PortEco logo

Gene Expression Omnibus (GEO)

From EcoliWiki
Jump to: navigation, search

You can help EcoliWiki by editing the content of this page. For information about becoming a registered user and obtaining editing privileges, see Help:Accounts.

Link/URL:

GEO

What:

NCBI archive of expression data

Who:

Ron Edgar NCBI

Updates:
Upcoming events:
Web Services:

Via NCBI EUtils

Contents

About Gene Expression Omnibus (GEO)

The entry point for 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

  • Platforms
  • Series
  • Samples
  • Datasets
  • Profiles: GEO profiles are expression patterns for specific genes over a dataset.



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

Samples

Samples are the individual array measurements. Sample accessions begin with GSM.

Series

Series are sets of samples. GEO Series accessions begin with GSE. Series are submitted by users.

Datasets

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 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

A view of hierarchical clustering for a dataset in GEO

GEO datasets include a variety of built-in analysis tools, such as views of hierarchical clustering within a specific dataset.

Profiles

Profile neighbors

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.



Other sites with related content

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

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. 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
  2. Barrett, T & Edgar, R (2006) Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Meth. Enzymol. 411 352-69 PubMed EcoliWiki page
  3. Barrett, T & Edgar, R (2006) Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*. Methods Mol. Biol. 338 175-90 PubMed EcoliWiki page
  4. Barrett, T et al. (2005) NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Res. 33 D562-6 PubMed EcoliWiki page
  5. 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

External Links

Discussion of Gene Expression Omnibus (GEO) on other websites