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expression_stage_search.html
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expression_stage_search.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Stage Expression Search - GExplore</title>
<link rel="stylesheet" href="style.css" type="text/css">
<link rel="icon" href="assets/favicon.png" type="image/png">
</head>
<body id="stage-expression-page">
<div class="search-wrapper">
<div id="header">
<a href="home.html">
<img src="assets/GExplore_logo.png" alt="GExplore Logo" class="logo">
</a>
<div id="topnav">
<ul>
<li class="active"><a href="home.html"><span class="text">Home</span></a></li>
<li><a><span class="text">Search</span> <span class="angle"></span></a>
<ul class="dropdown">
<li><a href="gene_search.html">Genes</a></li>
<li><a href="mutation_search.html">Mutations</a></li>
<li><a href="protein_search.html">Proteins</a></li>
<li><a href="expression_stage_search.html">Stage Expressions</a></li>
<li><a href="expression_tissue_search.html">Tissue Expressions</a></li>
<li><a href="expression_embryo_search.html">Embryo Expressions</a></li>
</ul>
</li>
<li><a><span class="text">Tools</span> <span class="angle"></span></a>
<ul class="dropdown">
<li><a href="compare.html">Compare</a></li>
<li><a href="convert.html">Convert</a></li>
</ul>
</li>
<li><a href="help.html"><span class="text">Help</span></a></li>
<li><a href="about.html"><span class="text">About</span></a></li>
</ul>
</div>
</div>
<div id="search-vertical-content">
<!-- Hero Section -->
<div id="search-intro">
<div class="search-hero-section">
<h2>Search for Stage-Specific Expression Profiles</h2>
<p>text</p>
<p>text</p>
<a href="help.html#expression-stages" target="_blank">Learn More</a>
</div>
</div>
<!-- Wrapper for padding -->
<div class="search-param-wrapper">
<div id="search-param">
<div class="search-param-column-full">
<!-- Gene Name Group -->
<div class="form-group">
<h4>
Gene Name
<img src="assets/help-icon.png" alt="Help" class="search-page-help-icon">
</h4>
<div class="search-page-help-content">
<p>Enter gene identifiers like WormBase gene IDs, locus names, or gene/protein sequence names. You can use commas, spaces, or wildcards to search multiple genes at once. <a href="help.html#gene-search-field" target="_blank">Learn more</a></p>
</div>
<textarea id="gene-names" name="gene-names" placeholder="Enter a gene name. Separate each additional name with a comma."></textarea>
</div>
</div>
<div class="search-param-column-full">
<h4>
Stage Expression Profiles
<img src="assets/help-icon.png" alt="Help" class="search-page-help-icon">
</h4>
<div class="search-page-help-content search-for-expression-help-content">
<p>
<strong>Time:</strong> Development post P<sub>0</sub> division based on the times given by <a href="https://www.sciencedirect.com/science/article/abs/pii/0012160677901580?via%3Dihub" target="_blank">Sulston et al.</a>
<br />
<strong>dcpm:</strong> Depth of coverage per million reads. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142569/" target="_blank">Suppl. Methods in Gerstein et al.</a>
</p>
</div>
</div>
<div class="search-param-column-full">
<!-- Time or Stage and Expression Fields -->
<div class="form-group">
<div class="two-column-wrapper">
<div class="form-column">
<h4>Time or Stage</h4>
<select name="el1" id="el1">
<option value="e0" selected="selected">4-cell stage</option>
<option value="e1" >44 min</option>
<option value="e2" >83 min (~ 27-cell)</option>
<option value="e3" >122 min (~ 53-cell)</option>
<option value="e4" >161 min (~ 128 AB stage)</option>
<option value="e5" >199 min</option>
<option value="e6" >238 min</option>
<option value="e7" >277 min</option>
<option value="e8" >316 min</option>
<option value="e9" >355 min</option>
<option value="e10" >393 min</option>
<option value="e11" >432 min (~2-fold)</option>
<option value="e12" >471 min</option>
<option value="e13" >510 min (3-fold)</option>
<option value="e14" >548 min</option>
<option value="e15" >587 min </option>
<option value="e16" >626 min</option>
<option value="e17" >665 min</option>
<option value="L1" >L1</option>
<option value="L2" >L2</option>
<option value="L3" >L3</option>
<option value="L4" >L4</option>
<option value="YA" >young adult</option>
