495 lines
No EOL
79 KiB
HTML
495 lines
No EOL
79 KiB
HTML
<?xml version="1.0" encoding="utf-8"?>
|
||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
||
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
||
|
||
<head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
||
<!-- AppResources meta begin -->
|
||
<meta name="paf-app-resources" content="" />
|
||
<script type="text/javascript">var ncbi_startTime = new Date();</script>
|
||
|
||
<!-- AppResources meta end -->
|
||
|
||
<!-- TemplateResources meta begin -->
|
||
<meta name="paf_template" content="" />
|
||
|
||
<!-- TemplateResources meta end -->
|
||
|
||
<!-- Logger begin -->
|
||
<meta name="ncbi_db" content="books" /><meta name="ncbi_pdid" content="book-part" /><meta name="ncbi_acc" content="NBK21093" /><meta name="ncbi_domain" content="handbook" /><meta name="ncbi_report" content="record" /><meta name="ncbi_type" content="fulltext" /><meta name="ncbi_objectid" content="" /><meta name="ncbi_pcid" content="/NBK21093/" /><meta name="ncbi_pagename" content="The Gene Expression Omnibus (GEO): A Gene Expression and Hybridization Repository - The NCBI Handbook - NCBI Bookshelf" /><meta name="ncbi_bookparttype" content="chapter" /><meta name="ncbi_app" content="bookshelf" />
|
||
<!-- Logger end -->
|
||
|
||
<title>The Gene Expression Omnibus (GEO): A Gene Expression and Hybridization Repository - The NCBI Handbook - NCBI Bookshelf</title>
|
||
|
||
<!-- AppResources external_resources begin -->
|
||
<link rel="stylesheet" href="/core/jig/1.15.2/css/jig.min.css" /><script type="text/javascript" src="/core/jig/1.15.2/js/jig.min.js"></script>
|
||
|
||
<!-- AppResources external_resources end -->
|
||
|
||
<!-- Page meta begin -->
|
||
<meta name="robots" content="NOINDEX,NOFOLLOW,NOARCHIVE,NOIMAGEINDEX" /><meta name="citation_inbook_title" content="The NCBI Handbook [Internet]" /><meta name="citation_title" content="The Gene Expression Omnibus (GEO): A Gene Expression and Hybridization Repository" /><meta name="citation_publisher" content="National Center for Biotechnology Information (US)" /><meta name="citation_date" content="2003/08/13" /><meta name="citation_author" content="Ron Edgar" /><meta name="citation_author" content="Alex Lash" /><meta name="citation_fulltext_html_url" content="https://www.ncbi.nlm.nih.gov/books/NBK21093/" /><link rel="schema.DC" href="http://purl.org/DC/elements/1.0/" /><meta name="DC.Title" content="The Gene Expression Omnibus (GEO): A Gene Expression and Hybridization Repository" /><meta name="DC.Type" content="Text" /><meta name="DC.Publisher" content="National Center for Biotechnology Information (US)" /><meta name="DC.Contributor" content="Ron Edgar" /><meta name="DC.Contributor" content="Alex Lash" /><meta name="DC.Date" content="2003/08/13" /><meta name="DC.Identifier" content="https://www.ncbi.nlm.nih.gov/books/NBK21093/" /><meta name="description" content="The Gene Expression Omnibus (GEO) project was initiated at NCBI in 1999 in response to the growing demand for a public repository for data generated from high-throughput microarray experiments. GEO has a flexible and open design that allows the submission, storage, and retrieval of many types of data sets, such as those from high-throughput gene expression, genomic hybridization, and antibody array experiments. GEO was never intended to replace lab-specific gene expression databases or laboratory information management systems (LIMS), both of which usually cater to a particular type of data set and analytical method. Rather, GEO complements these resources by acting as a central, molecular abundance–data distribution hub. GEO is available on the World Wide Web at http://www.ncbi.nih.gov/geo." /><meta name="og:title" content="The Gene Expression Omnibus (GEO): A Gene Expression and Hybridization Repository" /><meta name="og:type" content="book" /><meta name="og:description" content="The Gene Expression Omnibus (GEO) project was initiated at NCBI in 1999 in response to the growing demand for a public repository for data generated from high-throughput microarray experiments. GEO has a flexible and open design that allows the submission, storage, and retrieval of many types of data sets, such as those from high-throughput gene expression, genomic hybridization, and antibody array experiments. GEO was never intended to replace lab-specific gene expression databases or laboratory information management systems (LIMS), both of which usually cater to a particular type of data set and analytical method. Rather, GEO complements these resources by acting as a central, molecular abundance–data distribution hub. GEO is available on the World Wide Web at http://www.ncbi.nih.gov/geo." /><meta name="og:url" content="https://www.ncbi.nlm.nih.gov/books/NBK21093/" /><meta name="og:site_name" content="NCBI Bookshelf" /><meta name="og:image" content="https://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-handbook-lrg.png" /><meta name="twitter:card" content="summary" /><meta name="twitter:site" content="@ncbibooks" /><meta name="warning" content="This publication is provided for historical reference only and the information may be out of date." /><meta name="bk-non-canon-loc" content="/books/n/handbook/ch6/" /><link rel="canonical" href="https://www.ncbi.nlm.nih.gov/books/NBK21093/" /><link rel="stylesheet" href="/corehtml/pmc/css/figpopup.css" type="text/css" media="screen" /><link rel="stylesheet" href="/corehtml/pmc/css/bookshelf/2.26/css/books.min.css" type="text/css" /><link rel="stylesheet" href="/corehtml/pmc/css/bookshelf/2.26/css/books_print.min.css" type="text/css" media="print" /><style type="text/css">.main-content {background:transparent repeat-y top left;background-image:url(/corehtml/pmc/css/bookshelf/2.26/img/archive.png);background-size: auto, contain; padding:0 0 0 3em }</style><style type="text/css">p a.figpopup{display:inline !important} .bk_tt {font-family: monospace} .first-line-outdent .bk_ref {display: inline} .body-content h2, .body-content .h2 {border-bottom: 1px solid #97B0C8} .body-content h2.inline {border-bottom: none} a.page-toc-label , .jig-ncbismoothscroll a {text-decoration:none;border:0 !important} .temp-labeled-list .graphic {display:inline-block !important} .temp-labeled-list img{width:100%}</style><script type="text/javascript" src="/corehtml/pmc/js/jquery.hoverIntent.min.js"> </script><script type="text/javascript" src="/corehtml/pmc/js/common.min.js?_=3.18"> </script><script type="text/javascript" src="/corehtml/pmc/js/large-obj-scrollbars.min.js"> </script><script type="text/javascript">window.name="mainwindow";</script><script type="text/javascript" src="/corehtml/pmc/js/bookshelf/2.26/book-toc.min.js"> </script><script type="text/javascript" src="/corehtml/pmc/js/bookshelf/2.26/books.min.js"> </script><meta name="book-collection" content="NONE" />
|
||
|
||
<!-- Page meta end -->
|
||
<link rel="shortcut icon" href="//www.ncbi.nlm.nih.gov/favicon.ico" /><meta name="ncbi_phid" content="CE8DA8B57C7F458100000000010900D3.m_13" />
|
||
<meta name='referrer' content='origin-when-cross-origin'/><link type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4216699/css/3852956/3985586/3808861/4121862/3974050/3917732/251717/4216701/14534/45193/4113719/3849091/3984811/3751656/4033350/3840896/3577051/3852958/4008682/4207974/4206132/4062871/12930/3964959/3854974/36029/4128070/9685/3549676/3609192/3609193/3609213/3395586.css" /><link type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4216699/css/3411343/3882866.css" media="print" /></head>
|
||
<body class="book-part">
|
||
<div class="grid">
|
||
<div class="col twelve_col nomargin shadow">
|
||
<!-- System messages like service outage or JS required; this is handled by the TemplateResources portlet -->
|
||
<div class="sysmessages">
|
||
<noscript>
|
||
<p class="nojs">
|
||
<strong>Warning:</strong>
|
||
The NCBI web site requires JavaScript to function.
|
||
<a href="/guide/browsers/#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a>
|
||
</p>
|
||
</noscript>
|
||
</div>
|
||
<!--/.sysmessage-->
|
||
<div class="wrap">
|
||
<div class="page">
|
||
<div class="top">
|
||
<div id="universal_header">
|
||
<section class="usa-banner">
|
||
<div class="usa-accordion">
|
||
<header class="usa-banner-header">
|
||
<div class="usa-grid usa-banner-inner">
|
||
<img src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/favicons/favicon-57.png" alt="U.S. flag" />
|
||
<p>An official website of the United States government</p>
|
||
<button class="non-usa-accordion-button usa-banner-button" aria-expanded="false" aria-controls="gov-banner-top" type="button">
|
||
<span class="usa-banner-button-text">Here's how you know</span>
|
||
</button>
|
||
</div>
|
||
</header>
|
||
<div class="usa-banner-content usa-grid usa-accordion-content" id="gov-banner-top" aria-hidden="true">
|
||
<div class="usa-banner-guidance-gov usa-width-one-half">
|
||
<img class="usa-banner-icon usa-media_block-img" src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/icon-dot-gov.svg" alt="Dot gov" />
|
||
<div class="usa-media_block-body">
|
||
<p>
|
||
<strong>The .gov means it's official.</strong>
|
||
<br />
|
||
Federal government websites often end in .gov or .mil. Before
|
||
sharing sensitive information, make sure you're on a federal
|
||
government site.
|
||
</p>
|
||
</div>
|
||
</div>
|
||
<div class="usa-banner-guidance-ssl usa-width-one-half">
|
||
<img class="usa-banner-icon usa-media_block-img" src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/icon-https.svg" alt="Https" />
|
||
<div class="usa-media_block-body">
|
||
<p>
|
||
<strong>The site is secure.</strong>
|
||
<br />
|
||
The <strong>https://</strong> ensures that you are connecting to the
|
||
official website and that any information you provide is encrypted
|
||
and transmitted securely.
