541 lines
43 KiB
Text
541 lines
43 KiB
Text
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml">
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<head>
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<title>GEO2R - GEO - NCBI</title>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<meta name="author" content="geo"/>
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<meta name="keywords" content="NCBI, national institutes of health, nih, database, archive, central, bioinformatics, biomedicine, geo, gene, expression, omnibus, chips, microarrays, oligonucleotide, array, sage, CGH"/>
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<meta name="description" content="Gene Expression Omnibus (GEO) is a database repository of high throughput gene expression data and hybridization arrays, chips, microarrays."/>
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<meta name="ncbidialog" content="draggable: true"/>
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<meta name="ncbi_app" content="geo" />
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<meta name="ncbi_pdid" content="geo2r" />
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<script type="text/javascript">
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window.ncbi_startTime = new Date();
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</script>
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<script type="text/javascript" src="/geo/js/jquery.min.js"></script>
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<script type="text/javascript" src="/geo/js/jquery.cookie.js"></script>
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<script type="text/javascript" src="/geo/js/jquery-ui.min.js"></script>
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<script type="text/javascript" src="/geo/js/dd_menu.js"></script>
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<script type="text/javascript" src="/geo/js/login.js"></script>
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<script type="text/javascript" src="/geo/js/jquery.tablesorter.js"></script>
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<script type="text/javascript" src="/geo/js/jquery.tableselector.js"></script>
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<script type="text/javascript" src="/geo/js/jquery.dropdownChecklist.js"></script>
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<script type="text/javascript" src="geo2r.js"></script>
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<script type="text/javascript" src="geo2r_annotationDefaults.js"></script>
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<script type="text/javascript">
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jQuery.getScript("/core/alerts/alerts.js", function () {
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galert(['#crumbs_login_bar', 'body > *:nth-child(1)'])
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});
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</script>
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<link rel="shortcut icon" href="/geo/img/OmixIconBare.ico"/>
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<link rel="stylesheet" type="text/css" href="/geo/css/geo.css"/>
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<link rel="stylesheet" type="text/css" href="960grid.css"/>
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<link rel="stylesheet" type="text/css" href="geo2r.css"/>
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<link rel="stylesheet" href="/geo/css/jquery-ui.min.css">
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<!--link rel="stylesheet" type="text/css" href="glimma.min.css"/-->
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</head>
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<body class="g2r">
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<div id="all">
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<div id="page">
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<div id="header">
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<div id="ncbi_logo">
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<a href="/">
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<img src="/geo/img/ncbi_logo.gif" alt="NCBI Logo"/>
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</a>
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</div>
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<div id="geo_logo">
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<a href="/geo/"><img src="/geo/img/geo_main.gif" alt="GEO Logo"/></a>
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</div>
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</div>
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<div id="nav_bar">
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<ul id="geo_nav_bar">
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<li><a href="#">GEO Publications</a>
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<ul class="sublist">
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<li><a href="/geo/info/GEOHandoutFinal.pdf">Handout</a></li>
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<li><a href="/pmc/articles/PMC10767856/">NAR 2024 (latest)</a></li>
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<li><a href="/pmc/articles/PMC99122/">NAR 2002 (original)</a></li>
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<li><a href="/pmc/?term=10767856,4944384,3531084,3341798,3013736,2686538,2270403,1669752,1619900,1619899,539976,99122">All publications</a></li>
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</ul>
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</li>
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<li><a href="/geo/info/faq.html">FAQ</a></li>
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<li><a href="/geo/info/MIAME.html" title="Minimum Information About a Microarray Experiment">MIAME</a></li>
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<li><a href="mailto:geo@ncbi.nlm.nih.gov">Email GEO</a></li>
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</ul>
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</div>
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<div id="crumbs_login_bar">
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<a href="/" title="NCBI home page">NCBI</a> »
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<a href="/geo/" title="GEO home page" id="curr_page">GEO</a> »
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<span id="view"><a href="/geo/geo2r/" title="GEO2R home page">GEO2R</a></span>
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<span id="curr_acc"></span>
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<span id="login_status">
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<a href="/geo/submitter/" title="Click here to login. You need to do this only if you want to edit the contact information, submit data, see your unreleased data, or work with data already submitted by you. You do not need to login if you are here just to browse through public holdings">Login</a>