<option value="DauerEntry" >dauer entry</option>
<option value="Dauer" >dauer </option>
<option value="DauerExit" >dauer exit</option>
<option value="L4soma" >L4 soma</option>
<option value="L4male" >L4 male</option>
<option value="AdultSterile" >sterile adult</option>
<option value="AdultGonad" >adult gonad</option>
</select>
<select name="el2" id="el2">
<option value="e0">4-cell stage</option>
<option value="e1" >44 min</option>
<option value="e2" >83 min (~ 27-cell)</option>
<option value="e3" >122 min (~ 53-cell)</option>
<option value="e4" >161 min (~ 128 AB stage)</option>
<option value="e5" >199 min</option>
<option value="e6" >238 min</option>
<option value="e7" >277 min</option>
<option value="e8" >316 min</option>
<option value="e9" >355 min</option>
<option value="e10" >393 min</option>
<option value="e11" selected="selected">432 min (~2-fold)</option>
<option value="e12" >471 min</option>
<option value="e13" >510 min (3-fold)</option>
<option value="e14" >548 min</option>
<option value="e15" >587 min </option>
<option value="e16" >626 min</option>
<option value="e17" >665 min</option>
<option value="L1" >L1</option>
<option value="L2" >L2</option>
<option value="L3" >L3</option>
<option value="L4" >L4</option>
<option value="YA" >young adult</option>
<option value="DauerEntry" >dauer entry</option>
<option value="Dauer" >dauer </option>
<option value="DauerExit" >dauer exit</option>
<option value="L4soma" >L4 soma</option>
<option value="L4male" >L4 male</option>
<option value="AdultSterile" >sterile adult</option>
<option value="AdultGonad" >adult gonad</option>
</select>
<select name="el3" id="el3">
<option value="e0" >4-cell stage</option>
<option value="e1" >44 min</option>
<option value="e2" >83 min (~ 27-cell)</option>
<option value="e3" >122 min (~ 53-cell)</option>
<option value="e4" >161 min (~ 128 AB stage)</option>
<option value="e5" >199 min</option>
<option value="e6" >238 min</option>
<option value="e7" >277 min</option>
<option value="e8" >316 min</option>
<option value="e9" >355 min</option>
<option value="e10" >393 min</option>
<option value="e11" >432 min (~2-fold)</option>
<option value="e12" >471 min</option>
<option value="e13" >510 min (3-fold)</option>
<option value="e14" >548 min</option>
<option value="e15" >587 min </option>
<option value="e16" >626 min</option>
<option value="e17" >665 min</option>
<option value="L1" >L1</option>
<option value="L2" selected="selected">L2</option>
<option value="L3" >L3</option>
<option value="L4" >L4</option>
<option value="YA" >young adult</option>
<option value="DauerEntry" >dauer entry</option>
<option value="Dauer" >dauer </option>
<option value="DauerExit" >dauer exit</option>
<option value="L4soma" >L4 soma</option>
<option value="L4male" >L4 male</option>
<option value="AdultSterile" >sterile adult</option>
<option value="AdultGonad" >adult gonad</option>
</select>
<select name="el4" id="el4">
<option value="e0" >4-cell stage</option>
<option value="e1" >44 min</option>
<option value="e2" >83 min (~ 27-cell)</option>
<option value="e3" >122 min (~ 53-cell)</option>
<option value="e4" >161 min (~ 128 AB stage)</option>
<option value="e5" >199 min</option>
<option value="e6" >238 min</option>
<option value="e7" >277 min</option>
<option value="e8" >316 min</option>
<option value="e9" >355 min</option>
<option value="e10" >393 min</option>
<option value="e11" >432 min (~2-fold)</option>
<option value="e12" >471 min</option>
<option value="e13" >510 min (3-fold)</option>
<option value="e14" >548 min</option>
<option value="e15" >587 min </option>
<option value="e16" >626 min</option>
<option value="e17" >665 min</option>
<option value="L1" >L1</option>
<option value="L2" >L2</option>
<option value="L3" >L3</option>
<option value="L4" >L4</option>
<option value="YA" >young adult</option>
<option value="DauerEntry" >dauer entry</option>
<option value="Dauer" selected="selected">dauer </option>
<option value="DauerExit" >dauer exit</option>
<option value="L4soma" >L4 soma</option>
<option value="L4male" >L4 male</option>
<option value="AdultSterile" >sterile adult</option>
<option value="AdultGonad" >adult gonad</option>
</select>
<select name="el5" id="el5">
<option value="e0" >4-cell stage</option>
