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*id: [[id::{{{id}}}]]
{{Loading|loadingimage=sprites.gif}}<table>
*short_description: {{#show:{{PAGENAME}}|?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: {{#show:{{PAGENAME}}|?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: {{#show:{{PAGENAME}}|?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: {{#show:{{PAGENAME}}|?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: {{#show:{{PAGENAME}}|?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: {{#show:{{PAGENAME}}|?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>


{{#if:{{#pos:{{PAGENAME}}|hg19}}|
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{{Fontsize|3|View on UCSC genome browser}}
----
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{{Fontsize|3|CAGE Expression}}
----
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<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;
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<script type="text/javascript">
 
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// -->
</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:{{#pos:{{PAGENAME}}|mm9}}| yes | no}}
<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}}}|;|$
|{{#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>
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|<html>
|}}
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{{#arraymap:{{{short_description}}}|,|$|{{#set:short_description=$}}}}
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{{#arraymap:{{{description}}}|,|$|{{#set:description=$}}}}
Line 61: Line 294:
{{#arraymap:{{{HGNC}}}|,|$|{{#set:HGNC=$}}}}
{{#arraymap:{{{HGNC}}}|,|$|{{#set:HGNC=$}}}}
{{#arraymap:{{{UniProt}}}|,|$|{{#set:UniProt=$}}}}
{{#arraymap:{{{UniProt}}}|,|$|{{#set:UniProt=$}}}}
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{{#set:TSS_like_by_RIKEN_classifier={{{TSSclassifier}}}}}
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[[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


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.