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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");
Line 78: Line 79:
  
 
// 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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{{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;
Line 238: Line 239:
  
 
$(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>
Line 263: Line 262:
 
}}{{#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 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.