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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:

• 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 |

|---|---|

| ArrayTrack | ArrayTrack hosts both public and privat… |

| NCI mAdb | Hosts NCI data with integrated analysis… |

| ImmGen database | Open access across all immune system ce… |

| Genevestigator | Gene expression search engine based on… |

| Gene Expression Omnibus - NCBI | any curated MIAME compliant molecular a… |

| ArrayExpress at EBI | Any curated MIAME or MINSEQE compliant… |

| Stanford Microarray database | private and published microarray and mo… |

| The Cancer Genome Atlas (TCGA) | collection of expression data for diffe… |

| GeneNetwork system | Open access standard arrays, exons arra… |

| UNC modENCODE Microarray database | Nimblegen customer 2.1 million array |

| UPSC-BASE | data generated by microarray analysis w… |

| UPenn RAD database | MIAME compliant public and private stud… |

| UNC Microarray database | provides the service for microarray dat… |

| MUSC database | The database is a repository for DNA mi… |

| caArray at NCI | Cancer data, prepared for analysis on c… |

| Database | Microarray experiment sets | Sample profiles |

|---|---|---|

| ArrayTrack | 1622 | 50,093 |

| NCI mAdb | ? | 105,000 |

| ImmGen database | 267 | 1059 |

| Genevestigator | 3228 | 232,855 |

| Gene Expression Omnibus - NCBI | 25859 | 641770 |

| ArrayExpress at EBI | 24838 | 708914 |

| Stanford Microarray database | 82542 | ? |

| The Cancer Genome Atlas (TCGA) | 21229 | ? |

| GeneNetwork system | ~100 | ~10000 |

| UNC modENCODE Microarray database | ~6 | 180 |

| UPSC-BASE | ~100 | ? |

| UPenn RAD database | ~100 | ~2500 |

| UNC Microarray database | ~31 | 2093 |

| MUSC database | ~45 | 555 |

| caArray at NCI | 41 | 1741 |

| Database | As of date |

|---|---|

| ArrayTrack | Feb 2012 |

| NCI mAdb | Mar 2012 |

| ImmGen database | Jan 2012 |

| Genevestigator | October 2016 |

| Gene Expression Omnibus - NCBI | October 28, 2011 |

| ArrayExpress at EBI | October 28, 2011 |

| Stanford Microarray database | October 23, 2011 |

| The Cancer Genome Atlas (TCGA) | August 30, 2013 |

| GeneNetwork system | July, 2010 |

| UNC modENCODE Microarray database | July 17, 2009 |

| UPSC-BASE | November 15, 2007 |

| UPenn RAD database | Sept. 1, 2007 |

| UNC Microarray database | April 1, 2007 |

| MUSC database | April 1, 2007 |

| caArray at NCI | November 15, 2006 |

• See also

• External links

• Biological database

• List of biological databases

• DNA microarray

• DNA microarray § Data warehousing

• Microarray analysis techniques

• ArrayExpress: Quick Tour on EBI Train OnLine

• Exploring functional genomics data with the ArrayExpress Archive on EBI Train OnLine

• Investigating gene expression patterns with the Gene Expression Atlas on EBI Train OnLine

• ArrayExpress:Submitting data using MAGE-TAB on EBI Train OnLine

• ArrayExplorer - A free tool to compare microarrays side by side.