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Line 5: Line 5:
 
</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/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/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>
  
Line 69: Line 69:
 
----
 
----
 
{{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. }}}}
 +
<html><!-- tf enrich table: start-->
 +
<script type="text/javascript">
 +
var species="</html>{{#var:species_temp}}<html>";
 +
var mm_data = new Array();
 +
var enrichment_scores_data = "</html>{{{expression_enrichment_score}}}<html>";
 +
var sub_content = enrichment_scores_data.split(";;");
 +
 +
$(document).ready(function() {
 +
 +
for(i=0;i<sub_content.length;i++){
 +
var temp =sub_content[i];
 +
if(temp != null){
 +
if(temp.length>2){
 +
var sub_sub_content=sub_content[i].split("!");
 +
var built="FFCP_PHASE1:"+species+"::"+sub_sub_content[0];
 +
mm_data.push(sub_sub_content);
 +
}
 +
}
 +
}
 +
/*"sDom": '<"top"i>rt<"bottom"flp><"clear">' */
 +
 +
    $('#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>
 +
<span id="tf_enrich_table_export_tool"></span>
 +
<table cellpadding="0" cellspacing="0" border="0" id="ffcp_tf_enrichscore" class="stripe cell-border order-column compact"></table>
 +
</html>
 
}}
 
}}
 
{{#vardefine:isHumanOrMouse|{{#switch:{{{sample_species}}}|Human (Homo sapiens)=1|Mouse (Mus musculus)=1|0}}}}
 
{{#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]}}{{#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}}
+
{{#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() {
 +
 
 +
    if($('.relative-exp-of-coexp')[0]){
 +
        $('.relative-exp-of-coexp').DataTable({
 +
          dom: 'Blfrtip',
 +
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
 +
          lengthMenu: [[10, 50, -1], [10, 50, "All"]],
 +
          order: [[ 1, 'desc' ]]
 +
        });
 +
}
 +
});
 +
</script></html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?Coexpression_dpi_cluster_scores_median_value|intro=<table class="relative-exp-of-coexp stripe cell-border order-column compact"><html><thead></html><tr><th>Coexpression cluster</th><th>score</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table>|link=none|format=template|template=Coexpression_dpi_cluster_scores_median_in_ffsample|limit=5000|searchlabel=|default=No results for this sample}}
 
|<br><br>}}
 
|<br><br>}}
 
|Mouse (Mus musculus)=
 
|Mouse (Mus musculus)=
 
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
 
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|<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=}}
+
|<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 84: Line 142:
 