|
||
</p>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<div class="usa-overlay"></div>
|
||
<header class="ncbi-header" role="banner" data-section="Header">
|
||
|
||
<div class="usa-grid">
|
||
<div class="usa-width-one-whole">
|
||
|
||
<div class="ncbi-header__logo">
|
||
<a href="/" class="logo" aria-label="NCBI Logo" data-ga-action="click_image" data-ga-label="NIH NLM Logo">
|
||
<img src="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/logos/AgencyLogo.svg" alt="NIH NLM Logo" />
|
||
</a>
|
||
</div>
|
||
|
||
<div class="ncbi-header__account">
|
||
<a id="account_login" href="https://account.ncbi.nlm.nih.gov" class="usa-button header-button" style="display:none" data-ga-action="open_menu" data-ga-label="account_menu">Log in</a>
|
||
<button id="account_info" class="header-button" style="display:none" aria-controls="account_popup" type="button">
|
||
<span class="fa fa-user" aria-hidden="true">
|
||
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24" width="20px" height="20px">
|
||
<g style="fill: #fff">
|
||
<ellipse cx="12" cy="8" rx="5" ry="6"></ellipse>
|
||
<path d="M21.8,19.1c-0.9-1.8-2.6-3.3-4.8-4.2c-0.6-0.2-1.3-0.2-1.8,0.1c-1,0.6-2,0.9-3.2,0.9s-2.2-0.3-3.2-0.9 C8.3,14.8,7.6,14.7,7,15c-2.2,0.9-3.9,2.4-4.8,4.2C1.5,20.5,2.6,22,4.1,22h15.8C21.4,22,22.5,20.5,21.8,19.1z"></path>
|
||
</g>
|
||
</svg>
|
||
</span>
|
||
<span class="username desktop-only" aria-hidden="true" id="uname_short"></span>
|
||
<span class="sr-only">Show account info</span>
|
||
</button>
|
||
</div>
|
||
|
||
<div class="ncbi-popup-anchor">
|
||
<div class="ncbi-popup account-popup" id="account_popup" aria-hidden="true">
|
||
<div class="ncbi-popup-head">
|
||
<button class="ncbi-close-button" data-ga-action="close_menu" data-ga-label="account_menu" type="button">
|
||
<span class="fa fa-times">
|
||
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 48 48" width="24px" height="24px">
|
||
<path d="M38 12.83l-2.83-2.83-11.17 11.17-11.17-11.17-2.83 2.83 11.17 11.17-11.17 11.17 2.83 2.83 11.17-11.17 11.17 11.17 2.83-2.83-11.17-11.17z"></path>
|
||
</svg>
|
||
</span>
|
||
<span class="usa-sr-only">Close</span></button>
|
||
<h4>Account</h4>
|
||
</div>
|
||
<div class="account-user-info">
|
||
Logged in as:<br />
|
||
<b><span class="username" id="uname_long">username</span></b>
|
||
</div>
|
||
<div class="account-links">
|
||
<ul class="usa-unstyled-list">
|
||
<li><a id="account_myncbi" href="/myncbi/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_myncbi">Dashboard</a></li>
|
||
<li><a id="account_pubs" href="/myncbi/collections/bibliography/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_pubs">Publications</a></li>
|
||
<li><a id="account_settings" href="/account/settings/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_settings">Account settings</a></li>
|
||
<li><a id="account_logout" href="/account/signout/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_logout">Log out</a></li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
</div>
|
||
</div>
|
||
</header>
|
||
<div role="navigation" aria-label="access keys">
|
||
<a id="nws_header_accesskey_0" href="https://www.ncbi.nlm.nih.gov/guide/browsers/#ncbi_accesskeys" class="usa-sr-only" accesskey="0" tabindex="-1">Access keys</a>
|
||
<a id="nws_header_accesskey_1" href="https://www.ncbi.nlm.nih.gov" class="usa-sr-only" accesskey="1" tabindex="-1">NCBI Homepage</a>
|
||
<a id="nws_header_accesskey_2" href="/myncbi/" class="set-base-url usa-sr-only" accesskey="2" tabindex="-1">MyNCBI Homepage</a>
|
||
<a id="nws_header_accesskey_3" href="#maincontent" class="usa-sr-only" accesskey="3" tabindex="-1">Main Content</a>
|
||
<a id="nws_header_accesskey_4" href="#" class="usa-sr-only" accesskey="4" tabindex="-1">Main Navigation</a>
|
||
</div>
|
||
<section data-section="Alerts">
|
||
<div class="ncbi-alerts-placeholder"></div>
|
||
</section>
|
||
</div>
|
||
<div class="header">
|
||
<div class="res_logo"><h1 class="res_name"><a href="/books/" title="Bookshelf home">Bookshelf</a></h1><h2 class="res_tagline"></h2></div>
|
||
<div class="search"><form method="get" action="/books/"><div class="search_form"><label for="database" class="offscreen_noflow">Search database</label><select id="database"><optgroup label="Recent"><option value="books" selected="selected" data-ac_dict="bookshelf-search">Books</option><option value="gquery">All Databases</option><option value="refseq">RefSeq</option><option value="pubmed" class="last">PubMed</option></optgroup><optgroup label="All"><option value="gquery">All Databases</option><option value="assembly">Assembly</option><option value="biocollections">Biocollections</option><option value="bioproject">BioProject</option><option value="biosample">BioSample</option><option value="books" data-ac_dict="bookshelf-search">Books</option><option value="clinvar">ClinVar</option><option value="cdd">Conserved Domains</option><option value="gap">dbGaP</option><option value="dbvar">dbVar</option><option value="gene">Gene</option><option value="genome">Genome</option><option value="gds">GEO DataSets</option><option value="geoprofiles">GEO Profiles</option><option value="gtr">GTR</option><option value="ipg">Identical Protein Groups</option><option value="medgen">MedGen</option><option value="mesh">MeSH</option><option value="nlmcatalog">NLM Catalog</option><option value="nuccore">Nucleotide</option><option value="omim">OMIM</option><option value="pmc">PMC</option><option value="protein">Protein</option><option value="proteinclusters">Protein Clusters</option><option value="protfam">Protein Family Models</option><option value="pcassay">PubChem BioAssay</option><option value="pccompound">PubChem Compound</option><option value="pcsubstance">PubChem Substance</option><option value="pubmed">PubMed</option><option value="snp">SNP</option><option value="sra">SRA</option><option value="structure">Structure</option><option value="taxonomy">Taxonomy</option><option value="toolkit">ToolKit</option><option value="toolkitall">ToolKitAll</option><option value="toolkitbookgh">ToolKitBookgh</option></optgroup></select><div class="nowrap"><label for="term" class="offscreen_noflow" accesskey="/">Search term</label><div class="nowrap"><input type="text" name="term" id="term" title="Search Books. Use up and down arrows to choose an item from the autocomplete." value="" class="jig-ncbiclearbutton jig-ncbiautocomplete" data-jigconfig="dictionary:'bookshelf-search',disableUrl:'NcbiSearchBarAutoComplCtrl'" autocomplete="off" data-sbconfig="ds:'no',pjs:'no',afs:'no'" /></div><button id="search" type="submit" class="button_search nowrap" cmd="go">Search</button></div></div></form><ul class="searchlinks inline_list"><li>
|
||
<a href="/books/browse/">Browse Titles</a>
|
||
</li><li>
|
||
<a href="/books/advanced/">Advanced</a>
|
||
</li><li class="help">
|
||
<a href="/books/NBK3833/">Help</a>
|
||
</li><li class="disclaimer">
|
||
<a target="_blank" data-ga-category="literature_resources" data-ga-action="link_click" data-ga-label="disclaimer_link" href="https://www.ncbi.nlm.nih.gov/books/about/disclaimer/">Disclaimer</a>
|
||
</li></ul></div>
|
||
</div>
|
||
|
||
|
||
|
||
<!--<component id="Page" label="headcontent"/>-->
|
||
|
||
</div>
|
||
<div class="content">
|
||
<!-- site messages -->
|
||
<!-- Custom content 1 -->
|
||
<div class="col1">
|
||
|
||
</div>
|
||
|
||
<div class="container">
|
||
<div id="maincontent" class="content eight_col col">
|
||
<!-- Custom content in the left column above book nav -->
|
||
<div class="col2">
|
||
|
||
</div>
|
||
|
||
<!-- Book content -->
|
||
|
||
|
||
<!-- Custom content between navigation and content -->
|
||
<div class="col3">
|
||
|
||
</div>
|
||
|
||
<div class="document">
|
||
<div class="pre-content"><div><div class="bk_prnt"><p class="small">NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.</p><p>McEntyre J, Ostell J, editors. The NCBI Handbook [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2002-. </p></div><div class="bk_msg_box bk_bttm_mrgn clearfix bk_noprnt"><div class="iconblock clearfix"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/handbook2e/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-handbook2e-lrg.png" alt="Cover" height="100px" width="80px" /></a><div class="icnblk_cntnt"><ul class="messages"><li class="info icon"><span class="icon"><a href="/books/n/handbook2e/">See "The NCBI Handbook, 2nd Edition"</a></span></li></ul></div></div></div><div class="messagearea bk_noprnt" style="margin-bottom:1.3846em "><ul class="messages"><li class="warn icon"><span class="icon">This publication is provided for historical reference only and the information may be out of date.</span></li></ul></div><div class="bk_prnt"><p style="color:red;"><strong>This publication is provided for historical reference only and the information may be out of date.</strong></p></div><div class="iconblock clearfix whole_rhythm no_top_margin bk_noprnt"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/handbook/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-handbook-lrg.png" alt="Cover of The NCBI Handbook" height="100px" width="80px" /></a><div class="icnblk_cntnt eight_col"><h2>The NCBI Handbook [Internet].</h2><a data-jig="ncbitoggler" href="#__NBK21093_dtls__">Show details</a><div style="display:none" class="ui-widget" id="__NBK21093_dtls__"><div>McEntyre J, Ostell J, editors.</div><div>Bethesda (MD): <a href="https://www.ncbi.nlm.nih.gov/" ref="pagearea=page-banner&targetsite=external&targetcat=link&targettype=publisher">National Center for Biotechnology Information (US)</a>; 2002-.</div></div><div class="half_rhythm"><ul class="inline_list"><li style="margin-right:1em"><a class="bk_cntns" href="/books/n/handbook/">Contents</a></li></ul></div></div><div class="icnblk_cntnt two_col"><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/handbook/ch5/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/handbook/ch7/" title="Next page in this title">Next ></a></div></div></div></div></div>
|
||
