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<title>Microarray databases</title>

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<span id="openzim-page-title" class="mw-page-title-main"><span class="mw-page-title-main">Microarray databases</span></span>

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<div id="mw-content-text" class="mw-body-content mw-content-ltr" lang="en" dir="ltr"><div class="mw-content-ltr mw-parser-output" lang="en" dir="ltr"><p>A <b>microarray database</b> is a repository containing <a href="DNA_microarray" title="DNA microarray">microarray</a> <a href="Gene_expression" title="Gene expression">gene expression</a> 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).

</p><p>Microarray databases can fall into two distinct classes:

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<ol><li>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 <a href="Gene_Expression_Omnibus" title="Gene Expression Omnibus">Gene Expression Omnibus</a> (GEO) from <a href="National_Center_for_Biotechnology_Information" title="National Center for Biotechnology Information">NCBI</a> or ArrayExpress from <a href="European_Bioinformatics_Institute" title="European Bioinformatics Institute">EBI</a>.</li>

<li>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:

<ul><li>A subscription or license may be needed to gain full access,</li>

<li>The content may come primarily from a specific group (e.g. SMD, or UPSC-BASE), the Immunological Genome Project</li>

<li>There may be constraints on who can use the data or for what purpose data can be used,</li>

<li>Special permission may be required to submit new data, or there may be no obvious process at all,</li>

<li>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 <a href="CaBIG" title="CaBIG">caBIG</a>),</li>

<li>Further processing or reformatting of the data may be required for standard applications or analysis,</li>

<li>They claim to address the 'urgent need' to have a standard, centralized repository for microarray data. (See YMD, last updated in 2003, for example),</li>

<li>There is a claim to an incremental improvement over one of the public repositories,</li>

<li>A meta-analysis <i>application</i>, which incorporates studies from one or more public databases (e.g. Gemma primarily uses <a href="Gene_Expression_Omnibus" title="Gene Expression Omnibus">GEO</a> studies; NextBio uses various sources)</li></ul></li></ol>

<p>Some of the most known public, curated microarray <i>databases</i> are:

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<th>Database</th>

<th>Scope</th>

<th>Microarray experiment sets</th>

<th>Sample profiles</th>

<th>As of date

</th></tr>

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<td>ArrayTrack</td>

<td><a href="ArrayTrack" title="ArrayTrack">ArrayTrack</a> hosts both public and private data, including MAQC benchmark data, with integrated analysis tools</td>

<td>Feb 2012

</td></tr>

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<td>Hosts NCI data with integrated analysis and statistics tools</td>

<td>Mar 2012

</td></tr>

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<td>ImmGen database</td>

<td>Open access across all immune system cells; expression data, differential expression, coregulated clusters, regulation</td>

<td>Jan 2012

</td></tr>

<tr>

<td>Genevestigator</td>

<td>Gene expression search engine based on manually curated, well annotated public and proprietary microarray and RNA-seq datasets</td>

<td>October 2016

</td></tr>

<tr>

<td>Gene Expression Omnibus - NCBI</td>

<td>any curated <a href="MIAME" class="mw-redirect" title="MIAME">MIAME</a> compliant molecular abundance study</td>

<td>October 28, 2011

</td></tr>

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<td>ArrayExpress at EBI</td>

<td>Any curated <a href="MIAME" class="mw-redirect" title="MIAME">MIAME</a> or <a href="MINSEQE" class="mw-redirect" title="MINSEQE">MINSEQE</a> compliant transcriptomics data</td>

<td>October 28, 2011

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<td>Stanford Microarray database</td>

<td>private and published microarray and molecule abundance database (now defunct)</td>

<td>October 23, 2011

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<td>The Cancer Genome Atlas (TCGA)</td>

<td>collection of expression data for different cancers</td>

<td>August 30, 2013

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<td>GeneNetwork system</td>

<td>Open access standard arrays, exons arrays, and RNA-seq data for genetic analysis (eQTL studies) with analysis suite</td>

<td>July, 2010

</td></tr>

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<td>UNC modENCODE Microarray database</td>

<td>Nimblegen customer 2.1 million array</td>

<td>July 17, 2009

</td></tr>

<tr>

<td>data generated by microarray analysis within Umeå Plant Science Centre (UPSC).</td>

<td>November 15, 2007

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<td>UPenn RAD database</td>

<td><a href="MIAME" class="mw-redirect" title="MIAME">MIAME</a> compliant public and private studies, associated with <b>ArrayExpress</b></td>

<td>Sept. 1, 2007

</td></tr>

<tr>

<td>UNC Microarray database</td>

<td>provides the service for microarray data storage, retrieval, analysis, and visualization</td>

<td>April 1, 2007

</td></tr>

<tr>

<td>MUSC database</td>

<td>The database is a repository for DNA microarray data generated by MUSC investigators as well as researchers in the global research community.</td>

<td>April 1, 2007

</td></tr>

<tr>

<td>caArray at NCI</td>

<td>Cancer data, prepared for analysis on <a href="CaBIG" title="CaBIG">caBIG</a></td>

<td>November 15, 2006

</td></tr>

</tbody></table>

<ul><li><a href="Biological_database" title="Biological database">Biological database</a></li>

<li><a href="List_of_biological_databases" title="List of biological databases">List of biological databases</a></li>

<li><a href="DNA_microarray" title="DNA microarray">DNA microarray</a>

<ul><li><a href="DNA_microarray#Data_warehousing" title="DNA microarray">DNA microarray § Data warehousing</a></li></ul></li>

<li><a href="Microarray_analysis_techniques" title="Microarray analysis techniques">Microarray analysis techniques</a></li></ul>

<div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2></div>

<ul><li><a rel="nofollow" class="external text" href="http://www.ebi.ac.uk/training/online/course/arrayexpress-quick-tour">ArrayExpress: Quick Tour on EBI Train OnLine</a></li>

<li><a rel="nofollow" class="external text" href="http://www.ebi.ac.uk/training/online/course/arrayexpress-exploring-functional-genomics-data-ar">Exploring functional genomics data with the ArrayExpress Archive on EBI Train OnLine</a></li>

<li><a rel="nofollow" class="external text" href="http://www.ebi.ac.uk/training/online/course/arrayexpress-investigating-gene-expression-pattern-0">Investigating gene expression patterns with the Gene Expression Atlas on EBI Train OnLine</a></li>

<li><a rel="nofollow" class="external text" href="http://www.ebi.ac.uk/training/online/course/arrayexpress-submitting-data-using-mage-tab">ArrayExpress:Submitting data using MAGE-TAB on EBI Train OnLine</a></li>

<li><a rel="nofollow" class="external text" href="http://www.arrayexplorer.com">ArrayExplorer</a> - A free tool to compare microarrays side by side.</li></ul></div><div><div class="zim-footer">

This article is issued from <a class="external text" title="Last edited on 2023-09-21" href="https://en.wikipedia.org/wiki/?title=Microarray_databases&oldid=1176465799">Wikipedia</a>. The text is available under <a class="external text" href="https://creativecommons.org/licenses/by-sa/4.0/deed.en">Creative Commons Attribution-Share Alike 4.0</a> unless otherwise noted. Additional terms may apply for the media files.

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