<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>[http://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">
 +
$(document).ready(function() {
 +
var repeat_enrich_byfamily_data = [];
 +
var repeat_enrich_byfamily_repnames = [
 +
</html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)=<html>
 +
'Alu','Alu,Alu','Alu,ERVL-MaLR','Alu,L1','Alu,L2','Alu,Low_complexity','Alu,MIR','Alu,hAT-Charlie','Alu,hAT-Tip100','Alu,rRNA','Alu,snRNA','CR1','CR1,CR1','DNA','DNA?','Deu','ERV','ERV1','ERV1,ERV1','ERV1,ERVL','ERV1,ERVL-MaLR','ERV1,MIR','ERV1,snRNA','ERVK','ERVK,rRNA','ERVL','ERVL,ERV1','ERVL,ERVL','ERVL,ERVL-MaLR','ERVL,hAT-Charlie','ERVL,snRNA','ERVL-MaLR','ERVL-MaLR,ERVL-MaLR','ERVL-MaLR,snRNA','ERVL?','Gypsy','Gypsy?','Helitron','L1','L1,ERV1','L1,ERVL','L1,ERVL-MaLR','L1,L1','L1,TcMar-Mariner','L1,TcMar-Tigger','L1,hAT-Charlie','L1,rRNA','L1,snRNA','L1?','L2','L2,ERV1','L2,ERVL-MaLR','L2,L2','L2,MIR','L2,hAT-Blackjack','L2,hAT-Charlie','LTR','Low_complexity','Low_complexity,Alu','Low_complexity,ERV1','Low_complexity,L2','Low_complexity,Low_complexity','Low_complexity,Low_complexity,Low_complexity','Low_complexity,snRNA','MIR','MIR,ERVL-MaLR','MIR,Low_complexity','MIR,MIR','Merlin','MuDR','NA','Other','PiggyBac','PiggyBac?','RNA','RNA,MIR','RTE','RTE,CR1','RTE-BovB','SINE','SINE?','Satellite','Satellite,ERVL','Simple_repeat','Simple_repeat,Alu','Simple_repeat,ERV1','Simple_repeat,ERVL','Simple_repeat,ERVL-MaLR','Simple_repeat,L1','Simple_repeat,L2','Simple_repeat,Low_complexity','Simple_repeat,Low_complexity,Low_complexity','Simple_repeat,MIR','Simple_repeat,Other','Simple_repeat,Simple_repeat','Simple_repeat,Simple_repeat,Low_complexity','Simple_repeat,Simple_repeat,Simple_repeat','Simple_repeat,TcMar-Tigger','Simple_repeat,Unknown','Simple_repeat,hAT-Charlie','Simple_repeat,hAT-Tip100','Simple_repeat,scRNA','Simple_repeat,snRNA','TcMar','TcMar-Mariner','TcMar-Tc2','TcMar-Tc2,ERV1','TcMar-Tigger','TcMar-Tigger,TcMar-Tigger','TcMar-Tigger,snRNA','TcMar?','Unknown','Unknown?','acro','centr','hAT','hAT-Blackjack','hAT-Charlie','hAT-Charlie,ERVL-MaLR','hAT-Charlie,MIR','hAT-Charlie,hAT-Charlie','hAT-Charlie,snRNA','hAT-Tip100','hAT?','rRNA','rRNA,rRNA','scRNA','scRNA,L1','snRNA','srpRNA','tRNA','telo'
 +
</html>|Mouse (Mus musculus)=<html>
 +
'AcHobo','Alu','Alu,B4','Alu,B4,ERVL','Alu,ERVK','Alu,ERVL','Alu,L1','B2','B2,B4','B4','B4,Alu','B4,Low_complexity','CR1','ERV1','ERV1,ERVK','ERVK','ERVK,ERVK','ERVL','ERVL,Alu','ERVL,ERVK','ERVL,MaLR','ERVL?','Genie?','Gypsy','Gypsy?','Helitron','ID','ID,Satellite','L1','L1,ERVK','L1,L1','L1,snRNA','L1,tRNA','L2','L2,ERV1','L2,MaLR','LTR','Low_complexity','Low_complexity,Alu','Low_complexity,Low_complexity','Low_complexity,Low_complexity,Low_complexity','Low_complexity,MIR','Low_complexity,Tip100','Low_complexity,snRNA','MER1_type','MER1_type,B4','MER1_type?','MER2_type','MIR','MIR,MIR','MIR,MaLR','MaLR','MaLR,Alu','MaLR,ERV1','MaLR,ERVL','MaLR,MaLR','MuDR','NA','Other','PiggyBac','RNA','RTE','SINE','Satellite','Satellite,Satellite','Simple_repeat','Simple_repeat,Alu','Simple_repeat,Alu,B4','Simple_repeat,B2','Simple_repeat,B4','Simple_repeat,ERVK','Simple_repeat,L1','Simple_repeat,Low_complexity','Simple_repeat,Low_complexity,Low_complexity','Simple_repeat,MIR','Simple_repeat,MaLR','Simple_repeat,Simple_repeat','Simple_repeat,Simple_repeat,Low_complexity','Simple_repeat,rRNA','Tc2','TcMar','Tigger','Tip100','Unknown','hAT','hAT?','rRNA','rRNA,B4','rRNA,ERVK','scRNA','scRNA,B4','scRNA,Satellite','snRNA','tRNA'
 +
</html>}}<html>
 +
];
 +
var repeat_enrich_byfamily_values = [</html>{{{repeat_enrich_byfamily}}}<html>];
 +
for(i1=0;i1<repeat_enrich_byfamily_repnames.length;i1++){
 +
repeat_enrich_byfamily_data.push([repeat_enrich_byfamily_repnames[i1],repeat_enrich_byfamily_values[i1]]);
 +
}
 +
        $('#repeat_enrich_byfamily_table').DataTable({
 +
          data: repeat_enrich_byfamily_data,
 +
          dom: 'Blfrtip',
 +
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
 +
          lengthMenu: [[5, 50, -1], [5, 50, "All"]],
 +
          columns: [
 +
            { title: "Repeat family" },
 +
            { title: "Log10(Relative expression over median)" ,
 +
              render: function ( data, type, row, meta ) {
 +
                var num = row[1];
 +
                var numb = new Number(num);
 +
return  numb.toFixed(2);
 +
              }
 +
            }
 +
          ],
 +
          order: [[ 1, 'desc' ]]
 +
        });
 +
});
 +
</script>
 +
<span id="repeat_enrich_byfamily_table_export_tool"></span>
 +
<table id="repeat_enrich_byfamily_table" class="stripe cell-border order-column compact"></table><br>
  
