Gene Expression Omnibus (GEO)
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NCBI archive of expression data
Ron Edgar NCBI
About Gene Expression Omnibus (GEO)
- Microarray and other transcriptome data in MIAME compliant formats
- ChIP-chip data
Content in GEO has data describes as
- Profiles: GEO profiles are expression patterns for specific genes over a dataset.
A platform describes the physical setup of the assay. For example a platform might describe a specific product, such as the Affymetrix GeneChip E.coli Genome 2.0 Array. GEO platform accessions start with GPL
Samples are the individual array measurements. Sample accessions begin with GSM.
Series are sets of samples. GEO Series accessions begin with GSE. Series are submitted by users.
Datasets are curated by GEO curators at NCBI.
A DataSet represents a curated collection of biologically and statistically comparable GEO Samples and forms the basis of GEO's suite of data display and analysis tools. Samples within a DataSet refer to the same Platform, that is, they share a common set of array elements. Value measurements for each Sample within a DataSet are assumed to be calculated in an equivalent manner, that is, considerations such as background processing and normalization are consistent across the DataSet. Information reflecting experimental factors is provided through DataSet subsets.
Note that not all series are in datasets due to curation backlogs.
Using Gene Expression Omnibus (GEO)
The overview of how to use GEO is on the GEO website
Browsing and Searching
GEO datasets include a variety of built-in analysis tools, such as views of hierarchical clustering within a specific dataset.
Profiles show the expression of individual genes in a dataset. When viewing a gene profile, you can click on "Profile neighbors" above the graphic representation of the profile. This will return genes with similar profiles within the dataset.
Add links to additional pages describing success stories here.
GEO is queryable through the NCBI EUtils system. Brief documentation is provided at the GEO programmatic access page. Additional query documentation needed.
See Help:References for how to manage references in EcoliWiki.
- Barrett, T et al. (2007) NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res. 35 D760-5 PubMed EcoliWiki page
- Barrett, T & Edgar, R (2006) Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Meth. Enzymol. 411 352-69 PubMed EcoliWiki page
- Barrett, T & Edgar, R (2006) Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*. Methods Mol. Biol. 338 175-90 PubMed EcoliWiki page
- Barrett, T et al. (2005) NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Res. 33 D562-6 PubMed EcoliWiki page
- Edgar, R et al. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30 207-10 PubMed EcoliWiki page