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{{Loading|loadingimage=sprites.gif}}<table>
{{Loading|loadingimage=sprites.gif}}
<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">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>
{{#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">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}}
|{{#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}}
}}{{#if:{{#pos:{{PAGENAME}}|Mm9}}
|{{#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>
<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=<tr><th scope="row" align="right">Genome view:</th><td>[http://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>[http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=Uz8Jh3NEDl8qV47r6EGQ8B;loc={{#explode:{{PAGENAME}}|,|0}} ZENBU]</td></tr>
}}
</table>
 
<html>
<html>
<script language="javascript" type="text/javascript">
<style type="text/css" title="currentStyle">
$(document).ready(function() {
@import "/5/sstar/rb_js/html5button/datatables.css";
// hide-show animation for ucsc genome browser view
table.details td { width:30%; background-color: #EAEBFF;}
$("#ucsc_snap_view").hover(function(){
table.details th { width:10%; background-color: #5A5FB5; color: white;}
    $(this).stop(true, false).animate({ height: "600px"});
div.a {
}, function() {
  width: 80%;
    $(this).stop(true, false).animate({ height: "30px" });
  float: left;
});
  padding:5px;
});
  margin:5px;
</script>
}
</html><br>
{{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;">
Mouse over to see Genome browser image, Click image to go to Genome browser


{{#ucsc_gb_link:{{#if:{{#pos:{{FULLPAGENAME}}|Hg19}}|Hg19}}{{#if:{{#pos:{{FULLPAGENAME}}|Mm9}}|Mm9}}::{{{cluster_id}}}}}
div.b {
</div><br>
  width: 20%;
{{Fontsize|3|CAGE Expression}}
  float: right;
----
  padding:5px;
<html><script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.js"></script>
  margin:5px;
<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="/5/sstar/rb_js/flot/jquery.flot.min.js"></script>
<style type="text/css" title="currentStyle">
@import "/5/sstar/rb_js/html5button/datatables.css";
@import "/5/sstar/rb_js/datatables/extras/TableTools/media/css/TableTools.css";
</style>


div.description
{
width:auto;
height:auto;
overflow:auto;
}
</style>
</html>
</html>
<div class="description">
<table>
{{#if:{{{name}}}|<tr><th scope="row" align="right" valign="top">[[Property:Name|Name]]:</th><td>[[name::{{{name}}}]]</td></tr>|}}{{#if:{{{namespace}}}|<tr><th scope="row" align="right" valign="top">Namespace:</th><td>{{{namespace}}}</td></tr>|}}{{#if:{{{def}}}|<tr><th scope="row" align="right" valign="top">Definition:</th><td>{{{def}}}</td></tr>|}}{{#if:{{{xref}}}|<tr><th scope="row" align="right" valign="top">Xrefs:</th><td>{{XrefExternalRefs|{{{xref}}}|}}</td></tr>|}}{{#if:{{{synonym}}}|<tr><th scope="row" align="right" valign="top">Synonyms:</th><td>{{CollapsibleOntology|synonym|{{{synonym}}}|;;|<br>}}</td></tr>|}}
{{#if:{{{comment}}}|<tr><th scope="row" align="right" valign="top">Comments:</th><td>{{{comment}}}</td></tr>|}}{{#if:{{{alt_id}}}|<tr><th scope="row" align="right" valign="top">Alt_id:</th><td>{{CollapsibleOntology|alt_id|{{{alt_id}}}|;;|<br>}}</td></tr>|}}{{#if:{{{subset}}}|<tr><th scope="row" align="right" valign="top">Subset:</th><td>{{CollapsibleOntology|subset|{{{subset}}}|;;|<br>}}</td></tr>|}}{{#if:{{{created_by}}}|<tr><th scope="row" align="right" valign="top">Created by:</th><td>{{{created_by}}}</td></tr>|}}{{#if:{{{obo_creation_date}}}|<tr><th scope="row" align="right" valign="top">Creation date:</th><td>{{{obo_creation_date}}}</td></tr>|}}{{#if:{{{has_quality}}}|<tr><th scope="row" align="right" valign="top">Has quality:</th><td>{{{has_quality}}}</td></tr>|}}</table></div>
{{#if: {{#pos:{{{bp3d_img_id}}}|FMA:}}|<html><img width=100 height=100 src="http://lifesciencedb.jp/bp3d/API/image.cgi?%7B%22Common%22:%7B%22TreeName%22:%22partof%22%7D,%22Part%22:%5B%7B%22PartID%22:%22</html>{{#replace:{{{bp3d_img_id}}}|:|}}<html>%22%7D%5D%7D">
<!--
<img width=100 height=100 src="http://lifesciencedb.jp/bp3d/icon.cgi?i=</html>{{#replace:{{{bp3d_img_id}}}|:|}}<html>&p=front&v=3%2e0&t=conventional&c=1&m=bp3d&s=L">
-->
<span style="background:gainsboro;"> from <a href="http://lifesciencedb.jp/bp3d/">BodyParts3D</a></span>
</html>
{{#set:bp3d_img_id={{#replace:{{{bp3d_img_id}}}|:|}}}}
|{{#set:bp3d_img_id=}}
}}
<html>
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/jquery-1.7.1.min.js"></script>
<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" >


