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(Replaced content with "{{#ask:Category:FFCP |format=count}}")
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{{#ask:[[Category:FFCP]]
+
{{Loading|loadingimage=sprites.gif}}<html>
|format=count}}
+
<style type="text/css" title="currentStyle">
 +
@import "/5/sstar/rb_js/datatables/media/css/jquery.dataTables.css";
 +
@import "/5/sstar/rb_js/datatables/extras/TableTools/media/css/TableTools.css";
 +
 
 +
 
 +
</style>
 +
<script type="text/javascript" src="/5/sstar/rb_js/custom/expoconvert.js"></script>
 +
<script type="text/javascript" src="/5/sstar/rb_js/datatables/media/js/jquery.dataTables.min.js"></script>
 +
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
 +
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/extras/TableTools/media/js/ZeroClipboard.js"></script>
 +
 
 +
</html>{{#outerfile_existance: /5/sstar/sstar_img/f5samples/riken_cellimg/{{PAGENAME}}.jpg |<html>
 +
<div style="width:250px;height:250px;float:right;"><img width=250 src="/5/sstar/sstar_img/f5samples/riken_cellimg/</html>{{PAGENAME}}<html>.jpg">
 +
<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>}}
 +
{{#set:id={{{id}}}}}
 +
<table>
 +
<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:Library_accession_number|Library ID]]:</th><td>{{{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">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">CAGEd-oPOSSUM:</th><td>[http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/{{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | human | }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | mouse | }}/{{{id}}}/results.html 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|{{{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. }}}}
 +
<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">' */
 +
 +
var tf_enrich_table = $('#ffcp_tf_enrichscore').dataTable( {
 +
"bScrollCollapse": true,
 +
"bPaginate": true,
 +
"bFilter": true,
 +
"bInfo": true,
 +
                "iDisplayLength": 10,
 +
                "aLengthMenu": [[10,50,-1], [10,50,"All"]],
 +
"aaData": mm_data,
 +
"aoColumnDefs":[
 +
{"aTargets":[0],"sTitle": "CAGE peaks", "fnRender": function(obj) {
 +
var peak_loc = obj.aData[ obj.iDataColumn ];
 +
                var peak_name = obj.aData[ obj.iDataColumn+1 ];
 +
return sReturn = "<a href=\"/5/sstar/"+"FFCP_PHASE1:"+species+"::"+peak_loc +"\">"+peak_name+"</a>";
 +
}
 +
},
 +
{"aTargets":[1],"sTitle": "Log10(Relative expression over median)","fnRender": function(obj) {
 +
return sReturn = obj.aData[ obj.iDataColumn+1 ];
 +
}
 +
},
 +
{"aTargets":[2],"sTitle": "TPM","fnRender": function(obj) {
 +
return sReturn = obj.aData[ obj.iDataColumn+1 ];
 +
}
 +
},
 +
{"aTargets":[3],"sTitle": "TF","fnRender": function(obj) {
 +
return sReturn = obj.aData[ obj.iDataColumn+1 ];
 +
}
 +
}
 +
],
 +
"aaSorting": [[ 1, "desc" ]]
 +
} );
 +
 
 +
var tf_enrich_table_tool = new TableTools(tf_enrich_table, {"sSwfPath": "/5/sstar/rb_js/datatables/extras/TableTools/media/swf/copy_csv_xls_pdf.swf", "aButtons": [ {"sExtends": "copy", "mColumns": "visible"}, {"sExtends": "csv", "mColumns": "visible"},{"sExtends": "pdf", "mColumns": "visible"} ]});
 +
 
