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Line 110: 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>
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           order: [[ 1, 'desc' ]]
           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) ;
} }]
});
*/
}
}
});
});
Line 224: Line 172:
           order: [[ 1, 'desc' ]]
           order: [[ 1, 'desc' ]]
         });
         });
/*
  var repeat_enrich_byfamily_table_obj=  $('#repeat_enrich_byfamily_table').dataTable({
"bScrollCollapse": true,
"bPaginate": true,
"bFilter": true,
"bInfo": true,
                "iDisplayLength": 5,
                "aLengthMenu": [[5,50,-1], [5,50,"All"]],
"aaData": repeat_enrich_byfamily_data,
"aoColumns": [{ "sTitle": "Repeat family",  "bSortable": false },{ "sTitle": "Log10(Relative expression over median)", "sType": "numeric" ,"fnRender": function (obj) {
              var num =obj.aData[obj.iDataColumn];
              var numb = new Number(num);
                  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"} ]});
$('#repeat_enrich_byfamily_table_export_tool').before(repeat_enrich_byfamily_table_objtool.dom.container );
*/
});
});
</script>
</script>
Line 313: Line 241:
         });
         });


/*
var related_jaspar_table= $('.jaspar_motif_pval').dataTable({
"bScrollCollapse": true,
"bPaginate": true,
"bFilter": true,
"bInfo": true,
                "iDisplayLength": 5,
                "aLengthMenu": [[5,50,-1], [5,50,"All"]],
"aaSorting": [[2,'asc']],
"aoColumnDefs": [{"bSortable": false, "aTargets": [ 0 ]}, {  "fnRender": function(obj) {
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) {                   
                  var num =obj.aData[obj.iDataColumn];
                  return exp_converter(num,2,"e") ;
} }]
});
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"} ]});
$('#related_jaspar_table_export_tool').before(related_jaspar_table_tool.dom.container );
*/
     }
     }
});
});
Line 341: 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,           
"bPaginate": true,
"bFilter": true,
"bInfo": true,
                "iDisplayLength": 5,
                "aLengthMenu": [[5,50,-1], [5,50,"All"]],
"aaSorting": [[2,'asc']],
"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) {                   
                  var num =obj.aData[obj.iDataColumn];
                  return exp_converter(num,2,"e") ;
} }]
});
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 );
*/
$('.novel_motif_pval').DataTable({
$('.novel_motif_pval').DataTable({
               dom: 'Blfrtip',
               dom: 'Blfrtip',

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
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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