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GenVarX.blade.php
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GenVarX.blade.php
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@php
include resource_path() . '/views/system/config.blade.php';
$organism = $info['organism'];
$gene_array = $info['gene_array'];
$cnvr_array = $info['cnvr_array'];
$binding_TF_array = $info['binding_TF_array'];
$chromosome_array = $info['chromosome_array'];
@endphp
@extends('system.header')
@section('content')
<div class="title1">Genomic Variations Explorer</div>
<br />
<h2><b>Promoter Search</b></h2>
<table width="100%" cellspacing="14" cellpadding="14">
<tr>
<td width="50%" align="center" valign="top" style="border:1px solid #999999; padding:10px; background-color:#f8f8f8; text-align:left;">
<form action="{{ route('system.tools.GenVarX.viewPromotersByGenes', ['organism'=>$organism]) }}" method="get" target="_blank">
<h2>Search by Gene IDs</h2><br />
<label for="gene1"><b>Gene IDs:</b></label><br />
<span style="font-size:10pt">
(eg
@foreach($gene_array as $gene)
{{ $gene->Gene }}
@endforeach
)
</span><br />
<textarea id="gene1" name="gene1" rows="10" cols="40"></textarea>
<br /><br />
<label for="upstream_length_1"><b>Upstream length (bp):</b></label>
<span style="font-size:10pt">(eg 2000)</span>
<input type="text" id="upstream_length_1" name="upstream_length_1" size="40">
<br /><br />
<input type="submit" value="Search">
</form>
</td>
<td width="50%" align="center" valign="top" style="border:1px solid #999999; padding:10px; background-color:#f8f8f8; text-align:left;">
<form action="{{ route('system.tools.GenVarX.viewPromotersByBindingTFs', ['organism'=>$organism]) }}" method="get" target="_blank">
<h2>Search by Binding TFs</h2><br />
<label for="bindingTF1"><b>Binding TFs:</b></label><br />
<span style="font-size:10pt">
(eg
@foreach($binding_TF_array as $binding_TF)
{{ $binding_TF->Motif }}
@endforeach
)
</span><br />
<textarea id="bindingTF1" name="bindingTF1" rows="8" cols="40"></textarea>
<br /><br />
<label for="chromosome1"><b>Gene Binding Chromosome:</b></label>
<select name="chromosome1" id="chromosome1">
@php
for ($i = 0; $i < count($chromosome_array); $i++) {
echo "<option value=\"" . $chromosome_array[$i]->Chromosome . "\">" . $chromosome_array[$i]->Chromosome . "</option>";
}
@endphp
</select>
<br /><br />
<label for="upstream_length_1"><b>Upstream length (bp):</b></label>
<span style="font-size:10pt">(eg 2000)</span>
<input type="text" id="upstream_length_1" name="upstream_length_1" size="40">
<br /><br />
<input type="submit" value="Search">
</form>
</td>
</tr>
</table>
<br /><br />
<h2><b>Copy Number Variation Search</b></h2>
<table width="100%" cellspacing="14" cellpadding="14">
<tr>
<td width="50%" align="center" valign="top" style="border:1px solid #999999; padding:10px; background-color:#f8f8f8; text-align:left;">
<form action="{{ route('system.tools.GenVarX.viewAllCNVByGenes', ['organism'=>$organism]) }}" method="get" target="_blank">
<h2>Search by Gene IDs</h2><br />
<label for="gene_id_2"><b>Gene IDs:</b></label><br />
<span style="font-size:10pt">
(eg
@foreach($gene_array as $gene)
{{ $gene->Gene }}
@endforeach
)
</span><br />
<textarea id="gene_id_2" name="gene_id_2" rows="15" cols="40"></textarea>
<br /><br />
<label for="cnv_data_option_2"><b>Data Option:</b></label>
<select name="cnv_data_option_2" id="cnv_data_option_2">
<option value="Individual_Hits">Individual Hits</option>
<option value="Consensus_Regions" selected>Consensus Regions</option>
</select>
<br /><br />
<input type="submit" value="Search">
</form>
</td>
<td width="50%" align="center" valign="top" style="border:1px solid #999999; padding:10px; background-color:#f8f8f8; text-align:left;">
<form action="{{ route('system.tools.GenVarX.viewAllCNVByAccessionAndCopyNumbers', ['organism'=>$organism]) }}" method="get" target="_blank">
<h2>Search By Accession and Copy Numbers</h2><br />
<label for="accession_2"><b>Accession:</b></label>
<span style="font-size:10pt">
(eg
@foreach($cnvr_array as $cnvr)
{{ $cnvr->Accession }}
@endforeach
)
</span><br />
<input type="text" id="accession_2" name="accession_2" size="50">
<br /><br />
<label for="copy_number_2"><b>Copy Numbers:</b></label><br />
<span style="font-size:10pt">
(eg CN0 CN1 CN2 CN3 CN4 CN5 CN6 CN7 CN8)
</span><br />