<html>
<style type="text/css"> 
.rotate90 {
  -webkit-transform: rotate(-90deg);
  -moz-transform: rotate(-90deg);
-webkit-transform-origin: 6px 18px;
-moz-transform-origin: 6px 18px;
width:1px;
}
.highlight { background-color: yellow }
</style>
<script type="text/javascript">
$(document).ready(function() {
$(document).ready(function() {
    var oTable = $('#gene_exptable').DataTable({
 
         dom: 'frt',
if( $('.ont_enrich_ffcp').length ) {
var oTable= $('.ont_enrich_ffcp').DataTable({
         dom: 'Blfrti',
scrollY: "300px",
scrollY: "300px",
scrollCollapse: true,
paging: false,
paging: false,
scrollCollapse: true,
order: [[0,'asc']],
pageLength: -1,
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
order: [[1,'desc']],
        columnDefs: [{ width: "100px", targets: [0], type: "html-num"}],
columnDefs: [{ orderSequence: [ "desc", "asc" ], targets: [ 1 ] }, { type: "html-num", targets: [ 0 ] } ]
        columns: [null,
});
{ render: function ( data, type, row, meta ) {
$('#gene_exptable_wrapper .dataTables_scrollHead th').css("height", "100px").css("vertical-align", "bottom");
var title = data.split("#")[0];
 
return "<a href=\"/resource_browser/index.php/"+title+"\">"+title+"</a>";
 
},
var data = [];
},
var slist = [];
null
var plotdata = [];
]
 
});
 
// chart checkbox
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 + '">'
                                + $('#gene_exptable thead th:nth-child('+(i2+1)+')').text() + '</label><br/>');
}
}
 
else
function collectdata(){
{
data = [];
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": $('#gene_exptable thead th:nth-child('+(i2+1)+')').text(), "data": plots});
}
slist = [];
for (i1=2, len1=$('#gene_exptable tr').length; i1<len1; i1++) {
    slist.push($("#gene_exptable tr")[i1].cells[0].innerHTML);
}
//test
//slist[0] = "test";
}
}
 
 
 
function drawchart(){
 
plotdata = [];
 
$("#gene_exptable_chart_chkbox").find("input:checked").each(function () {
var key = $(this).attr("name");
plotdata.push(data[$(this).attr("name")]);
});
 
var plot1 = $.plot($("#gene_exptable_chart"), plotdata, {
                yaxis : { axisLabel : 'TPM' },
lines : { show : false },
points : { show : true },
                grid: { hoverable: true, clickable: true },
xaxis : { tickDecimals : 0, show: false },
                legend: { show: false }
});
 
//test
var data_series = plot1.getData();
 
$("#gene_exptable_chart_chkbox label").css("background-color", "white");
$.each(data_series , function(){
$("#gene_exptable_chart_chkbox label:contains(" + this.label + ")").css("background-color", this.color);
});
 
 
 
}
 
collectdata();
drawchart();
 
// re-draw chart event
$(window).resize(function() { drawchart(); });
$("th").click(function() {collectdata(); drawchart(); } );
$("#gene_exptable_paginate").click(function() {collectdata(); drawchart(); } );
$('#gene_exptable').bind('filter', function() {
setTimeout(function(){
collectdata(); drawchart();}, 1000);
} );
$('#gene_exptable_length').change(function() {collectdata(); drawchart(); } );
$("#gene_exptable_chart_chkbox").find("input").click(function() { drawchart(); });
 
