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- A microarray database is a repository containing 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: 1.
* 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. 2.
* 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: 3.
* A subscription or license may be needed to gain full access, 4.
* The content may come primarily from a specific group (e.g. SMD, or UPSC-BASE), the Immunological Genome Project 5.
* There may be constraints on who can use the data or for what purpose data can be used, 6.
* Special permission may be required to submit new data, or there may be no obvious process at all, 7.
* 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), 8.
* Further processing or reformatting of the data may be required for standard applications or analysis, 9.
* They claim to address the 'urgent need' to have a standard, centralized repository for microarray data. (See YMD, last updated in 2003, for example), 10.
* There is a claim to an incremental improvement over one of the public repositories, 11.
* 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: (en)
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