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See also: Correcting section link formatting, general fixes

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A '''microarray database''' is a repository containing [[DNA microarray|microarray]] [[gene expression]] data. The key uses of a microarray database are to store the measurement data, manage a searchable index, and make the data available to other applications for analysis and interpretation (either directly, or via user downloads).

Microarray databases can fall into two distinct classes:

# A peer reviewed, public repository that adheres to academic or industry standards and is designed to be used by many analysis applications and groups. A good example of this is the [[Gene Expression Omnibus]] (GEO) from [[National Center for Biotechnology Information|NCBI]] or ArrayExpress from [[European Bioinformatics Institute|EBI]].
# A specialized repository associated primarily with the brand of a particular entity (lab, company, university, consortium, group), an application suite, a topic, or an analysis method, whether it is commercial, non-profit, or academic. These databases might have one or more of the following characteristics:
#* A subscription or license may be needed to gain full access,
#* The content may come primarily from a specific group (e.g. SMD, or UPSC-BASE), the Immunological Genome Project
#* There may be constraints on who can use the data or for what purpose data can be used,
#* Special permission may be required to submit new data, or there may be no obvious process at all,
#* Only certain applications may be equipped to use the data, often also associated with the same entity (for example, caArray at NCI is specialized for the [[caBIG]]),
#* Further processing or reformatting of the data may be required for standard applications or analysis,
#* They claim to address the 'urgent need' to have a standard, centralized repository for microarray data. (See YMD, last updated in 2003, for example),
#* There is a claim to an incremental improvement over one of the public repositories,
#* A meta-analysis ''application'', which incorporates studies from one or more public databases (e.g. Gemma primarily uses [[Gene Expression Omnibus|GEO]] studies; NextBio uses various sources)

Some of the most known public, curated microarray ''databases'' are:



{| class = "wikitable sortable"
! Database || Scope || Microarray experiment sets || Sample profiles || As of date
|-
|| ArrayTrack || [[ArrayTrack]] hosts both public and private data, including MAQC benchmark data, with integrated analysis tools || 1622 || 50,093 || Feb 2012
|-
||NCI mAdb || Hosts NCI data with integrated analysis and statistics tools || ? || 105,000 || Mar 2012
|-
|| ImmGen database || Open access across all immune system cells; expression data, differential expression, coregulated clusters, regulation || 267 || 1059 || Jan 2012
|-
|| Genevestigator || Gene expression search engine based on manually curated, well annotated public and proprietary microarray and RNA-seq datasets || 3228 || 232,855 || October 2016
|-
|| Gene Expression Omnibus - NCBI || any curated [[MIAME]] compliant molecular abundance study || 25859 || 641770 || October 28, 2011
|-
|| ArrayExpress at EBI || Any curated [[MIAME]] or [[MINSEQE]] compliant transcriptomics data || 24838 || 708914 || October 28, 2011
|-
|| Stanford Microarray database || private and published microarray and molecule abundance database (now defunct) || 82542 || ? || October 23, 2011
|-
|| The Cancer Genome Atlas (TCGA) || collection of expression data for different cancers || 21229 || ? || August 30, 2013
|-
|| GeneNetwork system || Open access standard arrays, exons arrays, and RNA-seq data for genetic analysis (eQTL studies) with analysis suite || ~100 || ~10000 || July, 2010
|-
|| UNC modENCODE Microarray database || Nimblegen customer 2.1 million array || ~6 || 180 || July 17, 2009
|-
|| UPSC-BASE || data generated by microarray analysis within Umeå Plant Science Centre (UPSC). || ~100 || ? || November 15, 2007
|-
|| UPenn RAD database || [[MIAME]] compliant public and private studies, associated with '''ArrayExpress''' || ~100 || ~2500 || Sept. 1, 2007
|-
|| UNC Microarray database || provides the service for microarray data storage, retrieval, analysis, and visualization || ~31 || 2093 || April 1, 2007
|-
|| MUSC database || The database is a repository for DNA microarray data generated by MUSC investigators as well as researchers in the global research community. || ~45 || 555 || April 1, 2007
|-
|| caArray at NCI || Cancer data, prepared for analysis on [[caBIG]] || 41 || 1741 || November 15, 2006
|-
|}

==See also==
* [[Biological database]]
* [[List of biological databases]]
* [[DNA microarray]]
** {{section link|DNA microarray|Data warehousing}}
* [[Microarray analysis techniques]]

==External links==
* [http://www.ebi.ac.uk/training/online/course/arrayexpress-quick-tour ArrayExpress: Quick Tour on EBI Train OnLine]
* [http://www.ebi.ac.uk/training/online/course/arrayexpress-exploring-functional-genomics-data-ar Exploring functional genomics data with the ArrayExpress Archive on EBI Train OnLine]
* [http://www.ebi.ac.uk/training/online/course/arrayexpress-investigating-gene-expression-pattern-0 Investigating gene expression patterns with the Gene Expression Atlas on EBI Train OnLine]
* [http://www.ebi.ac.uk/training/online/course/arrayexpress-submitting-data-using-mage-tab ArrayExpress:Submitting data using MAGE-TAB on EBI Train OnLine]
* [http://www.arrayexplorer.com ArrayExplorer] - A free tool to compare microarrays side by side.

[[Category:Microarrays]]
[[Category:Genetics databases]]

Microarray databases - Revision history

imported>Sdkb: /* See also */Correcting section link formatting, general fixes