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Difference between revisions of "Template:EntrezGene" - resource_browser
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Difference between revisions of "Template:EntrezGene"

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{{Loading|loadingimage=sprites.gif}}<html><style type="text/css"
+
{{Loading|loadingimage=sprites.gif}}<html><script language="javascript" type="text/javascript" src="/resource_browser/rb_js/flot/jquery.flot.js"></script><script language="javascript" type="text/javascript" src="/resource_browser/rb_js/flot/jquery.flot.axislabels.js"></script>
table.detailinfo td { background-color: #FFFFFF;}
+
<script type="text/javascript" src="/resource_browser/rb_js/custom/expoconvert.js"></script></html>
table.detailinfo th { background-color: #fbfffb; color:#054950;}
+
<table>
</style></html>
+
<tr><th scope="row" align="right" valign="top">[[Property:Symbol|Symbol]]:</th><td>{{#if:{{{Symbol}}}|[[Symbol::{{{Symbol}}}]]|NA}}</td></tr>
<div style="width:100%; float:none;">
+
<tr><th scope="row" align="right" valign="top">[[Property:Description|Description]]:</th><td>{{#if:{{{description}}}|[[description::{{{description}}}]]|NA}}</td></tr>
<table class="detailinfo">
+
<tr><th scope="row" align="right" valign="top">[[Property:Synonyms|Synonyms]]:</th><td>{{#switch:{{{Synonyms}}}|- = NA| |#default = {{#show:{{FULLPAGENAME}}|?Synonyms}} }}</td></tr>
<tr><th scope="row" align="right" valign="top"> [[Property:Symbol|Symbol]]:</th><td>{{#if:{{{Symbol}}}|[[Symbol::{{{Symbol}}}]]|NA}}</td></tr>
+
<tr><th scope="row" align="right" valign="top">Species:</th><td>{{#set:tax_id={{{tax_id}}}}}{{#switch:{{{tax_id}}}|9606=Human (Homo sapiens)|10090=Mouse (Mus musculus)|NA}}</td></tr>
<tr><th scope="row" align="right" valign="top"> [[Property:Description|Description]]:</th><td>{{#if:{{{description}}}|[[description::{{{description}}}]]|NA}}</td></tr>
+
<!--
<tr><th scope="row" align="right" valign="top">[[Property:Synonyms|Synonyms]]:</th><td>{{#switch:{{{Synonyms}}}|- = NA| |#default = {{#show:{{FULLPAGENAME}}|?Synonyms}} }}</td></tr><tr><th scope="row" align="right" valign="top">Species:</th><td>{{#set:tax_id={{{tax_id}}}}}{{#switch:{{{tax_id}}}|9606=Human (Homo sapiens)|10090=Mouse (Mus musculus)|NA}}</td></tr>
+
<tr><th scope="row" align="right" valign="top">[[Property:tax_id|Tax ID]]:</th><td>{{#if:{{{tax_id}}}|[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=[[tax_id::{{{tax_id}}}]]&mode=Info {{{tax_id}}}]|NA}}</td></tr>
<!--<tr><th scope="row" align="right" valign="top">[[Property:tax_id|Tax ID]]:</th><td>[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=[[tax_id::{{{tax_id}}}]]&mode=Info {{{tax_id}}}]</td></tr>-->
+
--><tr><th scope="row" align="right" valign="top">Xrefs:</th><td>{{#if:{{{GeneID}}}|{{GeneExternalRefs|{{{tax_id}}}|{{{chromosome}}}|{{{GeneID}}}|{{{Symbol}}}|{{{Synonyms}}}|{{{dbXrefs}}}}}|NA}}</td></tr>
<tr><th scope="row" align="right" valign="top">Xrefs:</th><td>{{#if:{{{GeneID}}}|{{GeneExternalRefs|{{{tax_id}}}|{{{chromosome}}}|{{{GeneID}}}|{{{Symbol}}}|{{{Synonyms}}}|{{{dbXrefs}}}}}|NA}}</td></tr>
+
<tr><th scope="row" align="right" valign="top">Associated motifs:</th><td>{{#ifeq: {{#expr:{{#ask:[[Category:Motif]][[Name::~{{{Symbol}}}]]|?#|format=count}} }} | 0 | NA |{{#if:{{#ask:[[Category:Motif]][[Name::~{{{Symbol}}}]]|?Name}}|{{#ask:[[Category:Motif]][[Name::~{{{Symbol}}}]]|template=Jasparlogo_genepage|link=none}}|}}}}
<tr><th scope="row" align="right" valign="top">Associated motifs:</th><td>{{#ifeq:{{#expr:{{#ask:[[Category:SwissregulonMotif]][[EntrezGene::~{{{GeneID}}}]]|?name|format=count}}+{{#ask:[[Category:Motif]][[Name::~{{{Symbol}}}]]|?#|format=count}}+{{#ask:[[Category:NonRedundantMotifCluster]][[EntrezGene::~{{{GeneID}}}]]|?#|format=count}} }} | 0 | NA | {{#if:{{#ask:[[Category:SwissregulonMotif]][[EntrezGene::~{{{GeneID}}}]]}}|{{#ask:[[Category:SwissregulonMotif]][[EntrezGene::~{{{GeneID}}}]]
 
