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<html>
{{Loading|loadingimage=sprites.gif}}<html>
<style type="text/css" title="currentStyle">
<style type="text/css" title="currentStyle">
@import "/resource_browser/rb_js/datatables/media/css/jquery.dataTables.css";
@import "/5/sstar/rb_js/html5button/datatables.css";
@import "/resource_browser/rb_js/datatables/extras/TableTools/media/css/TableTools.css";
</style>
</style>
<script type="text/javascript" src="/5/sstar/rb_js/jquery-1.7.1.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" src="/5/sstar/rb_js/html5button/datatables.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" src="/5/sstar/rb_js/custom/expoconvert.js"></script>
 
</html>


</html>{{#outerfile_existance: /5/sstar/sstar_img/f5samples/riken_cellimg/{{PAGENAME}}.jpg |<html>
<div style="width:250px;height:250px;float:right;"><img width=250 src="/5/sstar/sstar_img/f5samples/riken_cellimg/</html>{{PAGENAME}}<html>.jpg">
<div align="right">&copy; RIKEN, 2013&nbsp;<a href="http://creativecommons.org/licenses/by-sa/2.1/jp"><img src="/5/sstar/sstar_img/f5samples/riken_cellimg/by-sa_s.png" alt="by-sa"></a></div>
</div></html>}}
{{#set:id={{{id}}}}}
{{#set:id={{{id}}}}}
<table>
<table>
<tr><th scope="row" align="right">Name:</th><td>[[name::{{{name}}}]]</td></tr>
<tr><th scope="row" align="right">Name:</th><td>[[name::{{{name}}}]]</td></tr>
<tr><th scope="row" align="right">[[Property:Sample_species|Species]]:</th><td>[[sample_species::{{{sample_species}}}]]</td></tr>
<tr><th scope="row" align="right">[[Property:Sample_species|Species]]:</th><td>[[sample_species::{{{sample_species}}}]]</td></tr>
<tr><th scope="row" align="right">Genomic View:</th><td>[https://fantom5-collaboration.gsc.riken.jp/zenbu/dex/#section=Experiments;search={{#replace:{{{id}}}|FF:|}} zenbu] , [https://fantom5-collaboration.gsc.riken.jp/ucsc/cgi-bin/hgTracks?db={{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | hg19 | }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | mm9 | }}{{#ifeq: {{{sample_species}}} | Rat (Rattus rattus) | rn4 | }}{{#ifeq: {{{sample_species}}} | Dog (Canis lupus familaris) | canFam2 | }}{{#ifeq: {{{sample_species}}} | Chicken (Gallus gallus) | galGal3 | }}&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC] </td></tr>
<tr><th scope="row" align="right">[[Property:Library_accession_number|Library ID]]:</th><td>{{#replace:{{{library_id}}}|!|, }}</td></tr>
</table>
{{#ifexpr: {{#pos:{{{cagescan_library_id}}}|Cig}}|<tr><th scope="row" align="right">CAGEScan Library ID:</th><td>{{#replace:{{{cagescan_library_id}}}|!|, }}</td></tr>|}}
<tr><th scope="row" align="right">[[Property:Sample_category|Sample type]]:</th><td>{{{sample_category}}}</td></tr>
{{#ifeq: {{{sample_species}}} | Human (Homo sapiens) |<tr><th scope="row" align="right">Genomic View:</th><td>{{#ifexpr: {{#pos:{{{zenbu_config}}}|ttp}}|[{{{zenbu_config}}} zenbu] |}} [http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC]</td></tr>|}}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) |<tr><th scope="row" align="right">Genomic View:</th><td>{{#ifexpr: {{#pos:{{{zenbu_config}}}|ttp}}|[{{{zenbu_config}}} zenbu] |}} [http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC]</td></tr>|}}
<!--
{{#ifexpr: {{#pos:{{{microRNAs_novel_cage}}}{{{microRNAs_novel_srna}}}|ttp}}|
{{#ifexpr: {{#pos:{{{microRNAs_novel_srna}}}|ttp}}
|{{#ifexpr: {{#pos:{{{microRNAs_novel_cage}}}|ttp}}|<tr><th scope="row" align="right">MicroRNAs:</th><td>Including candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_novel_cage}}} CAGE samples],&nbsp;[{{{microRNAs_novel_srna}}} sRNA samples])</span><br/>Excluding candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_nonnovel_cage}}} CAGE samples],&nbsp;[{{{microRNAs_nonnovel_srna}}} sRNA samples])</span></td></tr>|<tr><th scope="row" align="right">MicroRNAs:</th><td>Including candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_novel_srna}}} sRNA samples])</span><br/>Excluding candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_nonnovel_srna}}} sRNA samples])</span></td></tr>}}
|{{#ifexpr: {{#pos:{{{microRNAs_novel_cage}}}|ttp}}|<tr><th scope="row" align="right">MicroRNAs:</th><td>Including candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_novel_cage}}} CAGE samples])</span><br/>Excluding candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_nonnovel_cage}}} CAGE samples])</span></td></tr>|}}
}}
|}}
-->
{{#ifexpr: {{#pos:{{{refex}}}|ttp}}|
<tr><th scope="row" align="right">RefEX:</th><td>[{{#replace:{{#replace:{{{refex}}}|[|%5b}}|]|%5d}} Specific genes]  </td></tr>|}}
{{#ifexpr: {{#pos:{{{fantom_cat}}}|ttp}}|
<tr><th scope="row" align="right">FANTOM CAT:</th><td>{{ #vardefine: i | 1 }}{{#arraymap:{{{fantom_cat}}}|;;|$|[$ {{ #var: i }}{{ #vardefine: i | {{ #expr: {{ #var: i }} + 1 }} }}]|,&#32;}}</td></tr>|}}
{{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | <tr><th scope="row" align="right">CAGEd-oPOSSUM:</th><td>[http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/human/{{{id}}}/results.html link]  </td></tr> | }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | <tr><th scope="row" align="right">CAGEd-oPOSSUM:</th><td>[http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/mouse/{{{id}}}/results.html link]  </td></tr> | }}{{#ifexpr: {{#pos:{{{zenbu_report}}}|ttp}}|<tr><th scope="row" align="right">ZENBU report :</th><td><span class="plainlinks">[{{{zenbu_report}}} link]</span> </td></tr>|}} </table>
{|class="wikitable mw-collapsible mw-collapsed" style="width:auto"
! Additional information
|-
|<div style="width:50%; float:left;">Sample information<table cellspacing="0" border="1">
<tr><th>strain</th><td>{{#switch:{{{sample_strain}}}|,,,=NA| =NA |{{{sample_strain}}}}}</td></tr>
<tr><th>tissue</th><td>{{#switch:{{{sample_tissue}}}|,,,=NA| =NA |{{{sample_tissue}}}}}</td></tr>
<tr><th>dev stage</th><td>{{#switch:{{{sample_dev_stage}}}|,,,=NA| =NA |{{{sample_dev_stage}}}}}</td></tr>
<tr><th>sex</th><td>{{#switch:{{{sample_sex}}}|,,,=NA| =NA |{{{sample_sex}}}}}</td></tr>
<tr><th>age</th><td>{{#switch:{{{sample_age}}}|,,,=NA| =NA |{{{sample_age}}}}}</td></tr>
<tr><th>cell type</th><td>{{#switch:{{{sample_cell_type}}}|,,,=NA| =NA |{{{sample_cell_type}}}}}</td></tr>
<tr><th>cell line</th><td>{{#switch:{{{sample_cell_line}}}|,,,=NA| =NA |{{{sample_cell_line}}}}}</td></tr>
<tr><th>company</th><td>{{#switch:{{{sample_company}}}|,,,=NA| =NA |{{{sample_company}}}}}</td></tr>
<tr><th>collaboration</th><td>{{#switch:{{{sample_collaboration}}}|,,,=NA| =NA |{{{sample_collaboration}}}}}</td></tr>
{{#if:{{{sample_info_link}}}|<tr><th style="background-color: #4169e1;">External link for information</th><td style="background-color: #f0f8ff;">[{{#explode:{{{sample_info_link}}}|;|-1}} {{#explode:{{{sample_info_link}}}|;|0}}]</td></tr>}}</table></div>
<div style="width:50%; float:left;">
RNA information<table cellspacing="0" border="1">
<tr><th>lot number</th><td>{{#switch:{{{rna_lot_number}}}|,,,=NA| =NA |{{{rna_lot_number}}}}}</td></tr>
<tr><th>catalog number</th><td>{{#switch:{{{rna_catalog_number}}}|,,,=NA| =NA |{{{rna_catalog_number}}}}}</td></tr>
<tr><th>sample type</th><td>{{#switch:{{{rna_sample_type}}}|,,,=NA| =NA |{{{rna_sample_type}}}}}</td></tr>
<tr><th>extraction protocol <span style="background-color:white">[[Protocols:RNA_extraction|(Details)]]</span></th><td>{{#switch:{{{rna_extraction_protocol}}}|,,,=NA| =NA |{{{rna_extraction_protocol}}}}}</td></tr></table></div>
|}{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}|{{DRAAccessionNumbers|{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|CAGE}}|CAGE|{{#sub:{{{DRA_sample_Accession}}}|0|{{#pos:{{{DRA_sample_Accession}}}|@|0}}}}}}|{{{DRA_sample_Accession}}}|{{{accession_numbers}}}|{{{library_id}}}|{{{sample_species}}}}}|}}{{#if:{{#pos:{{{DRA_sample_Accession_Zoo}}}|@|0}}|{{DRAAccessionNumbers|sRNA|{{{DRA_sample_Accession_Zoo}}}|{{{accession_numbers_Zoo}}}|{{{zoo_library_id}}}|{{{sample_species}}}}}|}}{{#vardefine:species_temp|{{#switch: {{{sample_species}}} | Human (Homo sapiens) = Hg19 | Mouse (Mus musculus) = Mm9 }}}}{{#switch: {{{sample_species}}}
|Human (Homo sapiens) = {{FastaBamfileCTSS||Hg19|{{{hg19fasta}}}||{{{hg19bam}}}|{{{hg19ctss}}}|Hg38|{{#replace:{{{hg38bam}}}|hg38_v2|hg38_latest}}|{{#replace:{{{hg38ctss}}}|hg38_v2|hg38_latest}}}}
|Mouse (Mus musculus) = {{FastaBamfileCTSS||Mm9|{{{mm9fasta}}}||{{{mm9bam}}}|{{{mm9ctss}}}|Mm10|{{#replace:{{{mm10bam}}}|mm10_v2|mm10_latest}}|{{#replace:{{{mm10ctss}}}|mm10_v2|mm10_latest}}}}
|
}}{{#if:{{#pos:{{{DRA_sample_Accession_HumanCAGEScan}}}|@|0}}|{{DRAAccessionNumbers|HumanCAGEScan|{{{DRA_sample_Accession_HumanCAGEScan}}}|{{{accession_numbers_HumanCAGEScan}}}|{{{cagescan_library_id}}}|{{{sample_species}}}}}|}}{{#ifexpr: {{#pos:{{{hg38bam_cs1}}}{{{mm10ctss_cs}}}|ttp}}|
{{#switch: {{{sample_species}}}
|Human (Homo sapiens) = {{FastaBamfileCTSS|HumanCAGEScan|Hg19|{{{hg19fasta_cs3prime}}}|{{{hg19fasta_cs5prime}}}|{{{hg19bam_cs}}}|{{{hg19ctss_cs}}}|Hg38|{{{hg38bam_cs}}}|{{{hg38ctss_cs}}}}}
|Mouse (Mus musculus) = {{FastaBamfileCTSS|HumanCAGEScan|Mm9|{{{mm9fasta_cs}}}||{{{mm9bam_cs}}}|{{{mm9ctss_cs}}}|Mm10|{{{mm10bam_cs}}}|{{{mm10ctss_cs}}}}}
|
}}
|}}{{#ifexpr:{{#pos:{{{HumanCAGEScanFiles}}}|ttp}}|{{FastaBamfileCTSSforCAGEScan|{{{HumanCAGEScanFiles}}}}}
|}}{{#if:{{#pos:{{{DRA_sample_Accession_RNASeq}}}|@|0}}|{{DRAAccessionNumbers|RNA-Seq|{{{DRA_sample_Accession_RNASeq}}}|{{{accession_numbers_RNASeq}}}|{{{rnaseq_library_id}}}|{{{sample_species}}}}}|}}
{{#ifexpr:{{#pos:{{{RNASeqFiles}}}|ttp}}|{{FastaBamfileCTSSforCAGEScan|{{{RNASeqFiles}}}}}
|}}<br/>
{{#if: {{#pos:{{{expression_enrichment_score}}}|chr}}| {{Fontsize|3|Relative expression to median (log10)}}
----
{{Fontsize|3|Transcription factors with enriched expression in this sample}}{{nowrap|{{#info: Ranked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. }}}}
<html><!-- tf enrich table: start-->
<script type="text/javascript">
var species="</html>{{#var:species_temp}}<html>";
var mm_data = new Array();
var enrichment_scores_data = "</html>{{{expression_enrichment_score}}}<html>";
var sub_content = enrichment_scores_data.split(";;");


