The term microarray database is usually used to describe a repository containing microarray gene expression data. The key features 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 NCBI or ArrayExpress from 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 GEO studies; NextBio uses various sources)
Some of the most known public, curated microarray databases are:
|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 database||Gene expression search engine based on manually curated microarray data||2500||65000||Jan, 2012|
|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||82542||?||October 23, 2011|
|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|
- For a directory of Microarray Databases, see: Gene Expression Databases at the Open Directory Project
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