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


</html>{{#outerfile_existance: /5/sstar/sstar_img/f5samples/riken_cellimg/{{PAGENAME}}.jpg |<html>
</html>{{#outerfile_existance: /5/sstar/sstar_img/f5samples/riken_cellimg/{{PAGENAME}}.jpg |<html>
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{{#ifexpr: {{#pos:{{{cagescan_library_id}}}|Cig}}|<tr><th scope="row" align="right">CAGEScan Library ID:</th><td>{{#replace:{{{cagescan_library_id}}}|!|, }}</td></tr>|}}
{{#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>
<tr><th scope="row" align="right">[[Property:Sample_category|Sample type]]:</th><td>{{{sample_category}}}</td></tr>
{{#ifeq: {{{sample_species}}} | Gallus gallus ||<tr><th scope="row" align="right">Genomic View:</th><td>{{#ifexpr: {{#pos:{{{zenbu_config}}}|ttp}}|[{{{zenbu_config}}} zenbu] |}} {{#ifeq: {{{sample_species}}} | Human (Homo sapiens) |[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC]| }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) |[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC]| }}</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_cage}}}{{{microRNAs_novel_srna}}}|ttp}}|
{{#ifexpr: {{#pos:{{{microRNAs_novel_srna}}}|ttp}}
{{#ifexpr: {{#pos:{{{microRNAs_novel_srna}}}|ttp}}
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}}
}}
|}}
|}}
-->
{{#ifexpr: {{#pos:{{{refex}}}|ttp}}|
{{#ifexpr: {{#pos:{{{refex}}}|ttp}}|
<tr><th scope="row" align="right">RefEX:</th><td>[{{#replace:{{#replace:{{{refex}}}|[|%5b}}|]|%5d}} Specific genes]  </td></tr>|}}
<tr><th scope="row" align="right">RefEX:</th><td>[{{#replace:{{#replace:{{{refex}}}|[|%5b}}|]|%5d}} Specific genes]  </td></tr>|}}
{{#ifexpr: {{#pos:{{{fantom_cat}}}|ttp}}|
{{#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>|}}
<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> | }}</table>
{{#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>[{{{zenbu_report}}} link] </td></tr>|}} </table>
{|class="wikitable mw-collapsible mw-collapsed" style="width:auto"
{|class="wikitable mw-collapsible mw-collapsed" style="width:auto"
! Additional information
! Additional information
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<tr><th>sample type</th><td>{{#switch:{{{rna_sample_type}}}|,,,=NA| =NA |{{{rna_sample_type}}}}}</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>
<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||{{{DRA_sample_Accession}}}|{{{accession_numbers}}}|{{{library_id}}}|{{{sample_species}}}}}|}}{{#vardefine:species_temp|{{#switch: {{{sample_species}}} | Human (Homo sapiens) = Hg19 | Mouse (Mus musculus) = Mm9 }}}}{{#switch: {{{sample_species}}}
|}{{#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|{{{hg38bam}}}|{{{hg38ctss}}}}}
|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|{{{mm10bam}}}|{{{mm10ctss}}}}}
|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}}|
}}{{#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}}|
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for(i=0;i<sub_content.length;i++){
for(i=0;i<sub_content.length;i++){
var temp =sub_content[i];
var temp=sub_content[i];
if(temp != null){
if(temp!= null){
if(temp.length>2){
if(temp.length>2){
var sub_sub_content=sub_content[i].split("!");
var sub_sub_content=sub_content[i].split("!");
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     $('#ffcp_tf_enrichscore').DataTable( {
     $('#ffcp_tf_enrichscore').DataTable( {
         data: mm_data,
         data: mm_data,
         dom: 'Bfrtip',
         dom: 'Blfrtip',
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5', 'pageLength'],
         lengthMenu: [[10, 50, -1], [10, 50, "All"]],
         lengthMenu: [[10, 50, -1], [10, 50, "All"]],
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
         columnDefs: [{ targets: [1], visible: false}],
         columnDefs: [{ targets: [1], visible: false}],
         columns: [
         columns: [