$(document).ready(function() {


{{#if: {{#pos:{{{expression_enrichment_score}}}|chr}} |
for(i=0;i<sub_content.length;i++){
== TF expression and enrichment ==
var temp=sub_content[i];
<html>
if(temp!= null){
<br>
if(temp.length>2){
<!-- tf enrich table: start-->
var sub_sub_content=sub_content[i].split("!");
<script type="text/javascript" charset="utf-8">
var built="FFCP_PHASE1:"+species+"::"+sub_sub_content[0];
var ffcp_tf_enrichscore_d=
mm_data.push(sub_sub_content);
[
}
</html>
}
{{#exp_enrichscore_dtarr:{{{expression_enrichment_score}}}|FFCP_PHASE1:{{#switch: {{{sample_species}}} | Human (Homo sapiens) = Hg19 | Mouse (Mus musculus) = Mm9 }}::}}
}
<html>
/*"sDom": '<"top"i>rt<"bottom"flp><"clear">' */
];


$(document).ready(function() {
    $('#ffcp_tf_enrichscore').DataTable( {
$('#ffcp_tf_enrichscore').html( '<table cellpadding="0" cellspacing="0" border="0" class="display" id="ffcp_tf_enrichscore_cont"></table>' );
        data: mm_data,
var tf_enrich_tableex_obj = $('#ffcp_tf_enrichscore_cont').dataTable( {
        dom: 'Blfrtip',
"sScrollY": "300px",
        lengthMenu: [[10, 50, -1], [10, 50, "All"]],
"bPaginate": false,
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
"bScrollCollapse": true,
        columnDefs: [{ targets: [1], visible: false}],
"iDisplayLength": -1,
        columns: [
"aaData": ffcp_tf_enrichscore_d,
            { title: "CAGE peaks" ,
"aoColumns": [
              render: function ( data, type, row, meta ) {
{ "sTitle": "FFCP Phase1","sWidth": "30px",
                var peak_loc = row[0];
"fnRender": function(obj) {
                var peak_name = row[1];
var id = obj.aData[ obj.iDataColumn ].split("!");
return "<a href=\"/5/sstar/"+"FFCP_PHASE1:"+species+"::"+peak_loc +"\">"+peak_name+"</a>";
return sReturn = "<a href=\"/resource_browser/"+encodeURI(id[0])+"\">"+id[1]+"</a>";
              }
}
            },
},
            { title: "Log10(Relative expression over median)" },
{ "sTitle": "Enrichment Score","sWidth": "30px"},
            { title: "TPM" },
{ "sTitle": "TPM","sWidth": "30px"},
            { title: "TF." }
{ "sTitle": "TF","sWidth": "30px"}
        ],
 
        order: [[ 2, 'desc' ]]
],
    } );
"aaSorting": [[ 1, "desc" ]]
});
} );
</script>
 
