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(Created page with "<html> <style type="text/css" title="currentStyle"> @import "/resource_browser/rb_js/datatables/media/css/jquery.dataTables.css"; @import "/resource_browser/rb_js/datatables/e...")
 
(Undo revision 4578710 by A-Kondo (talk))
Tag: Undo
 
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<html>
{{Loading|loadingimage=sprites.gif}}<html>
<style type="text/css" title="currentStyle">
<style type="text/css" title="currentStyle">
@import "/resource_browser/rb_js/datatables/media/css/jquery.dataTables.css";
@import "/5/sstar/rb_js/html5button/datatables.css";
@import "/resource_browser/rb_js/datatables/extras/TableTools/media/css/TableTools.css";
@import "/5/sstar/rb_js/datatables/extras/TableTools/media/css/TableTools.css";
 
.content, .sidebar
{
display: inline-block;
      border:0px solid #a1a1a1;
      padding:5px 10px;
      border-radius:5px;
      background:#FEFEFE;
}
table.details td { width:40%; background-color: #EAEBFF;}
table.details th { width:10%; background-color: #5A5FB5; color: white;}
</style>
</style>
<script type="text/javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.min.js"></script>
<script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.js"></script>
<script type="text/javascript" src="/resource_browser/rb_js/datatables/extras/TableTools/media/js/TableTools.min.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() {
var m_sample
 
var h_sample = ['Adipocyte%20-%20breast%2c%20donor1.CNhs11051.11376-118A8','Adipocyte%20-%20breast%2c
var m_data = [];
var m_data = [];
for(i1=0;i1<m_sample.length;i1++){
for(i1=0;i1<m_sample.length;i1++){
m_data.push([m_sample[i1],m_pval[i1]]);
pval = m_pval[i1].split(";");
m_data.push([m_sample[i1],pval[1]]);
}
}