 +
$('#tf_enrich_table_export_tool').before(tf_enrich_table_tool.dom.container );
 +
});
 +
</script>
 +
<span id="tf_enrich_table_export_tool"></span>
 +
<table cellpadding="0" cellspacing="0" border="0" class="display" id="ffcp_tf_enrichscore"></table>
 +
</html>
 +
}}
 +
<br><br>{{Fontsize|3|Co-expression clusters with enriched expression in this sample}}{{#info:Ranked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters data]}}<html><script type="text/javascript">
 +
$(document).ready(function() {
 +
    if($('.relative-exp-of-coexp')[0]){
 +
var coexpression_dpi_cluster_scores_median_table= $('.relative-exp-of-coexp').dataTable({
 +
"bScrollCollapse": true,
 +
"bPaginate": true,
 +
"bFilter": true,
 +
"bInfo": true,
 +
                "iDisplayLength": 10,
 +
                "aLengthMenu": [[10,50,-1], [10,50,"All"]],
 +
"aaSorting": [[1,'desc']],
 +
"aoColumnDefs": [{ "sWidth": "150px", "sType": "numeric", "aTargets": [1] ,"fnRender": function (obj) {
 +
              var num =obj.aData[obj.iDataColumn];
 +
              var numb = new Number(num);
 +
                  return numb.toFixed(2) ;
 +
} }]
 +
});
 +
var coexpression_dpi_cluster_scores_median_table_export_tools = new TableTools(coexpression_dpi_cluster_scores_median_table, {"sSwfPath": "/5/sstar/rb_js/datatables/extras/TableTools/media/swf/copy_csv_xls_pdf.swf", "aButtons": [ {"sExtends": "copy", "mColumns": "visible"}, {"sExtends": "csv", "mColumns": "visible"}, {"sExtends": "pdf", "mColumns": "visible"} ]});
 +
$('#coexpression_dpi_cluster_scores_median_table_export_tool').before(coexpression_dpi_cluster_scores_median_table_export_tools.dom.container );}});</script></html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?Coexpression_dpi_cluster_scores_median_value|intro=<span id="coexpression_dpi_cluster_scores_median_table_export_tool"></span><table class="relative-exp-of-coexp"><html><thead></html><tr><th>Coexpression cluster</th><th>score</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table>|link=none|format=template|template=Coexpression_dpi_cluster_scores_median_in_ffsample|limit=5000|searchlabel=|default=No results for this sample}}
 +
|<br><br>}}
 +
|Mouse (Mus musculus)=
 +
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
 +
|<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=}}
 +
|<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>[http://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]]);
 +
}
 +
  var repeat_enrich_byfamily_table_obj=  $('#repeat_enrich_byfamily_table').dataTable({
 +
"bScrollCollapse": true,
 +
"bPaginate": true,
 +
"bFilter": true,
 +
"bInfo": true,
 +
                "iDisplayLength": 5,
 +
                "aLengthMenu": [[5,50,-1], [5,50,"All"]],
 +
"aaData": repeat_enrich_byfamily_data,
 +
"aoColumns": [{ "sTitle": "Repeat family",  "bSortable": false },{ "sTitle": "Log10(Relative expression over median)", "sType": "numeric" ,"fnRender": function (obj) {
 +
              var num =obj.aData[obj.iDataColumn];
 +
              var numb = new Number(num);
 +
                  return numb.toFixed(2) ;
 +
}}],
 +
"aaSorting": [[ 1, "desc" ]]
 +
});
 +
var repeat_enrich_byfamily_table_objtool = new TableTools( repeat_enrich_byfamily_table_obj, {"sSwfPath": "/5/sstar/rb_js/datatables/extras/TableTools/media/swf/copy_csv_xls_pdf.swf", "aButtons": [ {"sExtends": "copy", "mColumns": "visible"},{"sExtends": "csv", "mColumns": "visible"},{"sExtends": "pdf", "mColumns": "visible"} ]});
 +
 
 +
$('#repeat_enrich_byfamily_table_export_tool').before(repeat_enrich_byfamily_table_objtool.dom.container );
 +
});
 +
</script>
 +
<span id="repeat_enrich_byfamily_table_export_tool"></span>
 +
<table id="repeat_enrich_byfamily_table"></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>[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}}|&|$
 +
|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}}
 +
|<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>[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}}|&|$
 +
|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}}
 +
|<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]){
 +
var related_jaspar_table= $('.jaspar_motif_pval').dataTable({
 +
"bScrollCollapse": true,
 +
"bPaginate": true,
 +
"bFilter": true,
 +
"bInfo": true,
 +
                "iDisplayLength": 5,
 +
                "aLengthMenu": [[5,50,-1], [5,50,"All"]],
 +
"aaSorting": [[2,'asc']],
 +
"aoColumnDefs": [{"bSortable": false, "aTargets": [ 0 ]}, {  "fnRender": function(obj) {
 +
return sReturn = '<img src="/5/sstar/seqlogo/jaspar/' +  $(obj.aData[1]).text() + '.png" width ="80" height = "20">'}, "sClass": "bgwhite", "sWidth": "50", "bSortable": false, "aTargets": [1] }, { "sTitle": "p-value",  "sType": "numeric", "sWidth": "50pt", "aTargets":[2],"fnRender": function (obj) {                   
 +
                  var num =obj.aData[obj.iDataColumn];
 +
                  return exp_converter(num,2,"e") ;
 +
} }]
 +
});
 +
var related_jaspar_table_tool= new TableTools(related_jaspar_table, {"sSwfPath": "/5/sstar/rb_js/datatables/extras/TableTools/media/swf/copy_csv_xls_pdf.swf", "aButtons": [ {"sExtends": "copy", "mColumns": "visible"}, {"sExtends": "csv", "mColumns": "visible"},{"sExtends": "pdf", "mColumns": "visible"} ]});
 +
 
 +
$('#related_jaspar_table_export_tool').before(related_jaspar_table_tool.dom.container );
 +
    }
 +
});
 +
</script>
 +
</html>
 +
 