 +
</html>
 
|no result for this sample
 
|no result for this sample
 
}}
 
}}
Line 100: 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 stripe cell-border order-column compact|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 108: 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 stripe cell-border order-column compact|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 119: Line 213:
 
|<br>
 
|<br>
 
}}<br>
 
}}<br>
 +
<html>
 +
<script type="text/javascript">
 +
$(document).ready(function() {
 +
    if($('.jaspar_motif_pval')[0]){
 +
        $('.jaspar_motif_pval').DataTable({
 +
          dom: 'Blfrtip',
 +
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
 +
          lengthMenu: [[5, 50, -1], [5, 50, "All"]],
 +
          columnDefs: [
 +
            { targets: 0, orderable: false},
 +
            { targets: 1, orderable: false, width: "50pt", className: "bgwhite"}
 +
          ],
 +
          columns: [
 +
            { title: "Jaspar motif" },
 +
            { title: "Logo",
 +
              render: function ( data, type, row, meta ) {
 +
return "<img src=\"/5/sstar/seqlogo/jaspar/" +  $(row[0]).text() + ".png\" width =\"80\" height = \"20\">";
 +
              }
 +
            },
 +
            { title: "p-value",
 +
              render: function ( data, type, row, meta ) {
 +
                var num=row[2];
 +
return exp_converter(num,2,"e") ;
 +
              }
 +
            }
 +
          ],
 +
          order: [[ 2, 'asc' ]]
 +
        });
 +
 +
    }
 +
});
 +
</script>
 +
</html>
 +
 +
<html>
 +
<script type="text/javascript">
 +
$(document).ready(function() {
 +
    if($('.novel_motif_pval')[0]){
 +
 +
$('.novel_motif_pval').DataTable({
 +
              dom: 'Blfrtip',
 +
              buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
 +
              lengthMenu: [[5, 50, -1], [5, 50, "All"]],
 +
              columnDefs: [
 +
                { targets: 0, orderable: false},
 +
                { targets: 1, orderable: false, width: "50pt", className: "bgwhite"}
 +
              ],
 +
              columns: [
 +
                { title: "Novel motif" },
 +
                { title: "Logo",
 +
              render: function ( data, type, row, meta ) {
 +
return "<img src=\"/5/sstar/seqlogo/novel/" +  $(row[0]).text() + ".png\" width =\"80\" height = \"20\">";
 +
              }
 +
            },
 +
            { title: "p-value",
 +
              render: function ( data, type, row, meta ) {
 +
                var num=row[2];
 +
return exp_converter(num,2,"e") ;
 +
              }
 +
            }
 +
          ],
 +
          order: [[ 2, 'asc' ]]
 +
});
  
 +
    }
 +
});
 +
</script>
 +
</html>
  
 
<html>
 
<html>
Line 275: Line 436:
  
 
$('#homer_denovo_table_export_tool').before(homer_denovo_table_tool.dom.container );
 
$('#homer_denovo_table_export_tool').before(homer_denovo_table_tool.dom.container );
    }
 
});
 
</script>
 
</html>
 
<html>
 
<script type="text/javascript">
 
$(document).ready(function() {
 
    if($('.jaspar_motif_pval')[0]){
 
        $('.jaspar_motif_pval').DataTable({
 
          dom: 'Blfrtip',
 
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
 
          lengthMenu: [[5, 50, -1], [5, 50, "All"]],
 
          columnDefs: [
 
            { targets: 0, orderable: false},
 
            { targets: 1, orderable: false, width: "50pt", className: "bgwhite"}
 
          ],
 
          columns: [
 
            { title: "Jaspar motif" },
 
            { title: "Logo",
 
              render: function ( data, type, row, meta ) {
 
return "<img src=\"/5/sstar/seqlogo/jaspar/" +  $(row[0]).text() + ".png\" width =\"80\" height = \"20\">";
 
              }
 
            },
 
            { title: "p-value",
 
              render: function ( data, type, row, meta ) {
 
                var num=row[2];
 
return exp_converter(num,2,"e") ;
 
              }
 
            }
 
          ],
 
          order: [[ 2, 'asc' ]]
 
        });
 
 
    }
 
});
 
