Template:FFCP: Difference between revisions

Latest revision as of 12:09, 22 September 2021

Short description:
Species:
DPI dataset:	NA
TSS-like-by-RIKEN-classifier(Yes/No):	NA
DHS support(Yes/No):	NA
Description:
Coexpression cluster:
Association with transcript:
EntrezGene:	{{{EntrezGene}}}
HGNC:	NA
UniProt:	NA

View on UCSC genome browser

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

CAGE Expression

Click each plot point to find sample in table

Ontology-based sample term enrichment analysisSummary:This analysis has been performed by utilizing wilcoxon rank sum test.When the number of associated cells/tissues are > n , randomly sampled n cells/tissues are used for P value calculation with rank sum test. this process are repeated several times, and the P values are averaged on the log space Analyst: Hideya Kawaji link to source dataset data

Cell type
Ontology term	p-value	n

Uber anatomy
Ontology term	p-value	n

Disease
Ontology term	p-value	n

"FFCP" is not a number.

Property "Dpi dataset" (as page type) with input value "{{{DPIdataset}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. Property "TSS like by RIKEN classifier" (as page type) with input value "{{{TSSclassifier}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. Property "DHS support" (as page type) with input value "{{{DHSsupport}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.

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Template:FFCP: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 12:09, 22 September 2021

