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> | </style> | ||
<script type="text/javascript" src="/ | <script type="text/javascript" src="/5/sstar/rb_js/datatables/media/js/jquery.dataTables.min.js"></script> | ||
<script type="text/javascript" src="/ | <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{ | ||
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float: left; | float: left; | ||
display:inline; | display:inline; | ||
width: | width:370px; | ||
margin: 10px; | margin: 10px; | ||
background:#fff; | background:#fff; | ||
| Line 35: | Line 35: | ||
.thumbnail:hover{ | .thumbnail:hover{ | ||
background-color: transparent; | background-color: transparent; | ||
z-index: | z-index: 0; | ||
} | } | ||
.thumbnail span{ /*CSS for enlarged image*/ | .thumbnail span{ /*CSS for enlarged image*/ | ||
position: absolute; | position: absolute; | ||
background-color: | background-color: transparent; | ||
padding: | padding: 1px; | ||
left: - | left: -410px; | ||
border: 1px dashed gray; | border: 1px dashed gray; | ||
visibility: hidden; | visibility: hidden; | ||
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.thumbnail span img{ /*CSS for enlarged image*/ | .thumbnail span img{ /*CSS for enlarged image*/ | ||
border-width: 0; | border-width: 0; | ||
padding: | padding: 1px; | ||
} | } | ||
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visibility: visible; | visibility: visible; | ||
top: 0; | top: 0; | ||
right: 40px; /*position where enlarged image should offset horizontally */ | |||
} | } | ||
</style> | </style> | ||
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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> | if(subclusters.length>0 ){ | ||
var tmp; | var tmp; | ||
for(j=0;j<subclusters.length;j++){ | for(j=0;j<subclusters.length;j++){ | ||
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"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, | ||
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if(motif_db== "JASPAR"){ | if(motif_db== "JASPAR"){ | ||
sReturn =motif_db+"_motif:"+motif_id; | sReturn =motif_db+"_motif:"+motif_id; | ||
return '<a href=/ | return '<a href=/5/sstar/'+sReturn+'>'+motif_id+'</a>'; | ||
}else | }else | ||
{ | { | ||
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} | } | ||
}, | }, | ||
{"aTargets":[2],"sTitle": "motif_name" }, | {"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) { | {"aTargets":[3],"sTitle": "Sequence logo","fnRender": function (obj) { | ||
motif_id = motif_prefix; | motif_id = motif_prefix; | ||
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$('.dataTables_scrollBody').css("resize", "vertical"); | $('.dataTables_scrollBody').css("resize", "vertical"); | ||
motif_table_tools = new TableTools( motif_table, {"sSwfPath": "/ | 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 ); | $('#motif_export_tool').before( motif_table_tools.dom.container ); | ||
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var uri = decodeURIComponent(motif_id); | var uri = decodeURIComponent(motif_id); | ||
return '<a class="" href="/5/sstar/seqlogos/'+tmp+"/"+ uri + '.png"><img src="/5/sstar/seqlogos/'+tmp+"/"+ uri +'.png" width="80px" height="26px" border="0"/></a>'; | |||
<img src="/ | |||
} | } | ||
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<div id ="wrap" style="background-color:White; {round corners}} padding: 0.5em 1em;"> | <div id ="wrap" style="background-color:White; {round corners}} padding: 0.5em 1em;"> | ||
<div id="left_col"> | <div id="left_col"> | ||
{{#info:<br>Analyst: Ivan Kulakovskiy <br> | {{#info:<br>Analyst: Ivan Kulakovskiy,Ilya Vorontsov, Vsevolod Makeev, Michiel de Hoon <br> | ||
208 clusters of known motifs | May 2013, Collection Name: Non-redundant known motifs<br> | ||
Analysis information: 208 clusters of known motifs were produced by MACRO-APE [http://autosome.ru/macroape/] using the general phase1 motif clustering procedure applied for known motif collections. | |||
<br>207 of 208 clusters had at least one member passing motif-promoter correlation procedure.For these clusters representative motifs were selected based on motif-promoter correlation values.For each cluster only motifs with an average distance to of ther members not greater than mean+SD were considered as representatives. | |||
}} | |||
<br> | <br> | ||
* Name :[[knownname::{{{name}}}]] | * Name :[[knownname::{{{name}}}]] | ||
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* Id :[[motifid::{{{representative_motif_id}}}]] | * Id :[[motifid::{{{representative_motif_id}}}]] | ||
* name :[[motifname::{{{representative_motif_name}}}]] | * name :[[motifname::{{{representative_motif_name}}}]] | ||
* score :[[motifscore::{{{score}}}]] | * score :[[motifscore::{{{score}}}]]<br> | ||
* | * External refs: {{#arraymap:{{{entrez_gene_id}}}|,|$| | ||
<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}}--> | <!--{{#ifeq: {{{representative_motif_db}}} | JASPAR |[[JASPAR_motif:{{{representative_motif_id}}}|]] | not equal}}--> | ||
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} | } | ||
var tmp ="/ | 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 =" | return number_prefix='<img src="'+uri+'" id="pic" width ="310" height = "100">' | ||
; | |||
} | } | ||
</script> | </script> | ||
</html> | </html> | ||
</div> | </div> | ||
</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 == | == 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:
- Internal refs:
- [[EntrezGene:{{{entrez_gene_id}}}]]
| Motif matrix | |
|---|---|
|
Sub Motif Members