<span id="tf_enrich_table_export_tool"></span>
var tf_enrich_tableex_objtool = new TableTools( tf_enrich_tableex_obj, {"sSwfPath": "/resource_browser/rb_js/datatables/extras/TableTools/media/swf/copy_csv_xls_pdf.swf", "aButtons": [ {"sExtends": "copy", "mColumns": "visible"}, {"sExtends": "csv", "mColumns": "visible"}, {"sExtends": "pdf", "mColumns": "visible"} ]});
<table cellpadding="0" cellspacing="0" border="0" id="ffcp_tf_enrichscore" class="stripe cell-border order-column compact"></table>
 
$('#tf_enrich_export_button').before( tf_enrich_tableex_objtool.dom.container );
 
} );
</script>
<!-- tf enrich table: end-->
<div id="tf_enrich_export_button"></div>
<div id="ffcp_tf_enrichscore"></div>
</html>
</html>
}}
}}
{{#vardefine:isHumanOrMouse|{{#switch:{{{sample_species}}}|Human (Homo sapiens)=1|Mouse (Mus musculus)=1|0}}}}
{{#ifeq:{{#var:isHumanOrMouse}}|1|<br><br>{{Fontsize|3|Co-expression clusters with enriched expression in this sample}}{{#info:Ranked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters data]}}<html><script type="text/javascript">
$(document).ready(function() {


    if($('.relative-exp-of-coexp')[0]){
        $('.relative-exp-of-coexp').DataTable({
          dom: 'Blfrtip',
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
          lengthMenu: [[10, 50, -1], [10, 50, "All"]],
          columnDefs: [{ targets: [0], visible: true},{ targets: [0], visible: true}],
          columns:[
                {title:"MCL coexpression id", visible:true},
                {title:"Coexpression_dpi_cluster_scores_median_value", visible:true}
          ],
          order: [[ 1, 'desc' ]]
        });
}
});
</script></html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?Coexpression_dpi_cluster_scores_median_value|intro=<table class="relative-exp-of-coexp stripe cell-border order-column compact"><html><thead></html><tr><th>Coexpression cluster</th><th>score</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table>|link=none|format=template|template=Coexpression_dpi_cluster_scores_median_in_ffsample|limit=5000|searchlabel=|default=No results for this sample}}
|<br><br>}}
|Mouse (Mus musculus)=
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|<h3>$</h3>{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?=MCL coexpression id|?Coexpression_dpi_cluster_scores_median_value|format=ttable|class=relative-exp-of-coexp stripe cell-border order-column compact|headers=hide|searchlabel=}}
|<br><br>
}}}}
<br><br>
{{Fontsize|3|Repeat families with enriched expression in this sample}}{{nowrap|{{#info:<b>Summary:</b>Ranked list of repeat family expression in this sample relative to
the median expression in the FANTOM5 collection is shown. Value is log10
transformed.<br><b>Analyst:</b>NA
<br><br>link to dataset.<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression data]}}}}
{{#if: {{#pos:{{{repeat_enrich_byfamily}}}|,}} |
<html><script type="text/javascript">
$(document).ready(function() {
var repeat_enrich_byfamily_data = [];
var repeat_enrich_byfamily_repnames = [
</html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)=<html>
'Alu','Alu,Alu','Alu,ERVL-MaLR','Alu,L1','Alu,L2','Alu,Low_complexity','Alu,MIR','Alu,hAT-Charlie','Alu,hAT-Tip100','Alu,rRNA','Alu,snRNA','CR1','CR1,CR1','DNA','DNA?','Deu','ERV','ERV1','ERV1,ERV1','ERV1,ERVL','ERV1,ERVL-MaLR','ERV1,MIR','ERV1,snRNA','ERVK','ERVK,rRNA','ERVL','ERVL,ERV1','ERVL,ERVL','ERVL,ERVL-MaLR','ERVL,hAT-Charlie','ERVL,snRNA','ERVL-MaLR','ERVL-MaLR,ERVL-MaLR','ERVL-MaLR,snRNA','ERVL?','Gypsy','Gypsy?','Helitron','L1','L1,ERV1','L1,ERVL','L1,ERVL-MaLR','L1,L1','L1,TcMar-Mariner','L1,TcMar-Tigger','L1,hAT-Charlie','L1,rRNA','L1,snRNA','L1?','L2','L2,ERV1','L2,ERVL-MaLR','L2,L2','L2,MIR','L2,hAT-Blackjack','L2,hAT-Charlie','LTR','Low_complexity','Low_complexity,Alu','Low_complexity,ERV1','Low_complexity,L2','Low_complexity,Low_complexity','Low_complexity,Low_complexity,Low_complexity','Low_complexity,snRNA','MIR','MIR,ERVL-MaLR','MIR,Low_complexity','MIR,MIR','Merlin','MuDR','NA','Other','PiggyBac','PiggyBac?','RNA','RNA,MIR','RTE','RTE,CR1','RTE-BovB','SINE','SINE?','Satellite','Satellite,ERVL','Simple_repeat','Simple_repeat,Alu','Simple_repeat,ERV1','Simple_repeat,ERVL','Simple_repeat,ERVL-MaLR','Simple_repeat,L1','Simple_repeat,L2','Simple_repeat,Low_complexity','Simple_repeat,Low_complexity,Low_complexity','Simple_repeat,MIR','Simple_repeat,Other','Simple_repeat,Simple_repeat','Simple_repeat,Simple_repeat,Low_complexity','Simple_repeat,Simple_repeat,Simple_repeat','Simple_repeat,TcMar-Tigger','Simple_repeat,Unknown','Simple_repeat,hAT-Charlie','Simple_repeat,hAT-Tip100','Simple_repeat,scRNA','Simple_repeat,snRNA','TcMar','TcMar-Mariner','TcMar-Tc2','TcMar-Tc2,ERV1','TcMar-Tigger','TcMar-Tigger,TcMar-Tigger','TcMar-Tigger,snRNA','TcMar?','Unknown','Unknown?','acro','centr','hAT','hAT-Blackjack','hAT-Charlie','hAT-Charlie,ERVL-MaLR','hAT-Charlie,MIR','hAT-Charlie,hAT-Charlie','hAT-Charlie,snRNA','hAT-Tip100','hAT?','rRNA','rRNA,rRNA','scRNA','scRNA,L1','snRNA','srpRNA','tRNA','telo'
</html>|Mouse (Mus musculus)=<html>
'AcHobo','Alu','Alu,B4','Alu,B4,ERVL','Alu,ERVK','Alu,ERVL','Alu,L1','B2','B2,B4','B4','B4,Alu','B4,Low_complexity','CR1','ERV1','ERV1,ERVK','ERVK','ERVK,ERVK','ERVL','ERVL,Alu','ERVL,ERVK','ERVL,MaLR','ERVL?','Genie?','Gypsy','Gypsy?','Helitron','ID','ID,Satellite','L1','L1,ERVK','L1,L1','L1,snRNA','L1,tRNA','L2','L2,ERV1','L2,MaLR','LTR','Low_complexity','Low_complexity,Alu','Low_complexity,Low_complexity','Low_complexity,Low_complexity,Low_complexity','Low_complexity,MIR','Low_complexity,Tip100','Low_complexity,snRNA','MER1_type','MER1_type,B4','MER1_type?','MER2_type','MIR','MIR,MIR','MIR,MaLR','MaLR','MaLR,Alu','MaLR,ERV1','MaLR,ERVL','MaLR,MaLR','MuDR','NA','Other','PiggyBac','RNA','RTE','SINE','Satellite','Satellite,Satellite','Simple_repeat','Simple_repeat,Alu','Simple_repeat,Alu,B4','Simple_repeat,B2','Simple_repeat,B4','Simple_repeat,ERVK','Simple_repeat,L1','Simple_repeat,Low_complexity','Simple_repeat,Low_complexity,Low_complexity','Simple_repeat,MIR','Simple_repeat,MaLR','Simple_repeat,Simple_repeat','Simple_repeat,Simple_repeat,Low_complexity','Simple_repeat,rRNA','Tc2','TcMar','Tigger','Tip100','Unknown','hAT','hAT?','rRNA','rRNA,B4','rRNA,ERVK','scRNA','scRNA,B4','scRNA,Satellite','snRNA','tRNA'
</html>}}<html>
];
var repeat_enrich_byfamily_values = [</html>{{{repeat_enrich_byfamily}}}<html>];
for(i1=0;i1<repeat_enrich_byfamily_repnames.length;i1++){
repeat_enrich_byfamily_data.push([repeat_enrich_byfamily_repnames[i1],repeat_enrich_byfamily_values[i1]]);
}
        $('#repeat_enrich_byfamily_table').DataTable({
          data: repeat_enrich_byfamily_data,
          dom: 'Blfrtip',
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
          lengthMenu: [[5, 50, -1], [5, 50, "All"]],
          columns: [
            { title: "Repeat family" },
            { title: "Log10(Relative expression over median)" ,
              render: function ( data, type, row, meta ) {
                var num = row[1];
                var numb = new Number(num);
return  numb.toFixed(2);
              }
            }
          ],
          order: [[ 1, 'desc' ]]
        });
});
</script>
<span id="repeat_enrich_byfamily_table_export_tool"></span>
<table id="repeat_enrich_byfamily_table" class="stripe cell-border order-column compact"></table><br>