@@ Line 1: / Line 1: @@
-<table>
+{{Loading|loadingimage=sprites.gif}}<table>
-<tr><th scope="row" align="right">short description:</th><td> {{#show:{{FULLPAGENAME}}|?short_description}}</td></tr>
+<tr><th scope="row" align="right">Short description:</th><td>{{#show:{{FULLPAGENAME}}|?short_description}}</td></tr><tr><th scope="row" align="right">Species:</th><td>{{#if:{{#pos:{{FULLPAGENAME}}|Hg19}}|[[species::Human (Homo sapiens)]]}}{{#if:{{#pos:{{FULLPAGENAME}}|Mm9}}|[[species::Mouse (Mus musculus)]]}}</td></tr><tr><th scope="row" align="right">DPI dataset:</th><td> {{#switch:{{{DPIdataset}}} |robust=Robust|permissive=Permissive|#default = NA}}</td></tr>
-<tr><th scope="row" align="right">DPIdataset:</th><td> {{#if:{{{DPIdataset}}}|{{{DPIdataset}}}|NA}}</td></tr>
+<tr><th scope="row" align="right">TSS-like-by-RIKEN-classifier(Yes/No):</th><td> {{#switch: {{{TSSclassifier}}} | strong = Yes| #default = NA| weak= No|not=No}} </td></tr>
-<tr><th scope="row" align="right">TSS-like-by-RIKEN-classifier(Yes/No):</th><td> {{#switch: {{{TSSclassifier}}} | S = Yes| #default = NA| W= No|N=No}} </td></tr>
+<!--tr><th scope="row" align="right">[[Property:GencodeV16b_All_Build2_RSEM10_CPAT_consensus|GencodeV16b-All-Build2-RSEM10-CPAT_consensus:]]</th><td>
-<tr><th scope="row" align="right">GencodeV16b_All_Build2_RSEM10_CPAT_consensus:</th><td> {{#if:{{#pos:{{{GencodeV16b_All_Build2_RSEM10_CPAT_consensus}}}|Gencode}}|{{{GencodeV16b_All_Build2_RSEM10_CPAT_consensus}}}|NA}}</td></tr>
+{{#switch: {{{GencodeV16b_All_Build2_RSEM10_CPAT_consensus}}} | no_gencodeV16_or_build2_transcript = no_gencodeV16_or_build2_transcript| #default = NA|novel_noncoding=novel_noncoding|novel_coding=novel_coding|gencodeV16_ncRNA=gencodeV16_ncRNA|gencodeV16_protein_coding=gencodeV16_protein_coding}}</td></tr-->
-<tr><th scope="row" align="right">EntrezGene:</th><td> {{#ifeq:{{{EntrezGene}}}|NA|NA|[[EntrezGene::{{{EntrezGene}}}|{{{EntrezGene}}}]]}}</td></tr>
+<tr><th scope="row" align="right">DHS support(Yes/No):</th><td> {{#switch: {{{DHSsupport}}}|supported= Yes|not supported=No|#default=NA}} </td></tr>
-<tr><th scope="row" align="right">description:</th><td> {{#show:{{FULLPAGENAME}}|?description}}</td></tr>
+<tr><th scope="row" align="right">Description:</th><td> {{#show:{{FULLPAGENAME}}|?description}}</td></tr><tr><th scope="row" align="right">Coexpression cluster:</th><td>{{#if:{{#pos:{{PAGENAME}}|Hg19}}
-<tr><th scope="row" align="right">Species:</th><td>{{#if:{{#pos:{{FULLPAGENAME}}|Hg19}}|[[species::Human (Homo sapiens)]]}}{{#if:{{#pos:{{FULLPAGENAME}}|Mm9}}|[[species::Mouse (Mus musculus)]]}}</td></tr>
+|{{#ifeq:{{#pos:{{{coexpression_cluster_id}}}|C}}|0|[[coexpression_cluster_id::{{{coexpression_cluster_id}}}|]][[Coexpression cluster:{{{coexpression_cluster_id}}}|{{#show:Coexpression cluster:{{{coexpression_cluster_id}}}|?Full_id}}]]|NA}}
-<tr><th scope="row" align="right">association<br>with transcript:</th><td> {{#show:{{FULLPAGENAME}}|?association_with_transcript}}</td></tr>
+}}{{#if:{{#pos:{{PAGENAME}}|Mm9}}
-{{#if: {{{HGNC}}} | <tr><th scope="row" align="right">HGNC:</th><td> {{#show:{{FULLPAGENAME}}|?HGNC}}</td></tr> |}}
+|{{#if:{{#pos:{{{MCL_coexpression_id}}}|MCL}}|NA|[[MCL_coexpression_id::{{{MCL_coexpression_id}}}|]][[MCL_coexpression_mm9:{{{MCL_coexpression_id}}}]]}}
-<tr><th scope="row" align="right">UniProt:</th><td> {{#show:{{FULLPAGENAME}}|?UniProt}}</td></tr>
+}}</td></tr><tr><th scope="row" align="right">Association with transcript:</th><td> {{#show:{{FULLPAGENAME}}|?association_with_transcript}}</td></tr>
-<tr><th scope="row" align="right">coexpression_cluster:</th><td>{{#if:{{#pos:{{FULLPAGENAME}}|Hg19}}|{{#set:coexpression_cluster_id={{{coexpression_cluster_id}}}}}[[Coexpression_cluster:{{{coexpression_cluster_id}}}|{{#show:Coexpression_cluster:{{{coexpression_cluster_id}}}|?full_id}}]]}}{{#if:{{#pos:{{FULLPAGENAME}}|Mm9}}|{{#set:MCL_coexpression_id={{{MCL_coexpression_id}}}}}[[MCL_coexpression_mm9:{{{MCL_coexpression_id}}}]]}}</td></tr>
