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{{Loading|loadingimage=sprites.gif}}<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">[[Property:Species|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">[[Property:Dpi dataset|DPI dataset:]]</th><td> {{#switch:{{{DPIdataset}}} |robust=Robust|permissive=Permissive|#default = NA}}</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">[[Property:TSS_like_by_RIKEN_classifier|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}}} | strong = Yes| #default = NA| weak= No|not=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">[[Property:GencodeV16b_All_Build2_RSEM10_CPAT_consensus|GencodeV16b-All-Build2-RSEM10-CPAT_consensus:]]</th><td>  
{{#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>
{{#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">[[Property:DHS support|DHS support(Yes/No):]]</th><td> {{#switch: {{{DHSsupport}}}|supported= Yes|not supported=No|#default=NA}} </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">Coexpression cluster:</th><td>{{#if:{{#pos:{{PAGENAME}}|Hg19}}
<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}}
|{{#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}}
|{{#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}}
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|{{#if:{{#pos:{{{MCL_coexpression_id}}}|MCL}}|NA|[[MCL_coexpression_id::{{{MCL_coexpression_id}}}|]][[MCL_coexpression_mm9:{{{MCL_coexpression_id}}}]]}}
|{{#if:{{#pos:{{{MCL_coexpression_id}}}|MCL}}|NA|[[MCL_coexpression_id::{{{MCL_coexpression_id}}}|]][[MCL_coexpression_mm9:{{{MCL_coexpression_id}}}]]}}
}}</td></tr><tr><th scope="row" align="right">Association with transcript:</th><td> {{#show:{{FULLPAGENAME}}|?association_with_transcript}}</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">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={{{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={{#show:{{FULLPAGENAME}}|?HGNC}}&submit=Submit {{#show:{{FULLPAGENAME}}|?HGNC}}]|NA}}</td></tr> |}}{{#if: {{{HGNC}}} |<tr><th scope="row" align="right">UniProt:</th><td> {{#ifeq:{{#show:{{FULLPAGENAME}}|?UniProt}}|NA|NA|{{#arraymap:{{#show:{{FULLPAGENAME}}|?UniProt}}|,|$|[http://www.uniprot.org/uniprot/?query=$  $] |}}}}</td></tr>|}}
<tr><th scope="row" align="right">EntrezGene:</th><td>{{#if:{{{EntrezGene}}}|{{#ifeq:{{#show:{{FULLPAGENAME}}|?EntrezGene}}|NA|NA|{{#ifexist:EntrezGene:{{{EntrezGene}}}|[[EntrezGene:{{{EntrezGene}}}|{{#show:EntrezGene:{{{EntrezGene}}}|?Symbol}}]]|[http://www.ncbi.nlm.nih.gov/gene?term={{#replace:{{{EntrezGene}}}|entrezgene:|}}  {{#replace:{{{EntrezGene}}}|entrezgene:|}}] }}}}|NA}}</td></tr>{{#if: {{{HGNC}}} | <tr><th scope="row" align="right">HGNC:</th><td> {{#ifeq:{{#show:{{FULLPAGENAME}}|?HGNC}}| {{#if:{{#pos:{{FULLPAGENAME}}|Hg19}}|NA|}}|NA|[http://www.genenames.org/cgi-bin/quick_search.pl?.cgifields=type&num=50&search={{#replace:{{#show:{{FULLPAGENAME}}|?HGNC}}|HGNC:| }}&submit=Submit {{#replace:{{#show:{{FULLPAGENAME}}|?HGNC}}|HGNC:|}}]|NA}}</td></tr> |}}{{#if: {{{HGNC}}} |<tr><th scope="row" align="right">UniProt:</th><td> {{#ifeq:{{#show:{{FULLPAGENAME}}|?UniProt}}||NA|{{#arraymap:{{#show:{{FULLPAGENAME}}|?UniProt}}|,|$|[http://www.uniprot.org/uniprot/?query=$  $] |}}}}</td></tr>|}}
{{#switch:{{#explode:{{PAGENAME}}|:|0}}
{{#switch:{{#explode:{{PAGENAME}}|:|0}}
|Hg19=<tr><th scope="row" align="right">Link to Zenbu:</th><td>[https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=BQjFm9HSPlZkqiPpqgcJ8B;loc={{#explode:{{PAGENAME}}|,|0}} ZENBU]</td></tr>
|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>
|Mm9=<tr><th scope="row" align="right">Link to Zenbu:</th><td>[https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=3qebVNZHMB1tN8DyYkP1uD;loc={{#explode:{{PAGENAME}}|,|0}} ZENBU]</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>
}}
}}
</table>
</table>
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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:{{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}}
{{Fontsize|3|CAGE Expression}}
----
----
<html><script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.min.js"></script>
<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/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>
<script type="text/javascript" language="javascript" src="/resource_browser/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 "/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>
</style>


