NCBI GEO: mining millions of expression profiles—database and tools

By Tanya Barrett, Tugba Onal Suzek, Dennis B. Troup, Stephen E. Wilhite, W. Ngau, Pierre Ledoux, D. Rudnev, A. Lash, W. Fujibuchi, Ron Edgar. Nucleic Acids Res., 2004

1,236 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

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Citations in the corpus

The xenobiotic β‐aminobutyric acid enhances Arabidopsis thermotolerance (2008, neutral): “gov/geo/) under accession number GSE9515 (Barrett et al., 2005).”
Arabidopsis PEN3/PDR8, an ATP Binding Cassette Transporter, Contributes to Nonhost Resistance to Inappropriate Pathogens That Enter by Direct Penetration[W][OA] (2006, methodology): “Accession Numbers Microarray data sets were deposited in the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/; Barrett et al., 2005) under accession number GSE3220.”
A survey of current trends in computational drug repositioning (2016, background): “NCBI Gene Expression Omnibus (GEO)] [18], its data have been extensively explored in drug repositioning studies.”
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The microRNA miR-29 controls innate and adaptive immune responses to intracellular bacterial infection by targeting interferon-γ (2011, methodology): “We studied the miRNA expression profiles of various subsets and stages of T cells by analyzing databases such as Gene Expression Omnibu”
The joint graphical lasso for inverse covariance estimation across multiple classes (2011, methodology): “The data are publicly available from the Gene Expression Omnibus (Barrett et al. 2005) at accession number GDS2771.”
Genevestigator V3: A Reference Expression Database for the Meta-Analysis of Transcriptomes (2008, methodology): “Although gene expression data and statistical tools are now widely available [1–4], the simultaneous analysis of hundreds or thousands of gene expression arrays in their biological context remains a major challenge for biologists.”
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis (2006, methodology): “(2) Network 2 contains five genes that are enzymes for biosynthesis of flavonoid, one of the major secondary metabolites functioning as a phytoalexin or protectant against photodamage.”
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The presence of tumor associated macrophages in tumor stroma as a prognostic marker for breast cancer patients (2012, methodology): “Using a publically available gene expression array dataset [GenBank:GDS806] [22] from NCBI Gene Expression Omnibus profiles [23] we were able to identify that breast cancer patients receiving endocrine therapy, who had recurrence, had significantly higher gene expression levels of CD68 (Figure 3B).”
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