Line 107: Line 104:
               }
               }
             },
             },
            { title: "" },
             { title: "Log10(Relative expression over median)" },
             { title: "Log10(Relative expression over median)" },
             { title: "TPM" },
             { title: "TPM" },
Line 114: Line 110:
         order: [[ 2, 'desc' ]]
         order: [[ 2, 'desc' ]]
     } );
     } );
/*
var tf_enrich_table = $('#ffcp_tf_enrichscore').dataTable( {
"bScrollCollapse": true,
"bPaginate": true,
"bFilter": true,
"bInfo": true,
                "iDisplayLength": 10,
                "aLengthMenu": [[10,50,-1], [10,50,"All"]],
"aaData": mm_data,
"aoColumnDefs":[
{"aTargets":[0],"sTitle": "CAGE peaks", "fnRender": function(obj) {
var peak_loc = obj.aData[ obj.iDataColumn ];
                var peak_name = obj.aData[ obj.iDataColumn+1 ];
return sReturn = "<a href=\"/5/sstar/"+"FFCP_PHASE1:"+species+"::"+peak_loc +"\">"+peak_name+"</a>";
}
},
{"aTargets":[1],"sTitle": "Log10(Relative expression over median)","fnRender": function(obj) {
return sReturn = obj.aData[ obj.iDataColumn+1 ];
}
},
{"aTargets":[2],"sTitle": "TPM","fnRender": function(obj) {
return sReturn = obj.aData[ obj.iDataColumn+1 ];
}
},
{"aTargets":[3],"sTitle": "TF","fnRender": function(obj) {
return sReturn = obj.aData[ obj.iDataColumn+1 ];
}
}
],
"aaSorting": [[ 1, "desc" ]]
} );
var tf_enrich_table_tool = new TableTools(tf_enrich_table, {"sSwfPath": "/5/sstar/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"} ]});
$('#tf_enrich_table_export_tool').before(tf_enrich_table_tool.dom.container );
*/
});
});
</script>
</script>
<span id="tf_enrich_table_export_tool"></span>
<span id="tf_enrich_table_export_tool"></span>
<table cellpadding="0" cellspacing="0" border="0" class="display dataTable" id="ffcp_tf_enrichscore"></table>
<table cellpadding="0" cellspacing="0" border="0" id="ffcp_tf_enrichscore" class="stripe cell-border order-column compact"></table>
</html>
</html>
}}
}}
<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>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters data]}}<html><script type="text/javascript">
{{#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() {
$(document).ready(function() {
     if($('.relative-exp-of-coexp')[0]){
     if($('.relative-exp-of-coexp')[0]){
         $('.relative-exp-of-coexp').dataTable({
         $('.relative-exp-of-coexp').DataTable({
        dom: 'lBfrtip',
          dom: 'Blfrtip',
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5', 'pageLength'],
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
        lengthMenu: [[10, 50, -1], [10, 50, "All"]],
          lengthMenu: [[10, 50, -1], [10, 50, "All"]],
        order: [[ 1, 'desc' ]]
          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' ]]
         });
         });
/*
var coexpression_dpi_cluster_scores_median_table= $('.relative-exp-of-coexp').dataTable({
"bScrollCollapse": true,
"bPaginate": true,
"bFilter": true,
"bInfo": true,
                "iDisplayLength": 10,
                "aLengthMenu": [[10,50,-1], [10,50,"All"]],
"aaSorting": [[1,'desc']],
"aoColumnDefs": [{ "sWidth": "150px", "sType": "numeric", "aTargets": [1] ,"fnRender": function (obj) {
              var num =obj.aData[obj.iDataColumn];
              var numb = new Number(num);
                  return numb.toFixed(2) ;
} }]
});
*/
}
}
});
});
</script></html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?Coexpression_dpi_cluster_scores_median_value|intro=<span id="coexpression_dpi_cluster_scores_median_table_export_tool"></span><table class="relative-exp-of-coexp"><html><thead></html><tr><th>Coexpression cluster</th><th>score</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table>|link=none|format=template|template=Coexpression_dpi_cluster_scores_median_in_ffsample|limit=5000|searchlabel=|default=No results for this sample}}
