Personal tools

Template:Known motif: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(49 intermediate revisions by one other user not shown)
Line 1: Line 1:
<html>
<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/datatables/media/css/jquery.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";
</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/datatables/media/js/jquery.dataTables.min.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/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
<style type="text/css">
<style type="text/css">
#wrap{
#wrap{
Line 83: Line 83:
if( necessary_part.length>1 ){
if( necessary_part.length>1 ){
subclusters = necessary_part.split("~");
subclusters = necessary_part.split("~");
if(subclusters.length>1 ){
if(subclusters.length>0 ){
var tmp;
var tmp;
for(j=0;j<subclusters.length;j++){
for(j=0;j<subclusters.length;j++){
Line 111: Line 111:
"sScrollY": "500px",
"sScrollY": "500px",
"bScrollCollapse": true,
"bScrollCollapse": true,
                "iDisplayLength": 5,
"aLengthMenu": [[5, 10, -1], [5, 10, "All"]],
"bPaginate": true,
"bPaginate": true,
"bFilter": true,
"bFilter": true,
Line 123: Line 125:
if(motif_db== "JASPAR"){
if(motif_db== "JASPAR"){
  sReturn =motif_db+"_motif:"+motif_id;
  sReturn =motif_db+"_motif:"+motif_id;
                   return '<a href=/resource_browser/'+sReturn+'>'+motif_id+'</a>';
                   return '<a href=/5/sstar/'+sReturn+'>'+motif_id+'</a>';
}else
}else
{
{
Line 158: Line 160:


$('.dataTables_scrollBody').css("resize", "vertical");
$('.dataTables_scrollBody').css("resize", "vertical");
motif_table_tools = new TableTools( motif_table, {"sSwfPath": "/resource_browser/rb_js/datatables/extras/TableTools/media/swf/copy_csv_xls_pdf.swf", "aButtons": [ {"sExtends": "copy", "mColumns": "visible"}, {"sExtends": "csv", "mColumns": "visible"}, {"sExtends": "pdf", "mColumns": "visible"} ]});
motif_table_tools = new TableTools( motif_table, {"sSwfPath": "/5/sstar/rb_js/datatables/extras/TableTools/media/swf/copy_csv_xls_pdf.swf", "aButtons": [ {"sExtends": "copy", "mColumns": "visible"}, {"sExtends": "csv", "mColumns": "visible"}, {"sExtends": "pdf", "mColumns": "visible"} ]});


$('#motif_export_tool').before( motif_table_tools.dom.container );
$('#motif_export_tool').before( motif_table_tools.dom.container );
Line 181: Line 183:
var uri = decodeURIComponent(motif_id);
var uri = decodeURIComponent(motif_id);


return '<a class="thumbnail" href="#thumb"><img src="/resource_browser/seqlogos/'+tmp+"/"+ uri +'.png" width="80px" height="26px" border="0"/>'+
return '<a class="" href="/5/sstar/seqlogos/'+tmp+"/"+ uri + '.png"><img src="/5/sstar/seqlogos/'+tmp+"/"+ uri +'.png" width="80px" height="26px" border="0"/></a>';
'<span><img src="/resource_browser/seqlogos/'+tmp+"/"+ uri + '.png"/></span></a>';


    
    