{{#if: {{#pos:{{{top_motifs}}}|;}} |
== Top motif activities with MARA ==
<html>
<!-- top motif table: start-->
<script type="text/javascript" charset="utf-8">
var top_motif_d=
[
</html>
{{#top_motifs_dtarr:{{{top_motifs}}}}}
<html>
];
$(document).ready(function() {
$('#top_motiftb').html( '<table cellpadding="0" cellspacing="0" border="0" class="display" id="top_motiftb_cont"></table>' );
$('#top_motiftb_cont').dataTable( {
"sScrollY": "300px",
"bPaginate": false,
"bScrollCollapse": true,
"iDisplayLength": -1,
"aaData": top_motif_d,
"aoColumns": [
{ "sTitle": "Motifs","sWidth": "30px",
"fnRender": function(obj) {
var id = obj.aData[ obj.iDataColumn ].split("!");
return sReturn = "<a href=\"/resource_browser/"+id[0]+"\">"+id[1]+"</a>";
}
},
{ "sTitle": "Z-score", "sType": "numeric", "sWidth": "30px"},
],
"aaSorting": [[ 1, "desc" ]]
} );
$("#top_motiftb thead th").css('line-height', '34px');
} );
</script>
<!-- top motif table: end-->
<div id="top_motiftb"></div>
</html>
</html>
|no result for this sample
}}
}}


 
<br>
{{#if: {{#pos:{{{profile_hcage}}}|CNhs}} |
{{Fontsize|3|TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample}}
== TF to Motif to TF network ==
----
{{#info:Mouseover nodes and edges to see attributes. Motifs are shown in orange, TFs are shown in blue.  Promoter and z-score are attributes of the Motif to TF edges (blue arrow). TF to Motif edges are shown in orange.<br>Motifs shown are the top (maximum 30) motifs in the sample.  TFs shown have at least one CAGE promoter with at at least 10 TPM expression (RLE normalized) in the sample.  Edges shown have a z-score of at least 1.5 (based on correlation between motif activity and promoter expression).<br>Analyst: Erik Arner<br>Application Developer: Jayson HARSHBARGER}}
{{Fontsize|3|JASPAR motifs}}{{#info:<b>Summary:</b>Association of JASPAR motif to the promoter expression in this
sample. Pearson's correlation between the number of TFBSs estimated by
using the position-weight matrix for each promoter and its expression is
expressed as Z-score by taking the ones based on random position-weight
matrix, and the tail probability of the normal distribution corresponding
to the Z-score is taken as the resulting P-value. Lower P-value indicates
more (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br>
<br><br>link to dataset.<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression data]}}<br>
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|library id: $<span id="related_jaspar_table_export_tool"></span>{{#ask:[[jaspar_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]|?=Jaspar motif|?=Logo|?jaspar_motifs_sample_pval_pval=P-value|format=ttable|limit=1100|searchlabel=|class=jaspar_motif_pval stripe cell-border order-column compact|searchlabel=|default=This sample isn't target for the analysis}}
|<br>
}}
<br><br>
{{Fontsize|3|FANTOM5 phase1 novel unique motifs}}{{#info:<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in
169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br>
<br><br>link to dataset.<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression data]}}<br>
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|{{#outerfile_existance:/resource_browser/nwfiles/$.{{PAGENAME}}.xgmml|{{Tf_motif_cytoscapenw|CNhs=$|FFid={{PAGENAME}}}}
|library id: $<span id="related_novel_table_export_tool"></span>{{#ask:[[novel_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]|?=Novel motif|?=Logo|?novel_motifs_sample_pval_pval=P-value|format=ttable|limit=1100|searchlabel=|class=novel_motif_pval stripe cell-border order-column compact|searchlabel=|default=This sample isn't target for the analysis}}
|<br>
}}
}}
|<br>}}
<br><br>
{{Fontsize|3|de novo motifs identified by HOMER in promoters active in this sample}}{{#info:<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br>}}
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|library id: ${{#outerfile_existance:/5/sstar/Homer_de_novo_Motif_Results/$/homerResults.html
|<div id="homer_denovo_table_export_tool"></div><br>{{#homer_list:Homer_de_novo_Motif_Results/$/homerResults.html|homerResults!<TABLE cellpadding="2" cellspacing="0">!</div></TD></TR>!</TABLE>!Homer de novo Motif Results|/5/sstar/Homer_de_novo_Motif_Results/$/homerResults!<table class=homer-table><thead>!</div></TD></TR></thead><tbody>!</tbody></TABLE>|!}}
}}
}}
 
|<br>
 
}}<br>
 
{{#if: {{#pos:{{{sample_gostat}}}|;}} |
<html>
<html>
<script type="text/javascript">
<script type="text/javascript">
$(document).ready(function() {
$(document).ready(function() {
     $('.sample_gostat').dataTable({
     if($('.jaspar_motif_pval')[0]){
"sScrollY": "300px",
        $('.jaspar_motif_pval').DataTable({
"bPaginate": false,
          dom: 'Blfrtip',
"bScrollCollapse": true,
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
"iDisplayLength": -1,
          lengthMenu: [[5, 50, -1], [5, 50, "All"]],
"aaSorting": [[2,'asc']],
          columnDefs: [
"aoColumnDefs": [{"fnRender": function ( o, val ) {return "<a href=\"http://amigo.geneontology.org/cgi-bin/amigo/term_details?term="+o.aData[0]+"\">"+o.aData[0]+"</a>";}, "aTargets": [ 0 ]}, { "sWidth": "200px", "sType": "numeric", "aTargets": [2] }]
            { targets: 0, orderable: false},
});
            { targets: 1, orderable: false, width: "50pt", className: "bgwhite"}
          ],
          columns: [
            { title: "Jaspar motif" },
            { title: "Logo",
              render: function ( data, type, row, meta ) {
return "<img src=\"/5/sstar/seqlogo/jaspar/" + $(row[0]).text() + ".png\" width =\"80\" height = \"20\">";
              }
            },
            { title: "p-value",
              render: function ( data, type, row, meta ) {
                var num=row[2];
return exp_converter(num,2,"e");
              }
            }
          ],
          order: [[ 2, 'asc' ]]
        });
 
