title: NCBI GEO: mining tens of millions of expression profiles--database and tools update.
abstract: 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/
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: Dmitry
authors.initials: D
authors.lastname: Rudnev
authors.forename: Carlos
authors.initials: C
authors.lastname: Evangelista
authors.forename: Irene F
authors.initials: IF
authors.lastname: Kim
authors.forename: Alexandra
authors.initials: A
authors.lastname: Soboleva
authors.forename: Maxim
authors.initials: M
authors.lastname: Tomashevsky
authors.forename: Ron
authors.initials: R
authors.lastname: Edgar
mesh_terms: D003196:Computer Graphics; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D006801:Humans; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D014584:User-Computer Interface