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Template:Novel motif: Difference between revisions

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(Undo revision 4578710 by A-Kondo (talk))
Tag: Undo
 
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Line 15: Line 15:
table.details th { width:10%; background-color: #5A5FB5; color: white;}
table.details th { width:10%; background-color: #5A5FB5; color: white;}
</style>
</style>
<script type="text/javascript" src="/5/sstar/rb_js/jquery-1.7.1.min.js"></script>
<script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.js"></script>
<script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.js"></script>
<script type="text/javascript" src="/5/sstar/rb_js/custom/convert.js"></script>
<script type="text/javascript" src="/5/sstar/rb_js/custom/convert.js"></script>
</script>
<script type="text/javascript">
<script type="text/javascript">
$(document).ready(function() {
$(document).ready(function() {
Line 30: Line 32:
}
}


     $('#h_pval_table').dataTable({
     $('#h_pval_table').DataTable({
"sScrollY": "300px",
dom: 'lfrtip',
"bScrollCollapse": true,
scrollY: "300px",
"bPaginate": true,
scrollCollapse: true,
"bFilter": true,
pageLength: 10,
"bInfo": true,
lengthMenu: [[5,10,-1], [5,10,"All"]],
                "iDisplayLength": 10,
data: h_data,
                "aLengthMenu": [[5,10,-1], [5,10,"All"]],
columns: [
"aaData": h_data,
{ "title": "FF samples", "orderable": false, render: function(data, type, row, meta) {
"aoColumns": [{ "sTitle": "FF samples", "bSortable": false, "fnRender": function(obj) {
return '<a href="/5/sstar/index.php/FF:'+row[ 0 ].split('.').pop()+'">'+decodeURIComponent(row[ 0 ])+'</a>';
return sReturn = '<a href="/resource_browser/index.php/FF:'+obj.aData[ obj.iDataColumn ].split('.').pop()+'">'+decodeURIComponent(obj.aData[ obj.iDataColumn ])+'</a>';
} },
} },{ "sTitle": "p-value",  "sType": "numeric", "sWidth": "50pt" , "aTargets": [1],"fnRender": function (obj) {                     
{ title: "p-value",  type: "numeric", "width": "50pt", render: function (data, type, row, meta) {                     
                  var num =obj.aData[obj.iDataColumn];
        var num = row[1];
                  return exp_converter(num,2,"e") ;
          return exp_converter(num,2,"e");
} }],
} }
"aaSorting": [[ 1, "asc" ]],
],
order: [[ 1, "asc" ]],
});
});


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}
}


    $('#m_pval_table').DataTable({
$('#m_pval_table').DataTable({
dom: 'lfrtip',
dom: 'lfrtip',
scrollY: "300px",
scrollY: "300px",
scrollCollapse: true,
scrollCollapse: true,
                pLength: 10,
    pageLength: 10,
lengthMenu: [[5,10,-1], [5,10,"All"]],
lengthMenu: [[5,10,-1], [5,10,"All"]],
data: m_data,
data: m_data,
columnDefs: [
columns: [
          { targets: 0, orderable: false},
{ title: "FF samples", "orderable": false, render: function(data, type, row, meta) {
          { targets: 1, width: "50pt"}
return '<a href="/5/sstar/index.php/FF:'+row[0].split('.').pop()+'">'+decodeURIComponent(row[ 0 ])+'</a>';
],
}
columns: [{ title: "FF samples", orderable: false, render: function(data, type, row, meta) {
},
return '<a href="/resource_browser/index.php/FF:'+row[0].split('.').pop()+'">'+decodeURIComponent(row[ 0 ])+'</a>';
{ title: "p-value", width: "50pt", type: "numeric", render: function (data, type, row, meta) {                     
} },
              var num =row[1];
{ title: "p-value", type: "numeric", width: "50pt", render: function (data, type, row, meta) {                     
              return exp_converter(num,2,"e");
                  var num =row[1];
}
                  return exp_converter(num,2,"e") ;
}
}}],
],
order: [[ 1, "asc" ]],
order: [[ 1, "asc" ]],
});
});
 


// GREAT table for human start
// GREAT table for human start
$('#great_table_human').DataTable({
$('#great_table_human').DataTable({
dom: 'lfrtip',
dom:'lfrtip',
scrollY: "300px",
scrollY:"300px",
scrollCollapse: true,
scrollCollapse:true,
        pLength: 10,
    pageLength:10,
        lengthMenu: [[5,10,-1], [5,10,"All"]],
    lengthMenu:[[5,10,-1], [5,10,"All"]],
order: [[ 2, "asc" ]],
order:[[ 2, "asc" ]],
columnDefs: [
columns:[
{ targets: 0, orderable: false },
{"orderable":false},
{ targets: 1, orderable: false },
{"orderable":false},
{ targets: 2, type: "html-number", width: "80pt" }
{type: "html-number", width: "80pt", render: function(data, type, row, meta) {
],
              var num =row[2];
columns: [
              return exp_converter(num,2,"e");
{title: :""},
}
{title: :""},
}
{title: "FF samples", render: function(data, type, row, meta) {
]
                  var num =row[1];
});
                  return exp_converter(num,2,"e") ;
}}]
});
// GREAT table for human end
// GREAT table for human end