</script></html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?Coexpression_dpi_cluster_scores_median_value|intro=<table class="relative-exp-of-coexp stripe cell-border order-column compact"><html><thead></html><tr><th>Coexpression cluster</th><th>score</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table>|link=none|format=template|template=Coexpression_dpi_cluster_scores_median_in_ffsample|limit=5000|searchlabel=|default=No results for this sample}}
|<br><br>}}
|<br><br>}}
|Mouse (Mus musculus)=
|Mouse (Mus musculus)=
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|<h3>$</h3><span id="coexpression_dpi_cluster_scores_median_table_export_tool"></span>{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|mainlabel=MCL coexpression id|?Coexpression_dpi_cluster_scores_median_value|format=ttable|class=relative-exp-of-coexp|searchlabel=}}
|<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>
}}}}
}}}}
Line 194: Line 145:
the median expression in the FANTOM5 collection is shown. Value is log10
the median expression in the FANTOM5 collection is shown. Value is log10
transformed.<br><b>Analyst:</b>NA
transformed.<br><b>Analyst:</b>NA
<br><br>link to dataset.<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression data]}}}}
<br><br>link to dataset.<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression data]}}}}
{{#if: {{#pos:{{{repeat_enrich_byfamily}}}|,}} |
{{#if: {{#pos:{{{repeat_enrich_byfamily}}}|,}} |
<html><script type="text/javascript">
<html><script type="text/javascript">
Line 210: Line 161:
repeat_enrich_byfamily_data.push([repeat_enrich_byfamily_repnames[i1],repeat_enrich_byfamily_values[i1]]);
repeat_enrich_byfamily_data.push([repeat_enrich_byfamily_repnames[i1],repeat_enrich_byfamily_values[i1]]);
}
}
  var repeat_enrich_byfamily_table_obj=  $('#repeat_enrich_byfamily_table').dataTable({
        $('#repeat_enrich_byfamily_table').DataTable({
"bScrollCollapse": true,
          data: repeat_enrich_byfamily_data,
"bPaginate": true,
          dom: 'Blfrtip',
"bFilter": true,
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
"bInfo": true,
          lengthMenu: [[5, 50, -1], [5, 50, "All"]],
                "iDisplayLength": 5,
          columns: [
                "aLengthMenu": [[5,50,-1], [5,50,"All"]],
            { title: "Repeat family" },
"aaData": repeat_enrich_byfamily_data,
            { title: "Log10(Relative expression over median)" ,
"aoColumns": [{ "sTitle": "Repeat family",  "bSortable": false },{ "sTitle": "Log10(Relative expression over median)", "sType": "numeric" ,"fnRender": function (obj) {
              render: function ( data, type, row, meta ) {
              var num =obj.aData[obj.iDataColumn];
                var num = row[1];
              var numb = new Number(num);
                var numb = new Number(num);
                  return numb.toFixed(2) ;
return numb.toFixed(2);
}}],
              }
"aaSorting": [[ 1, "desc" ]]
            }
});
          ],
var repeat_enrich_byfamily_table_objtool = new TableTools( repeat_enrich_byfamily_table_obj, {"sSwfPath": "/5/sstar/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"} ]});
          order: [[ 1, 'desc' ]]
 
        });
$('#repeat_enrich_byfamily_table_export_tool').before(repeat_enrich_byfamily_table_objtool.dom.container );
});
});
</script>
</script>
<span id="repeat_enrich_byfamily_table_export_tool"></span>
<span id="repeat_enrich_byfamily_table_export_tool"></span>
<table id="repeat_enrich_byfamily_table"></table><br>
<table id="repeat_enrich_byfamily_table" class="stripe cell-border order-column compact"></table><br>


</html>
</html>
Line 247: Line 197:
to the Z-score is taken as the resulting P-value. Lower P-value indicates
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>
more (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br>
