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Template:Known motif: Difference between revisions

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<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>
<script type="text/javascript" src="/5/sstar/rb_js/datatables/media/js/jquery.dataTables.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">
#wrap{
clear: both;
width: 750px;
padding-bottom: 5px;
background:#fff;
overflow:hidden;
}
#left_col{
float: left;
display:inline;
width:370px;
margin: 10px;
background:#fff;
}
#right_col{
float: right;
width: 330px;
padding-top: 20px;
margin:15px;
background:#fff;
}
.thumbnail{
position: relative;
z-index: 0;
}
 
.thumbnail:hover{
background-color: transparent;
z-index: 0;
}
 
.thumbnail span{ /*CSS for enlarged image*/
position: absolute;
background-color: transparent;
padding: 1px;
left: -410px;
border: 1px dashed gray;
visibility: hidden;
color: black;
text-decoration: none;
}
 
.thumbnail span img{ /*CSS for enlarged image*/
border-width: 0;
padding: 1px;
}
 
.thumbnail:hover span{ /*CSS for enlarged image on hover*/
visibility: visible;
top: 0;
right: 40px; /*position where enlarged image should offset horizontally */
}
</style>
</style>
<script type="text/javascript" src="/resource_browser/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">
<script type="text/javascript">
var motif_prefix="";
var motif_prefix="";
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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 54: Line 108:




$('#example').dataTable({
motif_table = $('#example').dataTable({              
"sScrollY": "300px",
"sScrollY": "500px",
"bScrollCollapse": true,
"bScrollCollapse": true,
                "iDisplayLength": 5,
"aLengthMenu": [[5, 10, -1], [5, 10, "All"]],
"bPaginate": true,
"bPaginate": true,
"bFilter": true,
"bFilter": true,
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                   motif_prefix = motif_id ;
                   motif_prefix = motif_id ;
                   motif_db = obj.aData[ 0 ];
                   motif_db = obj.aData[ 0 ];
                  sReturn =motif_db+"_motif:"+motif_id;
if(motif_db== "JASPAR"){
                   return '<a href=/resource_browser/'+sReturn+'>'+motif_id+'</a>';}
sReturn =motif_db+"_motif:"+motif_id;
                   return '<a href=/5/sstar/'+sReturn+'>'+motif_id+'</a>';
}else
{
return motif_id;
}
                }
},
{"aTargets":[2],"sTitle": "motif_name", "fnRender": function (obj) {
                  motif_id = motif_prefix;
var ret ="";
if(motif_db=="HOCOMOCO" || motif_db=="UNIPROBE" || motif_db=="HOMER")
ret=motif_id.split(/_(.+)?/)[0];
else if (motif_db=="SWISSREGULON"){
var i = motif_id.lastIndexOf('.');
if (i != -1) {
    ret= motif_id.substr(0, i) ;
}
}
else ret ="";
return ret;
 
}
},
},
{"aTargets":[2],"sTitle": "motif_name" },
{"aTargets":[3],"sTitle": "Sequence logo","fnRender": function (obj) {
{"aTargets":[3],"sTitle": "Sequence logo","fnRender": function (obj) {
                   motif_id = motif_prefix;
                   motif_id = motif_prefix;
Line 81: Line 158:


});
});
$('.dataTables_scrollBody').css("resize", "vertical");
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 );


});
});


function logoLocator(motif_db,motif_id,number_prefix){
function logoLocator(motif_db,motif_id,number_prefix){
var tmp = "KNOWN"+"_"+motif_db +"_"+number_prefix+"_201304";
 
return '<img src="/resource_browser/seqlogos/' +tmp+"/"+ motif_id+ '.png" width ="80" height = "20">';  
motif_id= $.trim(motif_id);
 
if(motif_db=="SWISSREGULON"){
motif_id= motif_id.replace('(', '{');
    motif_id= motif_id.replace(')', '}');
 
}else{
    motif_id= motif_id.replace('{', '(');
    motif_id= motif_id.replace('}', ')');
}
 
 
var tmp ="KNOWN"+"_"+motif_db +"_"+number_prefix+"_201304";
var uri = decodeURIComponent(motif_id);
 
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>';
 
 
}
}


Line 119: Line 218:
</html>
</html>
== Representative Motif ==   
== Representative Motif ==   
{{#info:<br>Analyst: Ivan}}
<div id ="wrap" style="background-color:White; {round corners}} padding: 0.5em 1em;">
<div id="left_col">
{{#info:<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 [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>
* Name    :[[knownname::{{{name}}}]]
* Name    :[[knownname::{{{name}}}]]
* db      :[[database::{{{representative_motif_db}}}]]
* db      :[[motifdb::{{{representative_motif_db}}}]]
* Id      :[[motifid::{{{representative_motif_id}}}]]
* Id      :[[motifid::{{{representative_motif_id}}}]]
* name    :[[name::{{{representative_motif_name}}}]]
* name    :[[motifname::{{{representative_motif_name}}}]]
* score    :[[score::{{{score}}}]]
* score    :[[motifscore::{{{score}}}]]<br>
* Entry name : [http://www.uniprot.org/uniprot/{{{uniprot_entry_name}}} {{{uniprot_entry_name}}}]
* External refs: {{#arraymap:{{{entrez_gene_id}}}|,|$|
* Entrez GeneID :[http://www.ncbi.nlm.nih.gov/gene/{{{entrez_gene_id}}}  {{{entrez_gene_id}}}]
<span>
:[http://www.ncbi.nlm.nih.gov/gene?term=$  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}}-->
</div>
<div id="right_col">
<html>
<html>
<script type="text/javascript">
<script type="text/javascript">
var tmp = loqoNumberPrefixLocator(</html>{{{representative_motif_db}}}<html>);
var docs = document.getElementById("seqlogo");
  docs.setAttribute("src", "tmp");


var motif_id= "</html>{{{name}}}<html>";
document.write(logoLocator2(motif_id));


function loqoNumberPrefixLocator(motif-db)
function logoLocator2(motif_id){
{
var index = motif_id.indexOf(' ');
var number_prefix ="";


if(motif-db == "HOCOMOCO"){
if (index >= 0) {
number_prefix = "426";
    motif_id= motif_id.substr(0, index - 1) +"_"+ motif_id.substr(index);
}
}
else if(motif-db== "JASPAR"){
 
number_prefix = "130";
var tmp ="/5/sstar/seqlogos/"+ "known_motifs"+"_201304"+"/"+motif_id.toLowerCase()+".png";
var uri = encodeURI(tmp);
return number_prefix='<img src="'+uri+'" id="pic" width ="310" height = "100">'
;  
}
}
else if(motif-db == "HOMER"){
number_prefix = "138";
}
else if(motif-db == "SWISSREGULON"){
number_prefix = "190";
}
else if(motif-db == "UNIPROBE"){
number_prefix = "413";
}
else if(motif-db == "ENCODE"){
number_prefix = "683";
}
return number_prefix;
}
</script>
</script>
<img id="seqlogo" src='#'> 
</html>
</html>
== Sub Clusters ==
</div>
 
</div>
 
 
{| class="wikitable mw-collapsible mw-collapsed" style="width:500px"
! Motif matrix
|-
| <table cellspacing="0" border="1"><tr><td>{{#replace:{{#replace:{{{PWM}}}|!|</td></tr><tr><td>}}|;|</td><td>}}</tr></table>
|}
 
== Sub Motif Members ==
<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

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