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{{Loading|loadingimage=sprites.gif}}<html>
{{Loading|loadingimage=sprites.gif}}<html>
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.16/css/jquery.dataTables.min.css">
<style type="text/css" title="currentStyle">
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/buttons/1.5.0/css/buttons.dataTables.min.css">
@import "/5/sstar/rb_js/html5button/datatables.css";
<script type="text/javascript" language="javascript" src="//code.jquery.com/jquery-1.12.4.js">
</style>
</script>
<script type="text/javascript" src="/5/sstar/rb_js/jquery-1.7.1.min.js"></script>
<script type="text/javascript" language="javascript" src="https://cdn.datatables.net/1.10.16/js/jquery.dataTables.min.js">
<script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.js"></script>
</script>
<script type="text/javascript" src="/5/sstar/rb_js/custom/expoconvert.js"></script>
<script type="text/javascript" language="javascript" src="https://cdn.datatables.net/buttons/1.5.0/js/dataTables.buttons.min.js">
 
</script>
</html>{{#outerfile_existance: /5/sstar/sstar_img/f5samples/riken_cellimg/{{PAGENAME}}.jpg |<html>
<script type="text/javascript" language="javascript" src="//cdnjs.cloudflare.com/ajax/libs/jszip/3.1.3/jszip.min.js">
<div style="width:250px;height:250px;float:right;"><img width=250 src="/5/sstar/sstar_img/f5samples/riken_cellimg/</html>{{PAGENAME}}<html>.jpg">
</script>
<div align="right">&copy; RIKEN, 2013&nbsp;<a href="http://creativecommons.org/licenses/by-sa/2.1/jp"><img src="/5/sstar/sstar_img/f5samples/riken_cellimg/by-sa_s.png" alt="by-sa"></a></div>
<script type="text/javascript" language="javascript" src="//cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.32/pdfmake.min.js">
</div></html>}}
</script>
{{#set:id={{{id}}}}}
<script type="text/javascript" language="javascript" src="//cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.32/vfs_fonts.js">
<table>
</script>
<tr><th scope="row" align="right">Name:</th><td>[[name::{{{name}}}]]</td></tr>
<script type="text/javascript" language="javascript" src="//cdn.datatables.net/buttons/1.5.0/js/buttons.html5.min.js">
<tr><th scope="row" align="right">[[Property:Sample_species|Species]]:</th><td>[[sample_species::{{{sample_species}}}]]</td></tr>
        </script>
<tr><th scope="row" align="right">[[Property:Library_accession_number|Library ID]]:</th><td>{{#replace:{{{library_id}}}|!|, }}</td></tr>
</html>
{{#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>
{{#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_srna}}}|ttp}}
|{{#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> | }}{{#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"
! Additional information
|-
|<div style="width:50%; float:left;">Sample information<table cellspacing="0" border="1">
<tr><th>strain</th><td>{{#switch:{{{sample_strain}}}|,,,=NA| =NA |{{{sample_strain}}}}}</td></tr>
<tr><th>tissue</th><td>{{#switch:{{{sample_tissue}}}|,,,=NA| =NA |{{{sample_tissue}}}}}</td></tr>
<tr><th>dev stage</th><td>{{#switch:{{{sample_dev_stage}}}|,,,=NA| =NA |{{{sample_dev_stage}}}}}</td></tr>
<tr><th>sex</th><td>{{#switch:{{{sample_sex}}}|,,,=NA| =NA |{{{sample_sex}}}}}</td></tr>
<tr><th>age</th><td>{{#switch:{{{sample_age}}}|,,,=NA| =NA |{{{sample_age}}}}}</td></tr>
<tr><th>cell type</th><td>{{#switch:{{{sample_cell_type}}}|,,,=NA| =NA |{{{sample_cell_type}}}}}</td></tr>
<tr><th>cell line</th><td>{{#switch:{{{sample_cell_line}}}|,,,=NA| =NA |{{{sample_cell_line}}}}}</td></tr>
<tr><th>company</th><td>{{#switch:{{{sample_company}}}|,,,=NA| =NA |{{{sample_company}}}}}</td></tr>
<tr><th>collaboration</th><td>{{#switch:{{{sample_collaboration}}}|,,,=NA| =NA |{{{sample_collaboration}}}}}</td></tr>
{{#if:{{{sample_info_link}}}|<tr><th style="background-color: #4169e1;">External link for information</th><td style="background-color: #f0f8ff;">[{{#explode:{{{sample_info_link}}}|;|-1}} {{#explode:{{{sample_info_link}}}|;|0}}]</td></tr>}}</table></div>