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</span>
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</div>
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<div class="plotContent" id="plotContent">
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<div class="container_12 showgrid1">
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<div class="grid_12">
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<noscript>
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<div id="noScript" class="clear">
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<p class="highlight"> <strong>Warning:</strong> This tool requires JavaScript to function. <a href="https://www.google.com/support/adsense/bin/answer.py?answer=12654" title="Learn how to enable JavaScript" target="_blank">Learn how to enable javascript</a> </p>
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</div>
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</noscript>
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<div class="grid_121 rightColumn o1mega">
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<div class="pContent">
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<div class="plotForm">
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<form target="_blank" name="plotOptions" method="get" id="plotOptions" enctype="application/x-www-form-urlencoded" action="/geo/geo2r/">
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<p id="instr">
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Use GEO2R to compare two or more groups of Samples in order to identify genes that are
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differentially expressed across experimental conditions.
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Results are presented as a table of genes ordered by significance.
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<a href="/geo/info/geo2r.html" target="_blank">Full instructions</a>
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<a href="https://youtu.be/9RyWjzSnaE0" target="_blank" title="Tutorial video"><img id = "yt_icon" src= "/geo/img/yt_icon.png" alt="Tutorial video"/></a>
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</p>
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<div>
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<div>
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<div class="left"><span class="formeltitle formel">GEO accession</span></div>
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<div id="accOption-cell" class="left formel">
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<div class="input_wrapper">
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<input type="search" value="" name="gse" id="accOption" class="clearable"
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title="Enter a valid GEO accession"/>
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<a href="#" class="button secondary" id="setacc">Set</a>
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</div>
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</div>
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<div id="seriesTitle" class="formel"></div>
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<div id="rnaseq_label" class="hide">
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RNA-seq Series analysis <a href="/geo/info/geo2r.html#rnaseq" class="help_link" target="_blank">?</a>
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<span class="beta" id="beta_label">BETA</span>
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</div>
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</div>
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<div id="platformOptionsRow" class="clear hilite">
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<div class="left"><span class="formeltitle">Platform</span></div>
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<div>
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<select name="gpl" id="platformOptions" class="required" title="Select a platform">
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<option value="">Select a platform</option>
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</select>
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</div>
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</div>
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</div>
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<div class="formel togglerCont clear hide" id="sampOptions">
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<div id="sampOptions">
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<h6 class="steps">
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<a id="sampOptionsTitle" href="#sampOptionsBody">Samples</a>
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<span id="totalsDisplay"></span>
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</h6>
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<div id="sampOptionsBody" class="ui-widget" style="display:none">
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<div class="sampleSelector"></div>
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</div>
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<div id="samplesController"></div>
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</div>
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</div>
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<div class="formel clear" id="testOptions">
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<div class="defaultOptions">
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<div id="options_tabs">
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<ul class="ui-tabs-nav ui-helper-reset ui-helper-clearfix ui-widget-header ui-corner-all">
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<li class="ui-state-default ui-corner-top"><a href="#top_genes" id="top_genes_tab">GEO2R</a></li>
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<li class="ui-state-default ui-corner-top"><a href="#options" id="options_tab">Options</a></li>
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<li class="ui-state-default ui-corner-top"><a href="#profile_data" id="profile_data_tab">Profile graph</a></li>
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<li class="ui-state-default ui-corner-top"><a href="#r_script" id="r_script_tab">R script</a></li>
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</ul>
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<div id="top_genes">
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<h4><a id = "quickStartTitle" href='#introTxt'><span id="quickStartTitleContent">Quick start</span></a></h4>
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<div id="introTxt" style="display:none">
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<ul>
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<li>
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Specify a GEO Series accession and a Platform if prompted.
