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include $this->__viewFile;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/second_navigation.ctp'
$dataForView = array(
'sidebar_info' => array(
'gene_id' => 'Prupe.4G206500',
'species' => 'ppe',
'gene_type' => 'coding',
'default_gf_type' => 'HOMFAM',
'gf_info' => array(
'has_gf' => true,
'gf_id' => 'HOM05D163621',
'num_genes' => array(
[maximum depth reached]
)
),
'has_msa' => false,
'has_tree' => false,
'igv_info' => array(
'genome' => array(
[maximum depth reached]
),
'annotation' => array(
[maximum depth reached]
),
'synteny_scores' => array(
[maximum depth reached]
)
)
),
'sidebar' => 'gene_sidebar',
'navigation_bar_info' => array(
'num_colinearity_runs' => (int) 1,
'num_colinearity_with_dating_runs' => (int) 0,
'only_lvl2' => true,
'num_functional_clusters_runs' => (int) 6,
'has_pan_genomes' => false,
'has_blast_db' => true
),
'sidebar_information' => array(
'type' => 'gene_id',
'id' => 'Prupe.4G206500'
),
'external_sources_settings' => array(
'present' => 'TRUE',
'URL' => array(
'https' => '//bioinformatics.psb.ugent.be/plaza/external_sources/data/get_data_content'
)
),
'function_table_settings' => array(
'binding_sites' => 'true',
'go' => 'true',
'interpro' => 'true',
'mapman' => 'true'
),
'default_gf_type_id' => 'HOMFAM',
'annot' => array(
'gene_id' => 'Prupe.4G206500',
'species' => 'ppe',
'transcript' => 'Prupe.4G206500.1',
'coord_cds' => 'join(12888035..12888274)',
'start' => '12888035',
'stop' => '12888274',
'coord_transcript' => 'join(12888034..12888500)',
'seq' => 'ATGTGTACTTTTATTTCTAGAAAAACTATAAAAACTAAGTATGAAAAAAAAAAATTATCATTCGATTGGGTTGGTGAAACTGAAAACCATCAATTATTTGTTCTTTCCATAACTAAAGCAACGATCAAGACAAAAGTCTCAAAAACACAGCTTATTTACACACACACAGGCCAACAGAGAGGAATCGTAATCAGTCGTTTCTTGCCTCCTCTGATACCATACCAAGTAAAAGAGTCCTGA',
'strand' => 'positive',
'chr' => 'Pp04',
'type' => 'coding',
'check_transcript' => 'eq',
'check_protein' => 'eq',
'transl_table' => '1',
'common_name' => 'Prunus persica',
'tax_id' => '3760'
),
'is_transcription_factor' => false,
'duplication_info' => array(
'is_block' => (int) 0,
'is_tandem' => (int) 0,
'tandem_representative' => null,
'is_syntenic' => (int) 0,
'block' => (int) 0,
'tandem' => (int) 0,
'tandem_rep' => null
),
'gene_type_descriptions' => array(
'coding' => 'Coding gene',
'rna' => 'RNA gene',
'pseudo' => 'Pseudo gene',
'te' => 'Transposon'
),
'gene_descriptions' => array(
'ortholog' => array(
'is_ortholog' => true,
'content' => array(
[maximum depth reached]
),
'title' => 'Ortholog descriptions'
)
),
'gene_identifiers' => array(
(int) 0 => array(
'type' => 'id',
'value' => 'Prupe.4G206500.v2.1'
),
(int) 1 => array(
'type' => 'pacid',
'value' => '32091970'
)
),
'next_gene' => 'Prupe.4G206600',
'previous_gene' => 'Prupe.4G206400',
'splice_variants' => array(
(int) 0 => 'Prupe.4G206500.1'
),
'gene_families' => array(
'HOMFAM' => array(
'gf_id' => 'HOM05D163621',
'order' => '1',
'is_valid' => true,
'info' => array(
[maximum depth reached]
),
'profile' => array(
[maximum depth reached]
)
),
'ORTHOFAM' => array(
'gf_id' => 'ORTHO05D335230',
'order' => '2',
'is_valid' => true,
'info' => array(
[maximum depth reached]
),
'profile' => array(
[maximum depth reached]
)
)
),
'gene_id' => 'Prupe.4G206500',
'title_for_layout' => 'Dicots PLAZA 5.0 : gene pages',
'content_for_layout' => '
<h1>
<span class="dataTypeTitle">Gene:</span>
<span class="dataTitle">Prupe.4G206500</span>
</h1>
<!------------------------------------------------------------------------------------------------------------------>
<!-- General info layout -->
<h2>General Information</h2>
<div class="row">
<!-- first block : structural information -->
<div class="col-lg-4 col-md-12">
<h3>Structural Information</h3>
<ul class="list-group">
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Species</span>
<span class="ms-2 text-end text-break"><a href="/plaza.dev/_dev_instances/feedback/organism/view/ppe">Prunus persica</a></span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Gene Identifier</span>
<span class="ms-2 text-end text-break">Prupe.4G206500</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Transcript Identifier</span>
<span class="ms-2 text-end text-break">Prupe.4G206500.1</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Gene Type</span>
<span class="ms-2 text-end text-break">Coding gene</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Location</span>
<span class="ms-2 text-end text-break">Pp04 : 12888035-12888274 : positive</span>
</li>
</ul>
</div>
<!-- second block: gene family information -->
<div class="col-lg-4 col-md-12" id='family_information'>
<h3>Gene Family Information</h3>
<!-- Setup the navigation tabs-->
<ul class="nav nav-tabs">
<li class='nav-item'>
<a href='#GFTABHOMFAM' class='nav-link' data-bs-toggle='tab' style='margin-bottom:-2px'>Homologous GF</a>
</li>
<li class='nav-item'>
<a href='#GFTABORTHOFAM' class='nav-link' data-bs-toggle='tab' style='margin-bottom:-2px'>Orthologous GF</a>
</li>
</ul>
<!-- Setup the content for the navigation tabs -->
<div class='tab-content multitab-information'>
<div class='tab-pane' role='tabpanel' id='GFTABHOMFAM'>
<ul class="list-group mb-3" >
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="fw-bold">ID</span>
<span><a href="/plaza.dev/_dev_instances/feedback/gene_families/view/HOM05D163621" class="gf_id" data-id="HOM05D163621">HOM05D163621</a></span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class='fw-bold'>#Genes/#Species</span>
<span>1 / 1(orphan gene)</span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class="fw-bold">Phylogenetic origin</span>
<span class='gf_size_span'>
<span class='clade_specific_span' data-id='HOM05D163621'></span>
</span>
</li>
</ul>
</div>
<div class='tab-pane' role='tabpanel' id='GFTABORTHOFAM'>
<ul class="list-group mb-3" >
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="fw-bold">ID</span>
<span><a href="/plaza.dev/_dev_instances/feedback/gene_families/view/ORTHO05D335230" class="gf_id" data-id="ORTHO05D335230">ORTHO05D335230</a></span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class='fw-bold'>#Genes/#Species</span>
<span>1 / 1(orphan gene)</span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class="fw-bold">Phylogenetic origin</span>
<span class='gf_size_span'>
<span class='clade_specific_span' data-id='ORTHO05D335230'></span>
</span>
</li>
</ul>
</div>
</div>
</div>
<!-- third block : duplication information -->
<div class="col-lg-4 col-md-12" id="duplication_information">
<h3>Gene Duplication Information</h3>
<ul class="list-group">
</ul>
</div>
<!-- javascript for the content blocks in this row -->
<script type='text/javascript'>
//<![CDATA[
$(document).ready(function(){
//1) Disable display of gene family box if no gene families are defined
if($("#family_information ul:first li").length<1){$("#family_information").hide();}
//2) Set the "active" tab panes for the gene families to the first tab
$("#family_information ul.nav li.nav-item a.nav-link:first").addClass("active");
$("#family_information div.multitab-information div.tab-pane:first").addClass("show").addClass("active");
//3) Clade specificty analysis
$(".clade_specific_span").each(function (i, clade_specific_span) {
let gf_id = $(clade_specific_span).data('id');
