lect 16.7 - BIOINFORMATICS APPLICATIONS NOTE Gene...

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Vol. 23 no. 14 2007, pages 1846–1847 BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btm254 Gene expression GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor Sean Davis * and Paul S. Meltzer Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA Received on April 3, 2007; revised on April 30, 2007; accepted on May 4, 2007 Advance Access publication May 12, 2007 Associate Editor: Joaquin Dopazo ABSTRACT Microarray technology has become a standard molecular biology tool. Experimental data have been generated on a huge number of organisms, tissue types, treatment conditions and disease states. The Gene Expression Omnibus ( Barrett et al ., 2005), developed by the National Center for Bioinformatics (NCBI) at the National Institutes of Health is a repository of nearly 140 000 gene expression experiments. The BioConductor project (Gentleman et al ., 2004) is an open-source and open-development software project built in the R statistical programming environment (R Development core Team, 2005) for the analysis and comprehension of genomic data. The tools contained in the BioConductor project represent many state-of-the-art methods for the analysis of microarray and geno- mics data. We have developed a software tool that allows access to the wealth of information within GEO directly from BioConductor, eliminating many the formatting and parsing problems that have made such analyses labor-intensive in the past. The software, called GEOquery, effectively establishes a bridge between GEO and BioConductor. Easy access to GEO data from BioConductor will likely lead to new analyses of GEO data using novel and rigorous statistical and bioinformatic tools. Facilitating analyses and meta- analyses of microarray data will increase the efficiency with which biologically important conclusions can be drawn from published genomic data. Availability: GEOquery is available as part of the BioConductor project. Contact: sdavis2@mail.nih.gov 1 OVERVIEW OF GEO AND GEOQUERY The NCBI Gene Expression Omnibus (GEO) serves as a public repository for a wide range of high-throughput experimental data. These data include single and dual channel microarray- based experiments measuring mRNA, genomic DNA and protein abundance as well as non-array techniques, such as
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This note was uploaded on 07/29/2010 for the course BIOC BIOC2808 taught by Professor Dr.jjwang during the Fall '09 term at HKU.

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lect 16.7 - BIOINFORMATICS APPLICATIONS NOTE Gene...

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