NCBI GEO: mining millions of expression profiles--database and tools.
The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest fully public repository for high-throughput molecular abundance data, primarily gene expression data. The database has a flexible and open design that allows the submission, storage and retrieval of many data types. These data include microarray-based experiments measuring the abundance of mRNA, genomic DNA and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. GEO currently holds over 30,000 submissions representing approximately half a billion individual molecular abundance measurements, for over 100 organisms. Here, we describe recent database developments that facilitate effective mining and visualization of these data. Features are provided to examine data from both experiment- and gene-centric perspectives using user-friendly Web-based interfaces accessible to those without computational or microarray-related analytical expertise. The GEO database is publicly accessible through the World Wide Web 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, USA.
Suzek
Tugba O
TO
Troup
Dennis B
DB
Wilhite
Stephen E
SE
Ngau
Wing-Chi
WC
Ledoux
Pierre
P
Rudnev
Dmitry
D
Lash
Alex E
AE
Fujibuchi
Wataru
W
Edgar
Ron
R
D000818:Animals; D003196:Computer Graphics; D003628:Database Management Systems; D030541:Databases, Genetic / Q000592:standards; D020869:Gene Expression Profiling; D006801:Humans; D009317:National Library of Medicine (U.S.); D014481:United States; D014584:User-Computer Interface