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</li>
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<li>
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Click 'Define groups' and enter names for the groups of Samples you plan to compare,
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e.g., test and control.
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</li>
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<li>
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Assign Samples to each group.
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Highlight Sample rows then click the group name to assign those Samples to the group.
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Use the Sample metadata (title, source and characteristics) columns to help determine which Samples belong to which group.
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</li>
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<li>
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Click 'Analyze' to perform the calculation with default settings.
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</li>
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<li>
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You may change settings in the Options tab.
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</li>
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</ul>
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<p><a href="/geo/info/geo2r.html#how_to_use" target="_blank">How to use</a></p>
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</div>
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<p id = "log_trans_warn" class="highlight hidden">
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Log-transformation has been applied to the data. You can change this in the Options tab.
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</p>
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<span id="recalc_msg">
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<a id="getGeneExpressionData" class="button submitbutton" title="Run the differential expression analysis. Distribution plots can be viewed without specifying Sample groups.">Analyze</a><span id="recalc_text" class="hidden"> if you changed any options.</span>
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</span>
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<h4 id="visualize_title" class="hidden">Visualization <sup><a class="helper" href="#" title="Plots with a green border have additional interactive features">?</a></sup></h4>
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<div id="visualize" class="hidden"></div>
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<div id = "results_table" class="hidden">
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<h4 id="table_title">Top differentially expressed genes <sup><a class="helper" href="#" title="This is the top 250 table">?</a></sup></h4>
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<a href="#" id="getAllGeneExpressionData">Download full table</a>
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<a href="#" id="restore_cols">Show all columns</a>
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<a href="#" id="set_geo2r_cols" class="hide">
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Select columns
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</a>
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<div style="display: none;" title="Set columns" id="set_geo2r_cols_dialog">
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<div id="check_all_opts"><label><input type="checkbox" id="pl_all" name="pl_all"/><span class="example">Check all</span></label></div>
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<div id="cols_wrapper">
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<div id="set_columns">
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<h4>Data columns</h4>
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<input type="checkbox" name="threshold" value="adj.P.Val" id="adj-P-Val" checked="checked"/><label for="adj-P-Val">Adj P-value</label><br/>
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<input type="checkbox" name="threshold" value="P.Value" id="P-Value" checked="checked"/><label for="P-Value">P-value</label><br/>
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<span id = "enable_col_chkbx" class="disabled">
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<input type="checkbox" name="threshold" value="t" id="t-statistic" disabled="disabled"/><label for="t-statistic">t-statistic</label><br/>
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<input type="checkbox" name="threshold" value="B" id="B-value" disabled="disabled"/><label for="B-value">B-value</label><br/>
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<input type="checkbox" name="threshold" value="logFC" id="logFC" disabled="disabled"/><label for="logFC">logFC</label><br/>
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</span>
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<span id = "disable_col_chkbx">
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<input type="checkbox" name="threshold" value="F" id="F-statistic" checked="checked"/><label for="F-statistic">F-statistic</label>
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</span>
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</div>
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<div id="pl_opts" class="pl_options">
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<h4>Annotation columns</h4>
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</div>
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</div>
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<div id="col_btns" class="">
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<a id="setColsBtn" class="button" href="#">Set</a>
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<a id="cancelColsBtn" class="button" href="#">Cancel</a>
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<a id="restoreColsBtn" class="button" href="#">Restore defaults</a>
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</div>
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<div id="cols_wrapper_rnaseq" style="display:none;">
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<div id="set_columns_rnaseq">
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<h4>Data columns</h4>
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<input type="checkbox" name="threshold" value="padj" id="padj" checked="checked"/><label for="padj">padj</label><br/>
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<input type="checkbox" name="threshold" value="pvalue" id="pvalue" checked="checked"/><label for="pvalue">pvalue</label><br/>
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<input type="checkbox" name="threshold" value="lfcSE" id="lfcSE" checked="checked"/><label for="lfcSE">lfcSE</label><br/>
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<input type="checkbox" name="threshold" value="stat" id="stat" checked="checked"/><label for="stat">stat</label><br/>
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<input type="checkbox" name="threshold" value="log2FoldChange" id="log2FoldChange" checked="checked"/><label for="log2FoldChange">log2FoldChange</label><br/>
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<input type="checkbox" name="threshold" value="baseMean" id="baseMean" checked="checked"/><label for="baseMean">baseMean</label><br/>