<div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><h1 id="_NBK21093_"><span class="label">Chapter 6</span><span class="title" itemprop="name">The Gene Expression Omnibus (GEO): A Gene Expression and Hybridization Repository</span></h1><p class="contrib-group"><span itemprop="author">Ron Edgar</span> and <span itemprop="author">Alex Lash</span>.</p><p class="small">Created: <span itemprop="datePublished">October 9, 2002</span>; Last Update: <span itemprop="dateModified">August 13, 2003</span>.</p><p><em>Estimated reading time: 13 minutes</em></p></div><div class="jig-ncbiinpagenav body-content whole_rhythm" data-jigconfig="allHeadingLevels: ['h2'],smoothScroll: false" itemprop="text"><div id="_abs_rndgid_" itemprop="description"><h2 id="__abs_rndgid__">Summary</h2><p>The Gene Expression Omnibus (<a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a>) project was initiated at <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> in 1999 in response to the growing demand for a public repository for data generated from high-throughput microarray experiments. GEO has a flexible and open design that allows the submission, storage, and retrieval of many types of data sets, such as those from high-throughput gene expression, genomic hybridization, and antibody array experiments. GEO was never intended to replace lab-specific gene expression databases or laboratory information management systems (<a class="def" href="/books/n/handbook/A1237/def-item/app93/">LIMS</a>), both of which usually cater to a particular type of data set and analytical method. Rather, GEO complements these resources by acting as a central, molecular abundance–data distribution hub. GEO is available on the World Wide Web at <a href="http://www.ncbi.nih.gov/geo" ref="pagearea=abstract&targetsite=external&targetcat=link&targettype=uri">http://www.ncbi.nih.gov/geo</a>.</p></div><div id="A338"><h2 id="_A338_">Site Description</h2><p>High-throughput hybridization array- and sequencing-based experiments have become increasingly common in molecular biology laboratories in recent years (<a class="bk_pop" href="#A398">1</a>–<a class="bk_pop" href="#A401">4</a>). These techniques are used to measure the molecular abundance of <a class="def" href="/books/n/handbook/A1237/def-item/app114/">mRNA</a>, genomic <a class="def" href="/books/n/handbook/A1237/def-item/app37/">DNA</a>, and proteins in absolute or relative terms. The main attraction of these techniques is their highly parallel nature; large numbers of simultaneous molecular sampling events are performed under very similar conditions. This means that time and resources are saved, and complex biological systems can be represented in a more holistic manner. Furthermore, the development of tissue arrays means that it is possible to analyze, in parallel, the gene expression of large numbers of tumor tissue samples from patients at different stages of cancer development (<a class="bk_pop" href="#A402">5</a>).</p><p>Because of the plethora of measuring techniques for molecular abundance in use, our primary goal in creating the Gene Expression Omnibus (<a href="/geo" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">GEO</a>) was to cover the broadest possible spectrum of these techniques and remain flexible and responsive to future trends, rather than choosing only one of these techniques or setting rigid requirements and standards for entry. In taking this approach, however, we recognize that there are obvious, inherent limitations to functionality and analysis that can be provided on such heterogeneous data sets.</p><p>This chapter is both more current and more detailed than the previous literature report on <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> (<a class="bk_pop" href="#A403">6</a>). However, more detailed descriptions, tools, and news releases are available on the <a href="/geo" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">GEO Web site</a>.</p></div><div id="A339"><h2 id="_A339_">Design and Implementation</h2><p>The three principle components (or entities) of <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> are modeled after the three organizational units common to high-throughput gene expression and array-based methodologies. These entities are called <i>platforms</i>, <i>samples</i> and <i>series</i> (<a class="figpopup" href="/books/NBK21093/figure/A340/?report=objectonly" target="object" rid-figpopup="figA340" rid-ob="figobA340">Figure 1</a>; <a class="figpopup" href="/books/NBK21093/table/A341/?report=objectonly" target="object" rid-figpopup="figA341" rid-ob="figobA341">Table 1</a>). A <i>platform</i> is, essentially, a list of probes that defines what set of molecules may be detected in any experiment using that platform. A <i>sample</i> describes the set of molecules that are being probed and references a single platform used to generate molecular abundance data. Each sample has one, and only one, parent platform that must be defined previously. A <i>series</i> organizes samples into the meaningful data sets that make up an experiment and are bound together by a common attribute.</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA340" co-legend-rid="figlgndA340"><a href="/books/NBK21093/figure/A340/?report=objectonly" target="object" title="Figure 1" class="img_link icnblk_img figpopup" rid-figpopup="figA340" rid-ob="figobA340"><img class="small-thumb" src="/books/NBK21093/bin/ch6f1.gif" src-large="/books/NBK21093/bin/ch6f1.jpg" alt="Figure 1. GEO design." /></a><div class="icnblk_cntnt" id="figlgndA340"><h4 id="A340"><a href="/books/NBK21093/figure/A340/?report=objectonly" target="object" rid-ob="figobA340">Figure 1</a></h4><p class="float-caption no_bottom_margin">GEO design. The entity–relationship diagram for GEO. </p></div></div><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figA341"><a href="/books/NBK21093/table/A341/?report=objectonly" target="object" title="Table 1" class="img_link icnblk_img figpopup" rid-figpopup="figA341" rid-ob="figobA341"><img class="small-thumb" src="/books/NBK21093/table/A341/?report=thumb" src-large="/books/NBK21093/table/A341/?report=previmg" alt="Table 1. Entity prefixes, types, and subtypes in the GEO database." /></a><div class="icnblk_cntnt"><h4 id="A341"><a href="/books/NBK21093/table/A341/?report=objectonly" target="object" rid-ob="figobA341">Table 1</a></h4><p class="float-caption no_bottom_margin">Entity prefixes, types, and subtypes in the GEO database. </p></div></div><p>The <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> repository is a relational database, which required that some fundamental implementation decisions were made:</p><p>(<i>a</i>) <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> does not store raw hybridization-array image data, although “reference” images of less than 100 Kb may be stored. This decision was based on an assertion that most users of the data within the GEO repository would not be equipped to use raw image data (<a class="bk_pop" href="#A404">7</a>); although some may disagree, this means that repository storage requirements are reduced roughly by a factor of 20.</p><p>(<i>b</i>) We decided to use a different storage mechanism for data and metadata. Within the <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> repository, metadata are stored in designated fields within the database table. However, data from the entire set of probe attributes (for each platform) and molecular abundance measurements (for each sample) are stored as a single, text-compressed <a href="/books/n/handbook/A1237/#app14">BLOB</a>. This mode of data storage allows great flexibility in the amount and type of information stored in this <a class="def" href="/books/n/handbook/A1237/def-item/app14/">BLOB</a>. It allows any number of supplementary attributes or measurements to be provided by the submitter, including optional or submitter-defined information. For example, a microarray (the platform) consisting of several thousand spots (the probes) would have a set of probe attributes, some of which are defined by GEO. The GEO-defined attributes include, for each probe, the position within the array and biological reagent contents of each probe such as a <a href="/books/n/handbook/A1237/#app62">GenBank</a> <a class="def" href="/books/n/handbook/A1237/def-item/app208/">Accession number</a>, open reading frame (ORF) name, and clone identifier, as well as any number of submitter-defined columns. As another example, the set of probe-target measurements given in the data from a sample may contain the final, relevant abundance value of the probe defined in its platform, as well as any other GEO-defined (e.g., raw signal, background signal) and submitter-defined data.</p><p>Once a platform, sample, or series is defined by a submitter, an <a class="def" href="/books/n/handbook/A1237/def-item/app208/">Accession number</a> (i.e., a unique, stable identifier) is assigned (<a class="figpopup" href="/books/NBK21093/figure/A342/?report=objectonly" target="object" rid-figpopup="figA342" rid-ob="figobA342">Figure 2</a>). Whether a <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> Accession number refers to a platform, sample, or series can be understood by the Accession number “prefix”. Platforms have the prefix GPL, samples have the prefix GSM, and series have the prefix GSE.</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA342" co-legend-rid="figlgndA342"><a href="/books/NBK21093/figure/A342/?report=objectonly" target="object" title="Figure 2" class="img_link icnblk_img figpopup" rid-figpopup="figA342" rid-ob="figobA342"><img class="small-thumb" src="/books/NBK21093/bin/ch6f2.gif" src-large="/books/NBK21093/bin/ch6f2.jpg" alt="Figure 2. GEO implementation example." /></a><div class="icnblk_cntnt" id="figlgndA342"><h4 id="A342"><a href="/books/NBK21093/figure/A342/?report=objectonly" target="object" rid-ob="figobA342">Figure 2</a></h4><p class="float-caption no_bottom_margin">GEO implementation example. An actual example of three samples referencing one platform and contained in a single series. </p></div></div></div><div id="A343"><h2 id="_A343_">Retrieving Data</h2><p>A <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> <a class="def" href="/books/n/handbook/A1237/def-item/app208/">Accession number</a> is required to retrieve data from the GEO repository database (<a class="figpopup" href="/books/NBK21093/figure/A355/?report=objectonly" target="object" rid-figpopup="figA355" rid-ob="figobA355">Figure 3</a>). An Accession number may be acquired in any number of ways, including direct reference, such as from a publication citing data deposited to GEO, or through a query interface, such as through <a href="/books/n/handbook/A1237/#app116">NCBI</a>'s <a href="/books/n/handbook/A1237/#app45">Entrez</a> ProbeSet interface (covered below).</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA355" co-legend-rid="figlgndA355"><a href="/books/NBK21093/figure/A355/?report=objectonly" target="object" title="Figure 3" class="img_link icnblk_img figpopup" rid-figpopup="figA355" rid-ob="figobA355"><img class="small-thumb" src="/books/NBK21093/bin/ch6f3.gif" src-large="/books/NBK21093/bin/ch6f3.jpg" alt="Figure 3. GEO retrieval statistics." /></a><div class="icnblk_cntnt" id="figlgndA355"><h4 id="A355"><a href="/books/NBK21093/figure/A355/?report=objectonly" target="object" rid-ob="figobA355">Figure 3</a></h4><p class="float-caption no_bottom_margin">GEO retrieval statistics. Daily usage statistics evaluated over a 4-week period January 24 to February 20, 2002. Web server <i>GET</i> (<i>blue</i>) and <i>POST</i> (<i>magenta</i>) calls are evaluated for URL http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi. <i>GET</i> calls correspond roughly <a href="/books/NBK21093/figure/A355/?report=objectonly" target="object" rid-ob="figobA355">(more...)