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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 "/resource_browser/rb_js/datatables/media/css/jquery.dataTables.css";
@import "/5/sstar/rb_js/html5button/datatables.css";
@import "/resource_browser/rb_js/datatables/extras/TableTools/media/css/TableTools.css";
</style>
<script type="text/javascript" src="/5/sstar/rb_js/jquery-1.7.1.min.js"></script>
<script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.js"></script>
<script type="text/javascript" src="/5/sstar/rb_js/custom/expoconvert.js"></script>


</html>{{#outerfile_existance: /5/sstar/sstar_img/f5samples/riken_cellimg/{{PAGENAME}}.jpg |<html>
#css-table {  
<div style="width:250px;height:250px;float:right;"><img width=250 src="/5/sstar/sstar_img/f5samples/riken_cellimg/</html>{{PAGENAME}}<html>.jpg">
display: table;
<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>
}
</div></html>}}
#css-table .col {
display: table-cell;
width: 25%;  
padding: 5px;  
}
#css-table .col:nth-child(even) {
background: #eee;
}
#css-table .col:nth-child(odd) {
background: #eee;
}
</style>
<script type="text/javascript" src="/resource_browser/rb_js/custom/convert.js"></script>
<script type="text/javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.min.js"></script>
<script type="text/javascript" src="/resource_browser/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
</html>
{{#set:id={{{id}}}}}
{{#set:id={{{id}}}}}
<table>
<table>
<tr><th scope="row" align="right">Name:</th><td>[[name::{{{name}}}]]</td></tr>
<tr><th scope="row" align="right">Name:</th><td>[[name::{{{name}}}]]</td></tr>
<tr><th scope="row" align="right">[[Property:Sample_species|Species]]:</th><td>[[sample_species::{{{sample_species}}}]]</td></tr>
<tr><th scope="row" align="right">[[Property:Sample_species|Species]]:</th><td>[[sample_species::{{{sample_species}}}]]</td></tr>
<tr><th scope="row" align="right">[[Property:Library_accession_number|Library ID]]:</th><td>{{#replace:{{{library_id}}}|!|, }}</td></tr>
{{#ifexpr: {{#pos:{{{cagescan_library_id}}}|Cig}}|<tr><th scope="row" align="right">CAGEScan Library ID:</th><td>{{#replace:{{{cagescan_library_id}}}|!|, }}</td></tr>|}}
<tr><th scope="row" align="right">[[Property:Sample_category|Sample type]]:</th><td>{{{sample_category}}}</td></tr>
<tr><th scope="row" align="right">[[Property:Sample_category|Sample type]]:</th><td>{{{sample_category}}}</td></tr>
<tr><th scope="row" align="right">Genomic View:</th><td>[http://fantom.gsc.riken.jp/zenbu/dex/#section=Experiments;search={{#replace:{{{id}}}|FF:|}} zenbu] , [http://genome.ucsc.edu/cgi-bin/hgTracks?db={{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | hg19 | }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | mm9 | }}{{#ifeq: {{{sample_species}}} | Rat (Rattus rattus) | rn4 | }}{{#ifeq: {{{sample_species}}} | Dog (Canis lupus familaris) | canFam2 | }}{{#ifeq: {{{sample_species}}} | Chicken (Gallus gallus) | galGal3 | }}&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC] </td></tr><!--tr><th scope="row" align="right">[[Property:Library_id|Library]]:</th><td></td></tr--></table>
{{#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>|}}
{{LibraryIds|{{{library_id_phase_based}}}}}
<!--
{{#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><span class="plainlinks">[{{{zenbu_report}}} link]</span> </td></tr>|}} </table>
{|class="wikitable mw-collapsible mw-collapsed" style="width:auto"
{|class="wikitable mw-collapsible mw-collapsed" style="width:auto"
! Additional information
! Additional information
|-
|-
|<div id="css-table"><div class="col">Sample information<table cellspacing="0" border="1">
|<div style="width:50%; float:left;">Sample information<table cellspacing="0" border="1">
<tr><th>[[Property:sample_strain|strain]]: </th><td>{{#switch:{{{sample_strain}}}|,,,=NA| =NA |{{{sample_strain}}}}}</td></tr>
<tr><th>strain</th><td>{{#switch:{{{sample_strain}}}|,,,=NA| =NA |{{{sample_strain}}}}}</td></tr>
<tr><th>[[Property:sample_tissue|tissue]]:</th><td>{{#switch:{{{sample_tissue}}}|,,,=NA| =NA |{{{sample_tissue}}}}}</td></tr>