let analyze_url = "/plaza.dev/_dev_instances/feedback/api/family_smallest_encompassing_clade" + "/" + gf_id;
let clade_url_base = "/plaza.dev/_dev_instances/feedback/organism/group";
jQuery.ajax({url: analyze_url,type: 'GET',dataType: 'json', success: function (data) {
$(clade_specific_span).html("<a href='" + clade_url_base + "/" + data.result + "'>" + data.result + "</a>");
}});
});
//4)Hide duplication panel if no duplication is present
if($("#duplication_information ul li").length<1){$("#duplication_information").hide();}
});
//]]>
</script>
</div> <!-- end div containing overview and family information-->
<!------------------------------------------------------------------------------------------------------------------>
<!-- row with the gene structure visualization -->
<div class="row">
<div class="col-lg-7 col-md-12 mb-5">
<div class="d-flex flex-row px-2">
<div class="d-flex align-items-center">
<a href="/plaza.dev/_dev_instances/feedback/genes/view/Prupe.4G206400"><i class="bi bi-chevron-left display-8"></i></a> </div>
<div id='gene-structure-draw-container' class='w-100 h-100' data-gene='Prupe.4G206500'></div>
<div class="d-flex align-items-center">
<a href="/plaza.dev/_dev_instances/feedback/genes/view/Prupe.4G206600"><i class="bi bi-chevron-right display-8"></i></a> </div>
</div>
</div>
<!-- Javascript code for the gene structure row/block -->
<script type='text/javascript'>
//<![CDATA[
$(document).ready(function(){
let gene_structure_url = '/plaza.dev/_dev_instances/feedback/genes/draw_gene_structure/Prupe.4G206500';
$.ajax({url:gene_structure_url,type:"GET",dataType: "html",success:function(data){
$("#gene-structure-draw-container").html(data);
}});
});
//]]>
</script>
</div>
<!------------------------------------------------------------------------------------------------------------------>
<!-- Identifiers and descriptions row -->
<h2>Labels</h2>
<div class="row mb-6">
<!-- Identifiers block -->
<div class="col-lg-4 col-md-12" id="identifier_col">
<h3>Identifiers</h3>
<ul class="list-group">
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class='fw-bold'>id</span>
<span>Prupe.4G206500.v2.1</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class='fw-bold'>pacid</span>
<span>32091970</span>
</li>
</ul>
</div>
<!-- Descriptions block -->
<div class="col-lg-8 col-md-12" id="descriptions_col">
<h3 id="description_header">Descriptions</h3>
<!-- setup the navigation tabs -->
<ul class="nav nav-tabs">
<li class='nav-item'>
<a href="#DESCTABortholog" style='margin-bottom:-2px' class="nav-link" data-bs-toggle='tab'>Ortholog descriptions</a>
</li>
</ul>
<!-- setup content for the navigation tabs -->
<div class='tab-content multitab-information'>
<div class="tab-pane" role="tabpanel" id="DESCTABortholog">
<ul class="list-group mb-3">
<li class="d-flex justify-content-between list-group-item list-group-item-light ortholog-description" data-id='ath'>
<span class='fw-bold'>Loading (ortholog descriptions from ath)... </span>
<span></span>
</li>
</ul>
</div>
</div>
</div>
<!-- javascript for the content blocks in this row -->
<script type='text/javascript'>
//<![CDATA[
$(document).ready(function(){
//1) Disable display of identifiers box if no external identifiers are defined
if($("#identifier_col ul:first li").length<1){$("#identifier_col").hide();}
//2)Hide description panel if no descriptions are present
if($("#descriptions_col ul:first li").length<1){$("#descriptions_col").hide();}
//3) Set the "active" tab panes for the gene families to the first tab
$("#descriptions_col ul.nav li.nav-item a.nav-link:first").addClass("active");
$("#descriptions_col div.multitab-information div.tab-pane:first").addClass("show").addClass("active");
//4) Get the descriptions of orthologs
$("li.ortholog-description").each(function(odi,odli){
let ortho_species = $(odli).data("id");
let ortho_desc_url = '/plaza.dev/_dev_instances/feedback/genes/get_best_ortholog_descriptions/ppe/Prupe.4G206500/'+ortho_species;
let gene_url_base = '/plaza.dev/_dev_instances/feedback/genes/view';
$.ajax({url:ortho_desc_url,type:"GET",dataType:"json",success:function(data){
if('error' in data){$(odli).html("<span class='fw-bold'>Error</span><span>"+data.error+"</span>");}
else if("result" in data){
//Empty current list
let parent_ul = $(odli).parent();
parent_ul.empty();
//Add multiple <li> entries
data['result'].forEach(function(entry){
let ortholog_entry = "<li class='d-flex justify-content-between list-group-item list-group-item-light'>"+
"<span><a href='"+gene_url_base+"/"+entry.ortholog+"' target='_blank'>"+entry.ortholog+"</a></span>"+
"<span>"+entry.description+"</span>"+
"</li>";
parent_ul.append(ortholog_entry);
});
}
else{$(odli).html("<span class='fw-bold'>Error</span><span>Unknown error</span>");}
}});
});
});
//]]>
</script>
</div>
<!-- end of labels presence check -->
<!------------------------------------------------------------------------------------------------------------------>
<!-- Functional Data Tabs -->
<h2>Functional Annotation</h2>
<ul class="nav nav-tabs" id="bottom_gene_nav_tabs">
<li class="nav-item">
<a href="#geneontology" class="nav-link active" data-bs-toggle="tab">GeneOntology</a>
</li>
<li class="nav-item">
<a href="#interpro" class="nav-link" data-bs-toggle="tab">Interpro</a>
</li>
<li class="nav-item">
<a href="#mapman" class="nav-link" data-bs-toggle="tab">Mapman</a>
</li>
<li class="nav-item">
<a href="#external_sources" class="nav-link" data-bs-toggle="tab">External sources</a>
</li>
</ul>
<div class="tab-content">
<div class="tab-pane show active" id="geneontology">
<div class="pt-3">
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/genegotable.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/publication_tooltips_TAIR.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/publication_tooltips_PMID.js"></script>
<div>
<span>No GO associations found for this gene.</span>
</div>
</div>
</div>
<div class="tab-pane" id="interpro">
<div class="panel-body">
<div class="col-lg-12 pt-3">
<div>
<span>No InterPro domains detected for this gene.</span>
</div>
</div>
</div>
</div>
<div class="tab-pane" id="mapman">
<div class="panel-body">
<div class="col-lg-12 pt-3">
<div>
<table class="table table-condensed table-hover">
<tr>
<th style='width:20%'>Mapman id</th>
<th style='width:80%'>Description</th>
</tr>
<tr>
<td><a href="/plaza.dev/_dev_instances/feedback/mapman/view/35.2">35.2</a></td>
<td>not assigned.not annotate</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
<script type="text/javascript">
//<![CDATA[
$(document).ready(function () {
var tooltipTriggerList = [].slice.call(document.querySelectorAll('[data-bs-toggle="tooltip"]'));
var tooltipList = tooltipTriggerList.map(function (tooltipTriggerEl) {
return new bootstrap.Tooltip(tooltipTriggerEl)
})
});
//]]>
</script>',
'scripts_for_layout' => ''
)
$sidebar_info = array(
'gene_id' => 'Prupe.4G206500',
'species' => 'ppe',
'gene_type' => 'coding',
'default_gf_type' => 'HOMFAM',
'gf_info' => array(
'has_gf' => true,
'gf_id' => 'HOM05D163621',
'num_genes' => array(
'num_genes' => '1',
'num_species' => '1'
)
),
'has_msa' => false,
'has_tree' => false,
'igv_info' => array(
'genome' => array(
'content' => array(
[maximum depth reached]
),
'index' => array(
[maximum depth reached]
),
'compressed_index' => array(
[maximum depth reached]