</a></p></div></div><p>Given a valid <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> <a class="def" href="/books/n/handbook/A1237/def-item/app208/">Accession number</a>, the Accession Display tool available on the GEO Web site provides a number of options for the retrieval and display of repository contents (see <a href="/books/NBK21093/box/A344/?report=objectonly" target="object" rid-ob="figobA344">Box 1</a>).</p><div class="iconblock whole_rhythm clearfix ten_col boxed-text" id="figA344"><a href="/books/NBK21093/box/A344/?report=objectonly" target="object" title="Box 1" class="img_link icnblk_img" rid-ob="figobA344"><img class="small-thumb" src="/corehtml/pmc/css/bookshelf/2.26/img/box-icon.gif" alt="Box Icon" /></a><div class="icnblk_cntnt"><h4 id="A344"><a href="/books/NBK21093/box/A344/?report=objectonly" target="object" rid-ob="figobA344">Box 1</a></h4><p class="float-caption no_bottom_margin">GEO Web site Accession Display tool. </p></div></div></div><div id="A353"><h2 id="_A353_">Depositing Data</h2><p>There are several formats in which data can be deposited and retrieved from <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a>. For deposit: (1) a file containing an ASCII-encoded text table of data can be uploaded, and metadata fields can be interactively entered through a series of Web forms; or (2) both data and metadata for one or more platforms, samples, or series can be uploaded directly in a format we call Simple Omnibus Format in Text, or <a class="def" href="/books/n/handbook/A1237/def-item/app169/">SOFT</a> (<a href="/books/NBK21093/box/A354/?report=objectonly" target="object" rid-ob="figobA354">Box 2</a>).</p><p>Interactive and direct modes of communication are available for new data submissions and updating data submissions. The interactive Web form route is straightforward and most suited for occasional submissions of a relatively small number of samples. Bulk submissions of large data sets may be rapidly incorporated into <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> via direct deposit of <a class="def" href="/books/n/handbook/A1237/def-item/app169/">SOFT</a> formatted data.</p><p>Submissions may be held private for a maximum of 6 months; this policy allows data release concordant with manuscript publication. Such submissions are given a final <a class="def" href="/books/n/handbook/A1237/def-item/app208/">Accession number</a> at the time of submission, which may be quoted in a publication.</p><p>Currently, submissions are validated according to a limited set of criteria (see the <a href="/geo" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">GEO Web site</a> for more details). Submissions are scanned by our staff to assure that the submissions are organized correctly and include meaningful information. It is entirely up to the submitter to make the data useful to others.</p><p>A quarterly, cumulative graph of the number of individual molecular abundance measurements in public submissions made through the first quarter of 2002 is shown in <a class="figpopup" href="/books/NBK21093/figure/A355/?report=objectonly" target="object" rid-figpopup="figA355" rid-ob="figobA355">Figure 4</a>.</p><p>
|
||
|
||
</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA352" co-legend-rid="figlgndA352"><a href="/books/NBK21093/figure/A352/?report=objectonly" target="object" title="Figure 4" class="img_link icnblk_img figpopup" rid-figpopup="figA352" rid-ob="figobA352"><img class="small-thumb" src="/books/NBK21093/bin/ch6f4.gif" src-large="/books/NBK21093/bin/ch6f4.jpg" alt="Figure 4. GEO submission statistics." /></a><div class="icnblk_cntnt" id="figlgndA352"><h4 id="A352"><a href="/books/NBK21093/figure/A352/?report=objectonly" target="object" rid-ob="figobA352">Figure 4</a></h4><p class="float-caption no_bottom_margin">GEO submission statistics. Cumulative individual sample measurements submitted to GEO are shown. Data are presented by quarter since operations began on July 25, 2000. </p></div></div></div><div id="A356"><h2 id="_A356_">Search and Integration</h2><p>Extensive indexing and linking on the data in <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> are performed periodically and can be queried through <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> ProbeSet (<a href="/books/NBK21093/box/A357/?report=objectonly" target="object" rid-ob="figobA357">Box 3</a>). Many users of Entrez will recognize this interface as similar to that of other popular <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> resources such as <a href="/books/n/handbook/A1237/#app150">PubMed</a> and <a class="def" href="/books/n/handbook/A1237/def-item/app62/">GenBank</a>. As with any Entrez database, a <a href="/books/n/handbook/A1237/#app16">Boolean</a> phrase may be entered and restricted to any number of supported attribute fields (<a class="figpopup" href="/books/NBK21093/table/A358/?report=objectonly" target="object" rid-figpopup="figA358" rid-ob="figobA358">Table 2</a>). Matches are linked to the full GEO entry as well as to other Entrez databases, currently Nucleotide, Taxonomy, and <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a>, as well as related Entrez ProbeSet entries. (See <a href="/books/n/handbook/ch15/">Chapter 15</a> for more details.) Entrez ProbeSet is accessible through the <a href="/entrez/query.fcgi?db=geo" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Entrez Web site</a> as one of the drop-down menu selections.</p><div class="iconblock whole_rhythm clearfix ten_col boxed-text" id="figA357"><a href="/books/NBK21093/box/A357/?report=objectonly" target="object" title="Box 3" class="img_link icnblk_img" rid-ob="figobA357"><img class="small-thumb" src="/corehtml/pmc/css/bookshelf/2.26/img/box-icon.gif" alt="Box Icon" /></a><div class="icnblk_cntnt"><h4 id="A357"><a href="/books/NBK21093/box/A357/?report=objectonly" target="object" rid-ob="figobA357">Box 3</a></h4><p class="float-caption no_bottom_margin">Entrez ProbeSet indexing and linking process. </p></div></div><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figA358"><a href="/books/NBK21093/table/A358/?report=objectonly" target="object" title="Table 2" class="img_link icnblk_img figpopup" rid-figpopup="figA358" rid-ob="figobA358"><img class="small-thumb" src="/books/NBK21093/table/A358/?report=thumb" src-large="/books/NBK21093/table/A358/?report=previmg" alt="Table 2. Entrez ProbeSet fields." /></a><div class="icnblk_cntnt"><h4 id="A358"><a href="/books/NBK21093/table/A358/?report=objectonly" target="object" rid-ob="figobA358">Table 2</a></h4><p class="float-caption no_bottom_margin">Entrez ProbeSet fields. </p></div></div></div><div id="A359"><h2 id="_A359_">Example of Retrieving Data</h2><p>Because samples are oftentimes organized into meaningful data sets within series, an example of retrieving a series and all the data of its associated samples and platform(s) is illustrative of the retrieval capabilities of the <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> Web site. For this example, to select a series of interest, we scan down a list of series in the GEO repository. However, to arrive at our series of interest, we could have just as well performed an <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> ProbeSet query and followed GEO accession links to a sample and then to its related series, or followed links from <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> to Entrez ProbeSet, and then to GEO. A step-by-step example of selecting a series of data and retrieving the data for this series from the GEO repository follows:</p><dl class="temp-labeled-list"><dt>1.</dt><dd id="A360"><p class="no_top_margin">Select the linked number of public series from the table of Repository Contents given on the <a href="http://www.ncbi.nih.gov/geo" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">GEO homepage</a>:
|
||
</p><p>
|
||
<div class="graphic"><img src="/books/NBK21093/bin/ch6df1.jpg" alt="Image ch6df1.jpg" /></div>
|
||
</p></dd><dt>2.</dt><dd id="A361"><p class="no_top_margin">Scan down the list of <a href="/geo/query/browse.cgi?view=series" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">public series</a> in the <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> repository and select <a href="/geo/query/acc.cgi?acc=GSE27" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=geo">GSE27</a>, on sporulation in yeast:
|
||
</p><p>
|
||
<div class="graphic"><img src="/books/NBK21093/bin/ch6df2.jpg" alt="Image ch6df2.jpg" /></div>
|
||
</p></dd><dt>3.</dt><dd id="A362"><p class="no_top_margin">The description of <a href="/geo/query/acc.cgi?acc=GSE27" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=geo">GSE27</a> on the <a href="/geo/query/acc.cgi?acc=GSE27" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Accession Display</a> allows a summary assessment of the data. The data set can be downloaded in <a class="def" href="/books/n/handbook/A1237/def-item/app169/">SOFT</a> format:
|
||
</p><p>
|
||
<div class="graphic"><img src="/books/NBK21093/bin/ch6df3.jpg" alt="Image ch6df3.jpg" /></div>
|
||
</p></dd><dt>4.</dt><dd id="A363"><p class="no_top_margin">In the <b>Accession Display</b> options, select <b>Scope:</b>Family, <b>Format:</b><a class="def" href="/books/n/handbook/A1237/def-item/app169/">SOFT</a>, and <b>Amount:</b>Full and then press the <a href="/geo/query/acc.cgi?acc=GSE27&targ=all%20&form=text&view=full" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri"><b>go</b></a> button:
|
||
</p><p>
|
||
<div class="graphic"><img src="/books/NBK21093/bin/ch6df4.jpg" alt="Image ch6df4.jpg" /></div>
|
||
</p></dd><dt>5.</dt><dd id="A364"><p class="no_top_margin">A browser dialog states that it took 19 seconds to download the 5 <a class="def" href="/books/n/handbook/A1237/def-item/app100/">MB</a> <a class="def" href="/books/n/handbook/A1237/def-item/app169/">SOFT</a> file of data and metadata for one series (<a href="/geo/query/acc.cgi?acc=GSE27" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=geo">GSE27</a>), seven samples (<a href="/geo/query/acc.cgi?acc=GSM992" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=geo">GSM992</a> to <a href="/geo/query/acc.cgi?acc=GSM1000" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=geo">GSM1000</a>), and one platform (<a href="/geo/query/acc.cgi?acc=GPL67" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=geo">GPL67</a>).
