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Nucleic Acids Research Advance Access originally published online on November 11, 2006
Nucleic Acids Research 2007 35(Database issue):D760-D765; doi:10.1093/nar/gkl887
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Nucleic Acids Research, 2007, Vol. 35, Database issue D760-D765
Published by Oxford University Press 2006
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.

Articles

NCBI GEO: mining tens of millions of expression profiles—database and tools update

Tanya Barrett*, Dennis B. Troup, Stephen E. Wilhite, Pierre Ledoux, Dmitry Rudnev, Carlos Evangelista, Irene F. Kim, Alexandra Soboleva, Maxim Tomashevsky and Ron Edgar

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

*To whom correspondence should be addressed. Tel: +1 301 402 4057; Fax: +1 301 480 0109; Email: barrett{at}ncbi.nlm.nih.gov

Received September 15, 2006. Accepted October 9, 2006.

The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information (NCBI) archives and freely disseminates microarray and other forms of high-throughput data generated by the scientific community. The database has a minimum information about a microarray experiment (MIAME)-compliant infrastructure that captures fully annotated raw and processed data. Several data deposit options and formats are supported, including web forms, spreadsheets, XML and Simple Omnibus Format in Text (SOFT). In addition to data storage, a collection of user-friendly web-based interfaces and applications are available to help users effectively explore, visualize and download the thousands of experiments and tens of millions of gene expression patterns stored in GEO. This paper provides a summary of the GEO database structure and user facilities, and describes recent enhancements to database design, performance, submission format options, data query and retrieval utilities. GEO is accessible at http://www.ncbi.nlm.nih.gov/geo/


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