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</div>
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<div id="rnaseq_annot" class="select">
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<h4>Annotation columns</h4>
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<div class="pl_options">
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<ul>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="GeneID" name="columns" forTest="all" checked="checked" disabled="disabled"/>
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<span title="GeneID">GeneID</span></label>
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</span>
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</li>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="Symbol" name="columns" forTest="all" checked="checked"/>
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<span title="Symbol">Symbol</span></label>
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</span>
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</li>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="Description" name="columns" forTest="all" checked="checked"/>
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<span title="Description">Description</span></label>
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</span>
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</li>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="Synonyms" name="columns" forTest="all"/>
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<span title="Synonyms">Synonyms</span></label>
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</span>
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</li>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="GeneType" name="columns" forTest="all"/>
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<span title="GeneType">GeneType</span></label>
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</span>
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</li>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="EnsemblGeneID" name="columns" forTest="all"/>
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<span title="EnsemblGeneID">EnsemblGeneID</span></label>
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</span>
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</li>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="Status" name="columns" forTest="all"/>
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<span title="Status">Status</span></label>
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</span>
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</li>
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</ul>
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<ul>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="ChrAcc" name="columns" forTest="all"/>
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<span title="ChrAcc">ChrAcc</span></label>
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</span>
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</li>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="ChrStart" name="columns" forTest="all"/>
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<span title="ChrStart">ChrStart</span></label>
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</span>
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</li>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="ChrStop" name="columns" forTest="all"/>
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<span title="ChrStop">ChrStop</span></label>
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</span>
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</li>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="Orientation" name="columns" forTest="all"/>
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<span title="Orientation">Orientation</span></label>
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</span>
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</li>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="Length" name="columns" forTest="all"/>
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<span title="Length">Length</span></label>
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</span>
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</li>
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</ul>
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<ul>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="GOFunctionID" name="columns" forTest="all"/>
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<span title="GOFunctionID">GOFunctionID</span></label>
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</span>
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</li>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="GOProcessID" name="columns" forTest="all"/>
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<span title="GOProcessID">GOProcessID</span></label>
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</span>
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</li>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="GOComponentID" name="columns" forTest="all"/>
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<span title="GOComponentID">GOComponentID</span></label>
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</span>
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</li>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="GOFunction" name="columns" forTest="all"/>
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<span title="GOFunction">GOFunction</span></label>
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</span>
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</li>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="GOProcess" name="columns" forTest="all"/>
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<span title="GOProcess">GOProcess</span></label>
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</span>
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</li>
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<li>
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<span class="testColOpt">
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<label><input type="checkbox" value="GOComponent" name="columns" forTest="all"/>
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<span title="GOComponent">GOComponent</span></label>
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</span>
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</li>
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</ul>
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</div>
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</div>
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</div>
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</div>
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</div>
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<div id="exprDataPanel"></div>
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</div>
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<div id="options" class="editAdjustTitleContent">
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<div id="adj_sel" class="left">
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<p>
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Apply adjustment to the P-values.
