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--> | |||
<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"> | <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"> | |{{#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}} | ||
<tr><th scope="row" align="right">TSS-like-by-RIKEN-classifier(Yes/No):</th><td> {{#switch: {{{TSSclassifier}}} | | }}{{#if:{{#pos:{{PAGENAME}}|Mm9}} | ||
<tr><th scope="row" align="right">GencodeV16b_All_Build2_RSEM10_CPAT_consensus:</th><td> | |{{#if:{{#pos:{{{MCL_coexpression_id}}}|MCL}}|NA|[[MCL_coexpression_id::{{{MCL_coexpression_id}}}|]][[MCL_coexpression_mm9:{{{MCL_coexpression_id}}}]]}} | ||
{{#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> | }}</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"> | <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>|}} | ||
<tr><th scope="row" align="right"> | |||
<tr><th scope="row" align="right"> | |||
<tr><th scope="row" align="right"> | |||
{{#if: {{{ | |||
<tr><th scope="row" align="right"> | |||
{{# | |||
</td></tr> | |||
{{#switch:{{#explode:{{PAGENAME}}|:|0}} | {{#switch:{{#explode:{{PAGENAME}}|:|0}} | ||
|Hg19= | |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> | ||
<tr><th scope="row" align="right"> | |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> | ||
|Mm9= | |||
<tr><th scope="row" align="right">Link to Zenbu:</th><td>[ | |||
}} | }} | ||
</table> | </table> | ||
<html> | <html> | ||
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}); | }); | ||
</script> | </script> | ||
</html> | </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;"> | <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 | Mouse over to see Genome browser image, Click image to go to Genome browser | ||
{{#ucsc_gb_link:{{# | {{#ucsc_gb_link:{{#if:{{#pos:{{FULLPAGENAME}}|Hg19}}|Hg19}}{{#if:{{#pos:{{FULLPAGENAME}}|Mm9}}|Mm9}}::{{{cluster_id}}}}} | ||
</div> | </div><br> | ||
{{Fontsize|3|CAGE Expression}} | |||
---- | |||
<html> | <html><script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.js"></script> | ||
<script type="text/ | <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="/ | <script type="text/javascript" language="javascript" src="/5/sstar/rb_js/flot/jquery.flot.min.js"></script> | ||
<script type="text/javascript" language="javascript" src="/ | |||
<style type="text/css" title="currentStyle"> | <style type="text/css" title="currentStyle"> | ||
@import "/ | @import "/5/sstar/rb_js/html5button/datatables.css"; | ||
@import "/ | @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'). | 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"); | $('#gene_exptable_wrapper .dataTables_scrollHead th').css("height", "100px").css("vertical-align", "bottom"); | ||
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// chart checkbox | // chart checkbox | ||
for (var i2=1; i2< | for (var i2=1; i2<$('#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 + '">' | ||
+ $( | + $('#gene_exptable thead th:nth-child('+(i2+1)+')').text() + '</label><br/>'); | ||
} | } | ||
function collectdata(){ | function collectdata(){ | ||
data = []; | data = []; | ||
for (i2=1, len2= | for (i2=1, len2=$('#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": $( | data.push({"label": $('#gene_exptable thead th:nth-child('+(i2+1)+')').text(), "data": plots}); | ||
} | } | ||
slist = []; | slist = []; | ||
for (i1=2, len1=$('#gene_exptable tr').length; i1<len1; i1++) { | for (i1=2, len1=$('#gene_exptable tr').length; i1<len1; i1++) { | ||
slist.push($("#gene_exptable tr")[i1].cells[0]. | slist.push($("#gene_exptable tr")[i1].cells[0].innerHTML); | ||
} | } | ||
//test | |||
//slist[0] = "test"; | |||
} | } | ||
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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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showTooltip(item.pageX, item.pageY, | showTooltip(item.pageX, item.pageY, | ||
"Sample: "+slist[item.dataIndex]+"<br>TSS: "+ item.series.label +" TPM: "+y); | |||
} | } | ||
} | } | ||
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</html> | </html> | ||
{{#gene_exptable:{{#explode:{{PAGENAME}}|:|0}} | <includeonly>{{#gene_exptable:{{#explode:{{PAGENAME}}|:|0}} | ||
|{{#replace:{{{short_description}}}|,|}},{{{phase1_expression}}} | |{{#replace:{{{short_description}}}|,|}},{{{phase1_expression}}} | ||
}} | }}</includeonly> | ||
<br> | |||
<br> | |||
<div id="gene_exptable_chart" style="float:left;width:600px;height:300px;"></div> | <div id="gene_exptable_chart" style="float:left;width:600px;height:300px;"></div> | ||
<br> | <br> | ||
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*Click each plot point to find sample in table | *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> | <html> | ||
<script type="text/ | <script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.js"></script> | ||