<div style="width:50%; float:left;">
RNA information<table cellspacing="0" border="1">
<tr><th>lot number</th><td>{{#switch:{{{rna_lot_number}}}|,,,=NA| =NA |{{{rna_lot_number}}}}}</td></tr>
<tr><th>catalog number</th><td>{{#switch:{{{rna_catalog_number}}}|,,,=NA| =NA |{{{rna_catalog_number}}}}}</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>
|}{{#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|{{#replace:{{{hg38bam}}}|hg38_v2|hg38_latest}}|{{#replace:{{{hg38ctss}}}|hg38_v2|hg38_latest}}}}
|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}}|
{{#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. }}}}
<html><!-- tf enrich table: start-->
<html><!-- tf enrich table: start-->
<script type="text/javascript">
<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() {
$(document).ready(function() {
     $('#example').DataTable( {
 
         dom: 'Bfrtip',
for(i=0;i<sub_content.length;i++){
         buttons: [
var temp=sub_content[i];
            'copyHtml5',
if(temp!= null){
            'excelHtml5',
if(temp.length>2){
            'csvHtml5',
var sub_sub_content=sub_content[i].split("!");
            'pdfHtml5'
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}}}}
{{#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() {
 
    if($('.relative-exp-of-coexp')[0]){
        $('.relative-exp-of-coexp').DataTable({
          dom: 'Blfrtip',
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
          lengthMenu: [[10, 50, -1], [10, 50, "All"]],
          columnDefs: [{ targets: [0], visible: true},{ targets: [0], visible: true}],
          columns:[
                {title:"MCL coexpression id", visible:true},
                {title:"Coexpression_dpi_cluster_scores_median_value", visible:true}
          ],
          order: [[ 1, 'desc' ]]
        });
}
});
</script></html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?Coexpression_dpi_cluster_scores_median_value|intro=<table class="relative-exp-of-coexp stripe cell-border order-column compact"><html><thead></html><tr><th>Coexpression cluster</th><th>score</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table>|link=none|format=template|template=Coexpression_dpi_cluster_scores_median_in_ffsample|limit=5000|searchlabel=|default=No results for this sample}}
|<br><br>}}
|Mouse (Mus musculus)=
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|<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>
{{Fontsize|3|Repeat families with enriched expression in this sample}}{{nowrap|{{#info:<b>Summary:</b>Ranked list of repeat family expression in this sample relative to
the median expression in the FANTOM5 collection is shown. Value is log10
transformed.<br><b>Analyst:</b>NA
<br><br>link to dataset.<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression data]}}}}
{{#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
}}
 
<br>
{{Fontsize|3|TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample}}
----
{{Fontsize|3|JASPAR motifs}}{{#info:<b>Summary:</b>Association of JASPAR motif to the promoter expression in this
sample. Pearson's correlation between the number of TFBSs estimated by
using the position-weight matrix for each promoter and its expression is
expressed as Z-score by taking the ones based on random position-weight
matrix, and the tail probability of the normal distribution corresponding
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>
<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}}|&|$
|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><br>
{{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>
<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}}|&|$
|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><br>
{{Fontsize|3|de novo motifs identified by HOMER in promoters active in this sample}}{{#info:<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br>}}
