Template:F5samples: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
| (408 intermediate revisions by 6 users not shown) | |||
| Line 1: | Line 1: | ||
{{Loading|loadingimage=sprites.gif}}<html> | |||
<style type="text/css" title="currentStyle"> | |||
@import "/5/sstar/rb_js/html5button/datatables.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> | |||
<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">© RIKEN, 2013 <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}}}}} | {{#set:id={{{id}}}}} | ||
<table> | <table> | ||
<tr><th scope="row" align="right">Name:</th><td>{{{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">Genomic View:</th><td>[ | <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> | |||
{{#ifeq: {{{sample_species}}} | Human (Homo sapiens) |<tr><th scope="row" align="right">Genomic View:</th><td>{{#ifexpr: {{#pos:{{{zenbu_config}}}|ttp}}|[{{{zenbu_config}}} zenbu] |}} [http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC]</td></tr>|}}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) |<tr><th scope="row" align="right">Genomic View:</th><td>{{#ifexpr: {{#pos:{{{zenbu_config}}}|ttp}}|[{{{zenbu_config}}} zenbu] |}} [http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC]</td></tr>|}} | |||
<!-- | |||
{{#ifexpr: {{#pos:{{{microRNAs_novel_cage}}}{{{microRNAs_novel_srna}}}|ttp}}| | |||
{{#ifexpr: {{#pos:{{{microRNAs_novel_srna}}}|ttp}} | |||
|{{#ifexpr: {{#pos:{{{microRNAs_novel_cage}}}|ttp}}|<tr><th scope="row" align="right">MicroRNAs:</th><td>Including candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_novel_cage}}} CAGE samples], [{{{microRNAs_novel_srna}}} sRNA samples])</span><br/>Excluding candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_nonnovel_cage}}} CAGE samples], [{{{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 }} }}]|, }}</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" | |||
! Additional information | |||
|- | |||
|<div style="width:50%; float:left;">Sample information<table cellspacing="0" border="1"> | |||
<tr><th>strain</th><td>{{#switch:{{{sample_strain}}}|,,,=NA| =NA |{{{sample_strain}}}}}</td></tr> | |||
<tr><th>tissue</th><td>{{#switch:{{{sample_tissue}}}|,,,=NA| =NA |{{{sample_tissue}}}}}</td></tr> | |||
<tr><th>dev stage</th><td>{{#switch:{{{sample_dev_stage}}}|,,,=NA| =NA |{{{sample_dev_stage}}}}}</td></tr> | |||
<tr><th>sex</th><td>{{#switch:{{{sample_sex}}}|,,,=NA| =NA |{{{sample_sex}}}}}</td></tr> | |||
<tr><th>age</th><td>{{#switch:{{{sample_age}}}|,,,=NA| =NA |{{{sample_age}}}}}</td></tr> | |||
<tr><th>cell type</th><td>{{#switch:{{{sample_cell_type}}}|,,,=NA| =NA |{{{sample_cell_type}}}}}</td></tr> | |||
<tr><th>cell line</th><td>{{#switch:{{{sample_cell_line}}}|,,,=NA| =NA |{{{sample_cell_line}}}}}</td></tr> | |||
<tr><th>company</th><td>{{#switch:{{{sample_company}}}|,,,=NA| =NA |{{{sample_company}}}}}</td></tr> | |||
<tr><th>collaboration</th><td>{{#switch:{{{sample_collaboration}}}|,,,=NA| =NA |{{{sample_collaboration}}}}}</td></tr> | |||