    $('#m_pval_table').dataTable({
$('#m_pval_table').DataTable({
"sScrollY": "300px",
dom: 'lfrtip',
"bScrollCollapse": true,
scrollY: "300px",
"bPaginate": false,
scrollCollapse: true,
"bFilter": false,
    pageLength: 10,
"bInfo": false,
lengthMenu: [[5,10,-1], [5,10,"All"]],
"aaData": m_data,
data: m_data,
"aoColumns": [{ "sTitle": "Motifs", "sWidth": "200pt"},{ "sTitle": "-log10(p-value)" }],
columns: [
"aaSorting": [[ 1, "desc" ]],
{ title: "FF samples", "orderable": false, render: function(data, type, row, meta) {
return '<a href="/5/sstar/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];
              return exp_converter(num,2,"e");
}
}
],
order: [[ 1, "asc" ]],
});
});
// GREAT table for human start
$('#great_table_human').DataTable({
dom:'lfrtip',
scrollY:"300px",
scrollCollapse:true,
    pageLength:10,
    lengthMenu:[[5,10,-1], [5,10,"All"]],
order:[[ 2, "asc" ]],
columns:[
{"orderable":false},
{"orderable":false},
{type: "html-number", width: "80pt", render: function(data, type, row, meta) {
              var num =row[2];
              return exp_converter(num,2,"e");
}
}
]
});
// GREAT table for human end
// GREAT table for mouse start
$('#great_table_mouse').DataTable({
dom: 'lfrtip',
scrollY: "300px",
scrollCollapse: true,
    pageLength: 10,
    lengthMenu: [[5,10,-1], [5,10,"All"]],
order: [[ 2, "asc" ]],
columns: [
{"orderable": false},
{"orderable": false},
{type: "html-number", width: "80pt", render: function(data, type, row, meta) {
              var num =row[2];
              return exp_converter(num,2,"e");
}
}
]
});
// GREAT table for mouse end
});
});
</script>
</script>
</html>
</html><html>
== P-values for the mouse samples ==
<div class="container">
{{#info:<br>Analyst: Michiel de Hoon}}
  <div class="content">
<html>
    <table class="details">
<table id="m_pval_table"></table>
      <tr><th scope="row" align="right">name:</th><td></html>[[name::{{{name}}}]]<html></td></tr> 
</html>
    </table>
    </div>
  <div class="content">
        <img src="/5/sstar/seqlogos/novel/</html>{{PAGENAME}}<html>.png">
  </div>
</div></html>
{{Fontsize|3|Association to promoter expression in human samples}}{{#info:<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>
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/hg19.pvalues.txt data]
}}
----
<table id="h_pval_table" class="ff_sample_list stripe cell-border order-column compact dataTable no-footer"></table>
<br><br>
{{Fontsize|3|Association to promoter expression in mouse samples}}
{{#info:<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>
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/mm9.pvalues.txt data]
}}
----
<table id="m_pval_table" class="ff_sample_list stripe cell-border order-column compact dataTable no-footer"></table>
<br><br>
{{Fontsize|3|GREAT analysis results for human}}
{{#info:<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>
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/hg19.table.txt data]
}}
----
<table id="great_table_human" class="ff_sample_list stripe cell-border order-column compact dataTable no-footer">
<html><thead></html>
<th>GO ID</th><th>GO Term</th><th>p-value</th>
<html></thead><tbody></html>{{#arraydefine:tmp_go_stat_human|{{{great_results_human}}}|!}}
<!--{{#arraymap:{{{great_results_human}}}|!|$|<tr><td>{{#replace:$|;|</td><td>}}</td></tr>|}}-->
{{#loop:p
  | 0         
  | {{#arraysize:tmp_go_stat_human}}
  | <nowiki/><tr>{{#arraydefine:tmp_go_stat_human{{#var:p}}|{{#arrayindex:tmp_go_stat_human|{{#var:p}}}}|;}}{{#loop:j
  | 0         
  | {{#arraysize:tmp_go_stat_human{{#var:p}}}}
  | <nowiki/>
  {{#vardefine:inner_el_human|{{#arrayindex:tmp_go_stat_human{{#var:p}}|{{#var:j}} }}  }}
  <td>{{#ifeq:{{#sub:{{#var:inner_el_human}}|0|3}}|GO:|[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term={{#var:inner_el_human}} {{#var:inner_el_human}}]|{{#var:inner_el_human}} }}</td>}}</tr>}}
<html></tbody></html>
<table>
<br><br>
{{Fontsize|3|GREAT analysis results for mouse}}{{#info:Genomic Enrichment of Annotations Tool (GREAT, Nat Biotechnol. 2010 May;28(5):495-501) is used to identify, both in human and in mouse, the gene ontology terms of biological processes enriched given the predicted TFBSs, and evaluated the overlap in the top-500 gene ontology terms between human and mouse. For each novel motif, the P value for the overlap was then evaluated by calculating its relative rank with respect to this background distribution.<br>Analyst: Michiel de Hoon <br><br>
link to source dataset <br>
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/mm9.table.txt data]
}}
----
{{#if:{{{great_results_mouse}}}|
<table id="great_table_mouse" class="ff_sample_list stripe cell-border order-column compact dataTable no-footer">
<html><thead></html>
<th>GO ID</th><th>GO Term</th><th>p-value</th>{{#arraydefine:tmp_go_stat_mouse|{{{great_results_mouse}}}|!}}
<html></thead><tbody></html><!--{{#arraymap:{{{great_results_mouse}}}|!|$|<tr><td>{{#replace:$|;|</td><td>}}</td></tr>|}}-->
{{#loop:p
  | 0         
  | {{#arraysize:tmp_go_stat_mouse}}
  | <nowiki/><tr>{{#arraydefine:tmp_go_stat_mouse{{#var:p}}|{{#arrayindex:tmp_go_stat_mouse|{{#var:p}}}}|;}}{{#loop:j
  | 0         
  | {{#arraysize:tmp_go_stat_mouse{{#var:p}}}}
  | <nowiki/>
  {{#vardefine:inner_el_mouse|{{#arrayindex:tmp_go_stat_mouse{{#var:p}}|{{#var:j}} }}  }}
  <td>{{#ifeq:{{#sub:{{#var:inner_el_mouse}}|0|3}}|GO:|[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term={{#var:inner_el_mouse}} {{#var:inner_el_mouse}}]|{{#var:inner_el_mouse}} }}</td>}}</tr>}}
<html></tbody></html>
<table>
|no results for this motif
}}
 
 
 
 
{{#arraymap:{{{novel_motifs_mouse_sample_pval}}}|,|$
|{{#set:novel_motifs_sample_pval=$}}
}}
 
{{#arraymap:{{{novel_motifs_human_sample_pval}}}|,|$
|{{#set:novel_motifs_sample_pval=$}}
}}
 
 
[[Category:Novel_motif]]
[[Category:Motif]]

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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