 +
<html>
 +
<script type="text/javascript">
 +
$(document).ready(function() {
 +
    if($('.novel_motif_pval')[0]){
 +
var related_novel_table= $('.novel_motif_pval').dataTable({
 +
"bScrollCollapse": true,           
 +
"bPaginate": true,
 +
"bFilter": true,
 +
"bInfo": true,
 +
                "iDisplayLength": 5,
 +
                "aLengthMenu": [[5,50,-1], [5,50,"All"]],
 +
"aaSorting": [[2,'asc']],
 +
"aoColumnDefs": [{"bSortable": false, "aTargets": [ 0 ]}, {  "fnRender": function(obj) {
 +
return sReturn = '<img src="/5/sstar/seqlogo/novel/' +  $(obj.aData[1]).text() + '.png" width ="80" height = "20">'}, "sClass": "bgwhite", "sWidth": "50",  "bSortable": false, "aTargets": [1] }, { "sTitle": "p-value",  "sType": "numeric", "sWidth": "50pt", "aTargets":[2],"fnRender": function (obj) {                   
 +
                  var num =obj.aData[obj.iDataColumn];
 +
                  return exp_converter(num,2,"e") ;
 +
} }]
 +
});
 +
var related_novel_table_tool = new TableTools( related_novel_table, {"sSwfPath": "/5/sstar/rb_js/datatables/extras/TableTools/media/swf/copy_csv_xls_pdf.swf", "aButtons": [ {"sExtends": "copy", "mColumns": "visible"}, {"sExtends": "csv", "mColumns": "visible"},{"sExtends": "pdf", "mColumns": "visible"} ]});
 +
 
 +
$('#related_novel_table_export_tool').before(related_novel_table_tool.dom.container );
 +
    }
 +
});
 +
</script>
 +
</html>
 +
 
 +
<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>
 +
<script type="text/javascript">
 +
$(document).ready(function() {
 +
    if($('.homer-table')[0]){
 +
        var homer_denovo_table = $('.homer-table').dataTable({
 +
"bPaginate": true,
 +
"bInfo": true,
 +
"bScrollCollapse": true,
 +
        "iDisplayLength": 5,
 +
                "aLengthMenu": [[5,50,-1], [5,50,"All"]],
 +
"aaSorting": [],
 +
"aoColumnDefs": [{ "sType": "numeric", "sWidth": "100px", "aTargets": [2]}, {"sType": "percent", "aTargets": [ 3, 4] }, { "bSortable": false, "aTargets": [ 0, 1, 5] }]
 +
});
 +
 
 +
var homer_denovo_table_tool = new TableTools(homer_denovo_table, {"sSwfPath": "/5/sstar/rb_js/datatables/extras/TableTools/media/swf/copy_csv_xls_pdf.swf", "aButtons": [ {"sExtends": "copy", "mColumns": "visible"},{"sExtends": "csv", "mColumns": "visible"},{"sExtends": "pdf", "mColumns": "visible"} ]});
 +
 
 +
$('#homer_denovo_table_export_tool').before(homer_denovo_table_tool.dom.container );
 +
    }
 +
});
 +
</script>
 +
</html>
 +
<br>
 +
{{Fontsize|3|FANTOM5 (FF) ontology }}
 +
----
 +
{{Fontsize|3|Direct parent terms}}
 +
{{#if: {{{is_a}}} |
 +
<div style="width:25%; float:left;">
 +
'''is_a relathionship'''<br>{{#arraymap:{{{is_a}}}|;;|$|
 +
{{#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>
 +
[http://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>
 +
[http://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]]

Revision as of 05:00, 30 August 2016

Name:{{{name}}}
Species:{{{sample_species}}}
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View:zenbu , UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strain{{{sample_strain}}}
tissue{{{sample_tissue}}}
dev stage{{{sample_dev_stage}}}
sex{{{sample_sex}}}
age{{{sample_age}}}
cell type{{{sample_cell_type}}}
cell line{{{sample_cell_line}}}
company{{{sample_company}}}
collaboration{{{sample_collaboration}}}
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number{{{rna_lot_number}}}
catalog number{{{rna_catalog_number}}}
sample type{{{rna_sample_type}}}
extraction protocol (Details){{{rna_extraction_protocol}}}



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data


Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data
no result for this sample


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


JASPAR motifsSummary: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
Analyst: Michiel de Hoon


link to dataset.
data

library id: {{{profile_hcage}}}This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifsSummary: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
Analyst: Michiel de Hoon


link to dataset.
data

library id: {{{profile_hcage}}}This sample isn't target for the analysis

de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: {{{profile_hcage}}}


FANTOM5 (FF) ontology


Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

Ancestor terms (non development)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



















Property "Timecourse" (as page type) with input value "{{{timecourse}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.



Property "Sample seq library id" (as page type) with input value "{{{profile_hcage}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process. Property "Sample timecourse" (as page type) with input value "{{{sample_timecourse}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.