+<tr><th scope="row" align="right">EntrezGene:</th><td>{{#if:{{{EntrezGene}}}|{{#ifeq:{{#show:{{FULLPAGENAME}}|?EntrezGene}}|NA|NA|{{#ifexist:EntrezGene:{{{EntrezGene}}}|[[EntrezGene:{{{EntrezGene}}}|{{#show:EntrezGene:{{{EntrezGene}}}|?Symbol}}]]|[http://www.ncbi.nlm.nih.gov/gene?term={{#replace:{{{EntrezGene}}}|entrezgene:|}}   {{#replace:{{{EntrezGene}}}|entrezgene:|}}] }}}}|NA}}</td></tr>{{#if: {{{HGNC}}} | <tr><th scope="row" align="right">HGNC:</th><td> {{#ifeq:{{#show:{{FULLPAGENAME}}|?HGNC}}| {{#if:{{#pos:{{FULLPAGENAME}}|Hg19}}|NA|}}|NA|[http://www.genenames.org/cgi-bin/quick_search.pl?.cgifields=type&num=50&search={{#replace:{{#show:{{FULLPAGENAME}}|?HGNC}}|HGNC:| }}&submit=Submit {{#replace:{{#show:{{FULLPAGENAME}}|?HGNC}}|HGNC:|}}]|NA}}</td></tr> |}}{{#if: {{{HGNC}}} |<tr><th scope="row" align="right">UniProt:</th><td> {{#ifeq:{{#show:{{FULLPAGENAME}}|?UniProt}}||NA|{{#arraymap:{{#show:{{FULLPAGENAME}}|?UniProt}}|,|$|[http://www.uniprot.org/uniprot/?query=$  $] |}}}}</td></tr>|}}
 {{#switch:{{#explode:{{PAGENAME}}|:|0}}
-|Hg19=
+|Hg19=<tr><th scope="row" align="right">Genome view:</th><td>[//fantom.gsc.riken.jp/zenbu/gLyphs/#config=ONHzqgf2E5Xtmnpsh2gURB;loc={{#explode:{{PAGENAME}}|,|0}} ZENBU]</td></tr>
-<tr><th scope="row" align="right">Link to Zenbu:</th><td>[https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=Q81RCpp-A1KvX1V9Xdn99D;loc={{#explode:{{PAGENAME}}|,|0}}]</td></tr>
+|Mm9=<tr><th scope="row" align="right">Link to Zenbu:</th><td>[//fantom.gsc.riken.jp/zenbu/gLyphs/#config=Uz8Jh3NEDl8qV47r6EGQ8B;loc={{#explode:{{PAGENAME}}|,|0}} ZENBU]</td></tr>
-|Mm9=
-<tr><th scope="row" align="right">Link to Zenbu:</th><td>[https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=iYRQLujlGB1iDTf1H2ARBB;loc={{#explode:{{PAGENAME}}|,|0}}]</td></tr>
 }}
 </table>
@@ Line 31: / Line 28: @@
 });
 </script>
-</html>
+</html><br>
+{{Fontsize|3|View on UCSC genome browser}}
-== View on UCSC genome browser OSC local mirror ==
+----
 <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
-{{#ucsc_gb_link:{{#replace:{{FULLPAGENAME}}|FFCP PHASE1:|}}|https://fantom5-collaboration.gsc.riken.jp/ucsc/}}
+{{#ucsc_gb_link:{{#if:{{#pos:{{FULLPAGENAME}}|Hg19}}|Hg19}}{{#if:{{#pos:{{FULLPAGENAME}}|Mm9}}|Mm9}}::{{{cluster_id}}}}}
-</div>
+</div><br>
+{{Fontsize|3|CAGE Expression}}
-== CAGE Expression ==
+----
-<html>
+<html><script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.js"></script>
-<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="/5/sstar/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
-<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/extras/TableTools/media/js/TableTools.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="/resource_browser/rb_js/flot/jquery.flot.min.js"></script>
 	<style type="text/css" title="currentStyle">
-		@import "/resource_browser/rb_js/datatables/media/css/jquery.dataTables.css";
+		@import "/5/sstar/rb_js/html5button/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>
@@ Line 65: / Line 61: @@
 <script type="text/javascript">
 $(document).ready(function() {
-     var oTable =  $('#gene_exptable').dataTable({
+     var oTable =  $('#gene_exptable').DataTable({
-		"sScrollY": "300px",
+        dom: 'frt',
-		"bPaginate": false,
+		scrollY: "300px",
-		"bScrollCollapse": true,
+		paging: false,
-		"iDisplayLength": -1,
+		scrollCollapse: true,
-		"aaSorting": [[1,'desc']],
+		pageLength: -1,
-		"aoColumnDefs": [ { "asSorting": [ "desc", "asc" ], "aTargets": [ 1 ] }  , { "sType": "html", "aTargets": [ 0 ] }]
+		order: [[1,'desc']],
+		columnDefs: [{ orderSequence: [ "desc", "asc" ], targets: [ 1 ] }, { type: "html-num", targets: [ 0 ] } ]
 });
 $('#gene_exptable_wrapper .dataTables_scrollHead th').css("height", "100px").css("vertical-align", "bottom");
@@ Line 77: / Line 74: @@
 var data = [];