// tooltip function start
    function showTooltip(x, y, contents) {
        $('<div id="tooltip">' + contents + '</div>').css( {
            position: 'absolute',
            display: 'none',
            top: y + 5,
            left: x + 5,
            border: '1px solid #aaa',
            padding: '2px',
            'background-color': '#fff',
            opacity: 0.80
        }).appendTo("body").fadeIn(200);
    }
 
    var previousPoint = null;
    $("#gene_exptable_chart").bind("plothover", function (event, pos, item) {
        $("#x").text(pos.x.toFixed(2));
        $("#y").text(pos.y.toFixed(2));
            if (item) {
                if (previousPoint != item.dataIndex) {
                    previousPoint = item.dataIndex;
                   
                    $("#tooltip").remove();
                    x = item.datapoint[0].toFixed(0),
                    y = item.datapoint[1].toFixed(2);
                 
                    showTooltip(item.pageX, item.pageY,
                              "Sample: "+slist[item.dataIndex]+"<br>TSS: "+ item.series.label +"  TPM: "+y);
                }
            }
            else {
                $("#tooltip").remove();
                previousPoint = null;           
            }
    });
// tooltip function end
 
// clicking point function
    $("#gene_exptable_chart").bind("plotclick", function (event, pos, item) {
if (item){
var vdata = Math.round($('#gene_exptable').height())/item.series.data.length*item.dataIndex;
$('#gene_exptable_wrapper .dataTables_scrollBody').animate({ scrollTop: vdata-150 }, 'slow');
$("#gene_exptable_wrapper .dataTables_scrollBody tbody td").removeClass('highlight');
$('#gene_exptable_wrapper .dataTables_scrollBody tbody tr:eq(' + item.dataIndex+ ') td').addClass('highlight');
}
    });
// clicking point function end
 
 
 
 


