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Line 1: Line 1:
 
{{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/datatables/extras/TableTools/media/css/TableTools.css";
 
@import "/5/sstar/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" src="/5/sstar/rb_js/html5button/datatables.js"></script>
 
<script type="text/javascript" src="/5/sstar/rb_js/custom/expoconvert.js"></script>
 
<script type="text/javascript" src="/5/sstar/rb_js/custom/expoconvert.js"></script>
<script type="text/javascript" src="/5/sstar/rb_js/datatables/media/js/jquery.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/datatables/extras/TableTools/media/js/ZeroClipboard.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>
Line 19: Line 17:
 
<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">[[Property:Library_accession_number|Library ID]]:</th><td>{{{library_id}}}</td></tr>
+
<tr><th scope="row" align="right">[[Property:Library_accession_number|Library ID]]:</th><td>{{#replace:{{{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>
<tr><th scope="row" align="right">Genomic View:</th><td>[http://fantom.gsc.riken.jp/zenbu/dex/#section=Experiments;search={{#replace:{{{id}}}|FF:|}} zenbu] , [http://genome.ucsc.edu/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>
+
{{#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>}}
{{#ifexpr: {{#pos:{{{microRNAs_novel_cage}}}|ttp}}||
+
{{#ifexpr: {{#pos:{{{microRNAs_novel_cage}}}{{{microRNAs_novel_srna}}}|ttp}}|
<tr><th scope="row" align="right">MicroRNAs:</th><td>Including candidate novel miRNAs([{{{microRNAs_novel_cage}}} CAGE],[{{{microRNAs_novel_cage}}} sRNA])&nbsp;&nbsp;{{#ifexpr: {{#pos:{{{microRNAs_nn}}}|ttp}}||  Excluding candidate novel miRNAs([{{{microRNAs_nn}}} CAGE],[{{{microRNAs_nn}}} sRNA])}} </td></tr>}}
+
{{#ifexpr: {{#pos:{{{microRNAs_novel_srna}}}|ttp}}
<tr><th scope="row" align="right">CAGEd-oPOSSUM:</th><td>[http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/{{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | human | }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | mouse | }}/{{{id}}}/results.html link]  </td></tr></table>
+
|{{#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> | }}</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}}}}}|}}{{#vardefine:species_temp|{{#switch: {{{sample_species}}} | Human (Homo sapiens) = Hg19 | Mouse (Mus musculus) = Mm9 }}}}{{#if: {{#pos:{{{expression_enrichment_score}}}|chr}}| {{Fontsize|3|Relative expression to median (log10)}}  
+
|}{{#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}}}
 +
|Human (Homo sapiens) = {{FastaBamfileCTSS||Hg19|{{{hg19fasta}}}||{{{hg19bam}}}|{{{hg19ctss}}}|Hg38|{{{hg38bam}}}|{{{hg38ctss}}}}}
 +
|Mouse (Mus musculus) = {{FastaBamfileCTSS||Mm9|{{{mm9fasta}}}||{{{mm9bam}}}|{{{mm9ctss}}}|Mm10|{{{mm10bam}}}|{{{mm10ctss}}}}}
 +
|
 +
}}{{#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. }}}}
 
{{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. }}}}
Line 68: Line 89:
 
}
 
}
 
/*"sDom": '<"top"i>rt<"bottom"flp><"clear">' */
 
/*"sDom": '<"top"i>rt<"bottom"flp><"clear">' */
 
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 );
+
    $('#ffcp_tf_enrichscore').DataTable( {
 +
        data: mm_data,
 +
        dom: 'Blfrtip',
 +
        lengthMenu: [[10, 50, -1], [10, 50, "All"]],
 +
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
 +
        columnDefs: [{ targets: [1], visible: false}],
 +
        columns: [
 +
            { title: "CAGE peaks" ,
 +
              render: function ( data, type, row, meta ) {
 +
                var peak_loc = row[0];
 +
                var peak_name = row[1];
 +
return "<a href=\"/5/sstar/"+"FFCP_PHASE1:"+species+"::"+peak_loc +"\">"+peak_name+"</a>";
 +
              }
 +
            },
 +
            { title: "Log10(Relative expression over median)" },
 +
            { title: "TPM" },
 +
            { title: "TF." }
 +
        ],
 +
        order: [[ 2, 'desc' ]]
 +
    } );
 