</script>
 
</html>
 
<html><!-- tf enrich table: start-->
 
<script type="text/javascript">
 
var species="</html>{{#var:species_temp}}<html>";
 
var mm_data = new Array();
 
var enrichment_scores_data = "</html>{{{expression_enrichment_score}}}<html>";
 
var sub_content = enrichment_scores_data.split(";;");
 
 
$(document).ready(function() {
 
 
for(i=0;i<sub_content.length;i++){
 
var temp =sub_content[i];
 
if(temp != null){
 
if(temp.length>2){
 
var sub_sub_content=sub_content[i].split("!");
 
var built="FFCP_PHASE1:"+species+"::"+sub_sub_content[0];
 
mm_data.push(sub_sub_content);
 
}
 
}
 
}
 
/*"sDom": '<"top"i>rt<"bottom"flp><"clear">' */
 
 
    $('#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>
 
<span id="tf_enrich_table_export_tool"></span>
 
<table cellpadding="0" cellspacing="0" border="0" id="ffcp_tf_enrichscore" class="stripe cell-border order-column compact"></table>
 
</html>
 
<html><script type="text/javascript">
 
$(document).ready(function() {
 
 
    if($('.relative-exp-of-coexp')[0]){
 
        $('.relative-exp-of-coexp').DataTable({
 
          dom: 'Blfrtip',
 
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
 
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          order: [[ 1, 'desc' ]]
 
        });
 
}
 
});
 
</script></html>
 
<html><script type="text/javascript">
 
$(document).ready(function() {
 
var repeat_enrich_byfamily_data = [];
 
var repeat_enrich_byfamily_repnames = [
 
</html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)=<html>
 
'Alu','Alu,Alu','Alu,ERVL-MaLR','Alu,L1','Alu,L2','Alu,Low_complexity','Alu,MIR','Alu,hAT-Charlie','Alu,hAT-Tip100','Alu,rRNA','Alu,snRNA','CR1','CR1,CR1','DNA','DNA?','Deu','ERV','ERV1','ERV1,ERV1','ERV1,ERVL','ERV1,ERVL-MaLR','ERV1,MIR','ERV1,snRNA','ERVK','ERVK,rRNA','ERVL','ERVL,ERV1','ERVL,ERVL','ERVL,ERVL-MaLR','ERVL,hAT-Charlie','ERVL,snRNA','ERVL-MaLR','ERVL-MaLR,ERVL-MaLR','ERVL-MaLR,snRNA','ERVL?','Gypsy','Gypsy?','Helitron','L1','L1,ERV1','L1,ERVL','L1,ERVL-MaLR','L1,L1','L1,TcMar-Mariner','L1,TcMar-Tigger','L1,hAT-Charlie','L1,rRNA','L1,snRNA','L1?','L2','L2,ERV1','L2,ERVL-MaLR','L2,L2','L2,MIR','L2,hAT-Blackjack','L2,hAT-Charlie','LTR','Low_complexity','Low_complexity,Alu','Low_complexity,ERV1','Low_complexity,L2','Low_complexity,Low_complexity','Low_complexity,Low_complexity,Low_complexity','Low_complexity,snRNA','MIR','MIR,ERVL-MaLR','MIR,Low_complexity','MIR,MIR','Merlin','MuDR','NA','Other','PiggyBac','PiggyBac?','RNA','RNA,MIR','RTE','RTE,CR1','RTE-BovB','SINE','SINE?','Satellite','Satellite,ERVL','Simple_repeat','Simple_repeat,Alu','Simple_repeat,ERV1','Simple_repeat,ERVL','Simple_repeat,ERVL-MaLR','Simple_repeat,L1','Simple_repeat,L2','Simple_repeat,Low_complexity','Simple_repeat,Low_complexity,Low_complexity','Simple_repeat,MIR','Simple_repeat,Other','Simple_repeat,Simple_repeat','Simple_repeat,Simple_repeat,Low_complexity','Simple_repeat,Simple_repeat,Simple_repeat','Simple_repeat,TcMar-Tigger','Simple_repeat,Unknown','Simple_repeat,hAT-Charlie','Simple_repeat,hAT-Tip100','Simple_repeat,scRNA','Simple_repeat,snRNA','TcMar','TcMar-Mariner','TcMar-Tc2','TcMar-Tc2,ERV1','TcMar-Tigger','TcMar-Tigger,TcMar-Tigger','TcMar-Tigger,snRNA','TcMar?','Unknown','Unknown?','acro','centr','hAT','hAT-Blackjack','hAT-Charlie','hAT-Charlie,ERVL-MaLR','hAT-Charlie,MIR','hAT-Charlie,hAT-Charlie','hAT-Charlie,snRNA','hAT-Tip100','hAT?','rRNA','rRNA,rRNA','scRNA','scRNA,L1','snRNA','srpRNA','tRNA','telo'
 