} );
} );
Line 204: Line 76:
</html>
</html>


<includeonly>{{#gene_exptable:{{#explode:{{PAGENAME}}|:|0}}
{{Fontsize|3|Ontology association}}{{#info:<br>Each term has an is_a parent in the Uberon Ontology, which has a linkage to an another entity and FANTOM5 samples.Libraries were grouped into mutually exclusive facets according to the FANTOM5 sample ontology mapping to UBERON ontologies.
|{{#replace:{{{short_description}}}|,|}},{{{phase1_expression}}}
}}</includeonly>
<br>
<br>
<br>link to ontology dataset
<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ff-phase1-prerelease-20130717.obo  data]
}}
----
{{Fontsize|3|Parents}}
{{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{is_a}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{disjoint_from}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{union_of}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{derives_from}}}|:|0}}|1|0}} +{{#if:{{#pos:{{{has_quality}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{located_in}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{part_of}}}|:|0}}|1|0}} }} |NA|<table>
{{#if:{{{is_a}}}|<tr><th width=100 align="right">is_a:</th><td>{{#arraymap:{{{is_a}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}{{#if:{{{disjoint_from}}}|<tr><th width=100 align="right">disjoint_from:</th><td>{{#arraymap:{{{disjoint_from}}}|;;|$|[[$]]({{#show:$|?name}})|,}}</td></tr>}}{{#if:{{{union_of}}}|<tr><th width=100 align="right">union_of:</th><td>{{#arraymap:{{{union_of}}}|;;|$|[[$]]({{#show:$|?name}})|,}}</td></tr>}}{{#if:{{{derives_from}}}|<tr><th width=100 align="right">derives_from:</th><td>{{#arraymap:{{{derives_from}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}{{#if:{{{develops_from}}}|<tr><th width=100 align="right">develops_from:</th><td>{{#arraymap:{{{develops_from}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}{{#if:{{{has_quality}}}|<tr><th width=100 align="right">has_quality:</th><td>{{#arraymap:{{{has_quality}}}|;;|$|[[$]]({{#show:$|?name}})|,}}</td></tr>}}{{#if:{{{located_in}}}|<tr><th width=100 align="right">located_in:</th><td>{{#arraymap:{{{located_in}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}{{#if:{{{part_of}}}|<tr><th width=100 align="right">part_of:</th><td>{{#arraymap:{{{part_of}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}
</table>}}
<br><br>
{{Fontsize|3|Children}}
{{#vardefine:is_a_count|{{#ask:[[is_a::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:disjoint_from_count|{{#ask:[[disjoint_from::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:adjacent_to_count|{{#ask:[[adjacent_to::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:derives_from_count|{{#ask:[[derives_from::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:develops_from_count|{{#ask:[[develops_from::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:has_quality_count|{{#ask:[[has_quality::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:located_in_count|{{#ask:[[located_in::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:part_of_count|{{#ask:[[part_of::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:total_element_count|{{#expr:{{#var:is_a_count}}+{{#var:disjoint_from_count}}+{{#var:adjacent_to_count}}+{{#var:derives_from_count}}+{{#var:develops_from_count}}+{{#var:has_quality_count}}+{{#var:located_in_count}}+{{#var:part_of_count}} }} }}{{#ifexpr: {{#var:total_element_count}} > 0 | <table>
{{#ask:[[is_a::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">is_a:</th><td>|outro=</td></tr>}}{{#ask:[[disjoint_from::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">disjoint_from:</th><td>|outro=</td></tr>}}{{#ask:[[adjacent_to::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">adjacent_to:</th><td>|outro=</td></tr>}}{{#ask:[[derives_from::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">derives_from:</th><td>|outro=</td></tr>}}{{#ask:[[develops_from::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">develops_from:</th><td>|outro=</td></tr>}}{{#ask:[[has_quality::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">has_quality:</th><td>|outro=</td></tr>}}{{#ask:[[located_in::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">located_in:</th><td>|outro=</td></tr>}}{{#ask:[[part_of::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">part_of:</th><td>|outro=</td></tr>}}</table>|NA}}
<!-- comment out 2020.1.24
== Ontology Tree: Loaded from [http://purl.bioontology.org/ontology/UBERON BioPortal] ==
{{#ncbo_onttree2:{{#explode:{{{id}}}|:|0}}|{{#explode:{{{id}}}|:|1}}}}
-->
<!--
<html><object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" id="FlexoViz" width="100%" height="100%" codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab"><param name="movie" value="/resource_browser/rb_js/BasicFlexoViz.swf" /><param name="quality" value="high" /><param name="bgcolor" value="#ffffff" /><param name="allowScriptAccess" value="always" /><embed src="/resource_browser/rb_js/BasicFlexoViz.swf" bgcolor="#ffffff" width="750px" height="600px" name="FlexoViz" align="middle" play="true" loop="false" quality="high" allowScriptAccess="always" type="application/x-shockwave-flash" flashVars="widget=true&ontology=49804&nodeid=</html>{{{id}}}<html>&server=http://rest.bioontology.org/bioportal" pluginspage="http://www.adobe.com/go/getflashplayer"></embed></object></html>
-->
<br>
<br>
<div id="gene_exptable_chart" style="float:left;width:600px;height:300px;"></div>
{{Fontsize|3|FF samples}}{{#info:<br>It includes FANTOM5 samples that overlay the [http://uberon.org/  Uberon] ontology}}
----
{{#ifexpr: 0 ={{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]][[sample_species::Human (Homo sapiens)]][[name::+]][[datafreeze_phase::2]]|?name=|format=count}}||{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Human (Homo sapiens)]][[name::+]][[datafreeze_phase::2]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Human (Homo sapiens)</b>}} }}
{{#ifexpr: 0 ={{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]][[sample_species::Mouse (Mus musculus)]][[name::+]][[datafreeze_phase::2]]|?name=|format=count}}||{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Mouse (Mus musculus)]][[name::+]][[datafreeze_phase::2]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Mouse (Mus musculus)</b>}} }}
<!--{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Rat (Rattus rattus)]][[name::+]][[datafreeze_phase::1]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Rat (Rattus rattus)</b>}}
{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Dog (Canis lupus familaris)]][[name::+]][[datafreeze_phase::1]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Dog (Canis lupus familaris)</b>}}
{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Chicken (Gallus gallus)]][[name::+]][[datafreeze_phase::1]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Chicken (Gallus gallus)</b>}} -->
<br>
<br>
<div id="gene_exptable_chart_chkbox" style="float:left;"></div>
{{Fontsize|3|Enrichment analysis: top 100 FFCP enriched with this ontology term }}{{#info:TOP 100 FANTOM5 Cage Peaks enriched with {{{id}}} ({{{name}}}), sorted by p-values <br>Analyst: Hideya Kawaji
<div style="clear:both;"></div>
<br><br>
 
