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(Created page with "*id: [[id::{{{id}}}]] *short_description: [[short_description::{{{short_description}}}]] *description: [[description::{{{description}}}]] *association_with_transcript: [[assoc...")
 
 
(318 intermediate revisions by 5 users not shown)
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*id: [[id::{{{id}}}]]
+
{{Loading|loadingimage=sprites.gif}}<table>
*short_description: [[short_description::{{{short_description}}}]]
+
<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>
*description: [[description::{{{description}}}]]
+
<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>
*association_with_transcript: [[association_with_transcript::{{{association_with_transcript}}}]]
+
<!--tr><th scope="row" align="right">[[Property:GencodeV16b_All_Build2_RSEM10_CPAT_consensus|GencodeV16b-All-Build2-RSEM10-CPAT_consensus:]]</th><td>
*EntrezGene: [[EntrezGene::{{{EntrezGene}}}]]
+
{{#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-->
{{#if: {{{HGNC}}} | *HGNC: [[HGNC::{{{HGNC}}}]] |}}
+
<tr><th scope="row" align="right">DHS support(Yes/No):</th><td> {{#switch: {{{DHSsupport}}}|supported= Yes|not supported=No|#default=NA}} </td></tr>
*UniProt: [[UniProt::{{{UniProt}}}]]
+
<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>[//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>[//fantom.gsc.riken.jp/zenbu/gLyphs/#config=Uz8Jh3NEDl8qV47r6EGQ8B;loc={{#explode:{{PAGENAME}}|,|0}} ZENBU]</td></tr>
 +
}}
 +
</table>
  
phase1_expression:  
+
<html>
{{{phase1_expression}}}
+
<script language="javascript" type="text/javascript">
 +
$(document).ready(function() {
 +
// hide-show animation for ucsc genome browser view
 +
$("#ucsc_snap_view").hover(function(){
 +
    $(this).stop(true, false).animate({ height: "600px"});
 +
}, function() {
 +
    $(this).stop(true, false).animate({ height: "30px" });
 +
});
 +
});
 +
</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><br>
 +
{{Fontsize|3|CAGE Expression}}
 +
----
 +
<html><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/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>
 +
 
 +
</html>
 +
 
 +
<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() {
 +
    var oTable =  $('#gene_exptable').DataTable({
 +
        dom: 'frt',
 +
scrollY: "300px",
 +
paging: false,
 +
scrollCollapse: true,
 +
pageLength: -1,
 +
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");
 +
 
 +
 
 +
var data = [];
 +
var slist = [];
 +
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/>');
 +
}
 +
 
 +
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
 +
 
 +
 
 +
 
 +
 
 +
 
 +
} );
 +
</script>
 +
</html>
 +
 
 +
<includeonly>{{#gene_exptable:{{#explode:{{PAGENAME}}|:|0}}
 +
|{{#replace:{{{short_description}}}|,|}},{{{phase1_expression}}}
 +
}}</includeonly>
 +
<br>
 +
<br>
 +
<div id="gene_exptable_chart" style="float:left;width:600px;height:300px;"></div>
 +
<br>
 +
<div id="gene_exptable_chart_chkbox" style="float:left;"></div>
 +
<div style="clear:both;"></div>
 +
 
 +
 
 +
*Click each plot point to find sample in table
 +
<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>
 +
[//fantom.gsc.riken.jp/5/datafiles/latest/extra/Sample_ontology_enrichment_of_CAGE_peaks/ data]
 +
}}
 +
----
 +
<html>
 +
<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/datatables/extras/TableTools/media/js/TableTools.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";
 +
.table_title{
 +
text-align:left;
 +
font-size:small;
 +
text-decoration:underline;
 +
color:darkgoldenrod;
 +
}
 +
</style>
 +
<script type="text/javascript">
 +
 
 +
$(document).ready(function() {
 +
    var oTable =  $('.enrichment_list').DataTable({
 +
        dom: 'frtip',
 +
scrollCollapse: false,
 +
        columnDefs: [{ orderable: false, targets: [ 0 ] },  { type: "html-num", width: "50pt", targets: [1] }],
 +
order: [[ 1, "asc" ]]
 +
});
 +
 
 +
 
 +
});
 +
</script>
 +
</html>
 +
{{#if:{{{ontology_enrichment_celltype_v019_2}}}|
 +
<div style="float:left;width:33%;">
 +
<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>
 +
{{#arraymap:{{{ontology_enrichment_celltype_v019_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>| }}
 +
|}}
 +
<html></tbody></html></table>
 +
</div>
 +
}}{{#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>
 +
</div>
 +
}}{{#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}}}|;|$
 +
|{{#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>| }}
 +
|}}
 +
<html></tbody></html></table>
 +
</div>
 +
}}
 +
<div style="clear:both;"></div>
 +
<!--
 +
{{#ifexpr: {{#expr: {{REVISIONTIMESTAMP}}-20120731160000 }} > 0
 +
|<html>
 +
|}}
 +
-->
 +
{{#arraymap:{{{short_description}}}|,|$|{{#set:short_description=$}}}}
 +
{{#arraymap:{{{description}}}|,|$|{{#set:description=$}}}}
 +
{{#arraymap:{{{association_with_transcript}}}|,|$|{{#set:association_with_transcript=$}}}}
 +
{{#arraymap:{{{EntrezGene}}}|,|$|{{#set:EntrezGene=$}}}}
 +
{{#arraymap:{{{HGNC}}}|,|$|{{#set:HGNC=$}}}}
 +
{{#arraymap:{{{UniProt}}}|,|$|{{#set:UniProt=$}}}}
 +
{{#set:phase1_expression={{{phase1_expression}}}}}
 +
{{#set:id={{{id}}}}}
 +
{{#set:chromosome={{#replace:{{#explode:{{PAGENAME}}|:|2}}|chr|}}}}
 +
{{#set:genomic_location_start={{#explode:{{#explode:{{PAGENAME}}|:|3}}|..|0}}}}
 +
{{#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]]

Latest revision as of 06:57, 16 January 2020

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 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.