{{#if:{{{sample_info_link}}}|<tr><th style="background-color: #4169e1;">External link for information</th><td style="background-color: #f0f8ff;">[{{#explode:{{{sample_info_link}}}|;|-1}} {{#explode:{{{sample_info_link}}}|;|0}}]</td></tr>}}</table></div> | |||
<div style="width:50%; float:left;"> | |||
RNA information<table cellspacing="0" border="1"> | |||
<tr><th>lot number</th><td>{{#switch:{{{rna_lot_number}}}|,,,=NA| =NA |{{{rna_lot_number}}}}}</td></tr> | |||
<tr><th>catalog number</th><td>{{#switch:{{{rna_catalog_number}}}|,,,=NA| =NA |{{{rna_catalog_number}}}}}</td></tr> | |||
<tr><th>sample type</th><td>{{#switch:{{{rna_sample_type}}}|,,,=NA| =NA |{{{rna_sample_type}}}}}</td></tr> | |||
<tr><th>extraction protocol <span style="background-color:white">[[Protocols:RNA_extraction|(Details)]]</span></th><td>{{#switch:{{{rna_extraction_protocol}}}|,,,=NA| =NA |{{{rna_extraction_protocol}}}}}</td></tr></table></div> | |||
|}{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}|{{DRAAccessionNumbers|{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|CAGE}}|CAGE|{{#sub:{{{DRA_sample_Accession}}}|0|{{#pos:{{{DRA_sample_Accession}}}|@|0}}}}}}|{{{DRA_sample_Accession}}}|{{{accession_numbers}}}|{{{library_id}}}|{{{sample_species}}}}}|}}{{#if:{{#pos:{{{DRA_sample_Accession_Zoo}}}|@|0}}|{{DRAAccessionNumbers|sRNA|{{{DRA_sample_Accession_Zoo}}}|{{{accession_numbers_Zoo}}}|{{{zoo_library_id}}}|{{{sample_species}}}}}|}}{{#vardefine:species_temp|{{#switch: {{{sample_species}}} | Human (Homo sapiens) = Hg19 | Mouse (Mus musculus) = Mm9 }}}}{{#switch: {{{sample_species}}} | |||
|Human (Homo sapiens) = {{FastaBamfileCTSS||Hg19|{{{hg19fasta}}}||{{{hg19bam}}}|{{{hg19ctss}}}|Hg38|{{#replace:{{{hg38bam}}}|hg38_v2|hg38_latest}}|{{#replace:{{{hg38ctss}}}|hg38_v2|hg38_latest}}}} | |||
|Mouse (Mus musculus) = {{FastaBamfileCTSS||Mm9|{{{mm9fasta}}}||{{{mm9bam}}}|{{{mm9ctss}}}|Mm10|{{#replace:{{{mm10bam}}}|mm10_v2|mm10_latest}}|{{#replace:{{{mm10ctss}}}|mm10_v2|mm10_latest}}}} | |||
| | |||
}}{{#if:{{#pos:{{{DRA_sample_Accession_HumanCAGEScan}}}|@|0}}|{{DRAAccessionNumbers|HumanCAGEScan|{{{DRA_sample_Accession_HumanCAGEScan}}}|{{{accession_numbers_HumanCAGEScan}}}|{{{cagescan_library_id}}}|{{{sample_species}}}}}|}}{{#ifexpr: {{#pos:{{{hg38bam_cs1}}}{{{mm10ctss_cs}}}|ttp}}| | |||
{{#switch: {{{sample_species}}} | |||
|Human (Homo sapiens) = {{FastaBamfileCTSS|HumanCAGEScan|Hg19|{{{hg19fasta_cs3prime}}}|{{{hg19fasta_cs5prime}}}|{{{hg19bam_cs}}}|{{{hg19ctss_cs}}}|Hg38|{{{hg38bam_cs}}}|{{{hg38ctss_cs}}}}} | |||
|Mouse (Mus musculus) = {{FastaBamfileCTSS|HumanCAGEScan|Mm9|{{{mm9fasta_cs}}}||{{{mm9bam_cs}}}|{{{mm9ctss_cs}}}|Mm10|{{{mm10bam_cs}}}|{{{mm10ctss_cs}}}}} | |||
| | |||
}} | |||
|}}{{#ifexpr:{{#pos:{{{HumanCAGEScanFiles}}}|ttp}}|{{FastaBamfileCTSSforCAGEScan|{{{HumanCAGEScanFiles}}}}} | |||
|}}{{#if:{{#pos:{{{DRA_sample_Accession_RNASeq}}}|@|0}}|{{DRAAccessionNumbers|RNA-Seq|{{{DRA_sample_Accession_RNASeq}}}|{{{accession_numbers_RNASeq}}}|{{{rnaseq_library_id}}}|{{{sample_species}}}}}|}} | |||
{{#ifexpr:{{#pos:{{{RNASeqFiles}}}|ttp}}|{{FastaBamfileCTSSforCAGEScan|{{{RNASeqFiles}}}}} | |||
|}}<br/> | |||
{{#if: {{#pos:{{{expression_enrichment_score}}}|chr}}| {{Fontsize|3|Relative expression to median (log10)}} | |||