    }
});
});
</script>
</script>
</html>
</html>
== Gene Ontology GOstat analysis ==
{{#info:Sample GO (using GOStat) based on ranked expression for human libraries in phase 1 freeze  <br>Analyst: Erick Arner}}
<table class="sample_gostat"><html><thead></html><tr><th>GO id</th><th>GO term</th><th>P-value</th></tr><html></thead><tbody></html>
{{#arraymap:{{{sample_gostat}}}|!|$
|{{#set:sample_gostat=$}}<tr><td>{{#replace:$|;|</td><td>}}</td></tr>
|}}
<html></tbody></html></table>
}}


<html>
<script type="text/javascript">
$(document).ready(function() {
    if($('.novel_motif_pval')[0]){


$('.novel_motif_pval').DataTable({
              dom: 'Blfrtip',
              buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
              lengthMenu: [[5, 50, -1], [5, 50, "All"]],
              columnDefs: [
                { targets: 0, orderable: false},
                { targets: 1, orderable: false, width: "50pt", className: "bgwhite"}
              ],
              columns: [
                { title: "Novel motif" },
                { title: "Logo",
              render: function ( data, type, row, meta ) {
return "<img src=\"/5/sstar/seqlogo/novel/" +  $(row[0]).text() + ".png\" width =\"80\" height = \"20\">";
              }
            },
            { title: "p-value",
              render: function ( data, type, row, meta ) {
                var num=row[2];
return exp_converter(num,2,"e");
              }
            }
          ],
          order: [[ 2, 'asc' ]]
});


== Details ==
    }
});
</script>
</html>


 
<html>
=== Transcriptome profiling ===
<style type="text/css">
<table>
.white { background-color: white}
<tr><th scope="row" align="right"> [[Property:profile_hcage|hCAGE]] </th> <td> [[profile_hcage::{{{profile_hcage}}}]]</td>
table.homer-table td { padding: 1px }
<tr><th scope="row" align="right"> [[Property:profile_rnaseq|RNA-seq]] </th><td> [[profile_rnaseq::{{{profile_rnaseq}}}]]</td>
</style>
<tr><th scope="row" align="right"> [[Property:profile_srnaseq|smallRNA seq]] </th><td> [[profile_srnaseq::{{{profile_srnaseq}}}]]</td>
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/media/js/dataTables.Percentage.js"></script>
<tr><th scope="row" align="right"> [[Property:profile_cagescan|nanoCAGEscan]]</th><td> [[profile_cagescan::{{{profile_cagescan}}}]]
</html>
</table>
<br>|}}<!-- end of if(isHumanOrMouse) -->
 
{{Fontsize|3|FANTOM5 (FF) ontology }}
=== Sample info ===
----
<table>
{{Fontsize|3|Direct parent terms}}
<tr><th scope="row" align="right"> [[Property:sample_strain|strain]] </th><td> [[sample_strain::{{{sample_strain}}}]]</td>
<tr><th scope="row" align="right"> [[Property:sample_tissue|tissue]]</th><td> [[sample_tissue::{{{sample_tissue}}}]]</td>
<tr><th scope="row" align="right"> [[Property:sample_dev_stage|dev_stage]] </th><td> [[sample_dev_stage::{{{sample_dev_stage}}}]]</td>
<tr><th scope="row" align="right"> [[Property:sample_sex|sex]]</th><td> [[sample_sex::{{{sample_sex}}}]]</td>
<tr><th scope="row" align="right"> [[Property:sample_age|age]]</th><td> [[sample_age::{{{sample_age}}}]]</td>
<tr><th scope="row" align="right"> [[Property:sample_ethnicity|ethnicity]]</th><td> [[sample_ethnicity::{{{sample_ethnicity}}}]]</td>
<tr><th scope="row" align="right"> [[Property:sample_cell_type|cell_type]]</th><td> [[sample_cell_type::{{{sample_cell_type}}}]] </td>
<tr><th scope="row" align="right"> [[Property:sample_cell_line|cell_line]]</th><td> [[sample_cell_line::{{{sample_cell_line}}}]] </td>
<tr><th scope="row" align="right"> [[Property:sample_collaboration|collaboration]]</th><td> [[sample_collaboration::{{{sample_collaboration}}}]]</td>
<tr><th scope="row" align="right"> [[Property:sample_experimental_condition|Experimental condition]]</th><td>[[sample_experimental_condition::{{{sample_experimental_condition}}}]]</td>
<tr><th scope="row" align="right"> [[Property:sample_disease|disease]]</th><td> [[sample_disease::{{{sample_disease}}}]]</td>
<tr><th scope="row" align="right"> [[Property:sample_cell_lot|cell_lot]]</th><td> [[sample_cell_lot::{{{sample_cell_lot}}}]]</td>
<tr><th scope="row" align="right"> [[Property:sample_cell_catalog|cell_catalog]]</th><td> [[sample_cell_catalog::{{{sample_cell_catalog}}}]]</td>
<tr><th scope="row" align="right"> [[Property:sample_company|company]]</th><td> [[sample_company::{{{sample_company}}}]]</td>
<tr><th scope="row" align="right"> [[Property:sample_donor(cell lot)|donor(cell lot)]]</th><td> [[sample_donor(cell lot)::{{{sample_donor(cell lot)}}}]]</td>
<tr><th scope="row" align="right"> [[Property:sample_note|Note]]</th><td> [[sample_note::{{{sample_note}}}]]</td>
</table>
 
 
=== RNA info ===
<table>
<tr><th scope="row" align="right"> [[Property:sample_id|sample_id]] </th><td>[[sample_id::{{{sample_id}}}]]</td>
<tr><th scope="row" align="right"> [[Property:rna_tube_id|tube_id]]</th><td> [[rna_tube_id::{{{rna_tube_id}}}]]</td>
<tr><th scope="row" align="right"> [[Property:rna_box|box]]</th><td> [[rna_box::{{{rna_box}}}]]</td>
<tr><th scope="row" align="right"> [[Property:rna_position|position]]</th><td> [[rna_position::{{{rna_position}}}]]</td>
<tr><th scope="row" align="right"> [[Property:rna_lot_number|lot_number]]</th><td> [[rna_lot_number::{{{rna_lot_number}}}]]</td>
<tr><th scope="row" align="right"> [[Property:rna_catalog_number|catalog_number]]</th><td> [[rna_catalog_number::{{{rna_catalog_number}}}]]</td>
<tr><th scope="row" align="right"> [[Property:rna_rin|RIN]]</th><td> [[rna_rin::{{{rna_rin}}}]]</td>
<tr><th scope="row" align="right"> [[Property:rna_od260/230|OD260/230]]</th><td> [[rna_od260/230::{{{rna_od260/230}}}]]</td>
<tr><th scope="row" align="right"> [[Property:rna_od260/280|OD260/280]]</th><td> [[rna_od260/280::{{{rna_od260/280}}}]]</td>
<tr><th scope="row" align="right"> [[Property:rna_sample_type|sample_type]]</th><td> [[rna_sample_type::{{{rna_sample_type}}}]]</td>
<tr><th scope="row" align="right"> [[Property:rna_extraction_protocol|extraction_protocol]]</th><td> [[rna_extraction_protocol::{{{rna_extraction_protocol}}}]]</td>
<tr><th scope="row" align="right"> [[Property:rna_weight_ug|weight_ug]]</th><td> [[rna_weight_ug::{{{rna_weight_ug}}}]]</td>
<tr><th scope="row" align="right"> [[Property:rna_concentration|concentration]]</th><td>[[rna_concentration::{{{rna_concentration}}}]]</td>
</table>
 
