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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/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/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" src="/5/sstar/rb_js/html5button/datatables.min.js"></script>
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/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 91: Line 88:
}
}
/*"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: "" },
            { 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">
<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|}}]]|mainlabel=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 177: Line 155:
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 216: Line 193:
<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|_}}]]|mainlabel=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 224: Line 201:
<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|_}}]]|mainlabel=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 239: Line 216:
$(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 265: Line 250:
$(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 );
     }
     }
});
});

Revision as of 16:09, 24 January 2018


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}}}




Co-expression clusters with enriched expression in this sampleRanked 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>data

Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data
library id: {{{profile_hcage}}}This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifs<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 in169 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>data
library id: {{{profile_hcage}}}This sample isn't target for the analysis

de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: {{{profile_hcage}}}


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
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UBERON: Anatomy
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FF: FANTOM5
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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
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