<textarea id="copy_number_2" name="copy_number_2" rows="12" cols="50"></textarea>
<br /><br />
<label for="cnv_data_option_2"><b>Data Option:</b></label>
<select name="cnv_data_option_2" id="cnv_data_option_2">
<option value="Individual_Hits">Individual Hits</option>
<option value="Consensus_Regions" selected>Consensus Regions</option>
</select>
<br /><br />
<input type="submit" value="Search">
</form>
</td>
</tr>
<tr>
<td width="50%" align="center" valign="top" style="border:1px solid #999999; padding:10px; background-color:#f8f8f8; text-align:left;">
<form action="{{ route('system.tools.GenVarX.viewAllCNVByChromosomeAndRegion', ['organism'=>$organism]) }}" method="get" target="_blank">
<h2>Search By Chromosome and Region</h2><br />
<label for="chromosome_2"><b>Chromosome:</b></label>
<span style="font-size:10pt">
(eg
@foreach($cnvr_array as $cnvr)
{{ $cnvr->Chromosome }}
@endforeach
)
</span>
<input type="text" id="chromosome_2" name="chromosome_2" size="40">
<br /><br />
<label for="position_start_2"><b>Starting Position:</b></label>
<span style="font-size:10pt">
(eg
@foreach($cnvr_array as $cnvr)
{{ $cnvr->Start }}
@endforeach
)
</span>
<input type="text" id="position_start_2" name="position_start_2" size="40">
<br /><br />
<label for="position_end_2"><b>Ending Position:</b></label>
<span style="font-size:10pt">
(eg
@foreach($cnvr_array as $cnvr)
{{ $cnvr->End }}
@endforeach
)
</span>
<input type="text" id="position_end_2" name="position_end_2" size="40">
<br /><br />
<label for="cnv_data_option_2"><b>Data Option:</b></label>
<select name="cnv_data_option_2" id="cnv_data_option_2">
<option value="Individual_Hits">Individual Hits</option>
<option value="Consensus_Regions" selected>Consensus Regions</option>
</select>
<br /><br />
<input type="submit" value="Search">
</form>
</td>
<td>
</td>
</tr>
</table>
<br />
<br />
<br />
<br />
<div style="margin-top:10px;" align="center">
<button type="submit" onclick="downloadUserManual()" style="margin-right:20px;">Download User Manual</button>
</div>
<br />
<br />
<br />
<br />
<div>
<table>
<tr>
<td width="50%" align="center" valign="top" style="border:1px solid #999999; padding:10px; background-color:#f8f8f8; text-align:left;">
<h2>If you use the Genomic Variations Explorer in your work, please cite:</h2>
<br />
<p> Chan YO, Biova J, Mahmood A, Dietz N, Bilyeu K, Škrabišová M, Joshi T: <b> Genomic Variations Explorer (GenVarX): A Toolset for Annotating Promoter and CNV Regions Using Genotypic and Phenotypic Differences. </b> Frontiers in Genetics 2023, In Press. </p>
</td>
</tr>
</table>
</div>
@endsection
@section('javascript')
<script type="text/javascript">
let gene_array = <?php echo json_encode($gene_array); ?>;
let binding_TF_array = <?php echo json_encode($binding_TF_array); ?>;
// Populate gene1 textarea placeholder
gene1_placeholder = "\nPlease separate each gene into a new line.\n\nExample:\n";
for (let i = 0; i < gene_array.length; i++) {
gene1_placeholder += gene_array[i]['Gene'] + "\n";
}
document.getElementById('gene1').placeholder = gene1_placeholder;
// Populate bindingTF1 textarea placeholder
bindingTF1_placeholder = "\nPlease separate each gene into a new line.\n\nExample:\n";
for (let i = 0; i < binding_TF_array.length; i++) {
bindingTF1_placeholder += binding_TF_array[i]['Motif'] + "\n";
}
document.getElementById('bindingTF1').placeholder = bindingTF1_placeholder;
// Populate gene2 textarea placeholder
gene2_placeholder = "\nPlease separate each gene into a new line.\n\nExample:\n";
for (let i = 0; i < gene_array.length; i++) {
gene2_placeholder += gene_array[i]['Gene'] + "\n";
}
document.getElementById('gene_id_2').placeholder = gene2_placeholder;
// Populate copy_number_2 textarea placeholder
copy_number2_placeholder = "\nPlease separate each copy number into a new line.\n\nExample:\nCN0\nCN1\nCN3\n\n * CN2 represents normal.\n** CN2 is not in individual hits dataset.\n";
document.getElementById('copy_number_2').placeholder = copy_number2_placeholder;
function downloadUserManual() {
let downloadAnchorNode = document.createElement('a');
downloadAnchorNode.setAttribute("href", "{{ asset('system/home/GenVarX/assets/User_Manual/GenVarX_User_Manual.pdf') }}");
downloadAnchorNode.setAttribute("target", "_blank");
document.body.appendChild(downloadAnchorNode); // required for firefox
downloadAnchorNode.click();
downloadAnchorNode.remove();
}
</script>
@endsection