|?name
 
|format=template
 
|link=none
 
|template=SwissregulonResult_withSeqLogo
 
|sep=
 
}}|
 
}}
 
<span><br><br>
 
{{#if:{{#ask:[[Category:Motif]][[Name::~{{{Symbol}}}]]}}| {{#ask:[[Category:Motif]][[Name::~{{{Symbol}}}]]|template=Jasparlogo_genepage|link=none}}|}}
 
</span>
 
<span>{{#arraymap:{{{GeneID}}}|,|$|
 
{{NonRedundantMotifRender|$}}
 
}}</span>}}  
 
 
</td></tr>
 
</td></tr>
 
<tr><th scope="row" align="right" valign="top">Transcripton Factor?: </th><td>{{#switch:{{{tf?}}}|yes=[[tf?::Yes]]|[[tf?::No]]}}</td></tr>
 
<tr><th scope="row" align="right" valign="top">Transcripton Factor?: </th><td>{{#switch:{{{tf?}}}|yes=[[tf?::Yes]]|[[tf?::No]]}}</td></tr>
<tr><th scope="row" align="right" valign="top">TSS regions:</th><td>{{#ask:[[Category:FFCP]][[EntrezGene::{{{GeneID}}}]]
+
<tr><th scope="row" align="right" valign="top"> TSS regions:</th><td>{{#if:{{#ask:[[Category:FFCP]][[EntrezGene::{{{GeneID}}}]]
 
|?Short description
 
|?Short description
 
|format=ul
 
|format=ul
 
|headers=hide
 
|headers=hide
 
|sort=Short description
 
|sort=Short description
}}
+
}}|{{#ask:[[Category:FFCP]][[EntrezGene::{{{GeneID}}}]]
 +
|?Short description
 +
|format=ul
 +
|headers=hide
 +
|sort=Short description
 +
}}|NA}}
 
</td></tr>
 
</td></tr>
 
</table>
 
</table>
</div>
 
 
<html>
 
<html>
 
<script language="javascript" type="text/javascript">
 
<script language="javascript" type="text/javascript">
Line 46: Line 36:
 
});
 
});
 
</script>
 
</script>
</html>
+
</html><br>
<h2>View on UCSC genome browser OSC local mirror</h2>
+
{{Fontsize|3|View on UCSC genome browser }}
 +
----
 
<div id="ucsc_snap_view" style="width:750px; height:30px; border-style:solid; border-width:1px; border-color:#aaaaaa;  overflow:auto;">
 
<div id="ucsc_snap_view" style="width:750px; height:30px; border-style:solid; border-width:1px; border-color:#aaaaaa;  overflow:auto;">
 
Mouse over to see Genome browser image, Click image to go to Genome browser
 
Mouse over to see Genome browser image, Click image to go to Genome browser
{{#ucsc_gb_link:{{#replace:{{#ask:[[Category:FFCP]][[Short description::p1@{{{Symbol}}}]]|link=none|headers=hide|limit=1|searchlabel=}}|FFCP_PHASE1:|}}|https://fantom5-collaboration.gsc.riken.jp/ucsc/|3000}}
+
{{#ucsc_gb_link:{{#replace:{{#ask:[[Category:FFCP]][[Short description::p1@{{{Symbol}}}]]|link=none|headers=hide|limit=1|searchlabel=}}|FFCP_PHASE1:|}}}}
</div>
+
</div><br>
 
+
{{Fontsize|3|TSS expression}}
== TSS expression ==
+
----
 
<html>
 
<html>
 
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.min.js"></script>
 
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.min.js"></script>
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</html>
 
</html>
 +
 
<html>
 
<html>
 
<style type="text/css">   
 
<style type="text/css">   
Line 90: Line 82:
 
var data = [];
 
var data = [];
 
var plotdata = [];
 
var plotdata = [];
 
+
var slist = [];
  
 
// chart checkbox
 
// chart checkbox
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data.push({"label": $(oTable.fnSettings().aoColumns[i2].sTitle).text(), "data": plots});
 
data.push({"label": $(oTable.fnSettings().aoColumns[i2].sTitle).text(), "data": plots});
 
}
 
}
 +
slist = [];
 +
for (i1=2, len1=$('#gene_exptable tr').length; i1<len1; i1++) {
 +
    slist.push($("#gene_exptable tr")[i1].cells[0].innerHTML);
 +
}
 
