Microarray databases

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 may be characterized by:
- 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),
- There may be limits on how who can use the data, and for what purpose,
- 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
Gene Expression Omnibus - NCBI	any curated MIAME compliant molecular abundance study	8094	205148	March 11, 2008
Stanford Microarray database	private and published microarray and molecule abundance database	441	38925	March 27, 2009
Genevestigator database	Manually curated microarray data for expression meta-analysis	>500	20500	July, 2008
ArrayExpress at EBI	Any curated MIAME or MINSEQE compliant transcriptomics data	8037	239402	January, 2009
UPenn RAD database	MIAME compliant public and private studies, associated with ArrayExpress	~100	~2500	Sept. 1, 2007
UNC Microarray database	??	~31	2093	April 1, 2007
UNC modENCODE Microarray database	Nimblegen customer 2.1 million array	~6	180	July 17, 2009
MUSC database	??	~45	555	April 1, 2007
caArray at NCI	Cancer data, prepared for analysis on caBIG	41	1741	November 15, 2006
UPSC-BASE	data generated by microarray analysis within Umeå Plant Science Centre (UPSC).	~100	?	November 15, 2007

For a directory of Microarray Databases, see: Template:Dmoz

See also