</html>|Mouse (Mus musculus)=<html>
 
'AcHobo','Alu','Alu,B4','Alu,B4,ERVL','Alu,ERVK','Alu,ERVL','Alu,L1','B2','B2,B4','B4','B4,Alu','B4,Low_complexity','CR1','ERV1','ERV1,ERVK','ERVK','ERVK,ERVK','ERVL','ERVL,Alu','ERVL,ERVK','ERVL,MaLR','ERVL?','Genie?','Gypsy','Gypsy?','Helitron','ID','ID,Satellite','L1','L1,ERVK','L1,L1','L1,snRNA','L1,tRNA','L2','L2,ERV1','L2,MaLR','LTR','Low_complexity','Low_complexity,Alu','Low_complexity,Low_complexity','Low_complexity,Low_complexity,Low_complexity','Low_complexity,MIR','Low_complexity,Tip100','Low_complexity,snRNA','MER1_type','MER1_type,B4','MER1_type?','MER2_type','MIR','MIR,MIR','MIR,MaLR','MaLR','MaLR,Alu','MaLR,ERV1','MaLR,ERVL','MaLR,MaLR','MuDR','NA','Other','PiggyBac','RNA','RTE','SINE','Satellite','Satellite,Satellite','Simple_repeat','Simple_repeat,Alu','Simple_repeat,Alu,B4','Simple_repeat,B2','Simple_repeat,B4','Simple_repeat,ERVK','Simple_repeat,L1','Simple_repeat,Low_complexity','Simple_repeat,Low_complexity,Low_complexity','Simple_repeat,MIR','Simple_repeat,MaLR','Simple_repeat,Simple_repeat','Simple_repeat,Simple_repeat,Low_complexity','Simple_repeat,rRNA','Tc2','TcMar','Tigger','Tip100','Unknown','hAT','hAT?','rRNA','rRNA,B4','rRNA,ERVK','scRNA','scRNA,B4','scRNA,Satellite','snRNA','tRNA'
 
</html>}}<html>
 
];
 
var repeat_enrich_byfamily_values = [</html>{{{repeat_enrich_byfamily}}}<html>];
 
for(i1=0;i1<repeat_enrich_byfamily_repnames.length;i1++){
 
repeat_enrich_byfamily_data.push([repeat_enrich_byfamily_repnames[i1],repeat_enrich_byfamily_values[i1]]);
 
}
 
        $('#repeat_enrich_byfamily_table').DataTable({
 
          data: repeat_enrich_byfamily_data,
 
          dom: 'Blfrtip',
 
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
 
          lengthMenu: [[5, 50, -1], [5, 50, "All"]],
 
          columns: [
 
            { title: "Repeat family" },
 
            { title: "Log10(Relative expression over median)" ,
 
              render: function ( data, type, row, meta ) {
 
                var num = row[1];
 
                var numb = new Number(num);
 
return  numb.toFixed(2);
 
              }
 
            }
 
          ],
 
          order: [[ 1, 'desc' ]]
 
        });
 
});
 
</script>
 
<span id="repeat_enrich_byfamily_table_export_tool"></span>
 
<table id="repeat_enrich_byfamily_table" class="stripe cell-border order-column compact"></table><br>
 
 
</html>
 
<html>
 
<script type="text/javascript">
 
$(document).ready(function() {
 
    if($('.novel_motif_pval')[0]){
 
 
$('.novel_motif_pval').DataTable({
 
              dom: 'Blfrtip',
 
              buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
 
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                { targets: 0, orderable: false},
 
                { targets: 1, orderable: false, width: "50pt", className: "bgwhite"}
 
              ],
 
              columns: [
 
                { title: "Novel motif" },
 
                { title: "Logo",
 
              render: function ( data, type, row, meta ) {
 
return "<img src=\"/5/sstar/seqlogo/novel/" +  $(row[0]).text() + ".png\" width =\"80\" height = \"20\">";
 
              }
 
            },
 
            { title: "p-value",
 
              render: function ( data, type, row, meta ) {
 
                var num=row[2];
 
return exp_converter(num,2,"e") ;
 
              }
 
            }
 
          ],
 
          order: [[ 2, 'asc' ]]
 
});
 
 
 
     }
 
     }
 
});
 
});
 
</script>
 
</script>
 
</html>
 
</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