---- | |||
{{Fontsize|3|Transcription factors with enriched expression in this sample}}{{nowrap|{{#info: Ranked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. }}}} | |||
<html><!-- tf enrich table: start--> | |||
<script type="text/javascript"> | |||
var species="</html>{{#var:species_temp}}<html>"; | |||
var mm_data = new Array(); | |||
var enrichment_scores_data = "</html>{{{expression_enrichment_score}}}<html>"; | |||
var sub_content = enrichment_scores_data.split(";;"); | |||
$(document).ready(function() { | |||
for(i=0;i<sub_content.length;i++){ | |||
var temp=sub_content[i]; | |||
if(temp!= null){ | |||
if(temp.length>2){ | |||
var sub_sub_content=sub_content[i].split("!"); | |||
var built="FFCP_PHASE1:"+species+"::"+sub_sub_content[0]; | |||
mm_data.push(sub_sub_content); | |||
} | |||
} | |||
} | |||
/*"sDom": '<"top"i>rt<"bottom"flp><"clear">' */ | |||
{{ | $('#ffcp_tf_enrichscore').DataTable( { | ||
< | data: mm_data, | ||
dom: 'Blfrtip', | |||
{ | lengthMenu: [[10, 50, -1], [10, 50, "All"]], | ||
</ | buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | ||
</ | columnDefs: [{ targets: [1], visible: false}], | ||
columns: [ | |||
{ title: "CAGE peaks" , | |||
render: function ( data, type, row, meta ) { | |||
var peak_loc = row[0]; | |||
var peak_name = row[1]; | |||
return "<a href=\"/5/sstar/"+"FFCP_PHASE1:"+species+"::"+peak_loc +"\">"+peak_name+"</a>"; | |||
} | |||
}, | |||
{ title: "Log10(Relative expression over median)" }, | |||
{ title: "TPM" }, | |||
{ title: "TF." } | |||
], | |||
order: [[ 2, 'desc' ]] | |||
} ); | |||
}); | |||
</script> | |||
<span id="tf_enrich_table_export_tool"></span> | |||
<table cellpadding="0" cellspacing="0" border="0" id="ffcp_tf_enrichscore" class="stripe cell-border order-column compact"></table> | |||
</html> | |||
}} | }} | ||
{{#vardefine:isHumanOrMouse|{{#switch:{{{sample_species}}}|Human (Homo sapiens)=1|Mouse (Mus musculus)=1|0}}}} | |||
{{#ifeq:{{#var:isHumanOrMouse}}|1|<br><br>{{Fontsize|3|Co-expression clusters with enriched expression in this sample}}{{#info:Ranked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters data]}}<html><script type="text/javascript"> | |||
$(document).ready(function() { | |||
{{# | if($('.relative-exp-of-coexp')[0]){ | ||
<table class=" | $('.relative-exp-of-coexp').DataTable({ | ||
<tr><th> | dom: 'Blfrtip', | ||
< | buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | ||
{{# | lengthMenu: [[10, 50, -1], [10, 50, "All"]], | ||
</ | columnDefs: [{ targets: [0], visible: true},{ targets: [0], visible: true}], | ||
</ | columns:[ | ||
{title:"MCL coexpression id", visible:true}, | |||
{title:"Coexpression_dpi_cluster_scores_median_value", visible:true} | |||
], | |||
order: [[ 1, 'desc' ]] | |||
}); | |||
} | |||
}); | |||
</script></html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?Coexpression_dpi_cluster_scores_median_value|intro=<table class="relative-exp-of-coexp stripe cell-border order-column compact"><html><thead></html><tr><th>Coexpression cluster</th><th>score</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table>|link=none|format=template|template=Coexpression_dpi_cluster_scores_median_in_ffsample|limit=5000|searchlabel=|default=No results for this sample}} | |||
