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A `!microarray database`! is a repository containing `F33f`_`[microarray`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=DNA_microarray]`_`f `F33f`_`[gene expression`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Gene_expression]`_`f 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 `F33f`_`[Gene Expression Omnibus`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Gene_Expression_Omnibus]`_`f (GEO) from `F33f`_`[NCBI`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=National_Center_for_Biotechnology_Information]`_`f or ArrayExpress from `F33f`_`[EBI`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=European_Bioinformatics_Institute]`_`f.

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 `F33f`_`[caBIG`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=CaBIG]`_`f),

• 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 `F33f`_`[GEO`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Gene_Expression_Omnibus]`_`f studies; NextBio uses various sources)

Some of the most known public, curated microarray `*databases`* are:

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| 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 | Gene expression search engine based on manually curated, well annotated public and proprietary microarray and RNA-seq datasets | 3228 | 232,855 | October 2016 |

| 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 (now defunct) | 82542 | ? | October 23, 2011 |

| The Cancer Genome Atlas (TCGA) | collection of expression data for different cancers | 21229 | ? | August 30, 2013 |

| 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 |

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>>Contents

• `F0af`_`[See also`#see-also]`_`f

• `F0af`_`[External links`#external-links]`_`f

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>>See also

• `F33f`_`[Biological database`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Biological_database]`_`f

• `F33f`_`[List of biological databases`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=List_of_biological_databases]`_`f

• `F33f`_`[DNA microarray`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=DNA_microarray]`_`f

• `F33f`_`[DNA microarray § Data warehousing`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=DNA_microarray]`_`f

• `F33f`_`[Microarray analysis techniques`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Microarray_analysis_techniques]`_`f

>>External links

• 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.

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