BarleyBase--an expression profiling database for plant genomics

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 in...

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Published inNucleic acids research Vol. 33; no. 1; pp. D614 - D618
Main Authors Shen, L, Gong, J, Caldo, R.A, Nettleton, D, Cook, D, Wise, R.P, Dickerson, J.A
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.01.2005
Oxford Publishing Limited (England)
Subjects
Affymetrix microarrays
Arabidopsis
Arabidopsis - genetics
Arabidopsis - metabolism
barley
bioinformatics
Computer Graphics
Databases, Genetic
Edible Grain - genetics
gene banks
gene expression
Gene Expression Profiling
Genes, Plant
genome
Genome, Plant
Genomics
Hordeum - genetics
Hordeum - metabolism
Hordeum vulgare
messenger RNA
microarray technology
Oligonucleotide Array Sequence Analysis
Oryza sativa
Software
Triticum aestivum
Zea mays
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Summary: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.
Bibliography:http://www.nar.oupjournals.org/
Received August 12, 2004; Revised and Accepted October 21, 2004
local:gki123
To whom correspondence should be addressed. Tel: +1 515 294 7705; Fax: +1 515 294 8432; Email: julied@iastate.edu
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ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gki123