<tr><th>tissue</th><td>{{#switch:{{{sample_tissue}}}|,,,=NA| =NA |{{{sample_tissue}}}}}</td></tr>
<tr><th>[[Property:sample_dev_stage|dev_stage]]:</th><td>{{#switch:{{{sample_dev_stage}}}|,,,=NA| =NA |{{{sample_dev_stage}}}}}</td></tr>
<tr><th>dev stage</th><td>{{#switch:{{{sample_dev_stage}}}|,,,=NA| =NA |{{{sample_dev_stage}}}}}</td></tr>
<tr><th>[[Property:sample_sex|sex]]:</th><td>{{#switch:{{{sample_sex}}}|,,,=NA| =NA |{{{sample_sex}}}}}</td></tr>
<tr><th>sex</th><td>{{#switch:{{{sample_sex}}}|,,,=NA| =NA |{{{sample_sex}}}}}</td></tr>
<tr><th>[[Property:sample_age|age]]:</th><td>{{#switch:{{{sample_age}}}|,,,=NA| =NA |{{{sample_age}}}}}</td></tr>
<tr><th>age</th><td>{{#switch:{{{sample_age}}}|,,,=NA| =NA |{{{sample_age}}}}}</td></tr>
<tr><th>[[Property:sample_ethnicity|ethnicity]]:</th><td>{{#switch:{{{sample_ethnicity}}}|,,,=NA| =NA |{{{sample_ethnicity}}}}}</td></tr>
<tr><th>cell type</th><td>{{#switch:{{{sample_cell_type}}}|,,,=NA| =NA |{{{sample_cell_type}}}}}</td></tr>
<tr><th>[[Property:sample_cell_type|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>[[Property:sample_cell_line|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>[[Property:sample_collaboration|collaboration]]:</th><td>{{#switch:{{{sample_collaboration}}}|,,,=NA| =NA |{{{sample_collaboration}}}}}</td></tr>
<tr><th>collaboration</th><td>{{#switch:{{{sample_collaboration}}}|,,,=NA| =NA |{{{sample_collaboration}}}}}</td></tr>
<tr><th>[[Property:sample_experimental_condition|Experimental condition]]:</th><td>{{#switch:{{{sample_experimental_condition}}}|,,,=NA| =NA |{{{sample_experimental_condition}}}}}</td></tr>
<tr><th>[[Property:sample_disease|disease]]:</th><td>{{#switch:{{{sample_disease}}}|,,,=NA| =NA |{{{sample_disease}}}}}</td></tr>
<tr><th>[[Property:sample_cell_lot|cell_lot]];</th><td>{{#switch:{{{sample_cell_lot}}}|,,,=NA| =NA |{{{sample_cell_lot}}}}}</td></tr>
<tr><th>[[Property:sample_cell_catalog|cell_catalog]]:</th><td>{{#switch:{{{sample_cell_catalog}}}|,,,=NA| =NA |{{{sample_cell_catalog}}}}}</td></tr>
<tr><th>[[Property:sample_donor(cell lot)|donor(cell lot)]]:</th><td>{{#switch:{{{sample_donor(cell lot)}}}|,,,=NA| =NA |{{{sample_donor(cell lot)}}}}}</td></tr>
<tr><th>[[Property:sample_company|company]]:</th><td>{{#switch:{{{sample_company}}}|,,,=NA| =NA |{{{sample_company}}}}}</td></tr>
<tr><th>[[Property:sample_note|Note]]:</th><td>{{#switch:{{{sample_note}}}|,,,=NA| =NA |{{{sample_note}}}}}</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>
{{#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 class="col">Transcriptome profiling<table cellspacing="0" border="1">
<div style="width:50%; float:left;">
<tr><th>[[Property:profile_hcage|hCAGE]]:</th><td>{{#switch: {{{profile_hcage}}}|,,,=NA| =NA |{{{profile_hcage}}}}}</td></tr>
RNA information<table cellspacing="0" border="1">
<tr><th>[[Property:profile_rnaseq|RNA-seq]]:</th><td>{{#switch: {{{profile_rnaseq}}}|,,,=NA| =NA |{{{profile_rnaseq}}}}}</td></tr>
<tr><th>lot number</th><td>{{#switch:{{{rna_lot_number}}}|,,,=NA| =NA |{{{rna_lot_number}}}}}</td></tr>
<tr><th>[[Property:profile_srnaseq|smallRNA seq]]:</th><td>{{#switch: {{{profile_srnaseq}}}|,,,=NA| =NA |{{{profile_srnaseq}}}}} </td></tr>
<tr><th>catalog number</th><td>{{#switch:{{{rna_catalog_number}}}|,,,=NA| =NA |{{{rna_catalog_number}}}}}</td></tr>
<tr><th>[[Property:profile_cagescan|nanoCAGEscan]]:</th><td>{{#switch: {{{profile_cagescan}}}|,,,=NA| =NA |{{{profile_cagescan}}}}}</td></tr>
<tr><th>sample type</th><td>{{#switch:{{{rna_sample_type}}}|,,,=NA| =NA |{{{rna_sample_type}}}}}</td></tr>
</table>
<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>
<br>RNA information<br><table cellspacing="0" border="1">
|}{{#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}}}
<tr><th>[[Property:sample_id|sample_id]]:</th><td>{{#switch:{{{sample_id}}}|,,,=NA| =NA |{{{sample_id}}}}}</td></tr>
|Human (Homo sapiens) = {{FastaBamfileCTSS||Hg19|{{{hg19fasta}}}||{{{hg19bam}}}|{{{hg19ctss}}}|Hg38|{{#replace:{{{hg38bam}}}|hg38_v2|hg38_latest}}|{{#replace:{{{hg38ctss}}}|hg38_v2|hg38_latest}}}}