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<a href="/geo/info/geo2r.html#adjustment_references" target="_blank">More...</a>
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</p>
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<input type="radio" name="padj" id="padj-fdr" value="fdr" checked="checked"/>
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<label for="padj-fdr">Benjamini & Hochberg (False discovery rate)</label><br/>
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<input type="radio" name="padj" id="padj-BY" value="BY"/>
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<label for="padj-BY">Benjamini & Yekutieli</label><br/>
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<input type="radio" name="padj" id="padj-bonferroni" value="bonferroni"/>
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<label for="padj-bonferroni">Bonferroni</label><br/>
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<span class="rnaseq_only">
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<input type="radio" name="padj" id="padj-hochberg" value="hochberg"/>
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<label for="padj-hochberg">Hochberg</label><br/>
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</span>
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<input type="radio" name="padj" id="padj-holm" value="holm"/>
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<label for="padj-holm">Holm</label><br/>
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<span class="rnaseq_only">
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<input type="radio" name="padj" id="padj-hommel" value="hommel"/>
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<label for="padj-hommel">Hommel</label><br/>
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</span>
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</div>
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<div id="log_trans_sel" class="left">
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<p>
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Apply log transformation to the data.
|
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<a href="/geo/info/geo2r.html#logtransform" target="_blank">More...</a>
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</p>
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<input type="radio" name="log" id="log-auto" value="auto" checked="checked"/>
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<label for="log-auto">Auto-detect</label><br/>
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<input type="radio" name="log" id="log-yes" value="yes"/>
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<label for="log-yes">Yes</label><br/>
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<input type="radio" name="log" id="log-no" value="no"/>
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<label for="log-no">No</label><br/><br/>
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<p>
|
|
Apply limma precision weights (vooma).
|
|
<a href="/geo/info/geo2r.html#vooma" target="_blank">More...</a>
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</p>
|
|
<input type="radio" name="voom" id="voom-yes" value="yes"/>
|
|
<label for="voom-yes">Yes</label><br/>
|
|
<input type="radio" name="voom" id="voom-no" value="no" checked="checked"/>
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<label for="voom-no">No</label><br/><br/>
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<p>
|
|
Force normalization.
|
|
<a href="/geo/info/geo2r.html#normalization" target="_blank">More...</a>
|
|
</p>
|
|
<input type="radio" name="normalize" id="norm-yes" value="yes"/>
|
|
<label for="norm-yes">Yes</label><br/>
|
|
<input type="radio" name="normalize" id="norm-no" value="no" checked="checked"/>
|
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<label for="norm-no">No</label><br/><br/>
|
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</div>
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|
|
|
<div id="platformDefaultOptions" class="left">
|
|
<div id="choose_annot_type"><p>Category of Platform annotation to display on results.</p></div>
|
|
</div>
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|
|
|
<div id="plotsOptions" class="left">
|
|
<p>
|
|
Plot displays.
|
|
<a href="/geo/info/geo2r.html#visualization" target="_blank">More...</a>
|
|
</p>
|
|
<div class="inline_inputs">
|
|
<p id="pval_label">Significance level cut-off<br/>(enter number between 0 and 1)</p>
|
|
<input type="text" name="pval" id="pval" value="0.05"></input>
|
|
</div>
|
|
<div class="inline_inputs">
|
|
<p id="lfc_label">Log 2 fold change threshold</p>
|
|
<input type="text" name="lfc" id="lfc" value="0"></input>
|
|
</div>
|
|
<p id="contrasts_label">
|
|
Volcano and Mean-difference plot contrasts (select up to 5)<br/>
|
|
<span id="contrast_counter_message" style="display:none"><span id="contrast_counter">0</span> selected (<a href="" id="clear_contrasts">clear</a>)</span>
|
|
<span id="contrast_empty_message">Define two or more groups to select contrasts.</span>
|
|
</p>
|
|
<div id="contrasts">
|
|
|
|
</div>
|
|
</div>
|
|
|
|
<div class="options_msg">
|
|
If you edit <em>Options</em> after performing an analysis, click <em>Reanalyze</em> to apply the edits:
|
|
</div>
|
|
<a id="reanalyze_button" class="button submitbutton" title="Run the differential expression analysis. Distribution plots can be viewed without specifying Sample groups.">Reanalyze</a>
|
|
|
|
</div>
|
|
|
|
<div id="profile_data">
|
|
<div id="profile_data_container">
|
|
<label for="get_profile_graph">Enter ID: </label>
|
|
<div class="input_wrapper">
|
|
<input type="search" id="get_profile_graph" class="clearable"/>
|
|
<a href="#" class="button secondary" id="get_profile_graph_btn">Set</a>
|
|
</div>
|
|
<span id="platform_data"><a href="/geo/download/?format=file&type=rnaseq_counts&file=Human.GRCh38.p13.annot.tsv.gz" target="_blank" id="rnaseq_download_annot" class="hide">Download gene annotation</a></span>
|
|
|
|
<div id="profile_graph"></div>
|
|
|
|
<p>
|
|
This tab allows you to view a specific gene expression profile graph by entering the corresponding identifier from the ID column of the Platform record. This feature does not perform any calculations; it merely displays the expression values of the gene across Samples. Sample groups may or may not be defined for this feature to work.