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|library id: ${{#outerfile_existance:/5/sstar/Homer_de_novo_Motif_Results/$/homerResults.html
|<div id="homer_denovo_table_export_tool"></div><br>{{#homer_list:Homer_de_novo_Motif_Results/$/homerResults.html|homerResults!<TABLE cellpadding="2" cellspacing="0">!</div></TD></TR>!</TABLE>!Homer de novo Motif Results|/5/sstar/Homer_de_novo_Motif_Results/$/homerResults!<table class=homer-table><thead>!</div></TD></TR></thead><tbody>!</tbody></TABLE>|!}}
}}
|<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>
</script>
    <table id="example" class="display" cellspacing="0" width="100%">
</html>
        <thead>
            <tr>
                <th>PeakID</th>
                <th>TSS ID</th>
                <th>Category</th>
            </tr>
        </thead>
        <tfoot>
            <tr>
                <th>PeakID</th>
                <th>TSS ID</th>
                <th>Category</th>
            </tr>
        </tfoot>
        <tbody>
            <tr>
                <td>hg_233277.1</td>
                <td>12323512</td>
                <td>Edinburgh</td>
            </tr>
            <tr>
                <td>hg_234730.1</td>
                <td>21235255</td>
                <td>Tokyo</td>
            </tr>
            <tr>
                <td>hg_234953.1</td>
                <td>2536748</td>
                <td>San Francisco</td>
            </tr>
            <tr>
                <td>hg_233750.1</td>
                <td>833481</td>
                <td>Edinburgh</td>
            </tr>
        </tbody>
    </table>


<html>
<style type="text/css">
.white { background-color: white}
table.homer-table td { padding: 1px }
</style>
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/media/js/dataTables.Percentage.js"></script>
</html>
<br>|}}<!-- end of if(isHumanOrMouse) -->
{{Fontsize|3|FANTOM5 (FF) ontology }}
----
{{Fontsize|3|Direct parent terms}}
{{#if: {{{is_a}}} |
<div style="width:25%; float:left;">
'''is_a relathionship'''<br>{{#arraymap:{{{is_a}}}|;;|$|
{{#set:is_a=$}}{{#ifexist:$|[[$|$  {{#show:$|?name}}]]|$}}|<br>}}
</div>
|}}
{{#if: {{{part_of}}} |
<div style="width:25%; float:left;">
'''part_of relathionship'''<br>{{#arraymap:{{{part_of}}}|;;|$|
{{#set:part_of=$}}{{#ifexist:$|[[$|$  {{#show:$|?name}}]]|$}}|<br>}}
</div>
|}}
{{#if: {{{has_quality}}} |
<div style="width:25%; float:left;">
'''has_quality relathionship'''<br>{{#arraymap:{{{has_quality}}}|;;|$|
{{#set:has_quality=$}}{{#ifexist:$|[[$|$  {{#show:$|?name}}]]|$}}|<br>}}
</div>
|}}
<div style="clear:both;"></div>


{{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>
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data]
}}<br>
{{#if: {{{ancestors_in_cell_lineage_facet}}} |
<div style="width:25%; float:left;">
<b>CL: Cell type</b><br>
{{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ancestors_in_cell_lineage_facet}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ancestors_in_cell_lineage_facet}}}|,|$|{{#set:ancestors_in_cell_lineage_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}} }}
</div>
}}{{#if: {{{ancestors_in_disease_facet}}} |
<div style="width:25%; float:left;">
<b>DOID: Disease</b><br>
{{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ancestors_in_disease_facet}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ancestors_in_disease_facet}}}|,|$|{{#set:ancestors_in_disease_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}} }}
</div>
}}{{#if: {{{ancestors_in_anatomy_facet}}} |
<div style="width:25%; float:left;">
<b>UBERON: Anatomy</b><br>
{{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ancestors_in_anatomy_facet}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ancestors_in_anatomy_facet}}}|,|$|{{#set:ancestors_in_anatomy_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}} }}
</div>
}}{{#if: {{{ancestors_in_ff_facet}}} |
<div style="width:25%; float:left;">
<b>FF: FANTOM5</b><br>