|
||
</p><p>
|
||
<div class="graphic"><img src="/books/NBK21093/bin/ch6df5.jpg" alt="Image ch6df5.jpg" /></div>
|
||
</p></dd></dl></div><div id="A365"><h2 id="_A365_">Future Directions</h2><p>The <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> resource is under constant development and aims to improve its indexing, linking, searching, and display capabilities to allow vigorous data mining. Because the data sets stored within GEO are from heterogeneous techniques and sources, they are not necessarily comparable. For this reason, we have defined a ProbeSet to be a collection of GEO samples that contains comparable data. The selection of GEO samples into ProbeSets is necessary before integrating data in the GEO repository into other <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> resources (see <a href="/books/n/handbook/ch15/">Chapter 15</a>, <a href="/books/n/handbook/ch16/">Chapter 16</a>, and <a href="/books/n/handbook/ch20/">Chapter 20</a>), as well as for developing useful display tools for these data (<a class="figpopup" href="/books/NBK21093/figure/A366/?report=objectonly" target="object" rid-figpopup="figA366" rid-ob="figobA366">Figure 5</a>).</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA366" co-legend-rid="figlgndA366"><a href="/books/NBK21093/figure/A366/?report=objectonly" target="object" title="Figure 5" class="img_link icnblk_img figpopup" rid-figpopup="figA366" rid-ob="figobA366"><img class="small-thumb" src="/books/NBK21093/bin/ch6f5.gif" src-large="/books/NBK21093/bin/ch6f5.jpg" alt="Figure 5. Constellation of NCBI gene expression resources." /></a><div class="icnblk_cntnt" id="figlgndA366"><h4 id="A366"><a href="/books/NBK21093/figure/A366/?report=objectonly" target="object" rid-ob="figobA366">Figure 5</a></h4><p class="float-caption no_bottom_margin">Constellation of NCBI gene expression resources. Anticipated development of gene expression resources at NCBI is shown. <i>Blue spheres</i> represent Web sites, <i>orange cylinders</i> represent primary NCBI databases, <i>green cylinders</i> represent secondary databases, <a href="/books/NBK21093/figure/A366/?report=objectonly" target="object" rid-ob="figobA366">(more...)</a></p></div></div></div><div id="A367"><h2 id="_A367_">Frequently Asked Questions</h2><p>1. How do I submit my data?</p><blockquote><p>To submit data, an identity within the <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> resource must first be established. On first login, authentication and contact information must be provided. Authentication information (username and password) is used to identify users making submissions and updates to submissions. Contact information is displayed when repository contents are retrieved by others. This information is entered only once and can be updated at any time.</p></blockquote><p>2. Is there a “hold until date” feature in <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a>?</p><blockquote><p>Yes. This feature allows a submitter to submit data to <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> and receive a GEO <a class="def" href="/books/n/handbook/A1237/def-item/app208/">Accession number</a> before the data become public. There is currently a 6-month limit to this hold period. All private data are publicly released eventually.</p></blockquote><p>3. What kinds of data will <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> accept?</p><blockquote><p><a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> was designed around the common features of most of the high-throughput gene expression and array-based measuring technologies in use today. These technologies include hybridization filter, spotted microarray, high-density oligonucleotide array, serial analysis of gene expression, and Comparative Genomic Hybridization (<a class="def" href="/books/n/handbook/A1237/def-item/app24/">CGH</a>) and protein (antibody) arrays but may be expanded in the future.</p></blockquote><p>4. Does <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> archive raw data images?</p><blockquote><p>No. However, a reference image will be optionally accepted (limited to 100 Kb in size in JPEG format). In combination with optional references to horizontal and vertical coordinates, this image can be used to provide the user of the data with a qualitative assessment of the data.</p></blockquote><p>5. Are there any Quality Assurance (QA) measurements that are required by <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a>?</p><blockquote><p>Not at this time. These requirements may be added in the future.</p></blockquote><p>6. How can I submit QA measurements to <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a>?</p><blockquote><p>QA measurements are currently optional. If QA measurements are performed at the image-analysis step, these can be submitted as additional sample data.</p></blockquote><p>7. How can I make corrections to data that I have already submitted?</p><blockquote><p>By logging in with a username and password, an option to update a previous submission or your contact information is given. Accession updates can also be made through a link from the Accession Display after logging in. Updating the data of an already existing and valid <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> <a class="def" href="/books/n/handbook/A1237/def-item/app208/">Accession number</a> will cause a new version of that data element to be created. Alterations of metadata will not create a new version. All of the various versions of a data element will remain in the database.</p></blockquote><p>8. How are submitters authenticated?</p><blockquote><p>In their first submission to <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a>, submitters will be asked to select a username and password. This username and password can be used to submit additional data in the future without reentering contact information, as well as to authenticate the submitter when updating or resubmitting data elements under an existing GEO <a class="def" href="/books/n/handbook/A1237/def-item/app208/">Accession number</a>.</p></blockquote><p>9. How do I get data from <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a>?</p><blockquote><p>You need not login to retrieve data. All the data are available for downloading. <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> places no restrictions on the use of data whatsoever but does not guarantee that no restrictions exist from others. You should carefully read NCBI's data disclaimer, available on the <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> Web site.</p></blockquote><p>10. What kind of queries and retrievals will be possible in <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a>?</p><blockquote><p>Currently, there are three ways to retrieve submissions. One way is by entering a valid <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> <a class="def" href="/books/n/handbook/A1237/def-item/app208/">Accession number</a> into the query box on the header bar of this page; this will take you to the Accession Display. Another is to use the platform, sample, and series lists, located on the GEO Statistics page. Sophisticated queries of GEO data and linking to other <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> databases can be accomplished by using Entrez ProbeSet.</p></blockquote><p>11. What does <b>Scope</b> mean in the Accession Display?</p><blockquote><p><a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a> platforms (GPL prefix) may have related samples and, through those related samples, related series. GEO samples (GSM prefix) will always have one related platform and may have multiple, related series. GEO series (GSE prefix) will have at least one related sample and, through those related samples, will have at least one related platform. The <b>Family</b> setting will retrieve all accessions (of different types) related to self (including Self). Please see <a href="/books/NBK21093/box/A344/?report=objectonly" target="object" rid-ob="figobA344">Box 1</a> for more details.</p></blockquote><p>12. What is <a class="def" href="/books/n/handbook/A1237/def-item/app169/">SOFT</a>?