Template:EntrezGene: Difference between revisions
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{{Loading|loadingimage=sprites.gif}}<html><script language="javascript" type="text/javascript" src="/5/sstar/rb_js/flot/jquery.flot.js"></script><script language="javascript" type="text/javascript" src="/5/sstar/rb_js/flot/jquery.flot.axislabels.js"></script> | {{Loading|loadingimage=sprites.gif}}<html><script type="text/javascript" src="/5/sstar/rb_js/jquery-1.7.1.min.js"></script> | ||
<script language="javascript" type="text/javascript" src="/5/sstar/rb_js/flot/jquery.flot.js"></script><script language="javascript" type="text/javascript" src="/5/sstar/rb_js/flot/jquery.flot.axislabels.js"></script> | |||
<script type="text/javascript" src="/5/sstar/rb_js/custom/convert.js"></script></html> | <script type="text/javascript" src="/5/sstar/rb_js/custom/convert.js"></script></html> | ||
<table> | <table> | ||
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{{Fontsize|3|TSS regions }} | {{Fontsize|3|TSS regions }} | ||
---- | ---- | ||
{{#ask:[[FFCP PHASE2:+]][[Category:FFCP]][[EntrezGene::{{{GeneID}}}]]|?Short_description|format=table|class=ffcp_list stripe cell-border order-column compact|headers=hide|limit=20000|searchlabel= ... further results}} | |||
{{# | |||
<br> | <br> | ||
<html> | <html> | ||
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$(document).ready(function() { | $(document).ready(function() { | ||
// TSS regions list | // TSS regions list | ||
$('.ffcp_list').DataTable({ | |||
dom: 'Blfrtip', | |||
lengthMenu: [[10, 25, 50, -1], [10, 25, 50, "All"]], | |||
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | |||
columns: [{title:"TSS peak ID"},{title:"Short_description"}] | |||
}); | |||
// hide-show animation for ucsc genome browser view | // hide-show animation for ucsc genome browser view | ||
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<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}}}]][[FFCP PHASE1:+]]|link=none|headers=hide|limit=1|searchlabel=}}| | {{#ucsc_gb_link:{{#replace:{{#ask:[[Category:FFCP]][[Short description::p1@{{{Symbol}}}]][[FFCP PHASE1:+]]|link=none|headers=hide|limit=1|searchlabel=}}|FFCP PHASE1:|}}}} | ||
</div><br> | </div><br> | ||
{{Fontsize|3|TSS expression}} | {{Fontsize|3|TSS expression}} | ||
---- | ---- | ||
<html> | <html> | ||
<script type="text/ | <script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.js"></script> | ||
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/flot/jquery.flot.min.js"></script> | <script type="text/javascript" language="javascript" src="/5/sstar/rb_js/flot/jquery.flot.min.js"></script> | ||
<style type="text/css" title="currentStyle"> | <style type="text/css" title="currentStyle"> | ||
@import "/5/sstar/rb_js/ | @import "/5/sstar/rb_js/html5button/datatables.css"; | ||
</style> | </style> | ||
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<script type="text/javascript"> | <script type="text/javascript"> | ||
$(document).ready(function() { | $(document).ready(function() { | ||
var oTable = $('#gene_exptable'). | var orderArr; | ||
if($('#gene_exptable')[0].rows[1].cells.length>1){ | |||
orderArr = [[1,'desc']]; | |||
} else { | |||
orderArr = [[0,'asc']]; | |||
} | |||
var oTable = $('#gene_exptable').DataTable({ | |||
dom: 'Bfrti', | |||
scrollY: "300px", | |||
scrollCollapse: true, | |||
order: orderArr, | |||
paging: false, | |||
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | |||
columnDefs: [{ orderSequence: [ "asc", "desc" ], type: "html", targets: [ 0 ] }, { orderSequence: [ "desc", "asc" ], targets: [ "_all" ] } ] | |||
}); | }); | ||
$('#gene_exptable_wrapper .dataTables_scrollHead th').css("height", "100px").css("vertical-align", "bottom"); | $('#gene_exptable_wrapper .dataTables_scrollHead th').css("height", "100px").css("vertical-align", "bottom"); | ||
var data = []; | var data = []; | ||
var plotdata = []; | var plotdata = []; | ||
var slist = []; | var slist = []; | ||
// chart checkbox | // chart checkbox | ||
for (var i2=1; i2< | for (var i2=1; i2<$('#gene_exptable thead th').length; i2++){ | ||
key2 = i2-1; | key2 = i2-1; | ||
$("#gene_exptable_chart_chkbox").append('<input type="checkbox" name="' + key2 + | $("#gene_exptable_chart_chkbox").append('<input type="checkbox" name="' + key2 + | ||
'" checked="checked" id="id' + key2 + '"><label for="id' + key2 + '">' | '" checked="checked" id="id' + key2 + '"><label for="id' + key2 + '">' | ||
+ $( | + $('#gene_exptable thead th:nth-child('+(i2+1)+')').text() + '</label><br/>'); | ||
} | } | ||