<option value="e1" >44 min</option>
<option value="e2" >83 min (~ 27-cell)</option>
<option value="e3" >122 min (~ 53-cell)</option>
<option value="e4" >161 min (~ 128 AB stage)</option>
<option value="e5" >199 min</option>
<option value="e6" >238 min</option>
<option value="e7" >277 min</option>
<option value="e8" >316 min</option>
<option value="e9" >355 min</option>
<option value="e10" >393 min</option>
<option value="e11" >432 min (~2-fold)</option>
<option value="e12" >471 min</option>
<option value="e13" >510 min (3-fold)</option>
<option value="e14" >548 min</option>
<option value="e15" >587 min </option>
<option value="e16" >626 min</option>
<option value="e17" >665 min</option>
<option value="L1" >L1</option>
<option value="L2" >L2</option>
<option value="L3" >L3</option>
<option value="L4" >L4</option>
<option value="YA" >young adult</option>
<option value="DauerEntry" >dauer entry</option>
<option value="Dauer" >dauer </option>
<option value="DauerExit" >dauer exit</option>
<option value="L4soma" >L4 soma</option>
<option value="L4male" selected="selected">L4 male</option>
<option value="AdultSterile" >sterile adult</option>
<option value="AdultGonad" >adult gonad</option>
</select>
</div>
<div class="form-column">
<h4>Expression (dcpm)</h4>
<input name="ev1" type="text" value="">
<input name="ev2" type="text" value="">
<input name="ev3" type="text" value="">
<input name="ev4" type="text" value="">
<input name="ev5" type="text" value="">
</div>
</div>
</div>
</div>
<!-- Notes -->
<div class="search-param-column-full">
<div class="more-explanation">
<ul>
<li>In the expression field to specify a range use <code>>0.5</code> or <code><0.5</code> or <code>2-10</code>.</li>
<li>To compare relative expression levels between stages specify x-fold difference and stage for comparison in the following way: <code>>10x adult</code> translates into 'more than 10-fold higher than in the 'adult' stage' (compared to the stage specified by the value in the pull-down menu).</li>
<li>Use values from the drop-down menu (e.g. <code>44 min</code>, or <code>Dauer entry</code>) to specify times or stages.</li>
</ul>
</div>
</div>
<!-- Sample Profiles Section -->
<div class="search-param-column-full">
<h4>
Sample Profiles
<img src="assets/help-icon.png" alt="Help" class="search-page-help-icon">
</h4>
<div class="search-page-help-content search-for-expression-help-content">
<p>The Sample Profile field offers three pre-defined profiles: Maternally Enriched, Early Embryo Enriched, and Male Enriched. Selecting any of these profiles will automatically populate the Time or Stage and Expression fields with appropriate values based on each profile’s criteria.</p>
</div>
<select name="profile" id="profile" onchange="insert_values()">
<option value="" disabled selected>Select a sample profile</option>
<option value="el1,e0,ev1,,el2,e11,ev2,,el3,L2,ev3,,el4,Dauer,ev4,,el5,L4male,ev5,,">-</option>
<option value="el1,YA,ev1,>2x L4,el2,e1,ev2,>2x 122 min,el3,e1,ev3,>0.3,el4,,ev4,,el5,,ev5,,">Maternally Enriched</option>
<option value="el1,e2,ev1,>0.3,el2,e1,ev2,<0.5x 83 min,el3,e2,ev3,>3x 548 min,el4,,ev4,,el5,,ev5,,">Early Embryo Enriched</option>
<option value="el1,L4male,ev1,>0.1,el2,L4male,ev2,>10x L3,el3,L4male,ev3,>5x Young Adult,el4,L4male,ev4,>3x 626 min,el5,L4male,ev5,>3x Dauer">Male Enriched</option>
</select>
<script type="text/javascript">
// Dr. Hutter's JS for sample profile input population
function insert_values() {
var a = document.getElementById('profile').value.split(',');
for (var i = 0; i < a.length; i += 2) {
var input = document.getElementsByName(a[i])[0];
input.value = a[i + 1];
// Added JS to activate the Search button with above code
// Manually trigger the input event to ensure it's detected
var event = new Event('input', {
'bubbles': true,
'cancelable': true
});
input.dispatchEvent(event);
}
// Call the checkFormFields function after populating the fields (this is in script.js file)
checkFormFields();
}
</script>
</div>
</div>
</div>
<div class="form-actions">
<button type="reset">Clear</button>
<button type="submit" id="search-button" disabled>Search</button>
</div>
</div>
</div>
<!-- JavaScript file -->
<script src="script.js"></script>
</body>
</html>