Template:FFCP: Difference between revisions
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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| | <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: {{{ | |||
{{#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"> | ||
| Line 30: | Line 28: | ||
}); | }); | ||
</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 | ||
| Line 38: | Line 36: | ||
{{#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}} | |||
---- | |||
<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"; | |||
} | } | ||
| Line 175: | Line 174: | ||
showTooltip(item.pageX, item.pageY, | showTooltip(item.pageX, item.pageY, | ||
"Sample: "+slist[item.dataIndex]+"<br>TSS: "+ item.series.label +" TPM: "+y); | |||
} | } | ||
} | } | ||
| Line 207: | Line 206: | ||
|{{#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> | ||
| Line 215: | Line 215: | ||
*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> | |||
[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> | ||
| Line 243: | Line 247: | ||
"aaSorting": [[ 1, "asc" ]] | "aaSorting": [[ 1, "asc" ]] | ||
}); | }); | ||
}); | }); | ||
| Line 252: | Line 255: | ||
<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 | <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:$|,|2}}</td></tr>| }} | ||
|}} | |||
<html></tbody></html></table> | <html></tbody></html></table> | ||
</div> | </div> | ||
| Line 263: | Line 265: | ||
<table class="enrichment_list"><caption class="table_title">Uber anatomy</caption><html><thead></html> | <table class="enrichment_list"><caption class="table_title">Uber anatomy</caption><html><thead></html> | ||
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr> | <tr><th>Ontology term</th><th>p-value</th><th>n</th></tr> | ||
<html></thead><tbody></html | <html></thead><tbody></html> | ||
{{#arraymap:{{{ontology_enrichment_uberon_v019_2}}}|;|$ | {{#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:$|,|2}}</td></tr>| }} | ||
|}} | |||
<html></tbody></html></table> | <html></tbody></html></table> | ||
</div> | </div> | ||
| Line 274: | Line 276: | ||
<table class="enrichment_list"><caption class="table_title">Disease</caption><html><thead></html> | <table class="enrichment_list"><caption class="table_title">Disease</caption><html><thead></html> | ||
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr> | <tr><th>Ontology term</th><th>p-value</th><th>n</th></tr> | ||
<html></thead><tbody></html | <html></thead><tbody></html> | ||
{{#arraymap:{{{ontology_enrichment_disease_v019_2}}}|;|$ | {{#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:$|,|2}}</td></tr>| }} | ||
|}} | |||
<html></tbody></html></table> | <html></tbody></html></table> | ||
</div> | </div> | ||
}} | }} | ||
<div style="clear:both;"></div> | <div style="clear:both;"></div> | ||
<!-- | <!-- | ||
| Line 289: | Line 292: | ||
|}} | |}} | ||
--> | --> | ||
{{#arraymap:{{{short_description}}}|,|$|{{#set:short_description=$}}}} | {{#arraymap:{{{short_description}}}|,|$|{{#set:short_description=$}}}} | ||
| Line 304: | Line 308: | ||
{{#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 10:19, 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 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 "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.
