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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 "/5/sstar/rb_js/datatables/media/css/jquery.dataTables.css";
@import "/resource_browser/rb_js/datatables/media/css/jquery.dataTables.css";
@import "/5/sstar/rb_js/datatables/extras/TableTools/media/css/TableTools.css";
@import "/resource_browser/rb_js/datatables/extras/TableTools/media/css/TableTools.css";




</style>
</style>
<script type="text/javascript" src="/5/sstar/rb_js/custom/expoconvert.js"></script>
<script type="text/javascript" src="/resource_browser/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" src="/resource_browser/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="/resource_browser/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>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/extras/TableTools/media/js/ZeroClipboard.js"></script>


</html>{{#outerfile_existance: /5/sstar/sstar_img/f5samples/riken_cellimg/{{PAGENAME}}.jpg |<html>
</html>{{#outerfile_existance: /resource_browser/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 style="width:250px;height:250px;float:right;"><img width=250 src="/resource_browser/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 align="right">&copy; RIKEN, 2013&nbsp;<a href="http://creativecommons.org/licenses/by-sa/2.1/jp"><img src="/resource_browser/sstar_img/f5samples/riken_cellimg/by-sa_s.png" alt="by-sa"></a></div>
</div></html>}}
</div></html>}}
{{#set:id={{{id}}}}}
{{#set:id={{{id}}}}}
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var peak_loc = obj.aData[ obj.iDataColumn ];
var peak_loc = obj.aData[ obj.iDataColumn ];
                 var peak_name = obj.aData[ obj.iDataColumn+1 ];
                 var peak_name = obj.aData[ obj.iDataColumn+1 ];
return sReturn = "<a href=\"/5/sstar/"+"FFCP_PHASE1:"+species+"::"+peak_loc +"\">"+peak_name+"</a>";
return sReturn = "<a href=\"/resource_browser/"+"FFCP_PHASE1:"+species+"::"+peak_loc +"\">"+peak_name+"</a>";
}
}
},
},
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} );
} );


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"} ]});
var tf_enrich_table_tool = new TableTools(tf_enrich_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"} ]});


$('#tf_enrich_table_export_tool').before(tf_enrich_table_tool.dom.container );
$('#tf_enrich_table_export_tool').before(tf_enrich_table_tool.dom.container );
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} }]
} }]
});
});
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"} ]});
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"} ]});
$('#coexpression_dpi_cluster_scores_median_table_export_tool').before(coexpression_dpi_cluster_scores_median_table_export_tools.dom.container );});</script></html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#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}}
$('#coexpression_dpi_cluster_scores_median_table_export_tool').before(coexpression_dpi_cluster_scores_median_table_export_tools.dom.container );});</script></html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#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>}}
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"aaSorting": [[ 1, "desc" ]]
"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"} ]});
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"} ]});


$('#repeat_enrich_byfamily_table_export_tool').before(repeat_enrich_byfamily_table_objtool.dom.container );
$('#repeat_enrich_byfamily_table_export_tool').before(repeat_enrich_byfamily_table_objtool.dom.container );
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{{Fontsize|3|de novo motifs identified by HOMER in promoters active in this sample}}{{#info:<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br>}}
{{Fontsize|3|de novo motifs identified by HOMER in promoters active in this sample}}{{#info:<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br>}}
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|library id: ${{#outerfile_existance:/5/sstar/Homer_de_novo_Motif_Results/$/homerResults.html
|library id: ${{#outerfile_existance:/resource_browser/Homer_de_novo_Motif_Results/$/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>|!}}
|<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>|!}}
}}
}}
|<br>
|<br>
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"aaSorting": [[2,'asc']],
"aaSorting": [[2,'asc']],
"aoColumnDefs": [{"bSortable": false, "aTargets": [ 0 ]}, {  "fnRender": function(obj) {
"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) {                     
return sReturn = '<img src="/resource_browser/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];
                   var num =obj.aData[obj.iDataColumn];
                   return exp_converter(num,2,"e") ;
                   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"} ]});
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"} ]});


$('#related_jaspar_table_export_tool').before(related_jaspar_table_tool.dom.container );
$('#related_jaspar_table_export_tool').before(related_jaspar_table_tool.dom.container );
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"aaSorting": [[2,'asc']],
"aaSorting": [[2,'asc']],
"aoColumnDefs": [{"bSortable": false, "aTargets": [ 0 ]}, {  "fnRender": function(obj) {
"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) {                     
return sReturn = '<img src="/resource_browser/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];
                   var num =obj.aData[obj.iDataColumn];
                   return exp_converter(num,2,"e") ;
                   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"} ]});
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"} ]});


$('#related_novel_table_export_tool').before(related_novel_table_tool.dom.container );
$('#related_novel_table_export_tool').before(related_novel_table_tool.dom.container );
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table.homer_table td { padding: 1px }
table.homer_table td { padding: 1px }
</style>
</style>
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/media/js/dataTables.Percentage.js"></script>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/dataTables.Percentage.js"></script>
<script type="text/javascript">
<script type="text/javascript">
$(document).ready(function() {
$(document).ready(function() {
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});
});


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"} ]});
var homer_denovo_table_tool = new TableTools(homer_denovo_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"} ]});


$('#homer_denovo_table_export_tool').before(homer_denovo_table_tool.dom.container );
$('#homer_denovo_table_export_tool').before(homer_denovo_table_tool.dom.container );

Revision as of 14:16, 4 March 2015

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



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

Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


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


JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data
library id: {{{profile_hcage}}}This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data
library id: {{{profile_hcage}}}This sample isn't target for the analysis

de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: {{{profile_hcage}}}


FANTOM5 (FF) ontology


Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
NA

DOID: Disease
NA

UBERON: Anatomy
NA

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA




















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.