Template:FFCP: Difference between revisions
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{{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">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--> | |||
{{#if: {{{HGNC}}} | | <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>[//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> | |||
<html> | <html> | ||
<script type="text/javascript" src=" | <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"> | <script type="text/javascript"> | ||
$(document).ready(function() { | |||
var | 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 = $('.enrichment_list').DataTable({ | |||
dom: 'frtip', | |||
scrollCollapse: false, | |||
columnDefs: [{ orderable: false, targets: [ 0 ] }, { type: "html-num", width: "50pt", targets: [1] }], | |||
order: [[ 1, "asc" ]] | |||
}); | |||
}); | }); | ||
</script> | </script> | ||
</html> | </html> | ||
{{#if:{{{ontology_enrichment_celltype_v019_2}}}| | |||
<div style="float:left;width:33%;"> | |||
<table class="enrichment_list stripe cell-border order-column compact"><caption class="table_title">Cell type</caption><html><thead></html> | |||
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr> | |||
<html></thead><tbody></html> | |||
{{#arraymap:{{{ontology_enrichment_celltype_v019_2}}}|;|$ | |||
|{{#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>| }} | |||
|}} | |}} | ||
{{#if:{{# | <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:{{{short_description}}}|,|$|{{#set:short_description=$}}}} | ||
{{#arraymap:{{{description}}}|,|$|{{#set:description=$}}}} | {{#arraymap:{{{description}}}|,|$|{{#set:description=$}}}} | ||
| Line 61: | Line 294: | ||
{{#arraymap:{{{HGNC}}}|,|$|{{#set:HGNC=$}}}} | {{#arraymap:{{{HGNC}}}|,|$|{{#set:HGNC=$}}}} | ||
{{#arraymap:{{{UniProt}}}|,|$|{{#set:UniProt=$}}}} | {{#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]] | [[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
| Ontology term | p-value | n |
|---|
| Ontology term | p-value | n |
|---|
| 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.
