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gene_search.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Gene Search - GExplore</title>
<link rel="stylesheet" href="style.css" type="text/css">
<link rel="icon" href="assets/favicon.png" type="image/png">
</head>
<body>
<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 <i>C. elegans</i> Genes</h2>
<p>The database contains all protein-coding genes from WormBase release 292 (April 2024).</p>
<p>Search for genes with particular protein domains, expression patterns, phenotypes, GO terms or human disease associations.</p>
<a href="help.html#gene-database" target="_blank">Learn More</a>
</div>
</div>
<!-- Wrapper for padding -->
<div class="search-param-wrapper">
<div id="search-param">
<div class="search-param-column-1">
<!-- Gene Name(s) 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 class="splice-variant-row">
<label for="longest-splice-variant">
<input type="checkbox" id="longest-splice-variant" name="longest-splice-variant" checked>
<h5>Only longest splice variant</h5>
</label>
</div>
</div>
<!-- Protein Domain group -->
<div class="form-group">
<h4>
Protein Domain
<img src="assets/help-icon.png" alt="Help" class="search-page-help-icon">
</h4>
<div class="search-page-help-content">
<p>Enter domain abbreviations or SMART/Pfam IDs to search for specific protein domains. Use wildcards, numbers, or combinations of both to define complex domain patterns. <a href="help.html#protein-domain-search-fields" target="_blank">Learn more</a></p>
</div>
<h5>Domain</h5>
<textarea id="protein-domain" name="protein-domain" placeholder="Enter a protein domain. Separate each additional domain with a comma."></textarea>
<h5>Domain Pattern</h5>
<textarea id="domain-pattern" name="domain-pattern"></textarea>
</div>
<!-- Expression Group -->
<div class="form-group">
<h4>
Expression
<img src="assets/help-icon.png" alt="Help" class="search-page-help-icon">
</h4>
<div class="search-page-help-content">
<p>The expression fields use WormBase-defined vocabularies with autosuggest functionality. The Genomic Studies field contains data from single-cell RNAseq or enrichment analysis studies. <a href="help.html#text-search-fields" target="_blank">Learn more</a></p>
</div>
<h5>Tissues and stages</h5>
<textarea id="expression" name="expression" placeholder="Enter a text. Separate each additional text with a comma."></textarea>
<h5>Tissues and stages (Genomic Studies)</h5>
<textarea id="genomic-studies" name="genomic-studies" placeholder="Enter a text. Separate each additional text with a comma."></textarea>
</div>
</div>
<div class="search-param-column-2">
<!-- Location group -->
<div class="form-group">
<h4>
Location
<img src="assets/help-icon.png" alt="Help" class="search-page-help-icon">
</h4>
<div class="search-page-help-content">
<p>The Genetic position represents a value that indicates the position relative to a reference point on the chromosome. The Nucleotide position outputs the start and end nucleotide positions, along with the strand direction.</p>
</div>
<div class="location-type-row">
<label for="genetic">
<input type="radio" id="genetic" name="location-type" value="genetic" checked>
<h5>Genetic</h5>
</label>
<label for="nucleotide">
<input type="radio" id="nucleotide" name="location-type" value="nucleotide">
<h5>Nucleotide</h5>
</label>
</div>
<div class="location-row">
<h5>Chromosome</h5>
<select id="chromosome" name="chromosome">
<option value="" disabled selected>-</option>
<option value="I">I</option>
<option value="II">II</option>
<option value="III">III</option>
<option value="IV">IV</option>
<option value="V">V</option>
<option value="X">X</option>
<option value="MtDNA">MtDNA</option>
</select>
</div>
<div class="location-row">
<h5>From</h5>
<input type="text" id="location-from" name="location-from">
<h5>To</h5>
<input type="text" id="location-to" name="location-to">
</div>
</div>
<!-- Description and Phenotype group -->
<div class="form-group">
<h4>
Description and Phenotype
<img src="assets/help-icon.png" alt="Help" class="search-page-help-icon">
</h4>
<div class="search-page-help-content">
<p>The description field includes both legacy and automated descriptions from WormBase. The phenotype field uses WormBase-defined vocabularies and features autosuggest. <a href="help.html#text-search-fields" target="_blank">Learn more</a></p>
</div>
<div class="label-container">
<h5>Description</h5>
<div class="checkbox-container">
<label for="legacy">
<input type="checkbox" id="legacy" name="description-type" checked>
<h5>Legacy</h5>
</label>
<label for="automated">
<input type="checkbox" id="automated" name="description-type" checked>
<h5>Automated</h5>
</label>
</div>
</div>
<textarea id="description" name="description"></textarea>
<div class="label-container">
<h5>Phenotype</h5>
<div class="checkbox-container">
<label for="mutant">
<input type="checkbox" id="mutant" name="phenotypes" checked>
<h5>Mutant</h5>
</label>
<label for="rnai">
<input type="checkbox" id="rnai" name="phenotypes" checked>
<h5>RNAi</h5>
</label>
</div>
</div>
<textarea id="phenotype" name="phenotype" placeholder="Enter a phenotype. Separate each additional phenotype with a comma."></textarea>
</div>
<!-- Gene Ontology Group -->
<div class="form-group">
<h4>
Gene Ontology Term
<img src="assets/help-icon.png" alt="Help" class="search-page-help-icon">
</h4>
<div class="search-page-help-content">
<p>This search field uses defined vocabularies and have an autosuggest function. <a href="help.html#text-search-fields" target="_blank">Learn more</a></p>
</div>
<textarea id="go-terms" name="go-terms" placeholder="Enter a GO term. Separate each additional term with a semicolon."></textarea>
</div>
<!-- Disease Association Group -->
<div class="form-group">
<h4>
Association to Disease Name
<img src="assets/help-icon.png" alt="Help" class="search-page-help-icon">
</h4>
<div class="search-page-help-content">
<p>This search field uses defined vocabularies and have an autosuggest function. <a href="help.html#text-search-fields" target="_blank">Learn more</a></p>
</div>
<textarea id="disease-associations" name="disease-associations" placeholder="Enter a disease name. Separate each additional name with a comma."></textarea>
</div>
</div>
</div>
</div>
<div class="form-actions">
<button type="reset">Clear</button>
<button type="submit" id="search-button" disabled>Search</button>
</div>
</div>
</div>
<!-- Main JavaScript file -->
<script src="script.js"></script>
<!-- Autosuggest JavaScript files -->
<script src="javascript/autosuggest_list_domains.js"></script>
<script src="javascript/autosuggest_list_phenotype.js"></script>
<script src="javascript/autosuggest_list_expression.js"></script>
<script src="javascript/autosuggest_list_GOterms.js"></script>
<script src="javascript/autosuggest_list_disease.js"></script>
</body>
</html>