title: NCBI GEO: archive for functional genomics data sets--10 years on.
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/.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA. barrett@ncbi.nlm.nih.gov
authors.forename: Tanya
authors.initials: T
authors.lastname: Barrett
authors.forename: Dennis B
authors.initials: DB
authors.lastname: Troup
authors.forename: Stephen E
authors.initials: SE
authors.lastname: Wilhite
authors.forename: Pierre
authors.initials: P
authors.lastname: Ledoux
authors.forename: Carlos
authors.initials: C
authors.lastname: Evangelista
authors.forename: Irene F
authors.initials: IF
authors.lastname: Kim
authors.forename: Maxim
authors.initials: M
authors.lastname: Tomashevsky
authors.forename: Kimberly A
authors.initials: KA
authors.lastname: Marshall
authors.forename: Katherine H
authors.initials: KH
authors.lastname: Phillippy
authors.forename: Patti M
authors.initials: PM
authors.lastname: Sherman
authors.forename: Rolf N
authors.initials: RN
authors.lastname: Muertter
authors.forename: Michelle
authors.initials: M
authors.lastname: Holko
authors.forename: Oluwabukunmi
authors.initials: O
authors.lastname: Ayanbule
authors.forename: Andrey
authors.initials: A
authors.lastname: Yefanov
authors.forename: Alexandra
authors.initials: A
authors.lastname: Soboleva
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling; D023281:Genomics; D020411:Oligonucleotide Array Sequence Analysis; D014584:User-Computer Interface