+var slist = [];
 var plotdata = [];
 // chart checkbox
-for (var i2=1; i2<oTable.fnSettings().aoColumns.length; i2++){
+for (var i2=1; i2<$('#gene_exptable thead th').length; i2++){
 key2 = i2-1;
          $("#gene_exptable_chart_chkbox").append('<input type="checkbox" name="' + key2 +
                                 '" checked="checked" id="id' + key2 + '"><label for="id' + key2 + '">'
-                                 + $(oTable.fnSettings().aoColumns[i2].sTitle).text() + '</label><br/>');
+                                 + $('#gene_exptable thead th:nth-child('+(i2+1)+')').text() + '</label><br/>');
 }
 function collectdata(){
 data = [];
-		for (i2=1, len2=oTable.fnSettings().aoColumns.length; i2<len2; i2++){
+		for (i2=1, len2=$('#gene_exptable thead th').length; i2<len2; i2++){
 			var plots = [];
 			for (i1=2, len1=$('#gene_exptable tr').length; i1<len1; i1++) {
    		  		plots.push([i1,$("#gene_exptable tr")[i1].cells[i2].innerHTML]);
 		 	}
-		 	data.push({"label": $(oTable.fnSettings().aoColumns[i2].sTitle).text(), "data": plots});
+		 	data.push({"label": $('#gene_exptable thead th:nth-child('+(i2+1)+')').text(), "data": plots});
 		}
+slist = [];
+			for (i1=2, len1=$('#gene_exptable tr').length; i1<len1; i1++) {
+  		  		slist.push($("#gene_exptable tr")[i1].cells[0].innerHTML);
+		 	}
+//test
+//slist[0] = "test";
 }
@@ Line 110: / Line 114: @@
 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 }
 });
@@ Line 163: / Line 167: @@
          $("#y").text(pos.y.toFixed(2));
              if (item) {
-                 if (previousPoint != item.dataIndex) {
+                 if (previousPoint!=item.dataIndex) {
                      previousPoint = item.dataIndex;
@@ Line 171: / Line 175: @@
                      showTooltip(item.pageX, item.pageY,
-                                "TSS: "+ item.series.label +"<br>TPM: "+y);
+                                "Sample: "+slist[item.dataIndex]+"<br>TSS: "+ item.series.label +"  TPM: "+y);
                  }
              }
@@ Line 200: / Line 204: @@
 </html>
-{{#gene_exptable:{{#explode:{{PAGENAME}}|:|0}}
+<includeonly>{{#gene_exptable:{{#explode:{{PAGENAME}}|:|0}}
-|{{{short_description}}},{{{phase1_expression}}}
+|{{#replace:{{{short_description}}}|,|}},{{{phase1_expression}}}
-}}
+}}</includeonly>
+<br>
+<br>
 <div id="gene_exptable_chart" style="float:left;width:600px;height:300px;"></div>
 <br>
@@ Line 211: / Line 216: @@
 *Click each plot point to find sample in table
+<br>
-== Ontology-based sample term enrichment analysis ==
+{{Fontsize|3| Ontology-based sample term enrichment analysis}}{{#info:<b>Summary:</b>This analysis has been performed by utilizing wilcoxon rank sum test.When the number of associated cells/tissues are > n , randomly sampled n cells/tissues are used for P value calculation with rank sum test. this process are repeated several times, and the P values are averaged on the log space <br><b>Analyst:</b> Hideya Kawaji
+<br><br>link to source dataset<br>
+[//fantom.gsc.riken.jp/5/datafiles/latest/extra/Sample_ontology_enrichment_of_CAGE_peaks/ data]
+}}
+----
 <html>
-<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.js"></script>
+<script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.js"></script>
-<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
+<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
 	<style type="text/css" title="currentStyle">
-		@import "/resource_browser/rb_js/datatables/media/css/jquery.dataTables.css";
+		@import "/5/sstar/rb_js/html5button/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";
 .table_title{
 text-align:left;
@@ Line 230: / Line 239: @@
 $(document).ready(function() {
-     var oTable =  $('.enrichment_list').dataTable({
+     var oTable =  $('.enrichment_list').DataTable({
-		"sScrollY": "300px",
+        dom: 'frtip',
-		"bScrollCollapse": true,
+		scrollCollapse: false,
-		"bPaginate": false,