)
),
'annotation' => array(
'content' => array(
[maximum depth reached]
)
),
'synteny_scores' => array(
'content' => array(
[maximum depth reached]
)
)
)
)
$sidebar = 'gene_sidebar'
$navigation_bar_info = array(
'num_colinearity_runs' => (int) 1,
'num_colinearity_with_dating_runs' => (int) 0,
'only_lvl2' => true,
'num_functional_clusters_runs' => (int) 6,
'has_pan_genomes' => false,
'has_blast_db' => true
)
$sidebar_information = array(
'type' => 'gene_id',
'id' => 'Prupe.4G206500'
)
$external_sources_settings = array(
'present' => 'TRUE',
'URL' => array(
'https' => '//bioinformatics.psb.ugent.be/plaza/external_sources/data/get_data_content'
)
)
$function_table_settings = array(
'binding_sites' => 'true',
'go' => 'true',
'interpro' => 'true',
'mapman' => 'true'
)
$default_gf_type_id = 'HOMFAM'
$annot = array(
'gene_id' => 'Prupe.4G206500',
'species' => 'ppe',
'transcript' => 'Prupe.4G206500.1',
'coord_cds' => 'join(12888035..12888274)',
'start' => '12888035',
'stop' => '12888274',
'coord_transcript' => 'join(12888034..12888500)',
'seq' => 'ATGTGTACTTTTATTTCTAGAAAAACTATAAAAACTAAGTATGAAAAAAAAAAATTATCATTCGATTGGGTTGGTGAAACTGAAAACCATCAATTATTTGTTCTTTCCATAACTAAAGCAACGATCAAGACAAAAGTCTCAAAAACACAGCTTATTTACACACACACAGGCCAACAGAGAGGAATCGTAATCAGTCGTTTCTTGCCTCCTCTGATACCATACCAAGTAAAAGAGTCCTGA',
'strand' => 'positive',
'chr' => 'Pp04',
'type' => 'coding',
'check_transcript' => 'eq',
'check_protein' => 'eq',
'transl_table' => '1',
'common_name' => 'Prunus persica',
'tax_id' => '3760'
)
$is_transcription_factor = false
$duplication_info = array(
'is_block' => (int) 0,
'is_tandem' => (int) 0,
'tandem_representative' => null,
'is_syntenic' => (int) 0,
'block' => (int) 0,
'tandem' => (int) 0,
'tandem_rep' => null
)
$gene_type_descriptions = array(
'coding' => 'Coding gene',
'rna' => 'RNA gene',
'pseudo' => 'Pseudo gene',
'te' => 'Transposon'
)
$gene_descriptions = array(
'ortholog' => array(
'is_ortholog' => true,
'content' => array(
(int) 0 => 'ath'
),
'title' => 'Ortholog descriptions'
)
)
$gene_identifiers = array(
(int) 0 => array(
'type' => 'id',
'value' => 'Prupe.4G206500.v2.1'
),
(int) 1 => array(
'type' => 'pacid',
'value' => '32091970'
)
)
$next_gene = 'Prupe.4G206600'
$previous_gene = 'Prupe.4G206400'
$splice_variants = array(
(int) 0 => 'Prupe.4G206500.1'
)
$gene_families = array(
'HOMFAM' => array(
'gf_id' => 'HOM05D163621',
'order' => '1',
'is_valid' => true,
'info' => array(
'name' => 'Homologous gene family'
),
'profile' => array(
'num_genes' => '1',
'num_species' => '1'
)
),
'ORTHOFAM' => array(
'gf_id' => 'ORTHO05D335230',
'order' => '2',
'is_valid' => true,
'info' => array(
'name' => 'Orthologous gene family'
),
'profile' => array(
'num_genes' => '1',
'num_species' => '1'
)
)
)
$gene_id = 'Prupe.4G206500'
$title_for_layout = 'Dicots PLAZA 5.0 : gene pages'
$content_for_layout = '
<h1>
<span class="dataTypeTitle">Gene:</span>
<span class="dataTitle">Prupe.4G206500</span>
</h1>
<!------------------------------------------------------------------------------------------------------------------>
<!-- General info layout -->
<h2>General Information</h2>
<div class="row">
<!-- first block : structural information -->
<div class="col-lg-4 col-md-12">
<h3>Structural Information</h3>
<ul class="list-group">
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Species</span>
<span class="ms-2 text-end text-break"><a href="/plaza.dev/_dev_instances/feedback/organism/view/ppe">Prunus persica</a></span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Gene Identifier</span>
<span class="ms-2 text-end text-break">Prupe.4G206500</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Transcript Identifier</span>
<span class="ms-2 text-end text-break">Prupe.4G206500.1</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Gene Type</span>
<span class="ms-2 text-end text-break">Coding gene</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Location</span>
<span class="ms-2 text-end text-break">Pp04 : 12888035-12888274 : positive</span>
</li>
</ul>
</div>
<!-- second block: gene family information -->
<div class="col-lg-4 col-md-12" id='family_information'>
<h3>Gene Family Information</h3>
<!-- Setup the navigation tabs-->
<ul class="nav nav-tabs">
<li class='nav-item'>
<a href='#GFTABHOMFAM' class='nav-link' data-bs-toggle='tab' style='margin-bottom:-2px'>Homologous GF</a>
</li>
<li class='nav-item'>
<a href='#GFTABORTHOFAM' class='nav-link' data-bs-toggle='tab' style='margin-bottom:-2px'>Orthologous GF</a>
</li>
</ul>
<!-- Setup the content for the navigation tabs -->
<div class='tab-content multitab-information'>
<div class='tab-pane' role='tabpanel' id='GFTABHOMFAM'>
<ul class="list-group mb-3" >
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="fw-bold">ID</span>
<span><a href="/plaza.dev/_dev_instances/feedback/gene_families/view/HOM05D163621" class="gf_id" data-id="HOM05D163621">HOM05D163621</a></span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class='fw-bold'>#Genes/#Species</span>
<span>1 / 1(orphan gene)</span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class="fw-bold">Phylogenetic origin</span>
<span class='gf_size_span'>
<span class='clade_specific_span' data-id='HOM05D163621'></span>
</span>
</li>
</ul>
</div>
<div class='tab-pane' role='tabpanel' id='GFTABORTHOFAM'>
<ul class="list-group mb-3" >
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="fw-bold">ID</span>
<span><a href="/plaza.dev/_dev_instances/feedback/gene_families/view/ORTHO05D335230" class="gf_id" data-id="ORTHO05D335230">ORTHO05D335230</a></span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class='fw-bold'>#Genes/#Species</span>
<span>1 / 1(orphan gene)</span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class="fw-bold">Phylogenetic origin</span>
<span class='gf_size_span'>
<span class='clade_specific_span' data-id='ORTHO05D335230'></span>
</span>
</li>
</ul>
</div>
</div>
</div>
<!-- third block : duplication information -->
<div class="col-lg-4 col-md-12" id="duplication_information">
<h3>Gene Duplication Information</h3>
<ul class="list-group">
</ul>
</div>
<!-- javascript for the content blocks in this row -->
<script type='text/javascript'>
//<![CDATA[
$(document).ready(function(){
//1) Disable display of gene family box if no gene families are defined
if($("#family_information ul:first li").length<1){$("#family_information").hide();}
//2) Set the "active" tab panes for the gene families to the first tab
$("#family_information ul.nav li.nav-item a.nav-link:first").addClass("active");
$("#family_information div.multitab-information div.tab-pane:first").addClass("show").addClass("active");
//3) Clade specificty analysis
$(".clade_specific_span").each(function (i, clade_specific_span) {
let gf_id = $(clade_specific_span).data('id');
let analyze_url = "/plaza.dev/_dev_instances/feedback/api/family_smallest_encompassing_clade" + "/" + gf_id;
let clade_url_base = "/plaza.dev/_dev_instances/feedback/organism/group";
jQuery.ajax({url: analyze_url,type: 'GET',dataType: 'json', success: function (data) {
$(clade_specific_span).html("<a href='" + clade_url_base + "/" + data.result + "'>" + data.result + "</a>");
}});
});
//4)Hide duplication panel if no duplication is present
if($("#duplication_information ul li").length<1){$("#duplication_information").hide();}
