NCBI GEO: mining tens of millions of expression profiles--database and tools update.
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/
Barrett
Tanya
T
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
DB
Wilhite
Stephen E
SE
Ledoux
Pierre
P
Rudnev
Dmitry
D
Evangelista
Carlos
C
Kim
Irene F
IF
Soboleva
Alexandra
A
Tomashevsky
Maxim
M
Edgar
Ron
R
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