+        columnDefs: [{ orderable: false, targets: [ 0 ] },  { type: "html-num", width: "50pt", targets: [1] }],
-		"bFilter": false,
+		order: [[ 1, "asc" ]]
-		"bInfo": false,
-		"aoColumnDefs": [{ "bSortable": false, "aTargets": [ 0 ] },  { "sType": "numeric", "aTargets": [1] }, { "sWidth": "50pt", "aTargets": [ 1 ] }],
-		"aaSorting": [[ 1, "asc" ]]
 });
@@ Line 246: / Line 252: @@
 {{#if:{{{ontology_enrichment_celltype_v019_2}}}|
 <div style="float:left;width:33%;">
-<table class="enrichment_list"><caption class="table_title">Cell Type</caption><html><thead></html>
+<table class="enrichment_list stripe cell-border order-column compact"><caption class="table_title">Cell type</caption><html><thead></html>
 <tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
-<html></thead><tbody></html><tr><td>
+<html></thead><tbody></html>
 {{#arraymap:{{{ontology_enrichment_celltype_v019_2}}}|;|$
-|{{#set:ffcp_ontology_enrichment_celltype={{#replace:$|,|;}}}}[[{{#explode:$|,|0}}|{{#show:{{#explode:$|,|0}}|?name}}]]</td><td>{{#explode:$|,|1}}</td><td>{{#explode:$|,|2}}
+|{{#set:ffcp_ontology_enrichment_celltype={{#replace:$|,|;}}}}{{#ifexist:{{#explode:$|,|0}}|<tr><td>[[{{#explode:$|,|0}}|{{#show:{{#explode:$|,|0}}|?name}}]]</td><td>{{#explode:$|,|1}}</td><td>{{#explode:$|,|2}}</td></tr>| }}
-|</td></tr><tr><td>}}
+|}}
-</td></tr>
 <html></tbody></html></table>
 </div>
 }}{{#if:{{{ontology_enrichment_uberon_v019_2}}}|
 <div style="float:left;width:33%;">
-<table class="enrichment_list"><caption class="table_title">Uber Anatomy</caption><html><thead></html>
+<table class="enrichment_list stripe cell-border order-column compact"><caption class="table_title">Uber anatomy</caption><html><thead></html>
 <tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
-<html></thead><tbody></html><tr><td>
+<html></thead><tbody></html>
 {{#arraymap:{{{ontology_enrichment_uberon_v019_2}}}|;|$
-|{{#set:ffcp_ontology_enrichment_uberon={{#replace:$|,|;}}}}[[{{#explode:$|,|0}}|{{#show:{{#explode:$|,|0}}|?name}}]]</td><td>{{#explode:$|,|1}}</td><td>{{#explode:$|,|2}}
+|{{#set:ffcp_ontology_enrichment_uberon={{#replace:$|,|;}}}}{{#ifexist:{{#explode:$|,|0}}|<tr><td>[[{{#explode:$|,|0}}|{{#show:{{#explode:$|,|0}}|?name}}]]</td><td>{{#explode:$|,|1}}</td><td>{{#explode:$|,|2}}</td></tr>| }}
-|</td></tr><tr><td>}}
+|}}
-</td></tr>
 <html></tbody></html></table>
 </div>
@@ Line 270: / Line 275: @@
 <table class="enrichment_list"><caption class="table_title">Disease</caption><html><thead></html>
 <tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
-<html></thead><tbody></html><tr><td>
+<html></thead><tbody></html>
 {{#arraymap:{{{ontology_enrichment_disease_v019_2}}}|;|$
-|{{#set:ffcp_ontology_enrichment_disease={{#replace:$|,|;}}}}[[{{#explode:$|,|0}}|{{#show:{{#explode:$|,|0}}|?name}}]]</td><td>{{#explode:$|,|1}}</td><td>{{#explode:$|,|2}}
+|{{#set:ffcp_ontology_enrichment_disease={{#replace:$|,|;}}}}{{#ifexist:{{#explode:$|,|0}}|<tr><td>[[{{#explode:$|,|0}}|{{#show:{{#explode:$|,|0}}|?name}}]]</td><td>{{#explode:$|,|1}}</td><td>{{#explode:$|,|2}}</td></tr>| }}
-|</td></tr><tr><td>}}
+|}}
-</td></tr>
 <html></tbody></html></table>
 </div>
 }}
 <div style="clear:both;"></div>
 <!--
 {{#ifexpr: {{#expr: {{REVISIONTIMESTAMP}}-20120731160000 }} > 0
 |<html>
 |}}
 -->
 {{#arraymap:{{{short_description}}}|,|$|{{#set:short_description=$}}}}
 {{#arraymap:{{{description}}}|,|$|{{#set:description=$}}}}
@@ Line 303: / Line 300: @@
 {{#set:genomic_location_end={{#explode:{{#explode:{{PAGENAME}}|..|-1}}|,|0}}}}
 {{#set:strand={{#explode:{{PAGENAME}}|,|-1}}}}
+{{#set:dpi_dataset={{{DPIdataset}}}}}
+{{#set:TSS_like_by_RIKEN_classifier={{{TSSclassifier}}}}}
+<!--{{#set:GencodeV16b_All_Build2_RSEM10_CPAT_consensus={{{GencodeV16b_All_Build2_RSEM10_CPAT_consensus}}}}}-->{{#set:DHS_support={{{DHSsupport}}}}}
 [[Category:FFCP]]

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