</p><blockquote><p><a class="def" href="/books/n/handbook/A1237/def-item/app169/">SOFT</a> stands for Simple Omnibus Format in Text. SOFT is an ASCII text format that was designed to be a machine-readable representation of data retrieved from, or submitted to, <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a>. SOFT output is obtained by using the Accession Display, and SOFT can be used to submit data to GEO. Please see Box 2 for more details.</p></blockquote><p>13. What does the word “taxon” mean?</p><blockquote><p>The <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a>'s Taxonomy group has constructed and maintains a taxonomic hierarchy based upon the most recent information, which is described in <a href="/books/n/handbook/ch4/">Chapter 4</a> of this Handbook.</p></blockquote></div><div id="A394"><h2 id="_A394_">Acknowledgments</h2><p>We gratefully acknowledge the work of Vladimir Soussov, as well as the entire <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> team, especially Grisha Starchenko, Vladimir Sirotinin, Alexey Iskhakov, Anton Golikov, and Pramod Paranthaman. We thank Jim Ostell for guidance, Lou Staudt for discussions during our initial planning for <a class="def" href="/books/n/handbook/A1237/def-item/app66/">GEO</a>, and the extreme patience shown by Brian Oliver, Wolfgang Huber, and Gavin Sherlock when making the first data submissions. Admirable patience was also exhibited by Al Zhong during the development of the direct deposit validator. Special thanks go to Manish Inala and Wataru Fujibuchi for their continuing work on future features and tools.</p></div><div id="A395"><h2 id="_A395_">Contributors</h2><p>
|
||
<a class="figpopup" href="/books/NBK21093/table/A396/?report=objectonly" target="object" rid-figpopup="figA396" rid-ob="figobA396">Table 3</a> shows a collection of data sets from various sources. Ron Edgar, Michael Domrachev, Tugba Suzek, Tanya Barrett, and Alex E. Lash contributed to this <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> resource.</p><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figA396"><a href="/books/NBK21093/table/A396/?report=objectonly" target="object" title="Table 3" class="img_link icnblk_img figpopup" rid-figpopup="figA396" rid-ob="figobA396"><img class="small-thumb" src="/books/NBK21093/table/A396/?report=thumb" src-large="/books/NBK21093/table/A396/?report=previmg" alt="Table 3. Selective data set survey." /></a><div class="icnblk_cntnt"><h4 id="A396"><a href="/books/NBK21093/table/A396/?report=objectonly" target="object" rid-ob="figobA396">Table 3</a></h4><p class="float-caption no_bottom_margin">Selective data set survey. </p></div></div></div><div id="A397"><h2 id="_A397_">References</h2><dl class="temp-labeled-list"><dt>1.</dt><dd><div class="bk_ref" id="A398">Schena M , Shalon D , Davis RW , Brown PO . Quantitative monitoring of gene expression patterns with a complementary DNA microarray. <span><span class="ref-journal">Science. </span>1995;<span class="ref-vol">270</span>:467–470.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/7569999" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 7569999</span></a>]</div></dd><dt>2.</dt><dd><div class="bk_ref" id="A399">Lipshutz RJ , Morris D , Chee M , Hubbell E , Kozal MJ , Shah N , Shen N , Yang R , Fodor SP . Using oligonucleotide probe arrays to access genetic diversity. <span><span class="ref-journal">Biotechniques. </span>1995;<span class="ref-vol">19</span>:442–447.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/7495558" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 7495558</span></a>]</div></dd><dt>3.</dt><dd><div class="bk_ref" id="A400">Velculescu VE , Zhang L , Vogelstein B , Kinzler KW . Serial analysis of gene expression. <span><span class="ref-journal">Science. </span>1995;<span class="ref-vol">270</span>:484–487.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/7570003" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 7570003</span></a>]</div></dd><dt>4.</dt><dd><div class="bk_ref" id="A401">Emili AQ , Cagney G . Large-scale functional analysis using peptide or protein arrays. <span><span class="ref-journal">Nat Biotechnol. </span>2000;<span class="ref-vol">18</span>:393–397.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/10748518" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 10748518</span></a>]</div></dd><dt>5.</dt><dd><div class="bk_ref" id="A402">Leighton S , Torhorst J , Mihatsch MJ , Sauter G , Kallioniemi OP . Tissue microarrays for high-throughput molecular profiling of tumor specimens. <span><span class="ref-journal">Nat Med. </span>1998;<span class="ref-vol">4</span>:844–847.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/9662379" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 9662379</span></a>]</div></dd><dt>6.</dt><dd><div class="bk_ref" id="A403">Edgar R , Domrachev M , Lash AE . Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. <span><span class="ref-journal">Nucleic Acids Research. </span>2002;<span class="ref-vol">30</span>:207–210.</span> [<a href="/pmc/articles/PMC99122/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC99122</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/11752295" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 11752295</span></a>]</div></dd><dt>7.</dt><dd><div class="bk_ref" id="A404">Brazma A , Hingamp P , Quackenbush J , Sherlock G , Spellman P , Stoeckert C , Aach J , Ansorge W , Ball CA , Causton HC , Gaasterland T , Glenisson P , Holstege FC , Kim IF , Markowitz V , Matese JC , Parkinson H , Robinson A , Sarkans U , Schulze-Kremer S , Stewart J , Taylor R , Vilo J , Vingron M . Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. <span><span class="ref-journal">Nat Genet. </span>2001;<span class="ref-vol">29</span>:365–371.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/11726920" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 11726920</span></a>]</div></dd></dl></div><div id="bk_toc_contnr"></div></div></div>
|
||
<div class="post-content"><div><div class="half_rhythm"><a href="/books/about/copyright/">Copyright Notice</a></div><div class="small"><span class="label">Bookshelf ID: NBK21093</span></div><div style="margin-top:2em" class="bk_noprnt"><a class="bk_cntns" href="/books/n/handbook/">Contents</a><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/handbook/ch5/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/handbook/ch7/" title="Next page in this title">Next ></a></div></div></div></div>
|
||
|
||
</div>
|
||
|
||
<!-- Custom content below content -->
|
||
<div class="col4">
|
||
|
||
</div>
|
||
|
||
|
||
<!-- Book content -->
|
||
|
||
<!-- Custom contetnt below bottom nav -->
|
||
<div class="col5">
|
||
|
||
</div>
|
||
</div>
|
||
|
||
<div id="rightcolumn" class="four_col col last">
|
||
<!-- Custom content above discovery portlets -->
|
||
<div class="col6">
|
||
<div id="ncbi_share_book"><a href="#" class="ncbi_share" data-ncbi_share_config="popup:false,shorten:true" ref="id=NBK21093&db=books">Share</a></div>
|
||
|
||
</div>
|
||
<div xmlns:np="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"></div><div class="portlet"><div class="portlet_head"><div class="portlet_title"><h3><span>Views</span></h3></div><a name="Shutter" sid="1" href="#" class="portlet_shutter" title="Show/hide content" remembercollapsed="true" pgsec_name="PDF_download" id="Shutter"></a></div><div class="portlet_content"><ul xmlns:np="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" class="simple-list"><li><a href="/books/NBK21093/?report=reader">PubReader</a></li><li><a href="/books/NBK21093/?report=printable">Print View</a></li><li><a data-jig="ncbidialog" href="#_ncbi_dlg_citbx_NBK21093" data-jigconfig="width:400,modal:true">Cite this Page</a><div id="_ncbi_dlg_citbx_NBK21093" style="display:none" title="Cite this Page"><div class="bk_tt">Edgar R, Lash A. The Gene Expression Omnibus (GEO): A Gene Expression and Hybridization Repository. 2002 Oct 9 [Updated 2003 Aug 13]. In: McEntyre J, Ostell J, editors. The NCBI Handbook [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2002-. Chapter 6.