|<br><br>}} | |||
|Mouse (Mus musculus)= | |||
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | |||
|<h3>$</h3>{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?=MCL coexpression id|?Coexpression_dpi_cluster_scores_median_value|format=ttable|class=relative-exp-of-coexp stripe cell-border order-column compact|headers=hide|searchlabel=}} | |||
|<br><br> | |||
}}}} | |||
<br><br> | |||
{{Fontsize|3|Repeat families with enriched expression in this sample}}{{nowrap|{{#info:<b>Summary:</b>Ranked list of repeat family expression in this sample relative to | |||
the median expression in the FANTOM5 collection is shown. Value is log10 | |||
transformed.<br><b>Analyst:</b>NA | |||
<br><br>link to dataset.<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression data]}}}} | |||
{{#if: {{#pos:{{{repeat_enrich_byfamily}}}|,}} | | |||
<html><script type="text/javascript"> | |||
$(document).ready(function() { | |||
var repeat_enrich_byfamily_data = []; | |||
var repeat_enrich_byfamily_repnames = [ | |||
</html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)=<html> | |||
'Alu','Alu,Alu','Alu,ERVL-MaLR','Alu,L1','Alu,L2','Alu,Low_complexity','Alu,MIR','Alu,hAT-Charlie','Alu,hAT-Tip100','Alu,rRNA','Alu,snRNA','CR1','CR1,CR1','DNA','DNA?','Deu','ERV','ERV1','ERV1,ERV1','ERV1,ERVL','ERV1,ERVL-MaLR','ERV1,MIR','ERV1,snRNA','ERVK','ERVK,rRNA','ERVL','ERVL,ERV1','ERVL,ERVL','ERVL,ERVL-MaLR','ERVL,hAT-Charlie','ERVL,snRNA','ERVL-MaLR','ERVL-MaLR,ERVL-MaLR','ERVL-MaLR,snRNA','ERVL?','Gypsy','Gypsy?','Helitron','L1','L1,ERV1','L1,ERVL','L1,ERVL-MaLR','L1,L1','L1,TcMar-Mariner','L1,TcMar-Tigger','L1,hAT-Charlie','L1,rRNA','L1,snRNA','L1?','L2','L2,ERV1','L2,ERVL-MaLR','L2,L2','L2,MIR','L2,hAT-Blackjack','L2,hAT-Charlie','LTR','Low_complexity','Low_complexity,Alu','Low_complexity,ERV1','Low_complexity,L2','Low_complexity,Low_complexity','Low_complexity,Low_complexity,Low_complexity','Low_complexity,snRNA','MIR','MIR,ERVL-MaLR','MIR,Low_complexity','MIR,MIR','Merlin','MuDR','NA','Other','PiggyBac','PiggyBac?','RNA','RNA,MIR','RTE','RTE,CR1','RTE-BovB','SINE','SINE?','Satellite','Satellite,ERVL','Simple_repeat','Simple_repeat,Alu','Simple_repeat,ERV1','Simple_repeat,ERVL','Simple_repeat,ERVL-MaLR','Simple_repeat,L1','Simple_repeat,L2','Simple_repeat,Low_complexity','Simple_repeat,Low_complexity,Low_complexity','Simple_repeat,MIR','Simple_repeat,Other','Simple_repeat,Simple_repeat','Simple_repeat,Simple_repeat,Low_complexity','Simple_repeat,Simple_repeat,Simple_repeat','Simple_repeat,TcMar-Tigger','Simple_repeat,Unknown','Simple_repeat,hAT-Charlie','Simple_repeat,hAT-Tip100','Simple_repeat,scRNA','Simple_repeat,snRNA','TcMar','TcMar-Mariner','TcMar-Tc2','TcMar-Tc2,ERV1','TcMar-Tigger','TcMar-Tigger,TcMar-Tigger','TcMar-Tigger,snRNA','TcMar?','Unknown','Unknown?','acro','centr','hAT','hAT-Blackjack','hAT-Charlie','hAT-Charlie,ERVL-MaLR','hAT-Charlie,MIR','hAT-Charlie,hAT-Charlie','hAT-Charlie,snRNA','hAT-Tip100','hAT?','rRNA','rRNA,rRNA','scRNA','scRNA,L1','snRNA','srpRNA','tRNA','telo' | |||
