Campus Units

Plant Pathology and Microbiology, Statistics, Virtual Reality Applications Center

Document Type

Article

Publication Version

Published Version

Publication Date

1-1-2005

Journal or Book Title

Nucleic Acids Research

Volume

33

Issue

Issue suppl_1

First Page

D614

Last Page

D618

DOI

10.1093/nar/gki123

Abstract

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.

Comments

This article is published as Shen, Lishuang, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook, Roger P. Wise, and Julie A. Dickerson. "BarleyBase—an expression profiling database for plant genomics." Nucleic Acids Research 33, no. suppl_1 (2005): D614-D618. doi: 10.1093/nar/gki123.

Rights

Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.

Language

en

File Format

application/pdf

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