<tr><th>[[Property:rna_tube_id|tube_id]]:</th><td>{{#switch:{{{rna_tube_id}}}|,,,=NA| =NA |{{{rna_tube_id}}}}}</td></tr>
|Mouse (Mus musculus) = {{FastaBamfileCTSS||Mm9|{{{mm9fasta}}}||{{{mm9bam}}}|{{{mm9ctss}}}|Mm10|{{#replace:{{{mm10bam}}}|mm10_v2|mm10_latest}}|{{#replace:{{{mm10ctss}}}|mm10_v2|mm10_latest}}}}
<tr><th>[[Property:rna_box|box]]:</th><td>{{#switch:{{{rna_box}}}|,,,=NA| =NA |{{{rna_box}}}}}</td></tr>
|
<tr><th>[[Property:rna_position|position]]:</th><td>{{#switch:{{{rna_position}}}|,,,=NA| =NA |{{{rna_position}}}}}</td></tr>
}}{{#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}}|
<tr><th>[[Property:rna_tube_id|tube_id]]:</th><td>{{#switch:{{{rna_tube_id}}}|,,,=NA| =NA |{{{rna_tube_id}}}}}</td></tr>
{{#switch: {{{sample_species}}}
<tr><th>[[Property:rna_lot_number|lot_number]]:</th><td>{{#switch:{{{rna_lot_number}}}|,,,=NA| =NA |{{{rna_lot_number}}}}}</td></tr>
|Human (Homo sapiens) = {{FastaBamfileCTSS|HumanCAGEScan|Hg19|{{{hg19fasta_cs3prime}}}|{{{hg19fasta_cs5prime}}}|{{{hg19bam_cs}}}|{{{hg19ctss_cs}}}|Hg38|{{{hg38bam_cs}}}|{{{hg38ctss_cs}}}}}
<tr><th>[[Property:rna_catalog_number|catalog_number]]:</th><td>{{#switch:{{{rna_catalog_number}}}|,,,=NA| =NA |{{{rna_catalog_number}}}}}</td></tr>
|Mouse (Mus musculus) = {{FastaBamfileCTSS|HumanCAGEScan|Mm9|{{{mm9fasta_cs}}}||{{{mm9bam_cs}}}|{{{mm9ctss_cs}}}|Mm10|{{{mm10bam_cs}}}|{{{mm10ctss_cs}}}}}
<tr><th>[[Property:rna_rin|RIN]]:</th><td>{{#switch:{{{rna_rin}}}|,,,=NA| =NA |{{{rna_rin}}}}}</td></tr>
|
<tr><th>[[Property:rna_od260/230|OD260/230]]:</th><td>{{#switch:{{{rna_od260/230}}}|,,,=NA| =NA |{{{rna_od260/230}}}}}</td></tr>
}}
<tr><th>[[Property:rna_od260/280|OD260/280]]:</th><td>{{#switch:{{{rna_od260/280}}}|,,,=NA| =NA |{{{rna_od260/280}}}}}</td></tr>
|}}{{#ifexpr:{{#pos:{{{HumanCAGEScanFiles}}}|ttp}}|{{FastaBamfileCTSSforCAGEScan|{{{HumanCAGEScanFiles}}}}}
<tr><th>[[Property:rna_sample_type|sample_type]]:</th><td>{{#switch:{{{rna_sample_type}}}|,,,=NA| =NA |{{{rna_sample_type}}}}}</td></tr>
|}}{{#if:{{#pos:{{{DRA_sample_Accession_RNASeq}}}|@|0}}|{{DRAAccessionNumbers|RNA-Seq|{{{DRA_sample_Accession_RNASeq}}}|{{{accession_numbers_RNASeq}}}|{{{rnaseq_library_id}}}|{{{sample_species}}}}}|}}
<tr><th>[[Property:rna_weight_ug|weight_ug]]:</th><td>{{#switch:{{{rna_weight_ug}}}|,,,=NA| =NA |{{{rna_weight_ug}}}}}</td></tr>
{{#ifexpr:{{#pos:{{{RNASeqFiles}}}|ttp}}|{{FastaBamfileCTSSforCAGEScan|{{{RNASeqFiles}}}}}
<tr><th>[[Property:rna_concentration|concentration]]:</th><td>{{#switch:{{{rna_concentration}}}|,,,=NA| =NA |{{{rna_concentration}}}}}</td></tr>
|}}<br/>
<tr><th>[[Property:rna_extraction_protocol|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:{{{expression_enrichment_score}}}|chr}}| {{Fontsize|3|Relative expression to median (log10)}}  
<br style="clear: left;" /></div>
|}{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}|{{DRAAccessionNumbers|{{{DRA_sample_Accession}}}|{{{accession_numbers}}}|{{{library_id}}}}}|}}{{#vardefine:species_temp|{{#switch: {{{sample_species}}} | Human (Homo sapiens) = Hg19 | Mouse (Mus musculus) = Mm9 }}}}
{{#if: {{#pos:{{{expression_enrichment_score}}}|chr}} |{{Fontsize|3|Relative expression to median (log10)}}  
----
----
{{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. }}}}{{#vardefine:category|{{{sample_category}}}}}{{#vardefine:phase|{{{data_phase}}}}}{{#ifeq:{{#var:phase}}|2||<html>
{{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. }}}}
<!-- tf enrich table: start-->
<html><!-- tf enrich table: start-->
<script type="text/javascript" charset="utf-8">
<script type="text/javascript">
var ffcp_tf_enrichscore_d=
var species="</html>{{#var:species_temp}}<html>";
[
var mm_data = new Array();
</html>
var enrichment_scores_data = "</html>{{{expression_enrichment_score}}}<html>";
{{#exp_enrichscore_dtarr:{{{expression_enrichment_score}}}|FFCP_PHASE1:{{#switch: {{{sample_species}}} | Human (Homo sapiens) = Hg19 | Mouse (Mus musculus) = Mm9 }}::}}
var sub_content = enrichment_scores_data.split(";;");
<html>
];


