Gene Expression Omnibus (GEO): Difference between revisions

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{{Pagetop}}
[[Category:Databases]]
[[Category:Gene Expression Databases]]
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'''GEO'''
'''You can help [[EcoliWiki]] by editing the content of this page.  For information about obtaining editing privileges, see [[E._coli_Wiki:Membership]]''' 
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
|  colspan = '2' | '''{{PAGENAME}}'''
|-
|-
| width='30%' | Who:
!align=left {{table heading style}} |Link/URL:
| ''proprietor''
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[http://www.ncbi.nlm.nih.gov/geo/ GEO]
|-
|-
| width='30%' | What:
!align=left {{table heading style}} |What:
| ''short description''
||
NCBI archive of expression data
|-
|-
| Where:
!align=left {{table heading style}} |Who:
| [http://{{{1|link}}} {{PAGENAME}}]
||
Ron Edgar
NCBI
|-
|-
| Updates
!align=left {{table heading style}} |Updates:
|
||
 
|-
|-
| Upcoming events
!align=left {{table heading style}} |Upcoming events:
| ''link to event calendar, if applicable''
||
 
|-
|-
| Web Services
!align=left {{table heading style}} |Web Services:
|
||
[http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_paccess.html Via NCBI EUtils]
 
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=About {{PAGENAME}}=
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[http://{{{1|link}}} {{PAGENAME}}] is...
==About {{PAGENAME}}==
=Content=
[[Image:GEO home.jpg|right|The entry point for GEO|thumb|300px]]
=Using {{PAGENAME}}=
[http://www.ncbi.nlm.nih.gov/geo/ GEO] {{PAGENAME}}] is the public repository for high throughput data at NCBI<ref name='PMID:17099226'/><ref name='PMID:16939800'/><ref name='PMID:16888359'/><ref name='PMID:15608262'/><ref name='PMID:11752295'/>.  GEO contains
==Browsing==
* Microarray and other transcriptome data in MIAME compliant formats
==Searching==
* 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.
<blockquote>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.</blockquote>
Note that not all series are in datasets due to curation backlogs.
 
==Using {{PAGENAME}}==
The overview of how to use GEO is on the [http://www.ncbi.nlm.nih.gov/projects/geo/info/overview GEO website]
===Browsing and Searching===
GEO can be searched from either the [http://www.ncbi.nlm.nih.gov/projects/geo/index.cgi GEO search page] or from the [http://www.ncbi.nlm.nih.gov/sites/entrez Entrez] home page (use the pulldown menu to select GEO datasets or GEO profiles).
===Datasets===
[[Image:GEO clustering.jpg|thumb|300px|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===
[[Image:GEO profile neighbors.jpg|thumb|300px|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==
==Usage examples==
''Add links to additional pages describing success stories here.''
''Add links to additional pages describing success stories here.''


=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=
==Trackbacks==
[[Trackbacks|''What are trackbacks?'']]  ''This feature is not yet functional''


=References=
 
=External Links=
{{Clr}}
[http://{{{1|link}}} {{PAGENAME}}]
 
==Other sites with related content==
*[[ArrayExpress]]
 
==Technology==
===Web Services/API===
GEO is queryable through the NCBI EUtils system. Brief documentation is provided at the [http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_paccess.html GEO programmatic access page]. Additional query documentation needed.
 
==Discussion==
 
==References==
{{BacktoTop}}
{{RefHelp}}
<references />
 
==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/info/faq.html GEO FAQ]
 
==Discussion of {{PAGENAME}} on other websites==
==Discussion of {{PAGENAME}} on other websites==

Latest revision as of 00:11, 23 May 2010

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


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
  2. ↑ Barrett, T & Edgar, R (2006) Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Meth. Enzymol. 411 352-69 PubMed
  3. ↑ Barrett, T & Edgar, R (2006) Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*. Methods Mol. Biol. 338 175-90 PubMed
  4. ↑ Barrett, T et al. (2005) NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Res. 33 D562-6 PubMed
  5. ↑ Edgar, R et al. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30 207-10 PubMed

External Links

Discussion of Gene Expression Omnibus (GEO) on other websites

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