});
//]]>
</script>
</div> <!-- end div containing overview and family information-->
<!------------------------------------------------------------------------------------------------------------------>
<!-- row with the gene structure visualization -->
<div class="row">
<div class="col-lg-7 col-md-12 mb-5">
<div class="d-flex flex-row px-2">
<div class="d-flex align-items-center">
<a href="/plaza.dev/_dev_instances/feedback/genes/view/Prupe.4G206400"><i class="bi bi-chevron-left display-8"></i></a> </div>
<div id='gene-structure-draw-container' class='w-100 h-100' data-gene='Prupe.4G206500'></div>
<div class="d-flex align-items-center">
<a href="/plaza.dev/_dev_instances/feedback/genes/view/Prupe.4G206600"><i class="bi bi-chevron-right display-8"></i></a> </div>
</div>
</div>
<!-- Javascript code for the gene structure row/block -->
<script type='text/javascript'>
//<![CDATA[
$(document).ready(function(){
let gene_structure_url = '/plaza.dev/_dev_instances/feedback/genes/draw_gene_structure/Prupe.4G206500';
$.ajax({url:gene_structure_url,type:"GET",dataType: "html",success:function(data){
$("#gene-structure-draw-container").html(data);
}});
});
//]]>
</script>
</div>
<!------------------------------------------------------------------------------------------------------------------>
<!-- Identifiers and descriptions row -->
<h2>Labels</h2>
<div class="row mb-6">
<!-- Identifiers block -->
<div class="col-lg-4 col-md-12" id="identifier_col">
<h3>Identifiers</h3>
<ul class="list-group">
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class='fw-bold'>id</span>
<span>Prupe.4G206500.v2.1</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class='fw-bold'>pacid</span>
<span>32091970</span>
</li>
</ul>
</div>
<!-- Descriptions block -->
<div class="col-lg-8 col-md-12" id="descriptions_col">
<h3 id="description_header">Descriptions</h3>
<!-- setup the navigation tabs -->
<ul class="nav nav-tabs">
<li class='nav-item'>
<a href="#DESCTABortholog" style='margin-bottom:-2px' class="nav-link" data-bs-toggle='tab'>Ortholog descriptions</a>
</li>
</ul>
<!-- setup content for the navigation tabs -->
<div class='tab-content multitab-information'>
<div class="tab-pane" role="tabpanel" id="DESCTABortholog">
<ul class="list-group mb-3">
<li class="d-flex justify-content-between list-group-item list-group-item-light ortholog-description" data-id='ath'>
<span class='fw-bold'>Loading (ortholog descriptions from ath)... </span>
<span></span>
</li>
</ul>
</div>
</div>
</div>
<!-- javascript for the content blocks in this row -->
<script type='text/javascript'>
//<![CDATA[
$(document).ready(function(){
//1) Disable display of identifiers box if no external identifiers are defined
if($("#identifier_col ul:first li").length<1){$("#identifier_col").hide();}
//2)Hide description panel if no descriptions are present
if($("#descriptions_col ul:first li").length<1){$("#descriptions_col").hide();}
//3) Set the "active" tab panes for the gene families to the first tab
$("#descriptions_col ul.nav li.nav-item a.nav-link:first").addClass("active");
$("#descriptions_col div.multitab-information div.tab-pane:first").addClass("show").addClass("active");
//4) Get the descriptions of orthologs
$("li.ortholog-description").each(function(odi,odli){
let ortho_species = $(odli).data("id");
let ortho_desc_url = '/plaza.dev/_dev_instances/feedback/genes/get_best_ortholog_descriptions/ppe/Prupe.4G206500/'+ortho_species;
let gene_url_base = '/plaza.dev/_dev_instances/feedback/genes/view';
$.ajax({url:ortho_desc_url,type:"GET",dataType:"json",success:function(data){
if('error' in data){$(odli).html("<span class='fw-bold'>Error</span><span>"+data.error+"</span>");}
else if("result" in data){
//Empty current list
let parent_ul = $(odli).parent();
parent_ul.empty();
//Add multiple <li> entries
data['result'].forEach(function(entry){
let ortholog_entry = "<li class='d-flex justify-content-between list-group-item list-group-item-light'>"+
"<span><a href='"+gene_url_base+"/"+entry.ortholog+"' target='_blank'>"+entry.ortholog+"</a></span>"+
"<span>"+entry.description+"</span>"+
"</li>";
parent_ul.append(ortholog_entry);
});
}
else{$(odli).html("<span class='fw-bold'>Error</span><span>Unknown error</span>");}
}});
});
});
//]]>
</script>
</div>
<!-- end of labels presence check -->
<!------------------------------------------------------------------------------------------------------------------>
<!-- Functional Data Tabs -->
<h2>Functional Annotation</h2>
<ul class="nav nav-tabs" id="bottom_gene_nav_tabs">
<li class="nav-item">
<a href="#geneontology" class="nav-link active" data-bs-toggle="tab">GeneOntology</a>
</li>
<li class="nav-item">
<a href="#interpro" class="nav-link" data-bs-toggle="tab">Interpro</a>
</li>
<li class="nav-item">
<a href="#mapman" class="nav-link" data-bs-toggle="tab">Mapman</a>
</li>
<li class="nav-item">
<a href="#external_sources" class="nav-link" data-bs-toggle="tab">External sources</a>
</li>
</ul>
<div class="tab-content">
<div class="tab-pane show active" id="geneontology">
<div class="pt-3">
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/genegotable.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/publication_tooltips_TAIR.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/publication_tooltips_PMID.js"></script>
<div>
<span>No GO associations found for this gene.</span>
</div>
</div>
</div>
<div class="tab-pane" id="interpro">
<div class="panel-body">
<div class="col-lg-12 pt-3">
<div>
<span>No InterPro domains detected for this gene.</span>
</div>
</div>
</div>
</div>
<div class="tab-pane" id="mapman">
<div class="panel-body">
<div class="col-lg-12 pt-3">
<div>
<table class="table table-condensed table-hover">
<tr>
<th style='width:20%'>Mapman id</th>
<th style='width:80%'>Description</th>
</tr>
<tr>
<td><a href="/plaza.dev/_dev_instances/feedback/mapman/view/35.2">35.2</a></td>
<td>not assigned.not annotate</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
<script type="text/javascript">
//<![CDATA[
$(document).ready(function () {
var tooltipTriggerList = [].slice.call(document.querySelectorAll('[data-bs-toggle="tooltip"]'));
var tooltipList = tooltipTriggerList.map(function (tooltipTriggerEl) {
return new bootstrap.Tooltip(tooltipTriggerEl)
})
});
//]]>
</script>'
$scripts_for_layout = ''
include - CORE/Cake/View/View.php, line 971
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::_renderElement() - CORE/Cake/View/View.php, line 1224
View::element() - CORE/Cake/View/View.php, line 418
include - APP/View/Layouts/toolbox_layout.ctp, line 40
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::renderLayout() - CORE/Cake/View/View.php, line 546
View::render() - CORE/Cake/View/View.php, line 481
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 151
Warning (2): include() [<a href='http://php.net/function.include'>function.include</a>]: Failed opening '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/second_navigation.ctp' for inclusion (include_path='/www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib:.:/opt/remi/php74/root/usr/share/pear:/opt/remi/php74/root/usr/share/php:/usr/share/pear:/usr/share/php') [CORE/Cake/View/View.php, line 971]Code Context ob_start();
include $this->__viewFile;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/second_navigation.ctp'