<span class="bk_cite_avail"></span></div></div></li><li><a href="/books/NBK21093/pdf/Bookshelf_NBK21093.pdf">PDF version of this page</a> (295K)</li><li><a href="/books/n/handbook/pdf/">PDF version of this title</a> (7.2M)</li><li><a href="#" class="toggle-glossary-link" title="Enable/disable links to the glossary">Disable Glossary Links</a></li></ul></div></div><div class="portlet"><div class="portlet_head"><div class="portlet_title"><h3><span>In this Page</span></h3></div><a name="Shutter" sid="1" href="#" class="portlet_shutter" title="Show/hide content" remembercollapsed="true" pgsec_name="page-toc" id="Shutter"></a></div><div class="portlet_content"><ul xmlns:np="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" class="simple-list"><li><a href="#_abs_rndgid_" ref="log$=inpage&link_id=inpage">Summary</a></li><li><a href="#A338" ref="log$=inpage&link_id=inpage">Site Description</a></li><li><a href="#A339" ref="log$=inpage&link_id=inpage">Design and Implementation</a></li><li><a href="#A343" ref="log$=inpage&link_id=inpage">Retrieving Data</a></li><li><a href="#A353" ref="log$=inpage&link_id=inpage">Depositing Data</a></li><li><a href="#A356" ref="log$=inpage&link_id=inpage">Search and Integration</a></li><li><a href="#A359" ref="log$=inpage&link_id=inpage">Example of Retrieving Data</a></li><li><a href="#A365" ref="log$=inpage&link_id=inpage">Future Directions</a></li><li><a href="#A367" ref="log$=inpage&link_id=inpage">Frequently Asked Questions</a></li><li><a href="#A394" ref="log$=inpage&link_id=inpage">Acknowledgments</a></li><li><a href="#A395" ref="log$=inpage&link_id=inpage">Contributors</a></li><li><a href="#A397" ref="log$=inpage&link_id=inpage">References</a></li></ul></div></div><div class="portlet"><div class="portlet_head"><div class="portlet_title"><h3><span>Recent Activity</span></h3></div><a name="Shutter" sid="1" href="#" class="portlet_shutter" title="Show/hide content" remembercollapsed="true" pgsec_name="recent_activity" id="Shutter"></a></div><div class="portlet_content"><div xmlns:np="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="HTDisplay" class=""><div class="action"><a href="javascript:historyDisplayState('ClearHT')">Clear</a><a href="javascript:historyDisplayState('HTOff')" class="HTOn">Turn Off</a><a href="javascript:historyDisplayState('HTOn')" class="HTOff">Turn On</a></div><ul id="activity"><li class="ra_rcd ralinkpopper two_line"><a class="htb ralinkpopperctrl" ref="log$=activity&linkpos=1" href="/portal/utils/pageresolver.fcgi?recordid=67c8067bb70fbb1960ffc425">The Gene Expression Omnibus (GEO): A Gene Expression and Hybridization Repositor...</a><div class="ralinkpop offscreen_noflow">The Gene Expression Omnibus (GEO): A Gene Expression and Hybridization Repository - The NCBI Handbook<div class="brieflinkpopdesc"></div></div><div class="tertiary"></div></li><li class="ra_rcd ralinkpopper two_line"><a class="htb ralinkpopperctrl" ref="log$=activity&linkpos=2" href="/portal/utils/pageresolver.fcgi?recordid=67c80679d5edb449bf3daf33">GenBank: The Nucleotide Sequence Database - The NCBI Handbook</a><div class="ralinkpop offscreen_noflow">GenBank: The Nucleotide Sequence Database - The NCBI Handbook<div class="brieflinkpopdesc"></div></div><div class="tertiary"></div></li><li class="ra_rcd ralinkpopper two_line"><a class="htb ralinkpopperctrl" ref="log$=activity&linkpos=3" href="/portal/utils/pageresolver.fcgi?recordid=67c80676feee5b00acf9e97e">Gene: A Directory of Genes - The NCBI Handbook</a><div class="ralinkpop offscreen_noflow">Gene: A Directory of Genes - The NCBI Handbook<div class="brieflinkpopdesc"></div></div><div class="tertiary"></div></li><li class="ra_rcd ralinkpopper two_line"><a class="htb ralinkpopperctrl" ref="log$=activity&linkpos=4" href="/portal/utils/pageresolver.fcgi?recordid=67c80675b70fbb1960ff8ec9">The Entrez Search and Retrieval System - The NCBI Handbook</a><div class="ralinkpop offscreen_noflow">The Entrez Search and Retrieval System - The NCBI Handbook<div class="brieflinkpopdesc"></div></div><div class="tertiary"></div></li><li class="ra_rcd ralinkpopper two_line"><a class="htb ralinkpopperctrl" ref="log$=activity&linkpos=5" href="/portal/utils/pageresolver.fcgi?recordid=67c806676d1ec11b6f58f4c5">The BLAST Sequence Analysis Tool - The NCBI Handbook</a><div class="ralinkpop offscreen_noflow">The BLAST Sequence Analysis Tool - The NCBI Handbook<div class="brieflinkpopdesc"></div></div><div class="tertiary"></div></li></ul><p class="HTOn">Your browsing activity is empty.</p><p class="HTOff">Activity recording is turned off.</p><p id="turnOn" class="HTOff"><a href="javascript:historyDisplayState('HTOn')">Turn recording back on</a></p><a class="seemore" href="/sites/myncbi/recentactivity">See more...</a></div></div></div>
|
||
|
||
<!-- Custom content below discovery portlets -->
|
||
<div class="col7">
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
<!-- Custom content after all -->
|
||
<div class="col8">
|
||
|
||
</div>
|
||
<div class="col9">
|
||
|
||
</div>
|
||
|
||
<script type="text/javascript" src="/corehtml/pmc/js/jquery.scrollTo-1.4.2.js"></script>
|
||
<script type="text/javascript">
|
||
(function($){
|
||
$('.skiplink').each(function(i, item){
|
||
var href = $($(item).attr('href'));
|
||
href.attr('tabindex', '-1').addClass('skiptarget'); // ensure the target can receive focus
|
||
$(item).on('click', function(event){
|
||
event.preventDefault();
|
||
$.scrollTo(href, 0, {
|
||
onAfter: function(){
|
||
href.focus();
|
||
}
|
||
});
|
||
});
|
||
});
|
||
})(jQuery);
|
||
</script>
|
||
</div>
|
||
<div class="bottom">
|
||
|
||
<div id="NCBIFooter_dynamic">
|
||
<!--<component id="Breadcrumbs" label="breadcrumbs"/>
|
||
<component id="Breadcrumbs" label="helpdesk"/>-->
|
||
|
||
</div>
|
||
|
||
<div class="footer" id="footer">
|
||
<section class="icon-section">
|
||
<div id="icon-section-header" class="icon-section_header">Follow NCBI</div>
|
||
<div class="grid-container container">
|
||
<div class="icon-section_container">
|
||
<a class="footer-icon" id="footer_twitter" href="https://twitter.com/ncbi" aria-label="Twitter"><svg xmlns="http://www.w3.org/2000/svg" data-name="Layer 1" viewBox="0 0 300 300">
|
||
<defs>
|
||
<style>
|
||
.cls-11 {
|
||
fill: #737373;
|
||
}
|
||
</style>
|
||
</defs>
|
||
<title>Twitter</title>
|
||
<path class="cls-11" d="M250.11,105.48c-7,3.14-13,3.25-19.27.14,8.12-4.86,8.49-8.27,11.43-17.46a78.8,78.8,0,0,1-25,9.55,39.35,39.35,0,0,0-67,35.85,111.6,111.6,0,0,1-81-41.08A39.37,39.37,0,0,0,81.47,145a39.08,39.08,0,0,1-17.8-4.92c0,.17,0,.33,0,.5a39.32,39.32,0,0,0,31.53,38.54,39.26,39.26,0,0,1-17.75.68,39.37,39.37,0,0,0,36.72,27.3A79.07,79.07,0,0,1,56,223.34,111.31,111.31,0,0,0,116.22,241c72.3,0,111.83-59.9,111.83-111.84,0-1.71,0-3.4-.1-5.09C235.62,118.54,244.84,113.37,250.11,105.48Z">
|
||
</path>
|
||
</svg></a>
|
||
<a class="footer-icon" id="footer_facebook" href="https://www.facebook.com/ncbi.nlm" aria-label="Facebook"><svg xmlns="http://www.w3.org/2000/svg" data-name="Layer 1" viewBox="0 0 300 300">
|
||
<title>Facebook</title>
|
||
<path class="cls-11" d="M210.5,115.12H171.74V97.82c0-8.14,5.39-10,9.19-10h27.14V52l-39.32-.12c-35.66,0-42.42,26.68-42.42,43.77v19.48H99.09v36.32h27.24v109h45.41v-109h35Z">
|
||
</path>
|
||
</svg></a>
|
||
<a class="footer-icon" id="footer_linkedin" href="https://www.linkedin.com/company/ncbinlm" aria-label="LinkedIn"><svg xmlns="http://www.w3.org/2000/svg" data-name="Layer 1" viewBox="0 0 300 300">
|
||
<title>LinkedIn</title>
|
||
<path class="cls-11" d="M101.64,243.37H57.79v-114h43.85Zm-22-131.54h-.26c-13.25,0-21.82-10.36-21.82-21.76,0-11.65,8.84-21.15,22.33-21.15S101.7,78.72,102,90.38C102,101.77,93.4,111.83,79.63,111.83Zm100.93,52.61A17.54,17.54,0,0,0,163,182v61.39H119.18s.51-105.23,0-114H163v13a54.33,54.33,0,0,1,34.54-12.66c26,0,44.39,18.8,44.39,55.29v58.35H198.1V182A17.54,17.54,0,0,0,180.56,164.44Z">
|
||
</path>
|
||
</svg></a>
|
||
<a class="footer-icon" id="footer_github" href="https://github.com/ncbi" aria-label="GitHub"><svg xmlns="http://www.w3.org/2000/svg" data-name="Layer 1" viewBox="0 0 300 300">
|
||
<defs>
|
||
<style>
|
||
.cls-11,
|
||
.cls-12 {
|
||
fill: #737373;
|
||
}
|
||
|
||
.cls-11 {
|
||
fill-rule: evenodd;
|
||
}
|
||
</style>
|
||
</defs>
|
||
<title>GitHub</title>
|
||
<path class="cls-11" d="M151.36,47.28a105.76,105.76,0,0,0-33.43,206.1c5.28,1,7.22-2.3,7.22-5.09,0-2.52-.09-10.85-.14-19.69-29.42,6.4-35.63-12.48-35.63-12.48-4.81-12.22-11.74-15.47-11.74-15.47-9.59-6.56.73-6.43.73-6.43,10.61.75,16.21,10.9,16.21,10.9,9.43,16.17,24.73,11.49,30.77,8.79,1-6.83,3.69-11.5,6.71-14.14C108.57,197.1,83.88,188,83.88,147.51a40.92,40.92,0,0,1,10.9-28.39c-1.1-2.66-4.72-13.42,1-28,0,0,8.88-2.84,29.09,10.84a100.26,100.26,0,0,1,53,0C198,88.3,206.9,91.14,206.9,91.14c5.76,14.56,2.14,25.32,1,28a40.87,40.87,0,0,1,10.89,28.39c0,40.62-24.74,49.56-48.29,52.18,3.79,3.28,7.17,9.71,7.17,19.58,0,14.15-.12,25.54-.12,29,0,2.82,1.9,6.11,7.26,5.07A105.76,105.76,0,0,0,151.36,47.28Z">