<br><br>link to dataset.<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression data]}}<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}}|&|$
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|library id: $<span id="related_jaspar_table_export_tool"></span>{{#ask:[[jaspar_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]|mainlabel=Jaspar motif|?=Logo|?jaspar_motifs_sample_pval_pval=P-value|format=ttable|limit=1100|searchlabel=|class=jaspar_motif_pval|searchlabel=|default=This sample isn't target for the analysis}}
|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>
}}
}}
Line 255: Line 205:
{{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
{{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>
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>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression data]}}<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}}|&|$
|library id: $<span id="related_novel_table_export_tool"></span>{{#ask:[[novel_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]|mainlabel=Novel motif|?=Logo|?novel_motifs_sample_pval_pval=P-value|format=ttable|limit=1100|searchlabel=|class=novel_motif_pval|searchlabel=|default=This sample isn't target for the analysis}}
|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>
}}
}}
Line 272: Line 222:
$(document).ready(function() {
$(document).ready(function() {
     if($('.jaspar_motif_pval')[0]){
     if($('.jaspar_motif_pval')[0]){
var related_jaspar_table= $('.jaspar_motif_pval').dataTable({
        $('.jaspar_motif_pval').DataTable({
"bScrollCollapse": true,
          dom: 'Blfrtip',
"bPaginate": true,
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
"bFilter": true,
          lengthMenu: [[5, 50, -1], [5, 50, "All"]],
"bInfo": true,
          columnDefs: [
                "iDisplayLength": 5,
            { targets: 0, orderable: false},
                "aLengthMenu": [[5,50,-1], [5,50,"All"]],
            { targets: 1, orderable: false, width: "50pt", className: "bgwhite"}
"aaSorting": [[2,'asc']],
          ],
"aoColumnDefs": [{"bSortable": false, "aTargets": [ 0 ]}, { "fnRender": function(obj) {
          columns: [
return sReturn = '<img src="/5/sstar/seqlogo/jaspar/' +  $(obj.aData[1]).text() + '.png" width ="80" height = "20">'}, "sClass": "bgwhite", "sWidth": "50", "bSortable": false, "aTargets": [1] }, { "sTitle": "p-value", "sType": "numeric", "sWidth": "50pt", "aTargets":[2],"fnRender": function (obj) {                  
            { title: "Jaspar motif" },
                  var num =obj.aData[obj.iDataColumn];
            { title: "Logo",
                  return exp_converter(num,2,"e") ;
              render: function ( data, type, row, meta ) {
} }]
return "<img src=\"/5/sstar/seqlogo/jaspar/" +  $(row[0]).text() + ".png\" width =\"80\" height = \"20\">";
});
              }
var related_jaspar_table_tool= new TableTools(related_jaspar_table, {"sSwfPath": "/5/sstar/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"} ]});
            },
            { title: "p-value",
              render: function ( data, type, row, meta ) {
                var num=row[2];
return exp_converter(num,2,"e");
              }
            }
          ],
          order: [[ 2, 'asc' ]]
        });


$('#related_jaspar_table_export_tool').before(related_jaspar_table_tool.dom.container );
     }
     }
});
});
Line 298: Line 256:
$(document).ready(function() {
$(document).ready(function() {
     if($('.novel_motif_pval')[0]){
     if($('.novel_motif_pval')[0]){
var related_novel_table= $('.novel_motif_pval').dataTable({
 
"bScrollCollapse": true,            
$('.novel_motif_pval').DataTable({
"bPaginate": true,
              dom: 'Blfrtip',
"bFilter": true,
              buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
"bInfo": true,
              lengthMenu: [[5, 50, -1], [5, 50, "All"]],
                "iDisplayLength": 5,
              columnDefs: [