$dataForView = array(
'sidebar_info' => array(
'gene_id' => 'Prupe.4G206500',
'species' => 'ppe',
'gene_type' => 'coding',
'default_gf_type' => 'HOMFAM',
'gf_info' => array(
'has_gf' => true,
'gf_id' => 'HOM05D163621',
'num_genes' => array(
[maximum depth reached]
)
),
'has_msa' => false,
'has_tree' => false,
'igv_info' => array(
'genome' => array(
[maximum depth reached]
),
'annotation' => array(
[maximum depth reached]
),
'synteny_scores' => array(
[maximum depth reached]
)
)
),
'sidebar' => 'gene_sidebar',
'navigation_bar_info' => array(
'num_colinearity_runs' => (int) 1,
'num_colinearity_with_dating_runs' => (int) 0,
'only_lvl2' => true,
'num_functional_clusters_runs' => (int) 6,
'has_pan_genomes' => false,
'has_blast_db' => true
),
'sidebar_information' => array(
'type' => 'gene_id',
'id' => 'Prupe.4G206500'
),
'external_sources_settings' => array(
'present' => 'TRUE',
'URL' => array(
'https' => '//bioinformatics.psb.ugent.be/plaza/external_sources/data/get_data_content'
)
),
'function_table_settings' => array(
'binding_sites' => 'true',
'go' => 'true',
'interpro' => 'true',
'mapman' => 'true'
),
'default_gf_type_id' => 'HOMFAM',
'annot' => array(
'gene_id' => 'Prupe.4G206500',
'species' => 'ppe',
'transcript' => 'Prupe.4G206500.1',
'coord_cds' => 'join(12888035..12888274)',
'start' => '12888035',
'stop' => '12888274',
'coord_transcript' => 'join(12888034..12888500)',
'seq' => 'ATGTGTACTTTTATTTCTAGAAAAACTATAAAAACTAAGTATGAAAAAAAAAAATTATCATTCGATTGGGTTGGTGAAACTGAAAACCATCAATTATTTGTTCTTTCCATAACTAAAGCAACGATCAAGACAAAAGTCTCAAAAACACAGCTTATTTACACACACACAGGCCAACAGAGAGGAATCGTAATCAGTCGTTTCTTGCCTCCTCTGATACCATACCAAGTAAAAGAGTCCTGA',
'strand' => 'positive',
'chr' => 'Pp04',
'type' => 'coding',
'check_transcript' => 'eq',
'check_protein' => 'eq',
'transl_table' => '1',
'common_name' => 'Prunus persica',
'tax_id' => '3760'
),
'is_transcription_factor' => false,
'duplication_info' => array(
'is_block' => (int) 0,
'is_tandem' => (int) 0,
'tandem_representative' => null,
'is_syntenic' => (int) 0,
'block' => (int) 0,
'tandem' => (int) 0,
'tandem_rep' => null
),
'gene_type_descriptions' => array(
'coding' => 'Coding gene',
'rna' => 'RNA gene',
'pseudo' => 'Pseudo gene',
'te' => 'Transposon'
),
'gene_descriptions' => array(
'ortholog' => array(
'is_ortholog' => true,
'content' => array(
[maximum depth reached]
),
'title' => 'Ortholog descriptions'
)
),
'gene_identifiers' => array(
(int) 0 => array(
'type' => 'id',
'value' => 'Prupe.4G206500.v2.1'
),
(int) 1 => array(
'type' => 'pacid',
'value' => '32091970'
)
),
'next_gene' => 'Prupe.4G206600',
'previous_gene' => 'Prupe.4G206400',
'splice_variants' => array(
(int) 0 => 'Prupe.4G206500.1'
),
'gene_families' => array(
'HOMFAM' => array(
'gf_id' => 'HOM05D163621',
'order' => '1',
'is_valid' => true,
'info' => array(
[maximum depth reached]
),
'profile' => array(
[maximum depth reached]
)
),
'ORTHOFAM' => array(
'gf_id' => 'ORTHO05D335230',
'order' => '2',
'is_valid' => true,
'info' => array(
[maximum depth reached]
),
'profile' => array(
[maximum depth reached]
)
)
),
'gene_id' => 'Prupe.4G206500',
'title_for_layout' => 'Dicots PLAZA 5.0 : gene pages',
'content_for_layout' => '
<h1>
<span class="dataTypeTitle">Gene:</span>
<span class="dataTitle">Prupe.4G206500</span>
</h1>
<!------------------------------------------------------------------------------------------------------------------>
<!-- General info layout -->
<h2>General Information</h2>
<div class="row">
<!-- first block : structural information -->
<div class="col-lg-4 col-md-12">
<h3>Structural Information</h3>
<ul class="list-group">
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Species</span>
<span class="ms-2 text-end text-break"><a href="/plaza.dev/_dev_instances/feedback/organism/view/ppe">Prunus persica</a></span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Gene Identifier</span>
<span class="ms-2 text-end text-break">Prupe.4G206500</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Transcript Identifier</span>
<span class="ms-2 text-end text-break">Prupe.4G206500.1</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Gene Type</span>
<span class="ms-2 text-end text-break">Coding gene</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Location</span>
<span class="ms-2 text-end text-break">Pp04 : 12888035-12888274 : positive</span>
</li>
</ul>
</div>
<!-- second block: gene family information -->
<div class="col-lg-4 col-md-12" id='family_information'>
<h3>Gene Family Information</h3>
<!-- Setup the navigation tabs-->
<ul class="nav nav-tabs">
<li class='nav-item'>
<a href='#GFTABHOMFAM' class='nav-link' data-bs-toggle='tab' style='margin-bottom:-2px'>Homologous GF</a>
</li>
<li class='nav-item'>
<a href='#GFTABORTHOFAM' class='nav-link' data-bs-toggle='tab' style='margin-bottom:-2px'>Orthologous GF</a>
</li>
</ul>
<!-- Setup the content for the navigation tabs -->
<div class='tab-content multitab-information'>
<div class='tab-pane' role='tabpanel' id='GFTABHOMFAM'>
<ul class="list-group mb-3" >
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="fw-bold">ID</span>
<span><a href="/plaza.dev/_dev_instances/feedback/gene_families/view/HOM05D163621" class="gf_id" data-id="HOM05D163621">HOM05D163621</a></span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class='fw-bold'>#Genes/#Species</span>
<span>1 / 1(orphan gene)</span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class="fw-bold">Phylogenetic origin</span>
<span class='gf_size_span'>
<span class='clade_specific_span' data-id='HOM05D163621'></span>
</span>
</li>
</ul>
</div>
<div class='tab-pane' role='tabpanel' id='GFTABORTHOFAM'>
<ul class="list-group mb-3" >
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="fw-bold">ID</span>
<span><a href="/plaza.dev/_dev_instances/feedback/gene_families/view/ORTHO05D335230" class="gf_id" data-id="ORTHO05D335230">ORTHO05D335230</a></span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class='fw-bold'>#Genes/#Species</span>
<span>1 / 1(orphan gene)</span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class="fw-bold">Phylogenetic origin</span>
<span class='gf_size_span'>
<span class='clade_specific_span' data-id='ORTHO05D335230'></span>
</span>
</li>
</ul>
</div>
</div>
</div>
<!-- third block : duplication information -->
<div class="col-lg-4 col-md-12" id="duplication_information">
<h3>Gene Duplication Information</h3>
<ul class="list-group">
</ul>
</div>
<!-- javascript for the content blocks in this row -->
<script type='text/javascript'>
//<![CDATA[
$(document).ready(function(){
//1) Disable display of gene family box if no gene families are defined
if($("#family_information ul:first li").length<1){$("#family_information").hide();}
//2) Set the "active" tab panes for the gene families to the first tab
$("#family_information ul.nav li.nav-item a.nav-link:first").addClass("active");
$("#family_information div.multitab-information div.tab-pane:first").addClass("show").addClass("active");
//3) Clade specificty analysis
$(".clade_specific_span").each(function (i, clade_specific_span) {
let gf_id = $(clade_specific_span).data('id');
let analyze_url = "/plaza.dev/_dev_instances/feedback/api/family_smallest_encompassing_clade" + "/" + gf_id;
let clade_url_base = "/plaza.dev/_dev_instances/feedback/organism/group";