|
||
</path>
|
||
<path class="cls-12" d="M85.66,199.12c-.23.52-1.06.68-1.81.32s-1.2-1.06-.95-1.59,1.06-.69,1.82-.33,1.21,1.07.94,1.6Zm-1.3-1">
|
||
</path>
|
||
<path class="cls-12" d="M90,203.89c-.51.47-1.49.25-2.16-.49a1.61,1.61,0,0,1-.31-2.19c.52-.47,1.47-.25,2.17.49s.82,1.72.3,2.19Zm-1-1.08">
|
||
</path>
|
||
<path class="cls-12" d="M94.12,210c-.65.46-1.71,0-2.37-.91s-.64-2.07,0-2.52,1.7,0,2.36.89.65,2.08,0,2.54Zm0,0"></path>
|
||
<path class="cls-12" d="M99.83,215.87c-.58.64-1.82.47-2.72-.41s-1.18-2.06-.6-2.7,1.83-.46,2.74.41,1.2,2.07.58,2.7Zm0,0">
|
||
</path>
|
||
<path class="cls-12" d="M107.71,219.29c-.26.82-1.45,1.2-2.64.85s-2-1.34-1.74-2.17,1.44-1.23,2.65-.85,2,1.32,1.73,2.17Zm0,0">
|
||
</path>
|
||
<path class="cls-12" d="M116.36,219.92c0,.87-1,1.59-2.24,1.61s-2.29-.68-2.3-1.54,1-1.59,2.26-1.61,2.28.67,2.28,1.54Zm0,0">
|
||
</path>
|
||
<path class="cls-12" d="M124.42,218.55c.15.85-.73,1.72-2,1.95s-2.37-.3-2.52-1.14.73-1.75,2-2,2.37.29,2.53,1.16Zm0,0"></path>
|
||
</svg></a>
|
||
<a class="footer-icon" id="footer_blog" href="https://ncbiinsights.ncbi.nlm.nih.gov/" aria-label="Blog">
|
||
<svg xmlns="http://www.w3.org/2000/svg" id="Layer_1" data-name="Layer 1" viewBox="0 0 40 40">
|
||
<defs><style>.cls-1{fill:#737373;}</style></defs>
|
||
<title>NCBI Insights Blog</title>
|
||
<path class="cls-1" d="M14,30a4,4,0,1,1-4-4,4,4,0,0,1,4,4Zm11,3A19,19,0,0,0,7.05,15a1,1,0,0,0-1,1v3a1,1,0,0,0,.93,1A14,14,0,0,1,20,33.07,1,1,0,0,0,21,34h3a1,1,0,0,0,1-1Zm9,0A28,28,0,0,0,7,6,1,1,0,0,0,6,7v3a1,1,0,0,0,1,1A23,23,0,0,1,29,33a1,1,0,0,0,1,1h3A1,1,0,0,0,34,33Z"></path>
|
||
</svg>
|
||
</a>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
|
||
<section class="container-fluid bg-primary">
|
||
<div class="container pt-5">
|
||
<div class="row mt-3">
|
||
<div class="col-lg-3 col-12">
|
||
<p><a class="text-white" href="https://www.nlm.nih.gov/socialmedia/index.html">Connect with NLM</a></p>
|
||
<ul class="list-inline social_media">
|
||
<li class="list-inline-item"><a href="https://twitter.com/NLM_NIH" aria-label="Twitter" target="_blank" rel="noopener noreferrer"><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.1" x="0px" y="0px" viewBox="0 0 249 249" style="enable-background:new 0 0 249 249;" xml:space="preserve">
|
||
<style type="text/css">
|
||
.st20 {
|
||
fill: #FFFFFF;
|
||
}
|
||
|
||
.st30 {
|
||
fill: none;
|
||
stroke: #FFFFFF;
|
||
stroke-width: 8;
|
||
stroke-miterlimit: 10;
|
||
}
|
||
</style>
|
||
<title>Twitter</title>
|
||
<g>
|
||
<g>
|
||
<g>
|
||
<path class="st20" d="M192.9,88.1c-5,2.2-9.2,2.3-13.6,0.1c5.7-3.4,6-5.8,8.1-12.3c-5.4,3.2-11.4,5.5-17.6,6.7 c-10.5-11.2-28.1-11.7-39.2-1.2c-7.2,6.8-10.2,16.9-8,26.5c-22.3-1.1-43.1-11.7-57.2-29C58,91.6,61.8,107.9,74,116 c-4.4-0.1-8.7-1.3-12.6-3.4c0,0.1,0,0.2,0,0.4c0,13.2,9.3,24.6,22.3,27.2c-4.1,1.1-8.4,1.3-12.5,0.5c3.6,11.3,14,19,25.9,19.3 c-11.6,9.1-26.4,13.2-41.1,11.5c12.7,8.1,27.4,12.5,42.5,12.5c51,0,78.9-42.2,78.9-78.9c0-1.2,0-2.4-0.1-3.6 C182.7,97.4,189.2,93.7,192.9,88.1z"></path>
|
||
</g>
|
||
</g>
|
||
<circle class="st30" cx="124.4" cy="128.8" r="108.2"></circle>
|
||
</g>
|
||
</svg></a></li>
|
||
<li class="list-inline-item"><a href="https://www.facebook.com/nationallibraryofmedicine" aria-label="Facebook" rel="noopener noreferrer" target="_blank">
|
||
<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.1" x="0px" y="0px" viewBox="0 0 249 249" style="enable-background:new 0 0 249 249;" xml:space="preserve">
|
||
<style type="text/css">
|
||
.st10 {
|
||
fill: #FFFFFF;
|
||
}
|
||
|
||
.st110 {
|
||
fill: none;
|
||
stroke: #FFFFFF;
|
||
stroke-width: 8;
|
||
stroke-miterlimit: 10;
|
||
}
|
||
</style>
|
||
<title>Facebook</title>
|
||
<g>
|
||
<g>
|
||
<path class="st10" d="M159,99.1h-24V88.4c0-5,3.3-6.2,5.7-6.2h16.8V60l-24.4-0.1c-22.1,0-26.2,16.5-26.2,27.1v12.1H90v22.5h16.9 v67.5H135v-67.5h21.7L159,99.1z"></path>
|
||
</g>
|
||
</g>
|
||
<circle class="st110" cx="123.6" cy="123.2" r="108.2"></circle>
|
||
</svg>
|
||
</a></li>
|
||
<li class="list-inline-item"><a href="https://www.youtube.com/user/NLMNIH" aria-label="Youtube" target="_blank" rel="noopener noreferrer"><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.1" x="0px" y="0px" viewBox="0 0 249 249" style="enable-background:new 0 0 249 249;" xml:space="preserve">
|
||
<title>Youtube</title>
|
||
<style type="text/css">
|
||
.st4 {
|
||
fill: none;
|
||
stroke: #FFFFFF;
|
||
stroke-width: 8;
|
||
stroke-miterlimit: 10;
|
||
}
|
||
|
||
.st5 {
|
||
fill: #FFFFFF;
|
||
}
|
||
</style>
|
||
<circle class="st4" cx="124.2" cy="123.4" r="108.2"></circle>
|
||
<g transform="translate(0,-952.36218)">
|
||
<path class="st5" d="M88.4,1037.4c-10.4,0-18.7,8.3-18.7,18.7v40.1c0,10.4,8.3,18.7,18.7,18.7h72.1c10.4,0,18.7-8.3,18.7-18.7 v-40.1c0-10.4-8.3-18.7-18.7-18.7H88.4z M115.2,1058.8l29.4,17.4l-29.4,17.4V1058.8z"></path>
|
||
</g>
|
||
</svg></a></li>
|
||
</ul>
|
||
</div>
|
||
<div class="col-lg-3 col-12">
|
||
<p class="address_footer text-white">National Library of Medicine<br />
|
||
<a href="https://www.google.com/maps/place/8600+Rockville+Pike,+Bethesda,+MD+20894/@38.9959508,-77.101021,17z/data=!3m1!4b1!4m5!3m4!1s0x89b7c95e25765ddb:0x19156f88b27635b8!8m2!3d38.9959508!4d-77.0988323" class="text-white" target="_blank" rel="noopener noreferrer">8600 Rockville Pike<br />
|
||
Bethesda, MD 20894</a></p>
|
||
</div>
|
||
<div class="col-lg-3 col-12 centered-lg">
|
||
<p><a href="https://www.nlm.nih.gov/web_policies.html" class="text-white">Web Policies</a><br />
|
||
<a href="https://www.nih.gov/institutes-nih/nih-office-director/office-communications-public-liaison/freedom-information-act-office" class="text-white">FOIA</a><br />
|
||
<a href="https://www.hhs.gov/vulnerability-disclosure-policy/index.html" class="text-white" id="vdp">HHS Vulnerability Disclosure</a></p>
|
||
</div>
|
||
<div class="col-lg-3 col-12 centered-lg">
|
||
<p><a class="supportLink text-white" href="https://support.nlm.nih.gov/">Help</a><br />
|
||
<a href="https://www.nlm.nih.gov/accessibility.html" class="text-white">Accessibility</a><br />
|
||
<a href="https://www.nlm.nih.gov/careers/careers.html" class="text-white">Careers</a></p>
|
||
</div>
|
||
</div>
|
||
<div class="row">
|
||
<div class="col-lg-12 centered-lg">
|
||
<nav class="bottom-links">
|
||
<ul class="mt-3">
|
||
<li>
|
||
<a class="text-white" href="//www.nlm.nih.gov/">NLM</a>
|
||
</li>
|
||
<li>
|
||
<a class="text-white" href="https://www.nih.gov/">NIH</a>
|
||
</li>
|
||
<li>
|
||
<a class="text-white" href="https://www.hhs.gov/">HHS</a>
|
||
</li>
|
||
<li>
|
||
<a class="text-white" href="https://www.usa.gov/">USA.gov</a>
|
||
</li>
|
||
</ul>
|
||
</nav>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<script type="text/javascript" src="/portal/portal3rc.fcgi/rlib/js/InstrumentOmnitureBaseJS/InstrumentNCBIConfigJS/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js?v=1"> </script>
|
||
<script type="text/javascript" src="/portal/portal3rc.fcgi/static/js/hfjs2.js"> </script>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<!--/.page-->
|
||
</div>
|
||
<!--/.wrap-->
|
||
</div><!-- /.twelve_col -->
|
||
</div>
|
||
<!-- /.grid -->
|
||
|
||
<span class="PAFAppResources"></span>
|
||
|
||
<!-- BESelector tab -->
|
||
|
||
|
||
|
||
<noscript><img alt="statistics" src="/stat?jsdisabled=true&ncbi_db=books&ncbi_pdid=book-part&ncbi_acc=NBK21093&ncbi_domain=handbook&ncbi_report=record&ncbi_type=fulltext&ncbi_objectid=&ncbi_pcid=/NBK21093/&ncbi_pagename=The Gene Expression Omnibus (GEO): A Gene Expression and Hybridization Repository - The NCBI Handbook - NCBI Bookshelf&ncbi_bookparttype=chapter&ncbi_app=bookshelf" /></noscript>
|
||
|
||
|
||
<!-- usually for JS scripts at page bottom -->
|
||
<!--<component id="PageFixtures" label="styles"></component>-->
|
||
|
||
|
||
<!-- CE8B5AF87C7FFCB1_0191SID /projects/books/PBooks@9.11 portal106 v4.1.r689238 Tue, Oct 22 2024 16:10:51 -->
|
||
<span id="portal-csrf-token" style="display:none" data-token="CE8B5AF87C7FFCB1_0191SID"></span>
|
||
|
||
<script type="text/javascript" src="//static.pubmed.gov/portal/portal3rc.fcgi/4216699/js/3879255/4121861/3501987/4008961/3893018/3821238/4062932/4209313/4212053/4076480/3921943/3400083/3426610.js" snapshot="books"></script></body>
|
||
</html> |