Template:Known motif: Difference between revisions
From FANTOM5_SSTAR
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<html> | <html> | ||
<style type="text/css" title="currentStyle"> | <style type="text/css" title="currentStyle"> | ||
@import "/ | @import "/5/sstar/rb_js/datatables/media/css/jquery.dataTables.css"; | ||
@import "/ | @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"> | <script type="text/javascript"> | ||
var motif_prefix=""; | var motif_prefix=""; | ||
var sReturn =""; | var sReturn =""; | ||
var motif_id =""; | var motif_id =""; | ||
var motif_db ="UNDEFINED"; | |||
var m_data = new Array(); | |||
$(document).ready(function() { | $(document).ready(function() { | ||
var subclusters=""; | |||
var subclusters_content = "</html>{{{motif_cluster_2013_march_motif_members}}}<html>"; | |||
var subclusters_content = subclusters_content.split("/"); | |||
{ | for(i=0;i<subclusters_content.length;i++){ | ||
{" | var necessary_part=""; | ||
tmp_element = subclusters_content[i]; | |||
var total_length =tmp_element.length; | |||
if(total_length>1){ | |||
{" | var first_occurrence = tmp_element.indexOf(":"); | ||
{" | necessary_part = tmp_element.substring(first_occurrence+1,total_length); | ||
motif_db = tmp_element.substring(0,first_occurrence); | |||
}else{ | |||
} | |||
if( necessary_part.length>1 ){ | |||
subclusters = necessary_part.split("~"); | |||
if(subclusters.length>0 ){ | |||
var tmp; | |||
for(j=0;j<subclusters.length;j++){ | |||
tmp =new Array(); | |||
tmp.push(motif_db); | |||
var sub_tmp= subclusters[j].split(";"); | |||
if(sub_tmp.length>1){ | |||
var | for(k=0;k<sub_tmp.length;k++){ | ||
tmp.push(sub_tmp[k]); | |||
} | |||
}else{ | |||
motif_id = | tmp.push(sub_tmp[0]); | ||
if( | tmp.push(""); | ||
} | |||
motif_id = | tmp.push(""); | ||
m_data.push(tmp); | |||
} | |||
m_data.length; | |||
} | |||
} | |||
else{ | |||
} | |||
} | |||
motif_table = $('#example').dataTable({ | |||
"sScrollY": "500px", | |||
"bScrollCollapse": true, | |||
"iDisplayLength": 5, | |||
"aLengthMenu": [[5, 10, -1], [5, 10, "All"]], | |||
"bPaginate": true, | |||
"bFilter": true, | |||
"bInfo": true, | |||
"aaData": m_data, | |||
"aoColumnDefs":[ | |||
{"aTargets":[0],"sTitle": "motif_db"}, | |||
{"aTargets":[1],"sTitle": "motif_id", "fnRender": function ( obj ) { | |||
motif_id = obj.aData[ obj.iDataColumn ]; | |||
motif_prefix = motif_id ; | |||
motif_db = obj.aData[ 0 ]; | |||
if(motif_db== "JASPAR"){ | |||
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":[3],"sTitle": "Sequence logo","fnRender": function (obj) { | |||
motif_id = motif_prefix; | |||
var number_prefix =loqoNumberPrefixLocator(); | |||
return logoLocator(motif_db,motif_id,number_prefix); } | |||
} | |||
], | |||
"aaSorting": [[ 0, "asc" ]], | |||
}); | |||
$('.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){ | |||
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>'; | |||
} | |||
function loqoNumberPrefixLocator() | |||
{ | |||
var number_prefix =""; | var number_prefix =""; | ||
if(motif_db == "HOCOMOCO"){ | |||
if( | |||
number_prefix = "426"; | number_prefix = "426"; | ||
} | } | ||
else if( | else if(motif_db== "JASPAR"){ | ||
number_prefix = "130"; | number_prefix = "130"; | ||
} | } | ||
else if( | else if(motif_db == "HOMER"){ | ||
number_prefix = "138"; | number_prefix = "138"; | ||
} | } | ||
else if( | else if(motif_db == "SWISSREGULON"){ | ||
number_prefix = "190"; | number_prefix = "190"; | ||
} | } | ||
else if( | else if(motif_db == "UNIPROBE"){ | ||
number_prefix = "413"; | number_prefix = "413"; | ||
} | } | ||
else if( | else if(motif_db == "ENCODE"){ | ||
number_prefix = "683"; | number_prefix = "683"; | ||
} | |||
return number_prefix; | |||
} | } | ||
</script> | </script> | ||
</html> | |||
== Representative Motif == | |||
<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}}}]] | |||
* db :[[motifdb::{{{representative_motif_db}}}]] | |||
* Id :[[motifid::{{{representative_motif_id}}}]] | |||
* name :[[motifname::{{{representative_motif_name}}}]] | |||
* score :[[motifscore::{{{score}}}]]<br> | |||
* External refs: {{#arraymap:{{{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> | |||
<script type="text/javascript"> | |||
var motif_id= "</html>{{{name}}}<html>"; | |||
document.write(logoLocator2(motif_id)); | |||
function logoLocator2(motif_id){ | |||
var index = motif_id.indexOf(' '); | |||
if (index >= 0) { | |||
motif_id= motif_id.substr(0, index - 1) +"_"+ motif_id.substr(index); | |||
} | |||
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">' | |||
; | |||
} | |||
</script> | |||
</html> | </html> | ||
</div> | |||
== | |||
</div> | |||
<table cellpadding="0" cellspacing="0" border="0" class="display" id=" | |||
{| 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> | |||
{{#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:
- Internal refs:
- [[EntrezGene:{{{entrez_gene_id}}}]]
Motif matrix | |
---|---|
|
Sub Motif Members