|
|
</p>
|
|
</div>
|
|
<div id="profile_data_container_rnaseq" class="hide">
|
|
<label for="get_profile_graph_rnaseq" class="rnaseq_data">Enter gene symbol or ID: </label>
|
|
<div class="input_wrapper">
|
|
<input type="search" id="get_profile_graph_rnaseq" class="clearable"/>
|
|
<a href="#" class="button secondary" id="get_profile_graph_btn_rnaseq">Set</a>
|
|
</div>
|
|
<span id="platform_data_rnaseq"><a href="/geo/download/?format=file&type=rnaseq_counts&file=Human.GRCh38.p13.annot.tsv.gz" target="_blank">Download gene annotation</a></span>
|
|
|
|
<div id="profile_graph_rnaseq"></div>
|
|
|
|
<p>
|
|
This tab allows you to view a specific gene expression profile graph by entering a gene symbol or the corresponding
|
|
identifier from the GeneID column of the <a href="/geo/download/?format=file&type=rnaseq_counts&file=Human.GRCh38.p13.annot.tsv.gz">Human.GRCh38.p13.annot.tsv.gz</a>
|
|
annotation file. This feature does not perform any calculations; it merely displays the
|
|
<a href="/geo/info/rnaseqcounts.html#norm" target="_blank">TPM normalized</a> expression values of the gene across Samples.
|
|
Sample groups may or may not be defined for this feature to work.
|
|
</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
|
|
<div id="r_script">
|
|
|
|
<div id="r_script_content"></div>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
</form>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="footer">
|
|
<span class="helpbar">|<a
|
|
href="https://www.nlm.nih.gov"> NLM </a>|<a
|
|
href="https://www.nih.gov"> NIH </a>|<a
|
|
href="mailto:geo@ncbi.nlm.nih.gov"> Email GEO </a>|<a
|
|
href="/geo/info/disclaimer.html"> Disclaimer </a>|<a
|
|
href="https://www.nlm.nih.gov/accessibility.html"> Accessibility </a>|<a
|
|
href="https://www.hhs.gov/vulnerability-disclosure-policy/index.html"> HHS Vulnerability Disclosure </a>|
|
|
</span>
|
|
</div>
|
|
|
|
|
|
<div id="contextMenu"></div>
|
|
<div id="loading"><img src="/geo/img/loading_blue.gif" alt="loading" width="24" height="24"/> Loading... </div>
|
|
</div></div>
|
|
<script type="text/javascript" src="https://www.ncbi.nlm.nih.gov/portal/portal3rc.fcgi/rlib/js/InstrumentOmnitureBaseJS/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js"></script>
|
|
<script type="text/javascript" src="/core/pinger/pinger.js"></script>
|
|
</body>
|
|
</html>
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