== Parent ontology==
{{#if: {{{is_a}}} |
{{#if: {{{is_a}}} |
<div style="width:25%; float:left;">
<div style="width:25%; float:left;">
Line 214: Line 316:
</div>
</div>
|}}
|}}
<div style="clear:both;"></div>
<div style="clear:both;"></div>


== Ancestors in ontology (non-development) ==
{{Fontsize|3|Ancestor terms (non development)}}{{#info:<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship  <br><b>Analyst:</b> Hideya Kawaji
{{#info: Connected ontology terms with is_a, part_of or located_in relathionship  <br>Analyst: Hideya Kawaji}}
<br><br>link to source data<br>
<!--
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data]
{{#if: {{{ancestors_in_cell_lineage_facet}}} |'''Cell_lineage'''<br>{{#arraymap:{{{ancestors_in_cell_lineage_facet}}}|,|$|
}}<br>
{{#set:ancestors_in_cell_lineage_facet=$}}CL:{{#ask:[[id::$]]|?name=|format=list}}|<br>}}|}}
{{#if: {{{ancestors_in_disease_facet}}} |<br>'''Disease'''<br>{{#arraymap:{{{ancestors_in_disease_facet}}}|,|$|
{{#set:ancestors_in_disease_facet=$}}DOID:{{#ask:[[id::$]]|?name=|format=list}}|<br>}}|}}
{{#if: {{{ancestors_in_anatomy_facet}}} |<br>'''Anatomy'''<br>{{#arraymap:{{{ancestors_in_anatomy_facet}}}|,|$|
{{#set:ancestors_in_anatomy_facet=$}}UBERON:{{#ask:[[id::$]]|?name=|format=list}}|<br>}}|}}
<table>
<tr><th align="left">Anatomy</th><th align="left">Cell type</th> <th align="left">Disease</th>
<tr>
<td align="left" valign="top">
{{#arraymap:{{{ancestors_in_anatomy_facet}}}|,|$|{{#set:ancestors_in_anatomy_facet=$}}UBERON:{{#ask:[[id::$]]|?name=|format=list}}|<br>}}
</td>
<td align="left" valign="top">
{{#arraymap:{{{ancestors_in_cell_lineage_facet}}}|,|$|{{#set:ancestors_in_cell_lineage_facet=$}}CL:{{#ask:[[id::$]]|?name=|format=list}}|<br>}}
</td>
<td align="left" valign="top">
{{#arraymap:{{{ancestors_in_disease_facet}}}|,|$|{{#set:ancestors_in_disease_facet=$}}DOID:{{#ask:[[id::$]]|?name=|format=list}}|<br>}}
</td>
-->
{{#if: {{{ancestors_in_cell_lineage_facet}}} |
{{#if: {{{ancestors_in_cell_lineage_facet}}} |
<div style="width:25%; float:left;">
<div style="width:25%; float:left;">
<b>CL: Cell type</b><br>
<b>CL: Cell type</b><br>
{{#arraymap:{{{ancestors_in_cell_lineage_facet}}}|,|$|{{#set:ancestors_in_cell_lineage_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}}
{{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ancestors_in_cell_lineage_facet}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ancestors_in_cell_lineage_facet}}}|,|$|{{#set:ancestors_in_cell_lineage_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}} }}
</div>
</div>
}}{{#if: {{{ancestors_in_disease_facet}}} |
}}{{#if: {{{ancestors_in_disease_facet}}} |
<div style="width:25%; float:left;">
<div style="width:25%; float:left;">
<b>DOID: Disease</b><br>
<b>DOID: Disease</b><br>
{{#arraymap:{{{ancestors_in_disease_facet}}}|,|$|{{#set:ancestors_in_disease_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}}
{{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ancestors_in_disease_facet}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ancestors_in_disease_facet}}}|,|$|{{#set:ancestors_in_disease_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}} }}
</div>
</div>
}}{{#if: {{{ancestors_in_anatomy_facet}}} |
}}{{#if: {{{ancestors_in_anatomy_facet}}} |
<div style="width:25%; float:left;">
<div style="width:25%; float:left;">
<b>UBERON: Anatomy</b><br>
<b>UBERON: Anatomy</b><br>
{{#arraymap:{{{ancestors_in_anatomy_facet}}}|,|$|{{#set:ancestors_in_anatomy_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}}
{{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ancestors_in_anatomy_facet}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ancestors_in_anatomy_facet}}}|,|$|{{#set:ancestors_in_anatomy_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}} }}
 
</div>
</div>
}}{{#if: {{{ancestors_in_ff_facet}}} |
}}{{#if: {{{ancestors_in_ff_facet}}} |
<div style="width:25%; float:left;">
<div style="width:25%; float:left;">
<b>FF: FANTOM5</b><br>
<b>FF: FANTOM5</b><br>
{{#arraymap:{{{ancestors_in_ff_facet}}}|,|$|{{#set:ancestors_in_ff_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}}
{{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ancestors_in_ff_facet}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ancestors_in_ff_facet}}}|,|$|{{#set:ancestors_in_ff_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}} }}
 
</div>
</div>
}}
}}
<div style="clear:both;"></div>
<div style="clear:both;"></div>


== Ancestors in ontology (development) ==
{{Fontsize|3|Ancestor terms (development)}}{{#info:<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br>
{{#info: Connected ontology terms with develops_from, derives_from or preceded_by relathionship  <br>Analyst: Hideya Kawaji}}<br>
<b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>
{{#arraymap:{{{ffid_belonging_in_development}}}|,|$|{{#ifexist:$|{{#set:ffid_belonging_in_development=$}}[[$]] ({{#show:$|?name}})}}|<br>}}
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data]
}}
<br>
{{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ffid_belonging_in_development}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ffid_belonging_in_development}}}|,|$|{{#ifexist:$|{{#set:ffid_belonging_in_development=$}}[[$]] ({{#show:$|?name}})}}|<br>}} }}
<br><br>
{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}|
{{#set:sample_category={{{sample_category}}}}}
{{#arraymap:{{{library_id}}}|!|$
|{{#set:Library accession number=$}}
}}


{{#switch:{{{datafreeze_phase}}}|1={{#set:datafreeze_phase=1}}|{{#set:datafreeze_phase=-1}}}}
{{#arraydefine:accession_numbers_array|{{{accession_numbers}}}|!}}{{#loop: k
  | 0         
  | {{#arraysize:accession_numbers_array}}
  | <nowiki/>
{{#vardefine:exp_met|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|0}}}}
{{#if:{{#var:exp_met}}|{{#set:Experiment method={{#var:exp_met}}}}|}}
{{#vardefine:lib_exp|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|1}}}}
{{#if:{{#var:lib_exp}}|{{#set:Experiment accession number={{#var:lib_exp}}}}|}}
{{#vardefine:lib_run|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|2}}}}
{{#if:{{#var:lib_run}}|{{#set:Run accession number={{#var:lib_run}}}}|}}
{{#vardefine:lib_bam|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|3}}}}
{{#if:{{#var:lib_bam}}|{{#set:Bam accession number={{#var:lib_bam}}|BAM}}|}}
{{#vardefine:lib_ctss|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|4}}}}
{{#if:{{#var:lib_ctss}}|{{#set:CTSS accession number={{#var:lib_ctss}}}}|}}
}}
|}}