}
 
}
  
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                     x = item.datapoint[0].toFixed(0),
 
                     x = item.datapoint[0].toFixed(0),
 
                     y = item.datapoint[1].toFixed(2);
 
                     y = item.datapoint[1].toFixed(2);
                 
+
 
 
                     showTooltip(item.pageX, item.pageY,
 
                     showTooltip(item.pageX, item.pageY,
                               "TSS: "+ item.series.label +"<br>TPM: "+y);
+
                               "Sample: "+slist[item.dataIndex]+"<br>TSS: "+ item.series.label +" TPM: "+y);
 
                 }
 
                 }
 
             }
 
             }
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     });
 
     });
 
// clicking point function end
 
// clicking point function end
 +
 +
  
 
var oTableTools = new TableTools(oTable, {"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"} ]});
 
var oTableTools = new TableTools(oTable, {"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"} ]});
 
 
$('#export_tool').before( oTableTools.dom.container );
 
$('#export_tool').before( oTableTools.dom.container );
 
 
  
 
} );
 
} );
 
</script>
 
</script>
<span id="export_tool"></span>
+
<span id="export_tool"></span><br><br>
 
</html>
 
</html>
  
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<br><br>
 
<br><br>
 
<div id="gene_exptable_chart" style="float:left;width:600px;height:300px;"></div>
 
<div id="gene_exptable_chart" style="float:left;width:600px;height:300px;"></div>
<br>
+
<html><br><br></html>
 
<div id="gene_exptable_chart_chkbox" style="float:left;"></div>
 
<div id="gene_exptable_chart_chkbox" style="float:left;"></div>
 
<div style="clear:both;"></div>
 
<div style="clear:both;"></div>
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</style></html>
 
</style></html>
  
== ENCODE TF ChIP-seq peak enrichment analysis ==
+
{{Fontsize|3|ENCODE TF ChIP-seq peak enrichment analysis }}{{#info:Analyst: Erik Arner <br>Summary: For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <nowiki><=</nowiki>  0.05)  after Benjamini-Hochberg correction were retained.  <br>
{{#info: Method: For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <nowiki><=</nowiki>  0.05)  after Benjamini-Hochberg correction were retained.  <br>Analyst: Erick Arner}}  
+
<br><br>link to source dataset.<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters data]
 +
}}  
 +
----
 
{{#ifexpr: {{#ask:[[tf_chipseq_enrich_entregeneid::{{{GeneID}}}]]|format=count}} > 0 |
 
{{#ifexpr: {{#ask:[[tf_chipseq_enrich_entregeneid::{{{GeneID}}}]]|format=count}} > 0 |
 
(#promoters = Number of promoters in the coexpression cluster that have ChIP signal of the TF)  
 
(#promoters = Number of promoters in the coexpression cluster that have ChIP signal of the TF)  
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<script type="text/javascript">
 
<script type="text/javascript">
 
$(document).ready(function() {
 
$(document).ready(function() {
     var oTable2= $('#tf_chipseq_enrich').dataTable({
+
     var oTable2 = $('#tf_chipseq_enrich').dataTable({
 
"sScrollY": "300px",
 
"sScrollY": "300px",
"bPaginate": false,
 
 
"bScrollCollapse": true,
 
"bScrollCollapse": true,
"iDisplayLength": -1,
+
"bPaginate": true,
 +
"bFilter": true,
 +
"bInfo": true,
 +
                "iDisplayLength": 10,
 +
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
 
"aaSorting": [[4,'asc']],
 
"aaSorting": [[4,'asc']],
"aoColumnDefs": [{ "sWidth": "150px", "sType": "numeric", "aTargets": [3] },{ "sWidth": "150px", "sType": "numeric", "aTargets": [4] }]
+
"aoColumnDefs": [{"sType": "numeric", "aTargets": [2,3,4],"fnRender": function (obj) {                   
 +
                  var num =obj.aData[obj.iDataColumn];             
 +
                  return exp_converter(num,2,"e") ;
 +
} }]
 
});
 
});
var oTableTools2 = new TableTools( oTable2, {"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"} ]});
+
var oTableTools2 = new TableTools(oTable2, {"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"} ]});
  
 
$('#export_tool2').before( oTableTools2.dom.container );
 
$('#export_tool2').before( oTableTools2.dom.container );
Line 252: Line 255:
 
