB) (www.barleybase.org) is an online database for plant microarrays with integrated tools for data visualization and statistical analysis. BB houses raw and normalized expression data from the two publicly available Affymetrix genome arrays, Barley1 and Arabidopsis ATH1 with plans to include the new Affymetrix 61K wheat, maize, soybean and rice arrays, as they become available. BB contains a broad set of query and display options at all data levels, ranging from experiments to individual hybridizations to probe sets down to individual probes. Users can perform cross-experiment queries on probe sets based on observed expression profiles and/or based on known biological information. Probe set queries are integrated with visualization and analysis tools such as the R statistical toolbox, data filters and a large variety of plot types. Controlled vocabularies for gene and plant ontologies, as well as interconnecting links to physical or genetic map and other genomic data in PlantGDB, Gramene and GrainGenes, allow users to perform EST alignments and gene function prediction using Barley1 exemplar sequences, thus, enhancing cross-species comparison.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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