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BarleyBase


NAR Molecular Biology Database Collection entry number 599
Shen L.1, Gong J.1,5, Xin J.1,5, Caldo R.A.2, Nettleton D.3, Cook D.3, Wise R.P.2,4 and Dickerson J.A.1,5
1Virtual Reality Applications Center, Iowa State University, Ames, Iowa 50011, USA
2Department of Plant Pathology and Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, IA 50011-1020
3 Department of Statistics, Iowa State University, Ames, IA 50011-1210
4Corn Insects and Crop Genetics Research, USDA-ARS, Iowa State University, Ames, IA 50011-1020
5Electrical and Computer Engineering Department, Iowa State University, Ames, IA 50011-3060.

Database Description

BarleyBase (http://www.BarleyBase.org) is an online database for plant microarrays with integrated tools for data visualization and statistical analysis. It currently houses both raw and normalized expression data for over 1,000 hybridizations from the Affymetrix Barley1 GeneChip, and Arabidopsis ATH1 and AG genome arrays. BarleyBase is evolving to Plant Expression Database (PLEXdb) by supporting the emerging Affymetrix wheat, maize, soybean, rice and grape arrays, as well as spotted 20k rice and 58k maize long-oligo microarrays.

BarleyBase supports data query, retrieval and display 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 annotation. Probe set queries are integrated with visualization and analysis tools such as the R/Bioconductor packages, data filters, and a large variety of plot types. BarleyBase provides integrated web-based service for functional interpretation of large scale gene expression data. Multiple gene lists can be classified, compared and visualized according to functional annotations. The gene function information includes gene ontology, Interpro protein functional domain prediction, metabolic pathway and gene family information.

Controlled Plant Ontology and Gene Ontology vocabularies facilitate comparative genomic analysis through interconnecting links to PlantGDB (http://www.plantgdb.org/), Gramene (http://gramene.org/), and GrainGenes (http://wheat.pw.usda.gov/index.shtml) for sequence alignment and function prediction using BarleyBase microarray sequences.

Acknowledgements

The BarleyBase projected is funded by the USDA-NRI program (grant #2002-03582) and USDA-CSREES North American Barley Genome Project. The Nottingham Arabidopsis Stock Centre's microarray database (NASCarrays, http://128.243.111.177/narrays/experimentbrowse.pl), TAIR (http://www.arabidopsis.org/) and GEO (http://www.ncbi.nlm.nih.gov/geo/) share ATH1 data. HarvEST:Barley (http://harvest.ucr.edu/) provides exemplar sequences and BLASTX NR annotations.

Category: Plant databases

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