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Difference between revisions of "Template:FFCP"

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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">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">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">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">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">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">[[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">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}}
 
}}{{#if:{{#pos:{{PAGENAME}}|Mm9}}
 
}}{{#if:{{#pos:{{PAGENAME}}|Mm9}}
 
|{{#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>
+
<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}}|,|$|[http://www.uniprot.org/uniprot/?query=$  $] |}}}}</td></tr>|}}
{{#if: {{{HGNC}}} | <tr><th scope="row" align="right">HGNC:</th><td> {{#ifeq:{{#show:{{FULLPAGENAME}}|?HGNC}}| {{#if:{{#pos:{{FULLPAGENAME}}|Hg19}}|NA|}}|NA|[http://www.genenames.org/cgi-bin/quick_search.pl?.cgifields=type&num=50&search={{#show:{{FULLPAGENAME}}|?HGNC}}&submit=Submit {{#show:{{FULLPAGENAME}}|?HGNC}}]|NA}}</td></tr>|}}{{#if: {{{UniProt}}} | <tr><th scope="row" align="right">UniProt:</th><td> {{#ifeq:{{#show:{{FULLPAGENAME}}|?UniProt}}|NA|NA|{{#arraymap:{{#show:{{FULLPAGENAME}}|?UniProt}}|,|$|[http://www.uniprot.org/uniprot/?query=$  $] |}}}}</td></tr> |}}
 
 
{{#switch:{{#explode:{{PAGENAME}}|:|0}}
 
{{#switch:{{#explode:{{PAGENAME}}|:|0}}
|Hg19=
+
|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>
<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>
+
|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>[https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=3qebVNZHMB1tN8DyYkP1uD;loc={{#explode:{{PAGENAME}}|,|0}} ZENBU]</td></tr>
 
 
}}
 
}}
 
</table>
 
</table>
 +
 
<html>
 
<html>
 
<script language="javascript" type="text/javascript">
 
<script language="javascript" type="text/javascript">
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});
 
});
 
</script>
 
</script>
</html>
+
</html><br>
 
+
{{Fontsize|3|View on UCSC genome browser}}
== View on UCSC genome browser OSC local mirror ==
+
----
 
<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
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{{#ucsc_gb_link:{{#replace:{{FULLPAGENAME}}|FFCP PHASE1:|}}|https://fantom5-collaboration.gsc.riken.jp/ucsc/}}
 
{{#ucsc_gb_link:{{#replace:{{FULLPAGENAME}}|FFCP PHASE1:|}}|https://fantom5-collaboration.gsc.riken.jp/ucsc/}}
 
</div>
 
</div>
 
+
{{Fontsize|3|CAGE Expression}}
== CAGE Expression ==
+
----
<html>
+
<html><script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.min.js"></script>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.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="/resource_browser/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="/resource_browser/rb_js/flot/jquery.flot.min.js"></script>
Line 101: Line 98:
 
     slist.push($("#gene_exptable tr")[i1].cells[0].innerHTML);
 
     slist.push($("#gene_exptable tr")[i1].cells[0].innerHTML);
 
}
 
}
 +
//test
 +
//slist[0] = "test";
 
}
 
}
  
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                     showTooltip(item.pageX, item.pageY,
 
                     showTooltip(item.pageX, item.pageY,
                                "Sample: "+slist[item.dataIndex]+"<br>TSS: "+ item.series.label +"<br>TPM: "+y);
+
                              "Sample: "+slist[item.dataIndex]+"<br>TSS: "+ item.series.label +" TPM: "+y);
 
                 }
 
                 }
 
             }
 
             }
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|{{#replace:{{{short_description}}}|,|}},{{{phase1_expression}}}
 
|{{#replace:{{{short_description}}}|,|}},{{{phase1_expression}}}
 
}}</includeonly>
 
}}</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>
== Ontology-based sample term enrichment analysis ==
+
{{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>
 +
[http://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" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.js"></script>
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"aaSorting": [[ 1, "asc" ]]
 
"aaSorting": [[ 1, "asc" ]]
 
});
 
});
 
  
 
});
 
});
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<table class="enrichment_list"><caption class="table_title">Cell type</caption><html><thead></html>
 
<table class="enrichment_list"><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><tr><td>
+
<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>| }}
|</td></tr><tr><td>}}
+
|}}
</td></tr>
 
 
<html></tbody></html></table>
 
<html></tbody></html></table>
 
</div>
 
</div>
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<table class="enrichment_list"><caption class="table_title">Uber anatomy</caption><html><thead></html>
 
<table class="enrichment_list"><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><tr><td>
+
<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>| }}
|</td></tr><tr><td>}}
+
|}}
</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><tr><td>
+
<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>| }}
|</td></tr><tr><td>}}
+
|}}
</td></tr>
+
 
 
<html></tbody></html></table>
 
<html></tbody></html></table>
 
</div>
 
</div>
 
}}
 
}}
 
<div style="clear:both;"></div>
 
<div style="clear:both;"></div>
 +
  
 
<!--
 
<!--
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|}}
 
|}}
 
-->
 
-->
 +
  
 
{{#arraymap:{{{short_description}}}|,|$|{{#set:short_description=$}}}}
 
{{#arraymap:{{{short_description}}}|,|$|{{#set:short_description=$}}}}
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{{#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:GencodeV16b_All_Build2_RSEM10_CPAT_consensus={{{GencodeV16b_All_Build2_RSEM10_CPAT_consensus}}}}}{{#set:DHS_support={{{DHSsupport}}}}}
{{#set:DHS_support={{{DHSsupport}}}}}
 
 
 
  
 
[[Category:FFCP]]
 
[[Category:FFCP]]

Revision as of 01:19, 10 April 2014

Short description:
Species:
DPI dataset: NA
TSS-like-by-RIKEN-classifier(Yes/No): NA
GencodeV16b-All-Build2-RSEM10-CPAT_consensus: NA
DHS support(Yes/No): NA
Description:
Coexpression cluster:
Association with transcript:
EntrezGene:{{{EntrezGene}}}
HGNC: NA
UniProt:


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 "GencodeV16b All Build2 RSEM10 CPAT consensus" (as page type) with input value "{{{GencodeV16b_All_Build2_RSEM10_CPAT_consensus}}}" 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.