<script type="text/javascript" language="javascript" src="/ | <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 "/ | @import "/5/sstar/rb_js/html5button/datatables.css"; | ||
@import "/ | @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'). | var oTable = $('.enrichment_list').DataTable({ | ||
dom: 'frtip', | |||
scrollCollapse: false, | |||
columnDefs: [{ orderable: false, targets: [ 0 ] }, { type: "html-num", width: "50pt", targets: [1] }], | |||
order: [[ 1, "asc" ]] | |||
}); | }); | ||
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{{#if:{{{ontology_enrichment_celltype_v019_2}}}| | {{#if:{{{ontology_enrichment_celltype_v019_2}}}| | ||
<div style="float:left;width:33%;"> | <div style="float:left;width:33%;"> | ||
<table class="enrichment_list"><caption class="table_title">Cell | <table class="enrichment_list stripe cell-border order-column compact"><caption class="table_title">Cell type</caption><html><thead></html> | ||
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr> | <tr><th>Ontology term</th><th>p-value</th><th>n</th></tr> | ||
<html></thead><tbody></html | <html></thead><tbody></html> | ||
{{#arraymap:{{{ontology_enrichment_celltype_v019_2}}}|;|$ | {{#arraymap:{{{ontology_enrichment_celltype_v019_2}}}|;|$ | ||
|{{#set:ffcp_ontology_enrichment_celltype={{#replace:$|,|;}}}}[[{{#explode:$|,|0}}|{{#show:{{#explode:$|,|0}}|?name}}]]</td><td>{{#explode:$|,|1}}</td><td>{{#explode:$|,|2}} | |{{#set:ffcp_ontology_enrichment_celltype={{#replace:$|,|;}}}}{{#ifexist:{{#explode:$|,|0}}|<tr><td>[[{{#explode:$|,|0}}|{{#show:{{#explode:$|,|0}}|?name}}]]</td><td>{{#explode:$|,|1}}</td><td>{{#explode:$|,|2}}</td></tr>| }} | ||
|}} | |||
<html></tbody></html></table> | <html></tbody></html></table> | ||
</div> | </div> | ||
}}{{#if:{{{ontology_enrichment_uberon_v019_2}}}| | }}{{#if:{{{ontology_enrichment_uberon_v019_2}}}| | ||
<div style="float:left;width:33%;"> | <div style="float:left;width:33%;"> | ||
<table class="enrichment_list"><caption class="table_title">Uber | <table class="enrichment_list stripe cell-border order-column compact"><caption class="table_title">Uber anatomy</caption><html><thead></html> | ||
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr> | <tr><th>Ontology term</th><th>p-value</th><th>n</th></tr> | ||
<html></thead><tbody></html | <html></thead><tbody></html> | ||
{{#arraymap:{{{ontology_enrichment_uberon_v019_2}}}|;|$ | {{#arraymap:{{{ontology_enrichment_uberon_v019_2}}}|;|$ | ||
|{{#set:ffcp_ontology_enrichment_uberon={{#replace:$|,|;}}}}[[{{#explode:$|,|0}}|{{#show:{{#explode:$|,|0}}|?name}}]]</td><td>{{#explode:$|,|1}}</td><td>{{#explode:$|,|2}} | |{{#set:ffcp_ontology_enrichment_uberon={{#replace:$|,|;}}}}{{#ifexist:{{#explode:$|,|0}}|<tr><td>[[{{#explode:$|,|0}}|{{#show:{{#explode:$|,|0}}|?name}}]]</td><td>{{#explode:$|,|1}}</td><td>{{#explode:$|,|2}}</td></tr>| }} | ||
|}} | |||
<html></tbody></html></table> | <html></tbody></html></table> | ||
</div> | </div> | ||
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<table class="enrichment_list"><caption class="table_title">Disease</caption><html><thead></html> | <table class="enrichment_list"><caption class="table_title">Disease</caption><html><thead></html> | ||
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr> | <tr><th>Ontology term</th><th>p-value</th><th>n</th></tr> | ||
<html></thead><tbody></html | <html></thead><tbody></html> | ||
{{#arraymap:{{{ontology_enrichment_disease_v019_2}}}|;|$ | {{#arraymap:{{{ontology_enrichment_disease_v019_2}}}|;|$ | ||
|{{#set:ffcp_ontology_enrichment_disease={{#replace:$|,|;}}}}[[{{#explode:$|,|0}}|{{#show:{{#explode:$|,|0}}|?name}}]]</td><td>{{#explode:$|,|1}}</td><td>{{#explode:$|,|2}} | |{{#set:ffcp_ontology_enrichment_disease={{#replace:$|,|;}}}}{{#ifexist:{{#explode:$|,|0}}|<tr><td>[[{{#explode:$|,|0}}|{{#show:{{#explode:$|,|0}}|?name}}]]</td><td>{{#explode:$|,|1}}</td><td>{{#explode:$|,|2}}</td></tr>| }} | ||
|}} | |||
<html></tbody></html></table> | <html></tbody></html></table> | ||
</div> | </div> | ||
}} | }} | ||
<div style="clear:both;"></div> | <div style="clear:both;"></div> | ||
<!-- | <!-- | ||
{{#ifexpr: {{#expr: {{REVISIONTIMESTAMP}}-20120731160000 }} > 0 | {{#ifexpr: {{#expr: {{REVISIONTIMESTAMP}}-20120731160000 }} > 0 | ||
|<html> | |<html> | ||
|}} | |}} | ||
--> | --> | ||
{{#arraymap:{{{short_description}}}|,|$|{{#set:short_description=$}}}} | {{#arraymap:{{{short_description}}}|,|$|{{#set:short_description=$}}}} | ||
{{#arraymap:{{{description}}}|,|$|{{#set:description=$}}}} | {{#arraymap:{{{description}}}|,|$|{{#set:description=$}}}} | ||
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{{#set:genomic_location_end={{#explode:{{#explode:{{PAGENAME}}|..|-1}}|,|0}}}} | {{#set:genomic_location_end={{#explode:{{#explode:{{PAGENAME}}|..|-1}}|,|0}}}} | ||
{{#set:strand={{#explode:{{PAGENAME}}|,|-1}}}} | {{#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
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.