NCBI GEO: archive for high-throughput functional genomic data

Barrett, Tanya
Troup, Dennis B.
Wilhite, Stephen E.
Ledoux, Pierre
Rudnev, Dmitry
Evangelista, Carlos
Kim, Irene F.
Soboleva, Alexandra
Tomashevsky, Maxim
Marshall, Kimberly A.
Phillippy, Katherine H.
Sherman, Patti M.
Muertter, Rolf N.
Edgar, Ron

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA

Received September 26, 2008; Accepted October 6, 2008

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This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Nucleic Acids Research 37:p D885-D890, January 2009.

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest public repository for high-throughput gene expression data. Additionally, GEO hosts other categories of high-throughput functional genomic data, including those that examine genome copy number variations, chromatin structure, methylation status and transcription factor binding. These data are generated by the research community using high-throughput technologies like microarrays and, more recently, next-generation sequencing. The database has a flexible infrastructure that can capture fully annotated raw and processed data, enabling compliance with major community-derived scientific reporting standards such as ‘Minimum Information About a Microarray Experiment’ (MIAME). In addition to serving as a centralized data storage hub, GEO offers many tools and features that allow users to effectively explore, analyze and download expression data from both gene-centric and experiment-centric perspectives. This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.