== Related MacroAPE_1083 Motifs ==
{{#set:sample_category={{{sample_category}}}}}
{{#info:The values shown are the p-values of the motif in FANTOM5 samples. <br>Analyst: Michiel de Hoon}}
{{#set:profile_hcage={{{profile_hcage}}}}}
<html>
{{#set:profile_rnaseq={{{profile_rnaseq}}}}}
<script type="text/javascript">
{{#set:profile_srnaseq={{{profile_srnaseq}}}}}
$(document).ready(function() {
{{#set:profile_cagescan={{{profile_cagescan}}}}}
    $('.macroape_p_sample').dataTable({
{{#set:sample_strain={{{sample_strain}}}}}
"sScrollY": "300px",
{{#set:sample_tissue={{{sample_tissue}}}}}
"bPaginate": false,
{{#set:sample_dev_stage={{{sample_dev_stage}}}}}
"bScrollCollapse": true,
{{#set:sample_sex={{{sample_sex}}}}}
"iDisplayLength": -1,
{{#set:sample_age={{{sample_age}}}}}
"aaSorting": [[1,'asc']],
{{#set:sample_ethnicity={{{sample_ethnicity}}}}}
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{{#set:sample_cell_type={{{sample_cell_type}}}}}
});
{{#set:sample_cell_line={{{sample_cell_line}}}}}
});
{{#set:sample_collaboration={{{sample_collaboration}}}}}
</script>
{{#set:sample_experimental_condition={{{sample_experimental_condition}}}}}
</html>
{{#set:sample_disease={{{sample_disease}}}}}
{{#ask:[[Macroape_1083_sample_pvalue_ffid::{{PAGENAME}}]]
{{#set:sample_cell_lot={{{sample_cell_lot}}}}}
|?Macroape_1083_sample_pvalue_pvalue|format=template|template=Doublecolumn_to_tbrow|intro=<html><table class="macroape_p_sample"><thead><tr><th>Motif name</th><th>P-value</th></tr></thead><tbody></html>|outro=<html></tbody></table></html>|limit=1100|searchlabel=|default=This sample isn't target for the analysis}}
{{#set:sample_cell_catalog={{{sample_cell_catalog}}}}}
{{#set:sample_company={{{sample_company}}}}}
{{#set:sample_donor(cell lot)={{{sample_donor(cell lot)}}}}}
{{#set:sample_note={{{sample_note}}}}}
{{#set:sample_id={{{sample_id}}}}}
{{#set:rna_tube_id={{{rna_tube_id}}}}}
{{#set:rna_box={{{rna_box}}}}}
{{#set:rna_position={{{rna_position}}}}}
{{#set:rna_lot_number={{{rna_lot_number}}}}}
{{#set:rna_catalog_number={{{rna_catalog_number}}}}}
{{#set:rna_rin={{{rna_rin}}}}}
{{#set:rna_od260/230={{{rna_od260/230}}}}}
{{#set:rna_od260/280={{{rna_od260/280}}}}}
{{#set:rna_sample_type={{{rna_sample_type}}}}}
{{#set:rna_extraction_protocol={{{rna_extraction_protocol}}}}}
{{#set:rna_weight_ug={{{rna_weight_ug}}}}}
{{#set:rna_concentration={{{rna_concentration}}}}}
{{#if:{{{timecourse}}}|{{#arraymap:{{{timecourse|}}}|,|$| {{#set:timecourse=$}}}}|}}
{{#set:donor={{{donor}}}}}
{{#set:time={{{time}}}}}


{{#switch:{{{datafreeze_phase}}}|1={{#set:datafreeze_phase=1}}|2={{#set:datafreeze_phase=2}}|{{#set:datafreeze_phase=-1}}}}
{{#arraymap:{{#explode:{{{profile_hcage|}}}|,|0}}|&|$
|{{#set:sample_seq_library_id=$}}
}}
{{#set:sample_timecourse={{{sample_timecourse|}}}}}
[[Category:FF_Ontology]]
[[Category:FF_Samples]]