$(document).ready(function() {
$(document).ready(function() {
$('#ffcp_tf_enrichscore').html( '<table cellpadding="0" cellspacing="0" border="0" class="display" id="ffcp_tf_enrichscore_cont"></table>' );
var tf_enrich_tableex_obj = $('#ffcp_tf_enrichscore_cont').dataTable( {
"bScrollCollapse": true,
"bPaginate": true,
"bFilter": true,
"bInfo": true,
                "iDisplayLength": 10,
                "aLengthMenu": [[10,50,-1], [10,50,"All"]],
"aaData": ffcp_tf_enrichscore_d,
"aoColumns": [
{ "sTitle": "CAGE peaks","sWidth": "30px",
"fnRender": function(obj) {
var id = obj.aData[ obj.iDataColumn ].split("!");
return sReturn = "<a href=\"/resource_browser/"+id[0]+"\">"+id[1]+"</a>";
}
},
{ "sTitle": "Relative expression over median","sWidth": "50px"},
{ "sTitle": "TPM","sWidth": "10px"},
{ "sTitle": "TF","sWidth": "10px"}


],
for(i=0;i<sub_content.length;i++){
"aaSorting": [[ 1, "desc" ]]
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">' */


var tf_enrich_tableex_objtool = new TableTools( tf_enrich_tableex_obj, {"sSwfPath": "/resource_browser/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"} ]});
    $('#ffcp_tf_enrichscore').DataTable( {
 
        data: mm_data,
$('#tf_enrich_export_button').before( tf_enrich_tableex_objtool.dom.container );
        dom: 'Blfrtip',
 
        lengthMenu: [[10, 50, -1], [10, 50, "All"]],
} );
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
</script>
        columnDefs: [{ targets: [1], visible: false}],
<!-- tf enrich table: end-->
        columns: [
<div id="tf_enrich_export_button"></div><br>
            { title: "CAGE peaks" ,
<div id="ffcp_tf_enrichscore"></div>
              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>
}}
}}
<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]}}
{{#vardefine:isHumanOrMouse|{{#switch:{{{sample_species}}}|Human (Homo sapiens)=1|Mouse (Mus musculus)=1|0}}}}
<html><script type="text/javascript">
{{#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() {
$(document).ready(function() {
     var coexpression_dpi_cluster_scores_median_table= $('.relative_exp_of_coexp').dataTable({
 
"bScrollCollapse": true,
     if($('.relative-exp-of-coexp')[0]){
"bPaginate": true,
        $('.relative-exp-of-coexp').DataTable({
"bFilter": true,
          dom: 'Blfrtip',
"bInfo": true,
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
                "iDisplayLength": 10,
          lengthMenu: [[10, 50, -1], [10, 50, "All"]],
                "aLengthMenu": [[10,50,-1], [10,50,"All"]],
          columnDefs: [{ targets: [0], visible: true},{ targets: [0], visible: true}],
"aaSorting": [[1,'desc']],
          columns:[
"aoColumnDefs": [{ "sWidth": "150px", "sType": "numeric", "aTargets": [1] ,"fnRender": function (obj) {
                {title:"MCL coexpression id", visible:true},
              var num =obj.aData[obj.iDataColumn];
                {title:"Coexpression_dpi_cluster_scores_median_value", visible:true}
              var numb = new Number(num);
          ],
                  return numb.toFixed(2) ;
          order: [[ 1, 'desc' ]]
} }]
        });
}
});
});
var coexpression_dpi_cluster_scores_median_table_export_tools = new TableTools(coexpression_dpi_cluster_scores_median_table, {"sSwfPath": "/resource_browser/rb_js/datatables/extras/TableTools/media/swf/copy_csv_xls_pdf.swf", "aButtons": [ {"sExtends": "copy", "mColumns": "visible"}, {"sExtends": "csv", "mColumns": "visible"}, {"sExtends": "pdf", "mColumns": "visible"} ]});
</script></html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#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}}
$('#coexpression_dpi_cluster_scores_median_table_export_tool').before(coexpression_dpi_cluster_scores_median_table_export_tools.dom.container );});
</script>
</html>
{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?Coexpression_dpi_cluster_scores_median_value|intro=<span id="coexpression_dpi_cluster_scores_median_table_export_tool"></span><table class="relative_exp_of_coexp"><html><thead></html><tr><th>Coexpression cluster</th><th>score</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table>|link=none|format=template|template=Coexpression_dpi_cluster_scores_median_in_ffsample|limit=5000|searchlabel=|default=No results for this sample}}
|<br><br>}}
|<br><br>}}
|Mouse (Mus musculus)=
|Mouse (Mus musculus)=
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|<h3>$</h3><span id="coexpression_dpi_cluster_scores_median_table_export_tool"></span>{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|mainlabel=MCL coexpression id|?Coexpression_dpi_cluster_scores_median_value|format=ttable|class=relative_exp_of_coexp|searchlabel=}}
|<h3>$</h3>{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?=MCL coexpression id|?Coexpression_dpi_cluster_scores_median_value|format=ttable|class=relative-exp-of-coexp stripe cell-border order-column compact|headers=hide|searchlabel=}}
|<br><br>
|<br><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
{{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
the median expression in the FANTOM5 collection is shown. Value is log10
transformed.<br><b>Analyst:</b>NA
transformed.<br><b>Analyst:</b>NA
<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>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression data]}}}}
 
