Gene Expression Omnibus (GEO) - EcoliWiki
EcoliHub logo

E. coli is indeed the coolest thing on the planet - Carl Zimmer

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

edit table

Contents

About Gene Expression Omnibus (GEO)

The entry point for 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

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

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
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
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

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. Methods 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

GEO URL http://www.ncbi.nlm.nih.gov/geo/ GEO

Discussion of Gene Expression Omnibus (GEO) on other websites

Retrieved from "http://ecoliwiki.net/colipedia/index.php/Gene_Expression_Omnibus_%28GEO%29"
Personal tools