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 silicon t ...

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. The ...

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 The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...

or ArrayExpress from

EBI Ebrahim Hamedi ( fa, اِبراهیم حامدی, also Romanized as "Ebrāhim Hāmedi"; born 1949), better known by his stage name Ebi (Persian: ), is an Iranian pop singer who first started his career in Tehran, gaining fame as part of a ban ...

. # 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 The cancer Biomedical Informatics Grid (caBIG) was a US government program to develop an open-source, open access information network called caGrid for secure data exchange on cancer research. The initiative was developed by the National Cance ...

), #* 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 Geo- is a prefix derived from the Greek word ''γη'' or ''γαια'', meaning "earth", usually in the sense of "ground or land”. GEO or Geo may also refer to: Arts, entertainment, and media * ''GEO'' (magazine), a popular scientific magazine ...

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 Minimum information about a microarray experiment (MIAME) is a standard created by the FGED Society for reporting microarray experiments. MIAME is intended to specify all the information necessary to interpret the results of the experiment unam ...

compliant molecular abundance study , , 25859 , , 641770 , , October 28, 2011 , - , , ArrayExpress at EBI , , Any curated

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 , ,

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

, , 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