Gene Expression Omnibus (GEO): Difference between revisions
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==External Links== | ==External Links== | ||
[http://www.ncbi.nlm.nih.gov/geo/ GEO] URL http://www.ncbi.nlm.nih.gov/geo/ GEO | * [http://www.ncbi.nlm.nih.gov/geo/ GEO] URL http://www.ncbi.nlm.nih.gov/geo/ GEO | ||
* [http://www.ncbi.nlm.nih.gov/geo/info/faq.html GEO FAQ] | |||
==Discussion of {{PAGENAME}} on other websites== | ==Discussion of {{PAGENAME}} on other websites== | ||
Revision as of 20:31, 28 December 2009
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| Link/URL: | |
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| What: |
NCBI archive of expression data |
| Who: |
Ron Edgar NCBI |
| Updates: | |
| Upcoming events: | |
| Web Services: | |
| edit table |
About Gene Expression Omnibus (GEO)
GEO Gene Expression Omnibus (GEO)] is the public repository for high throughput data at NCBI[1][2][3][4][5]. GEO contains
- Microarray and other transcriptome data in MIAME compliant formats
- ChIP-chip data
Content
Content in GEO has data describes as
- Datasets
- Platforms
- Series
- Samples
- Profiles: GEO profiles are expression patterns for specific genes over a dataset.
Datasets
Platforms
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
Series
Series are sets of samples. GEO Series accessions begin with GSE
Samples
Samples are the individual array measurements. Sample accessions begin with GSM
Using Gene Expression Omnibus (GEO)
The overview of how to use GEO is on the GEO website
Browsing and Searching
GEO can be searched from either the GEO search page or from the Entrez home page (use the pulldown menu to select GEO datasets or GEO profiles).
Datasets
GEO datasets include a variety of built-in analysis tools, such as views of hierarchical clustering within a specific dataset.
Profiles
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.
Usage examples
Add links to additional pages describing success stories here.
Technology
Web Services/API
GEO is queryable through the NCBI EUtils system. Brief documentation is provided at the GEO programmatic access page. Additional query documentation needed.
Discussion
References
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
- ↑ Barrett, T & Edgar, R (2006) Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Meth. Enzymol. 411 352-69 PubMed
- ↑ Barrett, T & Edgar, R (2006) Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*. Methods Mol. Biol. 338 175-90 PubMed
- ↑ Barrett, T et al. (2005) NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Res. 33 D562-6 PubMed
- ↑ Edgar, R et al. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30 207-10 PubMed