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<script type="text/javascript">
<script type="text/javascript">
$(document).ready(function() {
$(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");
$('#gene_exptable_wrapper .dataTables_scrollHead th').css("height", "100px").css("vertical-align", "bottom");
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// chart checkbox
// chart checkbox
for (var i2=1; i2<oTable.fnSettings().aoColumns.length; i2++){
for (var i2=1; i2<$('#gene_exptable thead th').length; i2++){
key2 = i2-1;
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 + '">'
                                 + $(oTable.fnSettings().aoColumns[i2].sTitle).text() + '</label><br/>');
                                 + $('#gene_exptable thead th:nth-child('+(i2+1)+')').text() + '</label><br/>');
}
}


function collectdata(){
function collectdata(){
data = [];
data = [];
for (i2=1, len2=oTable.fnSettings().aoColumns.length; i2<len2; i2++){
for (i2=1, len2=$('#gene_exptable thead th').length; i2<len2; i2++){
var plots = [];
var plots = [];
for (i1=2, len1=$('#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": $(oTable.fnSettings().aoColumns[i2].sTitle).text(), "data": plots});
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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         $("#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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{{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
{{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>
<br><br>link to source dataset<br>
[http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Sample_ontology_enrichment_of_CAGE_peaks/ data]
[//fantom.gsc.riken.jp/5/datafiles/latest/extra/Sample_ontology_enrichment_of_CAGE_peaks/ data]
}}
}}
----
----
<html>
<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">
<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{
.table_title{
text-align:left;
text-align:left;
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$(document).ready(function() {
$(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" ]]
});
});


});
});
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{{#if:{{{ontology_enrichment_celltype_v019_2}}}|
{{#if:{{{ontology_enrichment_celltype_v019_2}}}|
<div style="float:left;width:33%;">
<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>
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
<html></thead><tbody></html>
<html></thead><tbody></html>
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}}{{#if:{{{ontology_enrichment_uberon_v019_2}}}|
}}{{#if:{{{ontology_enrichment_uberon_v019_2}}}|
<div style="float:left;width:33%;">
<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>
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
<html></thead><tbody></html>
<html></thead><tbody></html>
Line 303: Line 302:
{{#set:dpi_dataset={{{DPIdataset}}}}}
{{#set:dpi_dataset={{{DPIdataset}}}}}
{{#set:TSS_like_by_RIKEN_classifier={{{TSSclassifier}}}}}
{{#set:TSS_like_by_RIKEN_classifier={{{TSSclassifier}}}}}
{{#set:GencodeV16b_All_Build2_RSEM10_CPAT_consensus={{{GencodeV16b_All_Build2_RSEM10_CPAT_consensus}}}}}{{#set:DHS_support={{{DHSsupport}}}}}
<!--{{#set:GencodeV16b_All_Build2_RSEM10_CPAT_consensus={{{GencodeV16b_All_Build2_RSEM10_CPAT_consensus}}}}}-->{{#set:DHS_support={{{DHSsupport}}}}}
 
[[Category:FFCP]]
[[Category:FFCP]]

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 analysis<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>data

Cell type
Ontology termp-valuen


Uber anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen






"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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