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The Gene Expression Omnibus Database

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Statistical Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1418))

Abstract

The Gene Expression Omnibus (GEO) database is an international public repository that archives and freely distributes high-throughput gene expression and other functional genomics data sets. Created in 2000 as a worldwide resource for gene expression studies, GEO has evolved with rapidly changing technologies and now accepts high-throughput data for many other data applications, including those that examine genome methylation, chromatin structure, and genome–protein interactions. GEO supports community-derived reporting standards that specify provision of several critical study elements including raw data, processed data, and descriptive metadata. The database not only provides access to data for tens of thousands of studies, but also offers various Web-based tools and strategies that enable users to locate data relevant to their specific interests, as well as to visualize and analyze the data. This chapter includes detailed descriptions of methods to query and download GEO data and use the analysis and visualization tools. The GEO homepage is at http://www.ncbi.nlm.nih.gov/geo/.

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Acknowledgments

The authors acknowledge the expertise and efforts of the whole GEO curation and development team—Steve Wilhite, Pierre Ledoux, Carlos Evangelista, Irene Kim, Kimberly Marshall, Katherine Phillippy, Patti Sherman, Cynthia Robertson, Hyeseung Lee, Maxim Tomashevsky, Andrey Yefanov, Nadezhda Serova, Naigong Zhang, and Alexandra Soboleva.

Funding

This research was supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine. This chapter is an official contribution of the National Institutes of Health; not subject to copyright in the USA.

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Authors and Affiliations

  1. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, MSC 6510, Building 45, Room AS13B, Bethesda, MD, 20892-6510, USA

    Emily Clough & Tanya Barrett

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  1. Emily Clough
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  2. Tanya Barrett
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Correspondence to Tanya Barrett .

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Editors and Affiliations

  1. Ohio State University, Biomed Informatics, College of Medicine, Columbus, Ohio, USA

    Ewy Mathé

  2. National Cancer Institute, National Institutes of Health, Columbia, Maryland, USA

    Sean Davis

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Clough, E., Barrett, T. (2016). The Gene Expression Omnibus Database. In: Mathé, E., Davis, S. (eds) Statistical Genomics. Methods in Molecular Biology, vol 1418. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3578-9_5

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  • DOI: https://doi.org/10.1007/978-1-4939-3578-9_5

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