Microarray databases

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 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 2615 119,400 August 2014
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 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

See also

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