== Repeat Enrichment ==
{{#info: <br>Analyst: }}
{{#if: {{#pos:{{{repeat_enrich_byname}}}|,}} |
<html>
<html>
<script type="text/javascript">
<script type="text/javascript">
$(document).ready(function() {
$(document).ready(function() {
var data = [];
    if($('.homer-table')[0]){
var repnames = 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R37B','LTR38','LTR38-int','LTR38B','LTR39','LTR39-int','LTR3A','LTR3B','LTR3B_','LTR4','LTR40A1','LTR40a','LTR40b','LTR40c','LTR41','LTR41,LTR41B','LTR41B','LTR42','LTR43','LTR43-int','LTR43B','LTR44','LTR45B','LTR45B,LTR72B','LTR45C','LTR46','LTR46-int','LTR47A','LTR47B','LTR48','LTR48B','LTR48B,LTR49-int','LTR49','LTR49,MSTB2','LTR49-int','LTR50','LTR51','LTR52','LTR52-int','LTR53','LTR54','LTR54B','LTR55','LTR56','LTR57','LTR57-int','LTR58','LTR5A','LTR5B','LTR5_Hs','LTR61','LTR62','LTR64','LTR65','LTR66','LTR67B','LTR67B,LTR67B','LTR67B,MER5A','LTR67B,MLT1J','LTR69','LTR6A','LTR6B','LTR7','LTR7,MER4C','LTR71A','LTR71B','LTR72','LTR72B','LTR73','LTR75','LTR75B','LTR75_1','LTR76','LTR77','LTR78','LTR78B','LTR79','LTR79,LTR79','LTR7B','LTR7C','LTR7Y','LTR8','LTR80B','LTR81AB','LTR81B','LTR81C','LTR82A','LTR82B','LTR83','LTR84a','LTR84b','LTR84b,LTR84b','LTR85a','LTR85b','LTR85c','LTR86A1','LTR86B2','LTR87','LTR88a','LTR88b','LTR88c','LTR89','LTR8A','LTR9','LTR90A','LTR90B','LTR9B','Looper','MADE1','MADE2','MARNA','MER101','MER101-int','MER101B','MER102a','MER102b','MER102c','MER103C','MER104','MER105','MER106A','MER106B','MER110','MER110-int','MER110A','MER112','MER113','MER113A','MER115','MER117','MER119','MER119,MER119','MER11A','MER11C','MER11D','MER121','MER125','MER126','MER130','MER131','MER135','MER1A','MER1B','MER2','MER20','MER20,MER5A1','MER20B','MER21-int','MER21A','MER21A,MER39','MER21B','MER21C','MER2B','MER3','MER3,MLT1J','MER30','MER30B','MER31-int','MER31-int,MER31-int','MER31A','MER31B','MER33','MER34-int','MER34A','MER34A1','MER34B','MER34B-int','MER34B-int,MER34B-int','MER34C','MER34C2','MER34C_','MER39','MER39B','MER4-int','MER41-int','MER41A','MER41B','MER41C','MER41D','MER41E','MER41G','MER44A','MER44B','MER44C','MER44D','MER45A','MER45B','MER45C','MER46C','MER47A','MER47B','MER47C','MER48','MER49','MER4A','MER4A1','MER4A1_','MER4B','MER4B-int','MER4B-int,U3','MER4C','MER4D','MER4D0','MER4D1','MER4E','MER4E1','MER50','MER50,MER50','MER50-int','MER50B','MER50C','MER51-int','MER51A','MER51B','MER51C','MER51D','MER51E','MER52-int','MER52A','MER52A,MER52A','MER52C','MER52D','MER53','MER54A','MER54B','MER57-int','MER57A-int','MER57A1','MER57A1,MER57D','MER57B1','MER57B2','MER57C1','MER57C2','MER57D','MER57E1','MER57E2','MER57E3','MER57F','MER58A','MER58B','MER58C','MER58D','MER5A','MER5A1','MER5B','MER5B,MIRb','MER5C','MER5C1','MER6','MER61-int','MER61A','MER61B','MER61C','MER61D','MER61E','MER61E,MLT2B1','MER61F','MER63A','MER63B','MER63C','MER63D','MER65-int','MER65A','MER65B','MER65C','MER65D','MER66-int','MER66A','MER66B','MER66C','MER66D','MER67A','MER67B','MER67C','MER67D','MER68','MER68-int','MER68B','MER6A','MER6B','MER70-int','MER70A','MER70B','MER70C','MER72','MER73','MER74A','MER74A,MER74A','MER74B','MER74C','MER75A','MER76','MER77','MER77B','MER8','MER81','MER82','MER83','MER83A-int','MER83B','MER83C','MER84','MER84-int','MER85','MER87B','MER89','MER89,MER89','MER90','MER90a','MER91A','MER91B','MER91C','MER92A','MER92B','MER92C','MER94','MER94B','MER95','MER96','MER96B','MER97a','MER99','MER9a2','MIR','MIR,MIRc','MIR,T-rich','MIR3','MIR3,MIRb','MIR3,MLT1C','MIRb','MIRc','MLT-int','MLT1-int','MLT1A','MLT1A0','MLT1A0-int','MLT1A1','MLT1A1-int','MLT1B','MLT1B-int','MLT1C','MLT1C-int','MLT1D','MLT1D-int','MLT1E','MLT1E1','MLT1E1A','MLT1E1A,U4','MLT1E1A-int','MLT1E2','MLT1E3','MLT1E3-int','MLT1F','MLT1F,THE1B','MLT1F-int','MLT1F1','MLT1F2','MLT1F2-int','MLT1G','MLT1G-int','MLT1G1','MLT1G1,MSTA','MLT1G3','MLT1G3-int','MLT1H','MLT1H-int','MLT1H1','MLT1H2','MLT1I','MLT1I-int','MLT1J','MLT1J-int','MLT1J1','MLT1J1-int','MLT1J2','MLT1J2-int','MLT1K','MLT1L','MLT1M','MLT1N2','MLT2A1','MLT2A2','MLT2B1','MLT2B2','MLT2B3','MLT2B4','MLT2B5','MLT2C1','MLT2C2','MLT2D','MLT2E','MLT2F','MSR1','MSTA','MSTA-int','MSTB','MSTB-int','MSTB1','MSTB2','MSTB2-int','MSTC','MSTD','MSTD-int','MamGyp-int','MamGypLTR1a','MamGypLTR1b','MamGypLTR1c','MamGypLTR1d','MamGypLTR2c','MamGypLTR3','MamRep1161','MamRep137','MamRep1527','MamRep1879','MamRep38','MamRep4096','MamRep434','MamRep488','MamRep564','MamRep605','MamSINE1','Merlin1_HS','ORSL','ORSL-2a','ORSL-2b','PABL_A','PABL_A-int','PABL_B','PABL_B-int','PRIMA4-int','PRIMA41-int','PRIMA4_LTR','Plat_L3','PrimLTR79','REP522','Ricksha','Ricksha_0','Ricksha_c','SAR','SATR1','SST1','SSU-rRNA_Hsa','SUBTEL_sa','SVA_B','SVA_C','SVA_D','SVA_F','T-rich','TAR1','THE1-int','THE1A','THE1A-int','THE1B','THE1B-int','THE1C','THE1D','THE1D-int','Tigger1','Tigger1,U1','Tigger10','Tigger11a','Tigger12','Tigger12A','Tigger12c','Tigger13a','Tigger14a','Tigger15a','Tigger16a','Tigger16b','Tigger1a_Art','Tigger2','Tigger2a','Tigger2b_Pri','Tigger3','Tigger3,Tigger3','Tigger3a','Tigger3b','Tigger3c','Tigger4','Tigger4,Tigger4','Tigger4a','Tigger5','Tigger6a','Tigger6b','Tigger7','Tigger8','Tigger9a','Tigger9b','U1','U13','U13_','U14','U17','U2','U3','U4','U5','U6','U7','U8','UCON14','UCON2','UCON26','UCON29','UCON31','X3_LINE','X6A_LINE','X6B_LINE','X7A_LINE','X7B_LINE','X7C_LINE','X9_LINE','Zaphod','Zaphod3','polypurine','polypyrimidine','tRNA-Ala-GCY','tRNA-Ala-GCY_','tRNA-Arg-AGG','tRNA-Asn-AAC','tRNA-Asn-AAT','tRNA-Gln-CAA_','tRNA-Gly-GGA','tRNA-Leu-TTA','tRNA-Leu-TTA(m)','tRNA-Met-i','tRNA-Pro-CCA','tRNA-Ser-AGY','tRNA-Ser-TCA(m)'];
        var homer_denovo_table2 = $('.homer-table').DataTable({
var values = [</html>{{{repeat_enrich_byname}}}<html>];
                        dom: 'Blfrtip',
for(i1=0;i1<repnames.length;i1++){
                        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
//pval = pvals[i1].split(";");
                        lengthMenu: [[5, 50, -1], [5, 50, "All"]],
data.push([repnames[i1],values[i1]]);
scrollCollapse: true,
}
                        columnDefs: [
                            { targets: 0, orderable: false},
                            { targets: 1, orderable: false},
                            { targets: 2, width: "100pt", "type": "numeric"},
                            { targets: 3, orderable: false, type: "percent"},
                            { targets: 4, orderable: false, type: "percent"},
                            { targets: 5, orderable: false}
                        ]
        });


     $('#repeat_enrich_byname_table').dataTable({
     }
//"aaData": [["one", 1],["two", 3],["three", 0]],
"sScrollY": "300px",
"bScrollCollapse": true,
"bPaginate": false,
"bFilter": false,
"bInfo": false,
"aaData": data,
"aoColumns": [{ "sTitle": "Repeat sequence name",  "bSortable": false },{ "sTitle": "Enrichment score", "sType": "numeric" }],
"aaSorting": [[ 1, "desc" ]],
});
});
});
</script>
</script>
<table id="repeat_enrich_byname_table"></table>
</html>
</html>
|no result for this sample
}}
== Relative expression of the co-expression cluster ==
{{#info: <br>Analyst: }}
<html>
<script type="text/javascript">
$(document).ready(function() {
    $('.relative_exp_of_coexp').dataTable({
"sScrollY": "300px",
"bPaginate": false,
"bScrollCollapse": true,
"iDisplayLength": -1,
"aaSorting": [[1,'desc']],
"aoColumnDefs": [{ "sWidth": "150px", "sType": "numeric", "aTargets": [1] }]
});
});
</script>
</html>
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?Coexpression_dpi_cluster_scores_median_value|intro=<h3>$</h3><br><table class="relative_exp_of_coexp"><html><thead></html><tr><th>Coexpression cluster</th><th>score</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table>|link=none|format=template|template=Coexpression_dpi_cluster_scores_median_in_ffsample|limit=5000|searchlabel=|default=}}
|<br><br>
}}
[[Category:FF_Ontology]]
[[Category:FF_Samples]]

Latest revision as of 18:04, 14 March 2022


Name:{{{name}}}
Species:{{{sample_species}}}
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Additional information
Sample information
strain{{{sample_strain}}}
tissue{{{sample_tissue}}}
dev stage{{{sample_dev_stage}}}
sex{{{sample_sex}}}
age{{{sample_age}}}
cell type{{{sample_cell_type}}}
cell line{{{sample_cell_line}}}
company{{{sample_company}}}
collaboration{{{sample_collaboration}}}
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number{{{rna_lot_number}}}
catalog number{{{rna_catalog_number}}}
sample type{{{rna_sample_type}}}
extraction protocol (Details){{{rna_extraction_protocol}}}



FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
NA

DOID: Disease
NA

UBERON: Anatomy
NA

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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