$(oTable.settings().column(i2).title).text() | |||
function collectdata(){ | function collectdata(){ | ||
data = []; | data = []; | ||
// for (i2=1, len2=oTable.settings().columns.length; i2<len2; i2++){ | |||
for (i2=1, len2=$('#gene_exptable thead th').length; i2<len2; i2++){ | |||
var plots = []; | var plots = []; | ||
for (i1=2, len1=$('#gene_exptable tr').length; i1<len1; i1++) { | for (i1=2, len1=$('#gene_exptable tr').length; i1<len1; i1++) { | ||
plots.push([i1,$("#gene_exptable tr")[i1].cells[i2].innerHTML]); | plots.push([i1,$("#gene_exptable tr")[i1].cells[i2].innerHTML]); | ||
} | } | ||
data.push({"label": $( | data.push({"label": $('#gene_exptable thead th:nth-child('+(i2+1)+')').text(), "data": plots}); | ||
} | } | ||
slist = []; | slist = []; | ||
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var plot1 = $.plot($("#gene_exptable_chart"), plotdata, { | var plot1 = $.plot($("#gene_exptable_chart"), plotdata, { | ||
yaxis : { axisLabel : 'TPM' }, | yaxis: { axisLabel: 'TPM' }, | ||
lines : { show : false }, | lines: { show: false }, | ||
points : { show : true }, | points: { show: true }, | ||
grid: { hoverable: true, clickable: true }, | grid: { hoverable: true, clickable: true }, | ||
xaxis : { tickDecimals : 0, show: false }, | xaxis: { tickDecimals: 0, show: false }, | ||
legend: { show: false } | legend: { show: false } | ||
}); | }); | ||
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collectdata(); | collectdata(); | ||
drawchart(); | if($('#gene_exptable')[0].rows[1].cells.length>1){ | ||
drawchart(); | |||
} | |||
// re-draw chart event | // re-draw chart event | ||
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$("#y").text(pos.y.toFixed(2)); | $("#y").text(pos.y.toFixed(2)); | ||
if (item) { | if (item) { | ||
if (previousPoint != item.dataIndex) { | if (previousPoint!=item.dataIndex) { | ||
previousPoint = item.dataIndex; | previousPoint = item.dataIndex; | ||
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// clicking point function end | // clicking point function end | ||
} ); | } ); | ||
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{{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> | {{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> | ||
<br><br>link to source dataset.<br>[ | <br><br>link to source dataset.<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters data] | ||
}} | }} | ||
---- | ---- | ||
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<script type="text/javascript"> | <script type="text/javascript"> | ||
$(document).ready(function() { | $(document).ready(function() { | ||
var oTable2 = $('#tf_chipseq_enrich'). | var oTable2 = $('#tf_chipseq_enrich').DataTable({ | ||
dom: 'Blfrtip', | |||
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | |||
scrollY: "300px", | |||
scrollCollapse: true, | |||
pageLength: 10, | |||
lengthMenu: [[10, 50, -1], [10, 50, "All"]], | |||
order: [[4,'asc']], | |||
columnDefs: [{type: "numeric", targets: [2,3,4], | |||
render: function ( data, type, row, meta ) { | |||
var num = | var num =data; | ||
return exp_converter(num,2,"e") ; | return exp_converter(num,2,"e") ; | ||
} }] | } }] | ||
} | }); | ||
}); | }); | ||
</script> | </script> | ||
</html>{{#ask:[[tf_chipseq_enrich_entregeneid::{{{GeneID}}}]]|?Tf_chipseq_enrich_values|intro=<div style="width:100%; float:left;"><table id="tf_chipseq_enrich" class="stripe cell-border order-column compact"><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=}} | |||
</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 | ||
}} | }} | ||
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{{#set:Other_designations={{{Other_designations}}}}} | {{#set:Other_designations={{{Other_designations}}}}} | ||
<!-- | <!-- | ||
{{#set:Modification_date={{{Modification_date | {{#set:Modification_date={{{Modification_date}}}}} | ||
--> | --> | ||
Latest revision as of 11:48, 22 September 2021
Symbol: | {{{Symbol}}} | ||
---|---|---|---|
Description: | {{{description}}} | ||
Synonyms: | |||
Species: | NA | ||
Xrefs: |
| ||
Associated motifs: | NA | ||
Transcripton Factor?: | No |
TSS regions
View on UCSC genome browser
TSS expression
- Click each plot point to find sample in table
ENCODE TF ChIP-seq peak enrichment analysis 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 <= 0.05) after Benjamini-Hochberg correction were retained. <br><br><br>link to source dataset.<br>data
No analysis results for this cluster
Details<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>human <br>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. |