</html>|Mouse (Mus musculus)=<html> | |||
'AcHobo','Alu','Alu,B4','Alu,B4,ERVL','Alu,ERVK','Alu,ERVL','Alu,L1','B2','B2,B4','B4','B4,Alu','B4,Low_complexity','CR1','ERV1','ERV1,ERVK','ERVK','ERVK,ERVK','ERVL','ERVL,Alu','ERVL,ERVK','ERVL,MaLR','ERVL?','Genie?','Gypsy','Gypsy?','Helitron','ID','ID,Satellite','L1','L1,ERVK','L1,L1','L1,snRNA','L1,tRNA','L2','L2,ERV1','L2,MaLR','LTR','Low_complexity','Low_complexity,Alu','Low_complexity,Low_complexity','Low_complexity,Low_complexity,Low_complexity','Low_complexity,MIR','Low_complexity,Tip100','Low_complexity,snRNA','MER1_type','MER1_type,B4','MER1_type?','MER2_type','MIR','MIR,MIR','MIR,MaLR','MaLR','MaLR,Alu','MaLR,ERV1','MaLR,ERVL','MaLR,MaLR','MuDR','NA','Other','PiggyBac','RNA','RTE','SINE','Satellite','Satellite,Satellite','Simple_repeat','Simple_repeat,Alu','Simple_repeat,Alu,B4','Simple_repeat,B2','Simple_repeat,B4','Simple_repeat,ERVK','Simple_repeat,L1','Simple_repeat,Low_complexity','Simple_repeat,Low_complexity,Low_complexity','Simple_repeat,MIR','Simple_repeat,MaLR','Simple_repeat,Simple_repeat','Simple_repeat,Simple_repeat,Low_complexity','Simple_repeat,rRNA','Tc2','TcMar','Tigger','Tip100','Unknown','hAT','hAT?','rRNA','rRNA,B4','rRNA,ERVK','scRNA','scRNA,B4','scRNA,Satellite','snRNA','tRNA' | |||
</html>}}<html> | |||
]; | |||
var repeat_enrich_byfamily_values = [</html>{{{repeat_enrich_byfamily}}}<html>]; | |||
for(i1=0;i1<repeat_enrich_byfamily_repnames.length;i1++){ | |||
repeat_enrich_byfamily_data.push([repeat_enrich_byfamily_repnames[i1],repeat_enrich_byfamily_values[i1]]); | |||
} | |||
$('#repeat_enrich_byfamily_table').DataTable({ | |||
data: repeat_enrich_byfamily_data, | |||
dom: 'Blfrtip', | |||
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | |||
lengthMenu: [[5, 50, -1], [5, 50, "All"]], | |||
columns: [ | |||
{ title: "Repeat family" }, | |||
{ title: "Log10(Relative expression over median)" , | |||
render: function ( data, type, row, meta ) { | |||
var num = row[1]; | |||
var numb = new Number(num); | |||
return numb.toFixed(2); | |||
} | |||
} | |||
], | |||
order: [[ 1, 'desc' ]] | |||
}); | |||
}); | |||
</script> | |||
<span id="repeat_enrich_byfamily_table_export_tool"></span> | |||
<table id="repeat_enrich_byfamily_table" class="stripe cell-border order-column compact"></table><br> | |||
</html> | |||
|no result for this sample | |||
}} | }} | ||
<br> | |||
{{Fontsize|3|TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample}} | |||
---- | |||
{{Fontsize|3|JASPAR motifs}}{{#info:<b>Summary:</b>Association of JASPAR motif to the promoter expression in this | |||
sample. Pearson's correlation between the number of TFBSs estimated by | |||
using the position-weight matrix for each promoter and its expression is | |||
expressed as Z-score by taking the ones based on random position-weight | |||
matrix, and the tail probability of the normal distribution corresponding | |||
to the Z-score is taken as the resulting P-value. Lower P-value indicates | |||
more (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br> | |||