{{#if: {{#pos:{{{repeat_enrich_byfamily}}}|,}} |
{{#if: {{#pos:{{{repeat_enrich_byfamily}}}|,}} |
<html>
<html><script type="text/javascript">
<script type="text/javascript">
$(document).ready(function() {
$(document).ready(function() {
var repeat_enrich_byfamily_data = [];
var repeat_enrich_byfamily_data = [];
Line 173: Line 161:
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": "/resource_browser/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>
|no result for this sample
|no result for this sample
}}
}}
<br><br>
 
{{#if: {{#pos:{{{profile_hcage}}}|CNhs}}|{{Fontsize|3|TF to Motif to TF network }}{{#info:Mouseover nodes and edges to see attributes.  Motifs are shown in orange, TFs are shown in blue.  Promoter and z-score are attributes of the Motif to TF edges (blue arrow).  TF to Motif edges are shown in orange.<br>Motifs shown are the top (maximum 30) motifs in the sample.  TFs shown have at least one CAGE promoter with at at least 10 TPM expression (RLE normalized) in the sample.  Edges shown have a z-score of at least 1.5 (based on correlation between motif activity and promoter expression).<br>Analyst: Erik Arner<br>Application Developer: Jayson HARSHBARGER}}
<br>
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|{{#outerfile_existance:/resource_browser/nwfiles/$.{{PAGENAME}}.xgmml|{{Tf_motif_cytoscapenw|CNhs=$|FFid={{PAGENAME}}}}
}}
|<br>}}
}}
<html><div style="clear:both;"></div></html>
{{#if: {{#pos:{{{sample_gostat}}}|;}} |
<html>
<script type="text/javascript">
$(document).ready(function() {
    $('.sample_gostat').dataTable({
"sScrollY": "300px",
"bPaginate": false,
"bScrollCollapse": true,
"iDisplayLength": -1,
"aaSorting": [[2,'asc']],
"aoColumnDefs": [{"fnRender": function ( o, val ) {return "<a href=\"http://amigo.geneontology.org/cgi-bin/amigo/term_details?term="+o.aData[0]+"\">"+o.aData[0]+"</a>";}, "aTargets": [ 0 ]}, { "sWidth": "200px", "sType": "numeric", "aTargets": [2],"fnRender": function (obj) {                   
                  var num =obj.aData[obj.iDataColumn];
                  return exp_converter(num,2,"e") ;
} }]
});
});
</script>
</html> <br>
{{Fontsize|3|Gene Ontology GOstat analysis}}{{#info:Sample GO (using GOStat) based on ranked expression for human libraries in phase 1 freeze  <br>Analyst: Erik Arner}}
<table class="sample_gostat"><html><thead></html><tr><th>GO id</th><th>GO term</th><th>P-value</th></tr><html></thead><tbody></html>
{{#arraymap:{{{sample_gostat}}}|!|$
|{{#set:sample_gostat=$}}<tr><td>{{#replace:$|;|</td><td>}}</td></tr>
|}}
<html></tbody></html></table>
}}
<br><br>
{{Fontsize|3|TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample}}
{{Fontsize|3|TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample}}
----
----
Line 241: Line 197:
to the Z-score is taken as the resulting P-value. Lower P-value indicates
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>
more (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <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>
<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}}|&|$
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|library id: $<span id="related_jaspar_table_export_tool"></span>{{#ask:[[jaspar_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]|mainlabel=Jaspar motif|?=Logo|?jaspar_motifs_sample_pval_pval=P-value|format=ttable|limit=1100|searchlabel=|class=jaspar_motif_pval|searchlabel=|default=This sample isn't target for the analysis}}
|library id: $<span id="related_jaspar_table_export_tool"></span>{{#ask:[[jaspar_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]|?=Jaspar motif|?=Logo|?jaspar_motifs_sample_pval_pval=P-value|format=ttable|limit=1100|searchlabel=|class=jaspar_motif_pval stripe cell-border order-column compact|searchlabel=|default=This sample isn't target for the analysis}}
|<br>
|<br>
}}
}}
Line 250: Line 205:
{{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
{{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>
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>[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>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression data]}}<br>
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|library id: $<span id="related_novel_table_export_tool"></span>{{#ask:[[novel_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]|mainlabel=Novel motif|?=Logo|?novel_motifs_sample_pval_pval=P-value|format=ttable|limit=1100|searchlabel=|class=novel_motif_pval|searchlabel=|default=This sample isn't target for the analysis}}
|library id: $<span id="related_novel_table_export_tool"></span>{{#ask:[[novel_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]|?=Novel motif|?=Logo|?novel_motifs_sample_pval_pval=P-value|format=ttable|limit=1100|searchlabel=|class=novel_motif_pval stripe cell-border order-column compact|searchlabel=|default=This sample isn't target for the analysis}}
|<br>
|<br>
}}
}}
<br><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>}}
{{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}}|&|$
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|library id: ${{#outerfile_existance:/resource_browser/Homer_de_novo_Motif_Results/$/homerResults.html
|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/$/homerResults.html|homerResults!<TABLE cellpadding="2" cellspacing="0">!</div></TD></TR>!</TABLE>!Homer de novo Motif Results|/resource_browser/Homer_de_novo_Motif_Results/$/homerResults!<table class=homer_table><thead>!</div></TD></TR></thead><tbody>!</tbody></TABLE>|!}}
|<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>
}}<br>
}}<br>
<html>
<html>
<script type="text/javascript">
<script type="text/javascript">
$(document).ready(function() {
$(document).ready(function() {
  var related_jaspar_table= $('.jaspar_motif_pval').dataTable({
    if($('.jaspar_motif_pval')[0]){
"bScrollCollapse": true,
        $('.jaspar_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="/resource_browser/seqlogos/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) {                  
          columns: [
                  var num =obj.aData[obj.iDataColumn];
            { title: "Jaspar motif" },
                  return exp_converter(num,2,"e") ;
            { title: "Logo",
} }]
              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": "/resource_browser/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 );
    }
});
});
</script>
</script>
Line 292: Line 255:
<script type="text/javascript">
<script type="text/javascript">
$(document).ready(function() {
$(document).ready(function() {
  var related_novel_table= $('.novel_motif_pval').dataTable({
    if($('.novel_motif_pval')[0]){
"bScrollCollapse": true,            
 