link to source dataset <br>
 
human : [//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/hg19exp_uberon_general_term_excluded.txt.gz data]  <br>
*Click each plot point to find sample in table
mouse : [//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/mm9exp_uberon_general_term_excluded.txt.gz data]  
<br>
{{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>
[http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Sample_ontology_enrichment_of_CAGE_peaks/ data]
}}
}}
----
----
<html>
{{#ifexpr: 0 = {{#ask:[[ffcp_ontology_enrichment_uberon_id::{{{id}}}]]|?#|format=count}} | No analysis results |{{#ask:[[ffcp_ontology_enrichment_uberon_id::{{{id}}}]]
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{{#arraymap:{{{synonym}}}|;;|$|{{#set:synonym=$}}}}
order: [[ 1, "asc" ]]
{{#arraymap:{{{comment}}}|;;|$|{{#set:comment=$}}}}
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{{#arraymap:{{{alt_id}}}|;;|$|{{#set:alt_id=$}}}}
 
{{#arraymap:{{{disjoint_from}}}|;;|$|{{#set:disjoint_from=$}}}}
 
{{#arraymap:{{{union_of}}}|;;|$|{{#set:union_of=$}}}}
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{{#arraymap:{{{subset}}}|;;|$|{{#set:subset=$}}}}
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{{#if:{{{ontology_enrichment_celltype_v019_2}}}|
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{{#arraymap:{{{derives_from}}}|;;|$|{{#set:derives_from=$}}}}
<table class="enrichment_list stripe cell-border order-column compact"><caption class="table_title">Cell type</caption><html><thead></html>
{{#arraymap:{{{develops_from}}}|;;|$|{{#set:develops_from=$}}}}
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
{{#arraymap:{{{has_quality}}}|;;|$|{{#set:has_quality=$}}}}
<html></thead><tbody></html>
{{#arraymap:{{{located_in}}}|;;|$|{{#set:located_in=$}}}}
{{#arraymap:{{{ontology_enrichment_celltype_v019_2}}}|;|$
{{#arraymap:{{{part_of}}}|;;|$|{{#set:part_of=$}}}}
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{{#arraymap:{{{property_value}}}|;;|$|{{#set:property_value=$}}}}
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<html></tbody></html></table>
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}}{{#if:{{{ontology_enrichment_uberon_v019_2}}}|
<div style="float:left;width:33%;">
<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>
{{#arraymap:{{{ontology_enrichment_uberon_v019_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>| }}
|}}
 
<html></tbody></html></table>
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}}{{#if:{{{ontology_enrichment_disease_v019_2}}}|
<div style="float:left;width:33%;">
<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>
{{#arraymap:{{{ontology_enrichment_disease_v019_2}}}|;|$
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|}}
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[[Category:FFCP]]
[[Category:Uber_Anatomy_Ontology]]

Revision as of 13:34, 27 January 2020

Name:{{{name}}}
Namespace:{{{namespace}}}
Definition:{{{def}}}
Xrefs:
links:
{{{xref}}}:[1]
Synonyms: {{{synonym}}}
Comments:{{{comment}}}
Alt_id: {{{alt_id}}}
Subset: {{{subset}}}
Created by:{{{created_by}}}
Creation date:{{{obo_creation_date}}}
Has quality:{{{has_quality}}}

Ontology association<br>Each term has an is_a parent in the Uberon Ontology, which has a linkage to an another entity and FANTOM5 samples.Libraries were grouped into mutually exclusive facets according to the FANTOM5 sample ontology mapping to UBERON ontologies.<br><br>link to ontology dataset<br>data

Parents NA

Children NA
FF samples<br>It includes FANTOM5 samples that overlay the Uberon ontology



Enrichment analysis: top 100 FFCP enriched with this ontology term TOP 100 FANTOM5 Cage Peaks enriched with {{{id}}} ({{{name}}}), sorted by p-values <br>Analyst: Hideya Kawaji<br><br>link to source dataset <br>human : data <br>mouse : data

No analysis results







"{{{obo_creation_date}}}" contains an extrinsic dash or other characters that are invalid for a date interpretation.




Property "Property value" (as page type) with input value "{{{property_value}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.

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