                "aLengthMenu": [[5,50,-1], [5,50,"All"]],
                { targets: 0, orderable: false},
"aaSorting": [[2,'asc']],
                { targets: 1, orderable: false, width: "50pt", className: "bgwhite"}
"aoColumnDefs": [{"bSortable": false, "aTargets": [ 0 ]}, { "fnRender": function(obj) {
              ],
return sReturn = '<img src="/5/sstar/seqlogo/novel/' +  $(obj.aData[1]).text() + '.png" width ="80" height = "20">'}, "sClass": "bgwhite", "sWidth": "50",  "bSortable": false, "aTargets": [1] }, { "sTitle": "p-value", "sType": "numeric", "sWidth": "50pt", "aTargets":[2],"fnRender": function (obj) {                  
              columns: [
                  var num =obj.aData[obj.iDataColumn];
                { title: "Novel motif" },
                  return exp_converter(num,2,"e") ;
                { 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' ]]
});
});
var related_novel_table_tool = new TableTools( related_novel_table, {"sSwfPath": "/5/sstar/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"} ]});


$('#related_novel_table_export_tool').before(related_novel_table_tool.dom.container );
     }
     }
});
});
Line 326: Line 293:
</style>
</style>
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/media/js/dataTables.Percentage.js"></script>
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/media/js/dataTables.Percentage.js"></script>
<script type="text/javascript">
$(document).ready(function() {
    if($('.homer-table')[0]){
        var homer_denovo_table = $('.homer-table').dataTable({
"bPaginate": true,
"bInfo": true,
"bScrollCollapse": true,
        "iDisplayLength": 5,
                "aLengthMenu": [[5,50,-1], [5,50,"All"]],
"aaSorting": [],
"aoColumnDefs": [{ "sType": "numeric", "sWidth": "100px", "aTargets": [2]}, {"sType": "percent", "aTargets": [ 3, 4] }, { "bSortable": false, "aTargets": [ 0, 1, 5] }]
});
var homer_denovo_table_tool = new TableTools(homer_denovo_table, {"sSwfPath": "/5/sstar/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"} ]});
$('#homer_denovo_table_export_tool').before(homer_denovo_table_tool.dom.container );
    }
});
</script>
</html>
</html>
<br>
<br>|}}<!-- end of if(isHumanOrMouse) -->
{{Fontsize|3|FANTOM5 (FF) ontology }}
{{Fontsize|3|FANTOM5 (FF) ontology }}
----
----
Line 372: Line 320:
{{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
{{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
<br><br>link to source data<br>
<br><br>link to source data<br>
[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data]
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data]
}}<br>
}}<br>
{{#if: {{{ancestors_in_cell_lineage_facet}}} |
{{#if: {{{ancestors_in_cell_lineage_facet}}} |
Line 401: Line 349:
{{Fontsize|3|Ancestor terms (development)}}{{#info:<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br>
{{Fontsize|3|Ancestor terms (development)}}{{#info:<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>
<b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>
[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data]
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data]
}}
}}
<br>
<br>
Line 475: Line 423:
[[Category:FF_Ontology]]
[[Category:FF_Ontology]]
[[Category:FF_Samples]]
[[Category:FF_Samples]]
<html>
<script type="text/javascript">
$(document).ready(function() {
    if($('.homer-table')[0]){
        var homer_denovo_table2 = $('.homer-table').DataTable({
                        dom: 'Blfrtip',
                        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
                        lengthMenu: [[5, 50, -1], [5, 50, "All"]],
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}
                        ]
        });
    }
});
</script>
</html>

Latest revision as of 11:44, 24 September 2021


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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