A microarray database is a repository containing

microarray A microarray is a multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of genes from a sample (e.g. from a tissue). It is a two-dimensional array on a solid substrate—usually a glass slide or silic ...

gene expression Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. ...

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: # 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 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: {, class = "wikitable sortable" ! 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 , -

External links

ArrayExpress: Quick Tour on EBI Train OnLineExploring functional genomics data with the ArrayExpress Archive on EBI Train OnLineInvestigating gene expression patterns with the Gene Expression Atlas on EBI Train OnLineArrayExpress:Submitting data using MAGE-TAB on EBI Train OnLineArrayExplorer
- A free tool to compare microarrays side by side. Microarrays Biological databases

See also

External links