jQuery.ajax({url: analyze_url,type: 'GET',dataType: 'json', success: function (data) {
$(clade_specific_span).html("<a href='" + clade_url_base + "/" + data.result + "'>" + data.result + "</a>");
}});
});
//4)Hide duplication panel if no duplication is present
if($("#duplication_information ul li").length<1){$("#duplication_information").hide();}
});
//]]>
</script>
</div> <!-- end div containing overview and family information-->
<!------------------------------------------------------------------------------------------------------------------>
<!-- row with the gene structure visualization -->
<div class="row">
<div class="col-lg-7 col-md-12 mb-5">
<div class="d-flex flex-row px-2">
<div class="d-flex align-items-center">
<a href="/plaza.dev/_dev_instances/feedback/genes/view/Prupe.4G206400"><i class="bi bi-chevron-left display-8"></i></a> </div>
<div id='gene-structure-draw-container' class='w-100 h-100' data-gene='Prupe.4G206500'></div>
<div class="d-flex align-items-center">
<a href="/plaza.dev/_dev_instances/feedback/genes/view/Prupe.4G206600"><i class="bi bi-chevron-right display-8"></i></a> </div>
</div>
</div>
<!-- Javascript code for the gene structure row/block -->
<script type='text/javascript'>
//<![CDATA[
$(document).ready(function(){
let gene_structure_url = '/plaza.dev/_dev_instances/feedback/genes/draw_gene_structure/Prupe.4G206500';
$.ajax({url:gene_structure_url,type:"GET",dataType: "html",success:function(data){
$("#gene-structure-draw-container").html(data);
}});
});
//]]>
</script>
</div>
<!------------------------------------------------------------------------------------------------------------------>
<!-- Identifiers and descriptions row -->
<h2>Labels</h2>
<div class="row mb-6">
<!-- Identifiers block -->
<div class="col-lg-4 col-md-12" id="identifier_col">
<h3>Identifiers</h3>
<ul class="list-group">
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class='fw-bold'>id</span>
<span>Prupe.4G206500.v2.1</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class='fw-bold'>pacid</span>
<span>32091970</span>
</li>
</ul>
</div>
<!-- Descriptions block -->
<div class="col-lg-8 col-md-12" id="descriptions_col">
<h3 id="description_header">Descriptions</h3>
<!-- setup the navigation tabs -->
<ul class="nav nav-tabs">
<li class='nav-item'>
<a href="#DESCTABortholog" style='margin-bottom:-2px' class="nav-link" data-bs-toggle='tab'>Ortholog descriptions</a>
</li>
</ul>
<!-- setup content for the navigation tabs -->
<div class='tab-content multitab-information'>
<div class="tab-pane" role="tabpanel" id="DESCTABortholog">
<ul class="list-group mb-3">
<li class="d-flex justify-content-between list-group-item list-group-item-light ortholog-description" data-id='ath'>
<span class='fw-bold'>Loading (ortholog descriptions from ath)... </span>
<span></span>
</li>
</ul>
</div>
</div>
</div>
<!-- javascript for the content blocks in this row -->
<script type='text/javascript'>
//<![CDATA[
$(document).ready(function(){
//1) Disable display of identifiers box if no external identifiers are defined
if($("#identifier_col ul:first li").length<1){$("#identifier_col").hide();}
//2)Hide description panel if no descriptions are present
if($("#descriptions_col ul:first li").length<1){$("#descriptions_col").hide();}
//3) Set the "active" tab panes for the gene families to the first tab
$("#descriptions_col ul.nav li.nav-item a.nav-link:first").addClass("active");
$("#descriptions_col div.multitab-information div.tab-pane:first").addClass("show").addClass("active");
//4) Get the descriptions of orthologs
$("li.ortholog-description").each(function(odi,odli){
let ortho_species = $(odli).data("id");
let ortho_desc_url = '/plaza.dev/_dev_instances/feedback/genes/get_best_ortholog_descriptions/ppe/Prupe.4G206500/'+ortho_species;
let gene_url_base = '/plaza.dev/_dev_instances/feedback/genes/view';
$.ajax({url:ortho_desc_url,type:"GET",dataType:"json",success:function(data){
if('error' in data){$(odli).html("<span class='fw-bold'>Error</span><span>"+data.error+"</span>");}
else if("result" in data){
//Empty current list
let parent_ul = $(odli).parent();
parent_ul.empty();
//Add multiple <li> entries
data['result'].forEach(function(entry){
let ortholog_entry = "<li class='d-flex justify-content-between list-group-item list-group-item-light'>"+
"<span><a href='"+gene_url_base+"/"+entry.ortholog+"' target='_blank'>"+entry.ortholog+"</a></span>"+
"<span>"+entry.description+"</span>"+
"</li>";
parent_ul.append(ortholog_entry);
});
}
else{$(odli).html("<span class='fw-bold'>Error</span><span>Unknown error</span>");}
}});
});
});
//]]>
</script>
</div>
<!-- end of labels presence check -->
<!------------------------------------------------------------------------------------------------------------------>
<!-- Functional Data Tabs -->
<h2>Functional Annotation</h2>
<ul class="nav nav-tabs" id="bottom_gene_nav_tabs">
<li class="nav-item">
<a href="#geneontology" class="nav-link active" data-bs-toggle="tab">GeneOntology</a>
</li>
<li class="nav-item">
<a href="#interpro" class="nav-link" data-bs-toggle="tab">Interpro</a>
</li>
<li class="nav-item">
<a href="#mapman" class="nav-link" data-bs-toggle="tab">Mapman</a>
</li>
<li class="nav-item">
<a href="#external_sources" class="nav-link" data-bs-toggle="tab">External sources</a>
</li>
</ul>
<div class="tab-content">
<div class="tab-pane show active" id="geneontology">
<div class="pt-3">
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/genegotable.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/publication_tooltips_TAIR.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/publication_tooltips_PMID.js"></script>
<div>
<span>No GO associations found for this gene.</span>
</div>
</div>
</div>
<div class="tab-pane" id="interpro">
<div class="panel-body">
<div class="col-lg-12 pt-3">
<div>
<span>No InterPro domains detected for this gene.</span>
</div>
</div>
</div>
</div>
<div class="tab-pane" id="mapman">
<div class="panel-body">
<div class="col-lg-12 pt-3">
<div>
<table class="table table-condensed table-hover">
<tr>
<th style='width:20%'>Mapman id</th>
<th style='width:80%'>Description</th>
</tr>
<tr>
<td><a href="/plaza.dev/_dev_instances/feedback/mapman/view/35.2">35.2</a></td>
<td>not assigned.not annotate</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
<script type="text/javascript">
//<![CDATA[
$(document).ready(function () {
var tooltipTriggerList = [].slice.call(document.querySelectorAll('[data-bs-toggle="tooltip"]'));
var tooltipList = tooltipTriggerList.map(function (tooltipTriggerEl) {
return new bootstrap.Tooltip(tooltipTriggerEl)
})
});
//]]>
</script>',
'scripts_for_layout' => ''
)
$sidebar_info = array(
'gene_id' => 'Prupe.4G206500',
'species' => 'ppe',
'gene_type' => 'coding',
'default_gf_type' => 'HOMFAM',
'gf_info' => array(
'has_gf' => true,
'gf_id' => 'HOM05D163621',
'num_genes' => array(
'num_genes' => '1',
'num_species' => '1'
)
),
'has_msa' => false,
'has_tree' => false,
'igv_info' => array(
'genome' => array(
'content' => array(
[maximum depth reached]
),
'index' => array(
[maximum depth reached]
),
'compressed_index' => array(
[maximum depth reached]
)
),
'annotation' => array(
'content' => array(
[maximum depth reached]
)
),
'synteny_scores' => array(
'content' => array(
