NCBI GEO: Archive for Functional Genomics Data Sets--10 Years on

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2010 Nov 25

PMID 21097893

Citations 637

Authors

Tanya Barrett

Dennis B Troup

Stephen E Wilhite

Pierre Ledoux

Carlos Evangelista

Irene F Kim

Maxim Tomashevsky

Kimberly A Marshall

Katherine H Phillippy

Patti M Sherman

Rolf N Muertter

Michelle Holko

Oluwabukunmi Ayanbule

Andrey Yefanov

Alexandra Soboleva

Affiliations

Soon will be listed here.

Abstract

A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20,000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

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