</script>
 
</script>
 
<span id="export_tool2"></span>
 
<span id="export_tool2"></span>
</html>{{#ask:[[tf_chipseq_enrich_entregeneid::{{{GeneID}}}]]|?Tf_chipseq_enrich_values|intro=<table id="tf_chipseq_enrich"><html><thead></html><tr><th>Coexpression cluster</th><th>#promoters</th><th>Enrichment</th><th>p-value</th><th>q-value</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table>|link=none|format=template|template=Tf_chipseq_enrichlist_in_entregene|limit=5000|searchlabel=}}
+
</html>{{#ask:[[tf_chipseq_enrich_entregeneid::{{{GeneID}}}]]|?Tf_chipseq_enrich_values|intro=<div style="width:100%; float:left;"><table id="tf_chipseq_enrich"><html><thead></html><tr><th>Coexpression cluster</th><th>#promoters</th><th>Enrichment</th><th>p-value</th><th>q-value</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table></div>|link=none|format=template|template=Tf_chipseq_enrichlist_in_entregene|limit=5000|searchlabel=}}
 
|No analysis results for this cluster
 
|No analysis results for this cluster
 
}}
 
}}
 
<html><br><br></html>
 
<html><br><br></html>
== Details ==
+
 
{{#info:<b>Summary</b>:It includes sequences from the international sequence collaboration, Swiss-Prot, and RefSeq. The RefSeq subset of this file is also available as gene2refseq.<br>data source :<br>[https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/entrez_gene/2012-01-19/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz  human]
+
{{Fontsize|3|Details}}{{#info:<b>Summary:</b>It includes sequences from the international sequence collaboration, Swiss-Prot, and RefSeq. The RefSeq subset of this file is also available as gene2refseq.<br><br>links to source dataset.<br>[ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz  human] <br>
<br>[https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/entrez_gene/2012-01-19/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz  mouse]
+
[ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz  mouse]
 
}}
 
}}
 +
----
 
<table class="details">
 
<table class="details">
 
<tr><th scope="row" align="right">GeneID:</th><td>{{#if:{{{GeneID}}}|[[GeneID::{{{GeneID}}}]]|NA}}</td></tr>
 
<tr><th scope="row" align="right">GeneID:</th><td>{{#if:{{{GeneID}}}|[[GeneID::{{{GeneID}}}]]|NA}}</td></tr>
Line 270: Line 274:
 
<tr><th scope="row" align="right">Nomenclature status:</th><td>{{#if:{{{Nomenclature_status}}}|[[Nomenclature_status::{{{Nomenclature_status}}}]]|NA}}</td></tr>
 
<tr><th scope="row" align="right">Nomenclature status:</th><td>{{#if:{{{Nomenclature_status}}}|[[Nomenclature_status::{{{Nomenclature_status}}}]]|NA}}</td></tr>
 
<tr><th scope="row" align="right">Other designations:</th><td>{{#if:{{{Other_designations}}}|{{#show:{{FULLPAGENAME}}|?Other_designations}}|NA}}</td></tr>
 
<tr><th scope="row" align="right">Other designations:</th><td>{{#if:{{{Other_designations}}}|{{#show:{{FULLPAGENAME}}|?Other_designations}}|NA}}</td></tr>
<tr><th scope="row" align="right">Modification date:</th><td>{{#if:{{{Modification_date}}}|[[Modification_date::{{{Modification_date}}}]]|NA}}</td></tr>
+
<tr><th scope="row" align="right">Modification date:</th><td>{{#if:{{{Modification_date}}}|{{#time: d.m.Y |{{{Modification_date}}}}}|NA}}</td></tr>
 
</table>
 
</table>
 
 
 
  
  
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[[Category:EntrezGene]]
 
[[Category:EntrezGene]]
<html>
 
<script language="javascript" type="text/javascript" src="/resource_browser/rb_js/flot/jquery.flot.js"></script>
 
<script language="javascript" type="text/javascript" src="/resource_browser/rb_js/flot/jquery.flot.axislabels.js"></script>
 
</html>
 

Revision as of 00:45, 8 April 2014

Symbol:{{{Symbol}}}
Description:{{{description}}}
Synonyms:
Species:NA
Xrefs:
EntrezGene:{{{GeneID}}}
{{{dbXrefs}}}:[NA ]
Associated motifs:NA
Transcripton Factor?: No
TSS regions:NA


View on UCSC genome browser


Mouse over to see Genome browser image, Click image to go to Genome browser


TSS expression




Sample






  • Click each plot point to find sample in table

ENCODE TF ChIP-seq peak enrichment analysis Analyst: Erik Arner
Summary: For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained.


link to source dataset.
data


No analysis results for this cluster

DetailsSummary:It includes sequences from the international sequence collaboration, Swiss-Prot, and RefSeq. The RefSeq subset of this file is also available as gene2refseq.

links to source dataset.
human
mouse


GeneID:{{{GeneID}}}
LocusTag:{{{LocusTag}}}
chromosome:{{{chromosome}}}
map location:
type of gene:{{{type_of_gene}}}
Symbol from
nomenclature authority:
{{{Symbol_from_nomenclature_authority}}}
Full name from
nomenclature authority:
{{{Full_name_from_nomenclature_authority}}}
Nomenclature status:{{{Nomenclature_status}}}
Other designations:
Modification date:Error: Invalid time.