[maximum depth reached]
)
)
)
)
$sidebar = 'gene_sidebar'
$navigation_bar_info = array(
'num_colinearity_runs' => (int) 1,
'num_colinearity_with_dating_runs' => (int) 0,
'only_lvl2' => true,
'num_functional_clusters_runs' => (int) 6,
'has_pan_genomes' => false,
'has_blast_db' => true
)
$sidebar_information = array(
'type' => 'gene_id',
'id' => 'Prupe.4G206500'
)
$external_sources_settings = array(
'present' => 'TRUE',
'URL' => array(
'https' => '//bioinformatics.psb.ugent.be/plaza/external_sources/data/get_data_content'
)
)
$function_table_settings = array(
'binding_sites' => 'true',
'go' => 'true',
'interpro' => 'true',
'mapman' => 'true'
)
$default_gf_type_id = 'HOMFAM'
$annot = array(
'gene_id' => 'Prupe.4G206500',
'species' => 'ppe',
'transcript' => 'Prupe.4G206500.1',
'coord_cds' => 'join(12888035..12888274)',
'start' => '12888035',
'stop' => '12888274',
'coord_transcript' => 'join(12888034..12888500)',
'seq' => 'ATGTGTACTTTTATTTCTAGAAAAACTATAAAAACTAAGTATGAAAAAAAAAAATTATCATTCGATTGGGTTGGTGAAACTGAAAACCATCAATTATTTGTTCTTTCCATAACTAAAGCAACGATCAAGACAAAAGTCTCAAAAACACAGCTTATTTACACACACACAGGCCAACAGAGAGGAATCGTAATCAGTCGTTTCTTGCCTCCTCTGATACCATACCAAGTAAAAGAGTCCTGA',
'strand' => 'positive',
'chr' => 'Pp04',
'type' => 'coding',
'check_transcript' => 'eq',
'check_protein' => 'eq',
'transl_table' => '1',
'common_name' => 'Prunus persica',
'tax_id' => '3760'
)
$is_transcription_factor = false
$duplication_info = array(
'is_block' => (int) 0,
'is_tandem' => (int) 0,
'tandem_representative' => null,
'is_syntenic' => (int) 0,
'block' => (int) 0,
'tandem' => (int) 0,
'tandem_rep' => null
)
$gene_type_descriptions = array(
'coding' => 'Coding gene',
'rna' => 'RNA gene',
'pseudo' => 'Pseudo gene',
'te' => 'Transposon'
)
$gene_descriptions = array(
'ortholog' => array(
'is_ortholog' => true,
'content' => array(
(int) 0 => 'ath'
),
'title' => 'Ortholog descriptions'
)
)
$gene_identifiers = array(
(int) 0 => array(
'type' => 'id',
'value' => 'Prupe.4G206500.v2.1'
),
(int) 1 => array(
'type' => 'pacid',
'value' => '32091970'
)
)
$next_gene = 'Prupe.4G206600'
$previous_gene = 'Prupe.4G206400'
$splice_variants = array(
(int) 0 => 'Prupe.4G206500.1'
)
$gene_families = array(
'HOMFAM' => array(
'gf_id' => 'HOM05D163621',
'order' => '1',
'is_valid' => true,
'info' => array(
'name' => 'Homologous gene family'
),
'profile' => array(
'num_genes' => '1',
'num_species' => '1'
)
),
'ORTHOFAM' => array(
'gf_id' => 'ORTHO05D335230',
'order' => '2',
'is_valid' => true,
'info' => array(
'name' => 'Orthologous gene family'
),
'profile' => array(
'num_genes' => '1',
'num_species' => '1'
)
)
)
$gene_id = 'Prupe.4G206500'
$title_for_layout = 'Dicots PLAZA 5.0 : gene pages'
$content_for_layout = '
<h1>
<span class="dataTypeTitle">Gene:</span>
<span class="dataTitle">Prupe.4G206500</span>
</h1>
<!------------------------------------------------------------------------------------------------------------------>
<!-- General info layout -->
<h2>General Information</h2>
<div class="row">
<!-- first block : structural information -->
<div class="col-lg-4 col-md-12">
<h3>Structural Information</h3>
<ul class="list-group">
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Species</span>
<span class="ms-2 text-end text-break"><a href="/plaza.dev/_dev_instances/feedback/organism/view/ppe">Prunus persica</a></span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Gene Identifier</span>
<span class="ms-2 text-end text-break">Prupe.4G206500</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Transcript Identifier</span>
<span class="ms-2 text-end text-break">Prupe.4G206500.1</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Gene Type</span>
<span class="ms-2 text-end text-break">Coding gene</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="list_group_label">Location</span>
<span class="ms-2 text-end text-break">Pp04 : 12888035-12888274 : positive</span>
</li>
</ul>
</div>
<!-- second block: gene family information -->
<div class="col-lg-4 col-md-12" id='family_information'>
<h3>Gene Family Information</h3>
<!-- Setup the navigation tabs-->
<ul class="nav nav-tabs">
<li class='nav-item'>
<a href='#GFTABHOMFAM' class='nav-link' data-bs-toggle='tab' style='margin-bottom:-2px'>Homologous GF</a>
</li>
<li class='nav-item'>
<a href='#GFTABORTHOFAM' class='nav-link' data-bs-toggle='tab' style='margin-bottom:-2px'>Orthologous GF</a>
</li>
</ul>
<!-- Setup the content for the navigation tabs -->
<div class='tab-content multitab-information'>
<div class='tab-pane' role='tabpanel' id='GFTABHOMFAM'>
<ul class="list-group mb-3" >
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="fw-bold">ID</span>
<span><a href="/plaza.dev/_dev_instances/feedback/gene_families/view/HOM05D163621" class="gf_id" data-id="HOM05D163621">HOM05D163621</a></span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class='fw-bold'>#Genes/#Species</span>
<span>1 / 1(orphan gene)</span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class="fw-bold">Phylogenetic origin</span>
<span class='gf_size_span'>
<span class='clade_specific_span' data-id='HOM05D163621'></span>
</span>
</li>
</ul>
</div>
<div class='tab-pane' role='tabpanel' id='GFTABORTHOFAM'>
<ul class="list-group mb-3" >
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class="fw-bold">ID</span>
<span><a href="/plaza.dev/_dev_instances/feedback/gene_families/view/ORTHO05D335230" class="gf_id" data-id="ORTHO05D335230">ORTHO05D335230</a></span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class='fw-bold'>#Genes/#Species</span>
<span>1 / 1(orphan gene)</span>
</li>
<li class='d-flex justify-content-between list-group-item list-group-item-light'>
<span class="fw-bold">Phylogenetic origin</span>
<span class='gf_size_span'>
<span class='clade_specific_span' data-id='ORTHO05D335230'></span>
</span>
</li>
</ul>
</div>
</div>
</div>
<!-- third block : duplication information -->
<div class="col-lg-4 col-md-12" id="duplication_information">
<h3>Gene Duplication Information</h3>
<ul class="list-group">
</ul>
</div>
<!-- javascript for the content blocks in this row -->
<script type='text/javascript'>
//<![CDATA[
$(document).ready(function(){
//1) Disable display of gene family box if no gene families are defined
if($("#family_information ul:first li").length<1){$("#family_information").hide();}
//2) Set the "active" tab panes for the gene families to the first tab
$("#family_information ul.nav li.nav-item a.nav-link:first").addClass("active");
$("#family_information div.multitab-information div.tab-pane:first").addClass("show").addClass("active");
//3) Clade specificty analysis
$(".clade_specific_span").each(function (i, clade_specific_span) {
let gf_id = $(clade_specific_span).data('id');
let analyze_url = "/plaza.dev/_dev_instances/feedback/api/family_smallest_encompassing_clade" + "/" + gf_id;
let clade_url_base = "/plaza.dev/_dev_instances/feedback/organism/group";
jQuery.ajax({url: analyze_url,type: 'GET',dataType: 'json', success: function (data) {
$(clade_specific_span).html("<a href='" + clade_url_base + "/" + data.result + "'>" + data.result + "</a>");
}});
});
//4)Hide duplication panel if no duplication is present
if($("#duplication_information ul li").length<1){$("#duplication_information").hide();}
});
//]]>
</script>