Line 219: Line 220:
<div id ="wrap" style="background-color:White; {round corners}} padding: 0.5em 1em;">
<div id ="wrap" style="background-color:White; {round corners}} padding: 0.5em 1em;">
<div id="left_col">
<div id="left_col">
{{#info:<br>Analyst:  Ivan Kulakovskiy <br>
{{#info:<br>Analyst:  Ivan Kulakovskiy,Ilya Vorontsov, Vsevolod Makeev, Michiel de Hoon <br>
208 clusters of known motifs (with the phase1 procedure <br> to  select representative cluster members based on motif-promoter corelations}}
May 2013, Collection Name: Non-redundant known motifs<br>
Analysis information: 208 clusters of known motifs were produced by MACRO-APE [http://autosome.ru/macroape/]  using the general phase1 motif clustering procedure applied for known motif collections.
<br>207 of 208 clusters had at least one member passing motif-promoter correlation procedure.For these clusters representative motifs were selected based on motif-promoter correlation values.For each cluster only motifs with an average distance to of ther members not greater than mean+SD were considered as representatives.
}}
<br>
<br>
* Name    :[[knownname::{{{name}}}]]
* Name    :[[knownname::{{{name}}}]]
Line 226: Line 230:
* Id      :[[motifid::{{{representative_motif_id}}}]]
* Id      :[[motifid::{{{representative_motif_id}}}]]
* name    :[[motifname::{{{representative_motif_name}}}]]
* name    :[[motifname::{{{representative_motif_name}}}]]
* score    :[[motifscore::{{{score}}}]]
* score    :[[motifscore::{{{score}}}]]<br>
* Entry name : [http://www.uniprot.org/uniprot/?query={{{uniprot_entry_name}}} {{{uniprot_entry_name}}}]
* External refs: {{#arraymap:{{{entrez_gene_id}}}|,|$|
* Entrez GeneID :[http://www.ncbi.nlm.nih.gov/gene?term={{#if: {{{entrez_gene_id}}}==-|no |{{{entrez_gene_id}}}}}
<span>
{{{entrez_gene_id}}}  {{{entrez_gene_id}}}]
:[http://www.ncbi.nlm.nih.gov/gene?term=$  EntrezGene:[[GeneID::$]]]<html><br></html>[http://www.uniprot.org/uniprot/?query=$  UniProt:$]
</span>
|}}
 
* Internal refs: {{#arraymap:{{{entrez_gene_id}}}|,|$|
<span>
:[[EntrezGene:$]]<html><br></html>
</span>
|}}


<!--{{#ifeq: {{{representative_motif_db}}} | JASPAR |[[JASPAR_motif:{{{representative_motif_id}}}|]] | not equal}}-->  
<!--{{#ifeq: {{{representative_motif_db}}} | JASPAR |[[JASPAR_motif:{{{representative_motif_id}}}|]] | not equal}}-->  
Line 248: Line 260:
}
}


var tmp ="/resource_browser/seqlogos/"+ "known_motifs"+"_201304"+"/"+motif_id.toLowerCase()+".png";
var tmp ="/5/sstar/seqlogos/"+ "known_motifs"+"_201304"+"/"+motif_id.toLowerCase()+".png";
var uri = encodeURI(tmp);
var uri = encodeURI(tmp);
  return number_prefix='<img src="'+uri+'"  id="pic" width ="310" height = "100">'
  return number_prefix='<img src="'+uri+'"  id="pic" width ="310" height = "100">'
Line 265: Line 277:
| <table cellspacing="0" border="1"><tr><td>{{#replace:{{#replace:{{{PWM}}}|!|</td></tr><tr><td>}}|;|</td><td>}}</tr></table>
| <table cellspacing="0" border="1"><tr><td>{{#replace:{{#replace:{{{PWM}}}|!|</td></tr><tr><td>}}|;|</td><td>}}</tr></table>
|}
|}
== Sub Motif Members ==
== Sub Motif Members ==
<span id = "motif_export_tool"></span>
<span id = "motif_export_tool"></span>
<table cellpadding="0" cellspacing="0" border="0" class="display" id="example"></table>
<table cellpadding="0" cellspacing="0" border="0" class="display" id="example"></table>
{{#set:EntrezGene={{{entrez_gene_id}}}}}
[[Category:Motif]]
[[Category:NonRedundantMotifCluster]]

Latest revision as of 15:19, 24 August 2015

Representative Motif

<br>Analyst: Ivan Kulakovskiy,Ilya Vorontsov, Vsevolod Makeev, Michiel de Hoon <br>May 2013, Collection Name: Non-redundant known motifs<br>Analysis information: 208 clusters of known motifs were produced by MACRO-APE [1] using the general phase1 motif clustering procedure applied for known motif collections.<br>207 of 208 clusters had at least one member passing motif-promoter correlation procedure.For these clusters representative motifs were selected based on motif-promoter correlation values.For each cluster only motifs with an average distance to of ther members not greater than mean+SD were considered as representatives.

  • Name  :{{{name}}}
  • db  :{{{representative_motif_db}}}
  • Id  :{{{representative_motif_id}}}
  • name  :{{{representative_motif_name}}}
  • score  :{{{score}}}
  • External refs:
EntrezGene:{{{entrez_gene_id}}}
UniProt:{{{entrez_gene_id}}}

  • Internal refs:
[[EntrezGene:{{{entrez_gene_id}}}]]


Motif matrix
{{{PWM}}}

Sub Motif Members