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Template:FFCP others: Difference between revisions

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<tr><th scope="row" align="right">Score:</th><td>{{{score}}}</td></tr>
<tr><th scope="row" align="right">Score:</th><td>{{{score}}}</td></tr>
<tr><th scope="row" align="right">Strand:</th><td>{{{strand}}}</td></tr>
<tr><th scope="row" align="right">Strand:</th><td>{{{strand}}}</td></tr>
<tr><th scope="row" align="right">Ensembl_transcript_id:</th><td>{{{ensembl_transcript_id}}}</td></tr>
<tr><th scope="row" align="right">Ensembl_transcript_id:</th><td>{{#replace:{{{ensembl_transcript_id}}}|,|<br>}}</td></tr>
{{#ifeq:{{{species}}}|Gallus gallus||<tr><th scope="row" align="right">Ensembl_gene_id:</th><td>{{{ensembl_gene_id}}}</td></tr>}}
{{#if:{{{ensembl_gene_name|}}}|<tr><th scope="row" align="right">Ensembl_gene_name:</th><td>{{{ensembl_gene_name}}}</td></tr>|}}
<tr><th scope="row" align="right">Ensembl_gene_name:</th><td>{{{ensembl_gene_name}}}</td></tr>
<tr><th scope="row" align="right">Augustus_gene_name:</th><td>{{#replace:{{{augustus_gene_name}}}|,|<br>}}</td></tr>
<tr><th scope="row" align="right">Augustus_gene_name:</th><td>{{{augustus_gene_name}}}</td></tr>
<tr><th scope="row" align="right">RefSeq_transcript_id:</th><td>{{{refseq_transcript_id}}}</td></tr>
<tr><th scope="row" align="right">RefSeq_transcript_id:</th><td>{{{refseq_transcript_id}}}</td></tr>
<tr><th scope="row" align="right">Genscan_gene_name:</th><td>{{{genscan_gene_name}}}</td></tr>
<tr><th scope="row" align="right">Genscan_gene_name:</th><td>{{{genscan_gene_name}}}</td></tr>
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{{#ifeq:{{{species}}}|Gallus gallus|<tr><th scope="row" align="right">NONCODE:</th><td>{{{noncode}}}</td></tr>|}}
{{#ifeq:{{{species}}}|Gallus gallus|<tr><th scope="row" align="right">NONCODE:</th><td>{{{noncode}}}</td></tr>|}}
</table>
</table>
 
<br>
<html>
<script language="javascript" type="text/javascript">
$(document).ready(function() {
// hide-show animation for ucsc genome browser view
$("#ucsc_snap_view").hover(function(){
    $(this).stop(true, false).animate({ height: "600px"});
}, function() {
    $(this).stop(true, false).animate({ height: "30px" });
});
});
</script>
</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;">
Mouse over to see Genome browser image, Click image to go to Genome browser
 
{{#ucsc_gb_link:{{#if:{{#pos:{{FULLPAGENAME}}|Hg19}}|Hg19}}{{#if:{{#pos:{{FULLPAGENAME}}|Mm9}}|Mm9}}::{{{cluster_id}}}}}
</div><br>
{{Fontsize|3|CAGE Expression}}
{{Fontsize|3|CAGE Expression}}
----
----
<html><script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.js"></script>
<html><script type="text/javascript" language="javascript" src="/5/sstar/rb_js/jquery-1.7.1.min.js"></script>
<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>
<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="/5/sstar/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>
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<includeonly>{{#gene_exptable:{{#explode:{{PAGENAME}}|:|0}}
<includeonly>{{#gene_exptable:{{#explode:{{PAGENAME}}|:|0}}
|,{{{expression}}}
|value,{{{expression}}}<nowiki>|</nowiki>short_description=value
}}</includeonly>
}}</includeonly>
<br>
<br>
Line 216: Line 197:


*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>
<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;
}
</style>
<script type="text/javascript">


$(document).ready(function() {
    var oTable =  $('.enrichment_list').DataTable({
        dom: 'frtip',
scrollCollapse: false,
        columnDefs: [{ orderable: false, targets: [ 0 ] },  { type: "html-num", width: "50pt", targets: [1] }],
order: [[ 1, "asc" ]]
});
});
</script>
</html>
{{#if:{{{ontology_enrichment_celltype_v019_2}}}|
<div style="float:left;width:33%;">
<table class="enrichment_list stripe cell-border order-column compact"><caption class="table_title">Cell type</caption><html><thead></html>
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
<html></thead><tbody></html>
{{#arraymap:{{{ontology_enrichment_celltype_v019_2}}}|;|$
|{{#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>| }}
|}}
<html></tbody></html></table>
</div>
}}{{#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>
<!--
{{#ifexpr: {{#expr: {{REVISIONTIMESTAMP}}-20120731160000 }} > 0
|<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}}}}}


{{#set:cage_peaks_id={{{cage_peaks_id}}}}}
{{#set:cage_peaks_id={{{cage_peaks_id}}}}}
Line 310: Line 217:
{{#set:score={{{score}}}}}
{{#set:score={{{score}}}}}
{{#set:strand={{{strand}}}}}
{{#set:strand={{{strand}}}}}
{{#set:ensembl_transcript_id={{{ensembl_transcript_id}}}}}
{{#set:ensembl_transcript_id={{{ensembl_transcript_id|}}}}}
{{#set:ensembl_gene_id={{{ensembl_gene_id}}}}}
{{#set:ensembl_gene_id={{{ensembl_gene_id}}}}}
{{#set:ensembl_gene_name={{{ensembl_gene_name}}}}}
{{#set:ensembl_gene_name={{{ensembl_gene_name}}}}}
Line 317: Line 224:
{{#set:genscan_gene_name={{{genscan_gene_name}}}}}
{{#set:genscan_gene_name={{{genscan_gene_name}}}}}
{{#set:est_gene_name={{{est_gene_name}}}}}
{{#set:est_gene_name={{{est_gene_name}}}}}
{{#set:aldb_lincRNA={{{aldb_lincRNA}}}}}
{{#set:noncode={{{noncode}}}}}
{{#set:species={{{species}}}}}
{{#set:species={{{species}}}}}


[[Category:FFCP]]
[[Category:FFCP]]

Latest revision as of 13:07, 25 January 2019


CAGE_peaks_ID:{{{cage_peaks_id}}}
Chr:{{{chromosome}}}
Start:{{{start}}}
End:{{{end}}}
Score:{{{score}}}
Strand:{{{strand}}}
Ensembl_transcript_id:{{{ensembl_transcript_id}}}
Augustus_gene_name:{{{augustus_gene_name}}}
RefSeq_transcript_id:{{{refseq_transcript_id}}}
Genscan_gene_name:{{{genscan_gene_name}}}
EST_gene_name:{{{est_gene_name}}}


CAGE Expression






  • Click each plot point to find sample in table






"FFCP others" is not a number.


Property "Cage peaks id" (as page type) with input value "{{{cage_peaks_id}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.

Property "Start" (as page type) with input value "{{{start}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. Property "End" (as page type) with input value "{{{end}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. Property "Score" (as page type) with input value "{{{score}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.


Property "Ensembl gene id" (as page type) with input value "{{{ensembl_gene_id}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. Property "Ensembl gene name" (as page type) with input value "{{{ensembl_gene_name}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. Property "Augustus gene name" (as page type) with input value "{{{augustus_gene_name}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. Property "Refseq transcript id" (as page type) with input value "{{{refseq_transcript_id}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. Property "Genscan gene name" (as page type) with input value "{{{genscan_gene_name}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. Property "Est gene name" (as page type) with input value "{{{est_gene_name}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.

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