});
 
});
 
</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" 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>[http://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]){
var coexpression_dpi_cluster_scores_median_table= $('.relative-exp-of-coexp').dataTable({
+
        $('.relative-exp-of-coexp').DataTable({
"bScrollCollapse": true,
+
          dom: 'Blfrtip',
"bPaginate": true,
+
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
"bFilter": true,
+
          lengthMenu: [[10, 50, -1], [10, 50, "All"]],
"bInfo": true,
+
          order: [[ 1, 'desc' ]]
                "iDisplayLength": 10,
+
        });
                "aLengthMenu": [[10,50,-1], [10,50,"All"]],
+
}
"aaSorting": [[1,'desc']],
+
});
"aoColumnDefs": [{ "sWidth": "150px", "sType": "numeric", "aTargets": [1] ,"fnRender": function (obj) {
+
</script></html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#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}}
              var num =obj.aData[obj.iDataColumn];
 
              var numb = new Number(num);
 
                  return numb.toFixed(2) ;
 
} }]
 
});
 
var coexpression_dpi_cluster_scores_median_table_export_tools = new TableTools(coexpression_dpi_cluster_scores_median_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"} ]});
 
$('#coexpression_dpi_cluster_scores_median_table_export_tool').before(coexpression_dpi_cluster_scores_median_table_export_tools.dom.container );}});</script></html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#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}}
 
 
|<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|searchlabel=}}
 
|<br><br>
 
|<br><br>
 
}}}}
 
}}}}
Line 154: Line 156:
 
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 193: Line 194:
 
<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>[http://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 201: Line 202:
 
<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>[http://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 216: Line 217:
 
$(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 242: Line 251:
 
$(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 270: Line 288:
 
</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 408: Line 407:
 
{{#set:rna_weight_ug={{{rna_weight_ug}}}}}
 
{{#set:rna_weight_ug={{{rna_weight_ug}}}}}
 
{{#set:rna_concentration={{{rna_concentration}}}}}
 
{{#set:rna_concentration={{{rna_concentration}}}}}
{{#if:{{{timecourse}}}|{{#arraymap:{{{timecourse}}}|,|$| {{#set:timecourse=$}}}}|}}
+
{{#if:{{{timecourse}}}|{{#arraymap:{{{timecourse|}}}|,|$| {{#set:timecourse=$}}}}|}}
 
{{#set:donor={{{donor}}}}}
 
{{#set:donor={{{donor}}}}}
 
{{#set:time={{{time}}}}}
 
{{#set:time={{{time}}}}}
  
 
{{#switch:{{{datafreeze_phase}}}|1={{#set:datafreeze_phase=1}}|2={{#set:datafreeze_phase=2}}|{{#set:datafreeze_phase=-1}}}}
 
{{#switch:{{{datafreeze_phase}}}|1={{#set:datafreeze_phase=1}}|2={{#set:datafreeze_phase=2}}|{{#set:datafreeze_phase=-1}}}}
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
+
{{#arraymap:{{#explode:{{{profile_hcage|}}}|,|0}}|&|$
 
|{{#set:sample_seq_library_id=$}}
 
|{{#set:sample_seq_library_id=$}}
 
}}
 
}}
{{#set:sample_timecourse={{{sample_timecourse}}}}}
+
{{#set:sample_timecourse={{{sample_timecourse|}}}}}
 
[[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_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>

Latest revision as of 07:52, 23 May 2019


Name:{{{name}}}
Species:{{{sample_species}}}
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View:
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)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

CL: Cell type
NA

DOID: Disease
NA

UBERON: Anatomy
NA

FF: FANTOM5
NA

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

NA