</div> <!-- end div containing overview and family information-->
<!------------------------------------------------------------------------------------------------------------------>
<!-- row with the gene structure visualization -->
<div class="row">
<div class="col-lg-7 col-md-12 mb-5">
<div class="d-flex flex-row px-2">
<div class="d-flex align-items-center">
<a href="/plaza.dev/_dev_instances/feedback/genes/view/Prupe.4G206400"><i class="bi bi-chevron-left display-8"></i></a> </div>
<div id='gene-structure-draw-container' class='w-100 h-100' data-gene='Prupe.4G206500'></div>
<div class="d-flex align-items-center">
<a href="/plaza.dev/_dev_instances/feedback/genes/view/Prupe.4G206600"><i class="bi bi-chevron-right display-8"></i></a> </div>
</div>
</div>
<!-- Javascript code for the gene structure row/block -->
<script type='text/javascript'>
//<![CDATA[
$(document).ready(function(){
let gene_structure_url = '/plaza.dev/_dev_instances/feedback/genes/draw_gene_structure/Prupe.4G206500';
$.ajax({url:gene_structure_url,type:"GET",dataType: "html",success:function(data){
$("#gene-structure-draw-container").html(data);
}});
});
//]]>
</script>
</div>
<!------------------------------------------------------------------------------------------------------------------>
<!-- Identifiers and descriptions row -->
<h2>Labels</h2>
<div class="row mb-6">
<!-- Identifiers block -->
<div class="col-lg-4 col-md-12" id="identifier_col">
<h3>Identifiers</h3>
<ul class="list-group">
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class='fw-bold'>id</span>
<span>Prupe.4G206500.v2.1</span>
</li>
<li class="d-flex justify-content-between list-group-item list-group-item-light">
<span class='fw-bold'>pacid</span>
<span>32091970</span>
</li>
</ul>
</div>
<!-- Descriptions block -->
<div class="col-lg-8 col-md-12" id="descriptions_col">
<h3 id="description_header">Descriptions</h3>
<!-- setup the navigation tabs -->
<ul class="nav nav-tabs">
<li class='nav-item'>
<a href="#DESCTABortholog" style='margin-bottom:-2px' class="nav-link" data-bs-toggle='tab'>Ortholog descriptions</a>
</li>
</ul>
<!-- setup content for the navigation tabs -->
<div class='tab-content multitab-information'>
<div class="tab-pane" role="tabpanel" id="DESCTABortholog">
<ul class="list-group mb-3">
<li class="d-flex justify-content-between list-group-item list-group-item-light ortholog-description" data-id='ath'>
<span class='fw-bold'>Loading (ortholog descriptions from ath)... </span>
<span></span>
</li>
</ul>
</div>
</div>
</div>
<!-- javascript for the content blocks in this row -->
<script type='text/javascript'>
//<![CDATA[
$(document).ready(function(){
//1) Disable display of identifiers box if no external identifiers are defined
if($("#identifier_col ul:first li").length<1){$("#identifier_col").hide();}
//2)Hide description panel if no descriptions are present
if($("#descriptions_col ul:first li").length<1){$("#descriptions_col").hide();}
//3) Set the "active" tab panes for the gene families to the first tab
$("#descriptions_col ul.nav li.nav-item a.nav-link:first").addClass("active");
$("#descriptions_col div.multitab-information div.tab-pane:first").addClass("show").addClass("active");
//4) Get the descriptions of orthologs
$("li.ortholog-description").each(function(odi,odli){
let ortho_species = $(odli).data("id");
let ortho_desc_url = '/plaza.dev/_dev_instances/feedback/genes/get_best_ortholog_descriptions/ppe/Prupe.4G206500/'+ortho_species;
let gene_url_base = '/plaza.dev/_dev_instances/feedback/genes/view';
$.ajax({url:ortho_desc_url,type:"GET",dataType:"json",success:function(data){
if('error' in data){$(odli).html("<span class='fw-bold'>Error</span><span>"+data.error+"</span>");}
else if("result" in data){
//Empty current list
let parent_ul = $(odli).parent();
parent_ul.empty();
//Add multiple <li> entries
data['result'].forEach(function(entry){
let ortholog_entry = "<li class='d-flex justify-content-between list-group-item list-group-item-light'>"+
"<span><a href='"+gene_url_base+"/"+entry.ortholog+"' target='_blank'>"+entry.ortholog+"</a></span>"+
"<span>"+entry.description+"</span>"+
"</li>";
parent_ul.append(ortholog_entry);
});
}
else{$(odli).html("<span class='fw-bold'>Error</span><span>Unknown error</span>");}
}});
});
});
//]]>
</script>
</div>
<!-- end of labels presence check -->
<!------------------------------------------------------------------------------------------------------------------>
<!-- Functional Data Tabs -->
<h2>Functional Annotation</h2>
<ul class="nav nav-tabs" id="bottom_gene_nav_tabs">
<li class="nav-item">
<a href="#geneontology" class="nav-link active" data-bs-toggle="tab">GeneOntology</a>
</li>
<li class="nav-item">
<a href="#interpro" class="nav-link" data-bs-toggle="tab">Interpro</a>
</li>
<li class="nav-item">
<a href="#mapman" class="nav-link" data-bs-toggle="tab">Mapman</a>
</li>
<li class="nav-item">
<a href="#external_sources" class="nav-link" data-bs-toggle="tab">External sources</a>
</li>
</ul>
<div class="tab-content">
<div class="tab-pane show active" id="geneontology">
<div class="pt-3">
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/genegotable.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/publication_tooltips_TAIR.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/publication_tooltips_PMID.js"></script>
<div>
<span>No GO associations found for this gene.</span>
</div>
</div>
</div>
<div class="tab-pane" id="interpro">
<div class="panel-body">
<div class="col-lg-12 pt-3">
<div>
<span>No InterPro domains detected for this gene.</span>
</div>
</div>
</div>
</div>
<div class="tab-pane" id="mapman">
<div class="panel-body">
<div class="col-lg-12 pt-3">
<div>
<table class="table table-condensed table-hover">
<tr>
<th style='width:20%'>Mapman id</th>
<th style='width:80%'>Description</th>
</tr>
<tr>
<td><a href="/plaza.dev/_dev_instances/feedback/mapman/view/35.2">35.2</a></td>
<td>not assigned.not annotate</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
<script type="text/javascript">
//<![CDATA[
$(document).ready(function () {
var tooltipTriggerList = [].slice.call(document.querySelectorAll('[data-bs-toggle="tooltip"]'));
var tooltipList = tooltipTriggerList.map(function (tooltipTriggerEl) {
return new bootstrap.Tooltip(tooltipTriggerEl)
})
});
//]]>
</script>'
$scripts_for_layout = ''
include - CORE/Cake/View/View.php, line 971
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::_renderElement() - CORE/Cake/View/View.php, line 1224
View::element() - CORE/Cake/View/View.php, line 418
include - APP/View/Layouts/toolbox_layout.ctp, line 40
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::renderLayout() - CORE/Cake/View/View.php, line 546
View::render() - CORE/Cake/View/View.php, line 481
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 151
Gene:
Prupe.4G206500
General Information
Structural Information
-
Species
Prunus persica
-
Gene Identifier
Prupe.4G206500
-
Transcript Identifier
Prupe.4G206500.1
-
Gene Type
Coding gene
-
Location
Pp04 : 12888035-12888274 : positive
Labels
Identifiers
-
id
Prupe.4G206500.v2.1
-
pacid
32091970
-
Loading (ortholog descriptions from ath)...
Functional Annotation
No GO associations found for this gene.
No InterPro domains detected for this gene.
Mapman id |
Description |
35.2 |
not assigned.not annotate |