"bPaginate": true,
$('.novel_motif_pval').DataTable({
"bFilter": true,
              dom: 'Blfrtip',
"bInfo": true,
              buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
                "iDisplayLength": 5,
              lengthMenu: [[5, 50, -1], [5, 50, "All"]],
                "aLengthMenu": [[5,50,-1], [5,50,"All"]],
              columnDefs: [
"aaSorting": [[2,'asc']],
                { targets: 0, orderable: false},
"aoColumnDefs": [{"bSortable": false, "aTargets": [ 0 ]}, { "fnRender": function(obj) {
                { targets: 1, orderable: false, width: "50pt", className: "bgwhite"}
return sReturn = '<img src="/resource_browser/seqlogos/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];
              columns: [
                  return exp_converter(num,2,"e") ;
                { title: "Novel motif" },
} }]
                { title: "Logo",
});
              render: function ( data, type, row, meta ) {
var related_novel_table_tool = new TableTools( related_novel_table, {"sSwfPath": "/resource_browser/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"} ]});
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' ]]
});


$('#related_novel_table_export_tool').before(related_novel_table_tool.dom.container );
    }
});
});
</script>
</script>
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<style type="text/css">
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{{Fontsize|3|FANTOM5 (FF) ontology }}
{{Fontsize|3|FANTOM5 (FF) ontology }}
----
----
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{{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
{{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>
<br><br>link to source data<br>
[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data]
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data]
}}<br>
}}<br>
{{#if: {{{ancestors_in_cell_lineage_facet}}} |
{{#if: {{{ancestors_in_cell_lineage_facet}}} |
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{{Fontsize|3|Ancestor terms (development)}}{{#info:<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br>
{{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>
<b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>
[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data]
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data]
}}<br>
}}
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R37B','LTR38','LTR38-int','LTR38B','LTR39','LTR39-int','LTR3A','LTR3B','LTR3B_','LTR4','LTR40A1','LTR40a','LTR40b','LTR40c','LTR41','LTR41,LTR41B','LTR41B','LTR42','LTR43','LTR43-int','LTR43B','LTR44','LTR45B','LTR45B,LTR72B','LTR45C','LTR46','LTR46-int','LTR47A','LTR47B','LTR48','LTR48B','LTR48B,LTR49-int','LTR49','LTR49,MSTB2','LTR49-int','LTR50','LTR51','LTR52','LTR52-int','LTR53','LTR54','LTR54B','LTR55','LTR56','LTR57','LTR57-int','LTR58','LTR5A','LTR5B','LTR5_Hs','LTR61','LTR62','LTR64','LTR65','LTR66','LTR67B','LTR67B,LTR67B','LTR67B,MER5A','LTR67B,MLT1J','LTR69','LTR6A','LTR6B','LTR7','LTR7,MER4C','LTR71A','LTR71B','LTR72','LTR72B','LTR73','LTR75','LTR75B','LTR75_1','LTR76','LTR77','LTR78','LTR78B','LTR79','LTR79,LTR79','LTR7B','LTR7C','LTR7Y','LTR8','LTR80B','LTR81AB','LTR81B','LTR81C','LTR82A','LTR82B','LTR83','LTR84a','LTR84b','LTR84b,LTR84b','LTR85a','LTR85b','LTR85c','LTR86A1','LTR86B2','LTR87','LTR88a','LTR88b','LTR88c','LTR89','LTR8A','LTR9','LTR90A','LTR90B','LTR9B','Looper','MADE1','MADE2','MARNA','MER101','MER101-int','MER101B','MER102a','MER102b','MER102c','MER103C','MER104','MER105','MER106A','MER106B','MER110','MER110-int','MER110A','MER112','MER113','MER113A','MER115','MER117','MER119','MER119,MER119','MER11A','MER11C','MER11D','MER121','MER125','MER126','MER130','MER131','MER135','MER1A','MER1B','MER2','MER20','MER20,MER5A1','MER20B','MER21-int','MER21A','MER21A,MER39','MER21B','MER21C','MER2B','MER3','MER3,MLT1J','MER30','MER30B','MER31-int','MER31-int,MER31-int','MER31A','MER31B','MER33','MER34-int','MER34A','MER34A1','MER34B','MER34B-int','MER34B-int,MER34B-int','MER34C','MER34C2','MER34C_','MER39','MER39B','MER4-int','MER41-int','MER41A','MER41B','MER41C','MER41D','MER41E','MER41G','MER44A','MER44B','MER44C','MER44D','MER45A','MER45B','MER45C','MER46C','MER47A','MER47B','MER47C','MER48','MER49','MER4A','MER4A1','MER4A1_','MER4B','MER4B-int','MER4B-int,U3','MER4C','MER4D','MER4D0','MER4D1','MER4E','MER4E1','MER50','MER50,MER50','MER50-int','MER50B','MER50C','MER51-int','MER51A','MER51B','MER51C','MER51D','MER51E','MER52-int','MER52A','MER52A,MER52A','MER52C','MER52D','MER53','MER54A','MER54B','MER57-int','MER57A-