{{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ancestors_in_ff_facet}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ancestors_in_ff_facet}}}|,|$|{{#set:ancestors_in_ff_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}} }}
</div>
}}
<div style="clear:both;"></div>
{{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>
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data]
}}
<br>
{{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ffid_belonging_in_development}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ffid_belonging_in_development}}}|,|$|{{#ifexist:$|{{#set:ffid_belonging_in_development=$}}[[$]] ({{#show:$|?name}})}}|<br>}} }}
<br><br>
{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}|
{{#set:sample_category={{{sample_category}}}}}
{{#arraymap:{{{library_id}}}|!|$
|{{#set:Library accession number=$}}
}}
{{#arraydefine:accession_numbers_array|{{{accession_numbers}}}|!}}{{#loop: k
  | 0         
  | {{#arraysize:accession_numbers_array}}
  | <nowiki/>
{{#vardefine:exp_met|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|0}}}}
{{#if:{{#var:exp_met}}|{{#set:Experiment method={{#var:exp_met}}}}|}}
{{#vardefine:lib_exp|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|1}}}}
{{#if:{{#var:lib_exp}}|{{#set:Experiment accession number={{#var:lib_exp}}}}|}}
{{#vardefine:lib_run|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|2}}}}
{{#if:{{#var:lib_run}}|{{#set:Run accession number={{#var:lib_run}}}}|}}
{{#vardefine:lib_bam|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|3}}}}
{{#if:{{#var:lib_bam}}|{{#set:Bam accession number={{#var:lib_bam}}|BAM}}|}}
{{#vardefine:lib_ctss|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|4}}}}
{{#if:{{#var:lib_ctss}}|{{#set:CTSS accession number={{#var:lib_ctss}}}}|}}
}}
|}}
{{#set:sample_category={{{sample_category}}}}}
{{#set:profile_hcage={{{profile_hcage}}}}}
{{#set:profile_rnaseq={{{profile_rnaseq}}}}}
{{#set:profile_srnaseq={{{profile_srnaseq}}}}}
{{#set:profile_cagescan={{{profile_cagescan}}}}}
{{#set:sample_strain={{{sample_strain}}}}}
{{#set:sample_tissue={{{sample_tissue}}}}}
{{#set:sample_dev_stage={{{sample_dev_stage}}}}}
{{#set:sample_sex={{{sample_sex}}}}}
{{#set:sample_age={{{sample_age}}}}}
{{#set:sample_ethnicity={{{sample_ethnicity}}}}}
{{#set:sample_cell_type={{{sample_cell_type}}}}}
{{#set:sample_cell_line={{{sample_cell_line}}}}}
{{#set:sample_collaboration={{{sample_collaboration}}}}}
{{#set:sample_experimental_condition={{{sample_experimental_condition}}}}}
{{#set:sample_disease={{{sample_disease}}}}}
{{#set:sample_cell_lot={{{sample_cell_lot}}}}}
{{#set:sample_cell_catalog={{{sample_cell_catalog}}}}}
{{#set:sample_company={{{sample_company}}}}}
{{#set:sample_donor(cell lot)={{{sample_donor(cell lot)}}}}}
{{#set:sample_note={{{sample_note}}}}}
{{#set:sample_id={{{sample_id}}}}}
{{#set:rna_tube_id={{{rna_tube_id}}}}}
{{#set:rna_box={{{rna_box}}}}}
{{#set:rna_position={{{rna_position}}}}}
{{#set:rna_lot_number={{{rna_lot_number}}}}}
{{#set:rna_catalog_number={{{rna_catalog_number}}}}}
{{#set:rna_rin={{{rna_rin}}}}}
{{#set:rna_od260/230={{{rna_od260/230}}}}}
{{#set:rna_od260/280={{{rna_od260/280}}}}}
{{#set:rna_sample_type={{{rna_sample_type}}}}}
{{#set:rna_extraction_protocol={{{rna_extraction_protocol}}}}}
{{#set:rna_weight_ug={{{rna_weight_ug}}}}}
{{#set:rna_concentration={{{rna_concentration}}}}}
{{#if:{{{timecourse}}}|{{#arraymap:{{{timecourse|}}}|,|$| {{#set:timecourse=$}}}}|}}
{{#set:donor={{{donor}}}}}
{{#set:time={{{time}}}}}
{{#switch:{{{datafreeze_phase}}}|1={{#set:datafreeze_phase=1}}|2={{#set:datafreeze_phase=2}}|{{#set:datafreeze_phase=-1}}}}
{{#arraymap:{{#explode:{{{profile_hcage|}}}|,|0}}|&|$
|{{#set:sample_seq_library_id=$}}
}}
{{#set:sample_timecourse={{{sample_timecourse|}}}}}
[[Category:FF_Ontology]]
[[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>
</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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