// GREAT table for mouse start
// GREAT table for mouse start
$('#great_table_mouse').DataTable({
$('#great_table_mouse').DataTable({
scrollY: "300px",
dom: 'lfrtip',
scrollCollapse: true,
scrollY: "300px",
        pLength: 10,
scrollCollapse: true,
        lengthMenu: [[5,10,-1], [5,10,"All"]],
    pageLength: 10,
order: [[ 2, "asc" ]],
    lengthMenu: [[5,10,-1], [5,10,"All"]],
columnDefs: [
order: [[ 2, "asc" ]],
{ targets: 0, orderable: false },
columns: [
{ targets: 1, orderable: false },
{"orderable": false},
{ targets: 2, type: "html-number", width: "80pt" }
{"orderable": false},
columns: [
{type: "html-number", width: "80pt", render: function(data, type, row, meta) {
{title: :""},
              var num =row[2];
{title: :""},
              return exp_converter(num,2,"e");
{title: "FF samples", render: function(data, type, row, meta) {
}
                  var num =row[1];
}
                  return exp_converter(num,2,"e") ;
]
}}]
});
});
});
// GREAT table for mouse end
// GREAT table for mouse end
Line 134: Line 131:
     </div>
     </div>
   <div class="content">
   <div class="content">
         <img src="/resource_browser/seqlogos/novel/</html>{{PAGENAME}}<html>.png">
         <img src="/5/sstar/seqlogos/novel/</html>{{PAGENAME}}<html>.png">
   </div>
   </div>
  </div></html>
  </div></html>
Line 143: Line 140:
}}
}}
----
----
<table id="h_pval_table"></table>
<table id="h_pval_table" class="ff_sample_list stripe cell-border order-column compact dataTable no-footer"></table>
<br><br>
<br><br>
{{Fontsize|3|Association to promoter expression in mouse samples}}
{{Fontsize|3|Association to promoter expression in mouse samples}}
Line 152: Line 149:
}}
}}
----
----
<!--
<table id="m_pval_table" class="ff_sample_list stripe cell-border order-column compact dataTable no-footer"></table>
<span id="export_tool"></span>
-->
<table id="m_pval_table"></table>
<br><br>
<br><br>
{{Fontsize|3|GREAT analysis results for human}}
{{Fontsize|3|GREAT analysis results for human}}
Line 164: Line 158:
}}
}}
----
----
<table id="great_table_human">
<table id="great_table_human" class="ff_sample_list stripe cell-border order-column compact dataTable no-footer">
<html><thead></html>
<html><thead></html>
<th>GO ID</th><th>GO Term</th><th>p-value</th>
<th>GO ID</th><th>GO Term</th><th>p-value</th>
Line 187: Line 181:
----
----
{{#if:{{{great_results_mouse}}}|
{{#if:{{{great_results_mouse}}}|
<table id="great_table_mouse">
<table id="great_table_mouse" class="ff_sample_list stripe cell-border order-column compact dataTable no-footer">
<html><thead></html>
<html><thead></html>
<th>GO ID</th><th>GO Term</th><th>p-value</th>{{#arraydefine:tmp_go_stat_mouse|{{{great_results_mouse}}}|!}}
<th>GO ID</th><th>GO Term</th><th>p-value</th>{{#arraydefine:tmp_go_stat_mouse|{{{great_results_mouse}}}|!}}

Latest revision as of 16:22, 24 September 2021

name:{{{name}}}

Association to promoter expression in human samples<b>Summary:</b>Significance of the correlation with CAGE expression, human <br><b>Analyst:</b> Michiel de Hoon<br><br>link to source dataset <br>data



Association to promoter expression in mouse samples <b>Summary:</b>Significance of the correlation with CAGE expression, mouse <br><b>Analyst:</b> Michiel de Hoon<br><br>link to source dataset <br>data



GREAT analysis results for human <b>Summary:</b>Genomic Enrichment of Annotations Tool (GREAT, Nat Biotechnol. 2010 May;28(5):495-501) is used to identify, both in human and in mouse, the gene ontology terms of biological processes enriched given the predicted TFBSs, and evaluated the overlap in the top-500 gene ontology terms between human and mouse. For each novel motif, the P value for the overlap was then evaluated by calculating its relative rank with respect to this background distribution.<br>Analyst: Michiel de Hoon<br><br>link to source dataset <br>data



GREAT analysis results for mouseGenomic Enrichment of Annotations Tool (GREAT, Nat Biotechnol. 2010 May;28(5):495-501) is used to identify, both in human and in mouse, the gene ontology terms of biological processes enriched given the predicted TFBSs, and evaluated the overlap in the top-500 gene ontology terms between human and mouse. For each novel motif, the P value for the overlap was then evaluated by calculating its relative rank with respect to this background distribution.<br>Analyst: Michiel de Hoon <br><br>link to source dataset <br>data

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