int','MER57A1','MER57A1,MER57D','MER57B1','MER57B2','MER57C1','MER57C2','MER57D','MER57E1','MER57E2','MER57E3','MER57F','MER58A','MER58B','MER58C','MER58D','MER5A','MER5A1','MER5B','MER5B,MIRb','MER5C','MER5C1','MER6','MER61-int','MER61A','MER61B','MER61C','MER61D','MER61E','MER61E,MLT2B1','MER61F','MER63A','MER63B','MER63C','MER63D','MER65-int','MER65A','MER65B','MER65C','MER65D','MER66-int','MER66A','MER66B','MER66C','MER66D','MER67A','MER67B','MER67C','MER67D','MER68','MER68-int','MER68B','MER6A','MER6B','MER70-int','MER70A','MER70B','MER70C','MER72','MER73','MER74A','MER74A,MER74A','MER74B','MER74C','MER75A','MER76','MER77','MER77B','MER8','MER81','MER82','MER83','MER83A-int','MER83B','MER83C','MER84','MER84-int','MER85','MER87B','MER89','MER89,MER89','MER90','MER90a','MER91A','MER91B','MER91C','MER92A','MER92B','MER92C','MER94','MER94B','MER95','MER96','MER96B','MER97a','MER99','MER9a2','MIR','MIR,MIRc','MIR,T-rich','MIR3','MIR3,MIRb','MIR3,MLT1C','MIRb','MIRc','MLT-int','MLT1-int','MLT1A','MLT1A0','MLT1A0-int','MLT1A1','MLT1A1-int','MLT1B','MLT1B-int','MLT1C','MLT1C-int','MLT1D','MLT1D-int','MLT1E','MLT1E1','MLT1E1A','MLT1E1A,U4','MLT1E1A-int','MLT1E2','MLT1E3','MLT1E3-int','MLT1F','MLT1F,THE1B','MLT1F-int','MLT1F1','MLT1F2','MLT1F2-int','MLT1G','MLT1G-int','MLT1G1','MLT1G1,MSTA','MLT1G3','MLT1G3-int','MLT1H','MLT1H-int','MLT1H1','MLT1H2','MLT1I','MLT1I-int','MLT1J','MLT1J-int','MLT1J1','MLT1J1-int','MLT1J2','MLT1J2-int','MLT1K','MLT1L','MLT1M','MLT1N2','MLT2A1','MLT2A2','MLT2B1','MLT2B2','MLT2B3','MLT2B4','MLT2B5','MLT2C1','MLT2C2','MLT2D','MLT2E','MLT2F','MSR1','MSTA','MSTA-int','MSTB','MSTB-int','MSTB1','MSTB2','MSTB2-int','MSTC','MSTD','MSTD-int','MamGyp-int','MamGypLTR1a','MamGypLTR1b','MamGypLTR1c','MamGypLTR1d','MamGypLTR2c','MamGypLTR3','MamRep1161','MamRep137','MamRep1527','MamRep1879','MamRep38','MamRep4096','MamRep434','MamRep488','MamRep564','MamRep605','MamSINE1','Merlin1_HS','ORSL','ORSL-2a','ORSL-2b','PABL_A','PABL_A-int','PABL_B','PABL_B-int','PRIMA4-int','PRIMA41-int','PRIMA4_LTR','Plat_L3','PrimLTR79','REP522','Ricksha','Ricksha_0','Ricksha_c','SAR','SATR1','SST1','SSU-rRNA_Hsa','SUBTEL_sa','SVA_B','SVA_C','SVA_D','SVA_F','T-rich','TAR1','THE1-int','THE1A','THE1A-int','THE1B','THE1B-int','THE1C','THE1D','THE1D-int','Tigger1','Tigger1,U1','Tigger10','Tigger11a','Tigger12','Tigger12A','Tigger12c','Tigger13a','Tigger14a','Tigger15a','Tigger16a','Tigger16b','Tigger1a_Art','Tigger2','Tigger2a','Tigger2b_Pri','Tigger3','Tigger3,Tigger3','Tigger3a','Tigger3b','Tigger3c','Tigger4','Tigger4,Tigger4','Tigger4a','Tigger5','Tigger6a','Tigger6b','Tigger7','Tigger8','Tigger9a','Tigger9b','U1','U13','U13_','U14','U17','U2','U3','U4','U5','U6','U7','U8','UCON14','UCON2','UCON26','UCON29','UCON31','X3_LINE','X6A_LINE','X6B_LINE','X7A_LINE','X7B_LINE','X7C_LINE','X9_LINE','Zaphod','Zaphod3','polypurine','polypyrimidine','tRNA-Ala-GCY','tRNA-Ala-GCY_','tRNA-Arg-AGG','tRNA-Asn-AAC','tRNA-Asn-AAT','tRNA-Gln-CAA_','tRNA-Gly-GGA','tRNA-Leu-TTA','tRNA-Leu-TTA(m)','tRNA-Met-i','tRNA-Pro-CCA','tRNA-Ser-AGY','tRNA-Ser-TCA(m)'];
var values = [</html>{{{repeat_enrich_byname}}}<html>];
for(i1=0;i1<repnames.length;i1++){
//pval = pvals[i1].split(";");
data.push([repnames[i1],values[i1]]);
}
    $('#repeat_enrich_byname_table').dataTable({
//"aaData": [["one", 1],["two", 3],["three", 0]],
"sScrollY": "300px",
"bScrollCollapse": true,
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"bInfo": false,
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"aoColumns": [{ "sTitle": "Repeat sequence name",  "bSortable": false },{ "sTitle": "Enrichment score", "sType": "numeric" }],
"aaSorting": [[ 1, "desc" ]],
});
});
</script>
<table id="repeat_enrich_byname_table"></table>
</html>
|no result for this sample
}}
-->
<!--
== Related MacroAPE_1083 Motifs ==
{{#info:The values shown are the p-values of the motif in FANTOM5 samples. <br>Analyst: Michiel de Hoon}}
<html>
<script type="text/javascript">
$(document).ready(function() {
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{{#ask:[[Macroape_1083_sample_pvalue_ffid::{{PAGENAME}}]]|mainlabel=Motif page name|?Macroape_1083_sample_pvalue_pvalue=P-value|format=ttable|limit=1100|searchlabel=|class=macroape_p_sample|default=This sample isn't target for the analysis}}
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<br><br>
<br><br>
{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}|
{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}|
{{#set:sample_category={{{sample_category}}}}}
{{#set:sample_category={{{sample_category}}}}}
 
