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:
   • 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: