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PMID: 17099226 Published · ppublish English Journal Article Research Support, N.I.H., Intramural

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

Nucleic acids research ·Vol. 35 ·No. Database issue ·2007-01-00 ·Pages D760-5

Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R

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/

MeSH Terms
Computer Graphics Databases, Genetic Gene Expression Profiling Humans Internet Oligonucleotide Array Sequence Analysis Software User-Computer Interface
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Barrett Tanya
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
Troup Dennis B
Wilhite Stephen E
Ledoux Pierre
Rudnev Dmitry
Evangelista Carlos
Kim Irene F
Soboleva Alexandra
Tomashevsky Maxim
Edgar Ron
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkl887
Email
barrett@ncbi.nlm.nih.gov
Published
2007-01-00
Epub
2006-00-11
Pages
D760-5
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1669752
Subset
IM
Grants
Intramural NIH HHS · United States
External Links
PubMed source DOI: 10.1093/nar/gkl887 PMC Full Text View journal details
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