{{#arraymap:{{{library_id}}}|!|$
|{{#set:Library accession number=$}}
}}


{{#arraydefine:accession_numbers_array|{{{accession_numbers}}}|!}}{{#loop: k
{{#arraydefine:accession_numbers_array|{{{accession_numbers}}}|!}}{{#loop: k
Line 470: Line 376:
}}
}}
|}}
|}}


{{#set:sample_category={{{sample_category}}}}}
{{#set:sample_category={{{sample_category}}}}}
Line 505: Line 412:
{{#set:rna_weight_ug={{{rna_weight_ug}}}}}
{{#set:rna_weight_ug={{{rna_weight_ug}}}}}
{{#set:rna_concentration={{{rna_concentration}}}}}
{{#set:rna_concentration={{{rna_concentration}}}}}
{{#if:{{{timecourse}}}|{{#arraymap:{{{timecourse|}}}|,|$| {{#set:timecourse=$}}}}|}}
{{#set:donor={{{donor}}}}}
{{#set:time={{{time}}}}}
{{#switch:{{{datafreeze_phase}}}|1={{#set:datafreeze_phase=1}}|2={{#set:datafreeze_phase=2}}|{{#set:datafreeze_phase=-1}}}}
{{#switch:{{{datafreeze_phase}}}|1={{#set:datafreeze_phase=1}}|2={{#set:datafreeze_phase=2}}|{{#set:datafreeze_phase=-1}}}}
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
{{#arraymap:{{#explode:{{{profile_hcage|}}}|,|0}}|&|$
|{{#set:sample_seq_library_id=$}}
|{{#set:sample_seq_library_id=$}}
}}
}}
{{#if:{{{timecourse}}}|{{#arraymap:{{{timecourse}}}|,|$| {{#set:timecourse=[[TimeCourse:$]]}}}}|}}
{{#set:sample_timecourse={{{sample_timecourse|}}}}}
{{#arraymap:{{{data_phase}}}|,|$|{{#set:data phase=$}} }}
[[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},
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                            { targets: 3, orderable: false, type: "percent"},
                            { targets: 4, orderable: false, type: "percent"},
                            { targets: 5, orderable: false}
                        ]
        });


[[Category:FF_Ontology]]
    }
[[Category:FF_Samples]]
});
</script>
</html>

Latest revision as of 18:04, 14 March 2022


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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