<br><br>link to dataset.<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression data]}}<br> | |||
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | |||
|library id: $<span id="related_jaspar_table_export_tool"></span>{{#ask:[[jaspar_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]|?=Jaspar motif|?=Logo|?jaspar_motifs_sample_pval_pval=P-value|format=ttable|limit=1100|searchlabel=|class=jaspar_motif_pval stripe cell-border order-column compact|searchlabel=|default=This sample isn't target for the analysis}} | |||
|<br> | |||
}} | |||
<br><br> | |||
{{Fontsize|3|FANTOM5 phase1 novel unique motifs}}{{#info:<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in | |||
169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br> | |||
<br><br>link to dataset.<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression data]}}<br> | |||
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | |||
|library id: $<span id="related_novel_table_export_tool"></span>{{#ask:[[novel_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]|?=Novel motif|?=Logo|?novel_motifs_sample_pval_pval=P-value|format=ttable|limit=1100|searchlabel=|class=novel_motif_pval stripe cell-border order-column compact|searchlabel=|default=This sample isn't target for the analysis}} | |||
|<br> | |||
}} | |||
<br><br> | |||
{{Fontsize|3|de novo motifs identified by HOMER in promoters active in this sample}}{{#info:<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br>}} | |||
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | |||
|library id: ${{#outerfile_existance:/5/sstar/Homer_de_novo_Motif_Results/$/homerResults.html | |||
|<div id="homer_denovo_table_export_tool"></div><br>{{#homer_list:Homer_de_novo_Motif_Results/$/homerResults.html|homerResults!<TABLE cellpadding="2" cellspacing="0">!</div></TD></TR>!</TABLE>!Homer de novo Motif Results|/5/sstar/Homer_de_novo_Motif_Results/$/homerResults!<table class=homer-table><thead>!</div></TD></TR></thead><tbody>!</tbody></TABLE>|!}} | |||
}} | |||
|<br> | |||
}}<br> | |||
<html> | |||
<script type="text/javascript"> | |||
$(document).ready(function() { | |||
if($('.jaspar_motif_pval')[0]){ | |||
$('.jaspar_motif_pval').DataTable({ | |||
dom: 'Blfrtip', | |||
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | |||
lengthMenu: [[5, 50, -1], [5, 50, "All"]], | |||
columnDefs: [ | |||
{ targets: 0, orderable: false}, | |||
{ targets: 1, orderable: false, width: "50pt", className: "bgwhite"} | |||
], | |||
columns: [ | |||
{ title: "Jaspar motif" }, | |||
{ title: "Logo", | |||
render: function ( data, type, row, meta ) { | |||
return "<img src=\"/5/sstar/seqlogo/jaspar/" + $(row[0]).text() + ".png\" width =\"80\" height = \"20\">"; | |||
} | |||
}, | |||
{ title: "p-value", | |||
render: function ( data, type, row, meta ) { | |||
var num=row[2]; | |||
return exp_converter(num,2,"e"); | |||
} | |||
} | |||
], | |||
order: [[ 2, 'asc' ]] | |||
}); | |||
} | |||
}); | |||
</script> | |||
</html> | |||
<html> | |||
< | <script type="text/javascript"> | ||
< | $(document).ready(function() { | ||
if($('.novel_motif_pval')[0]){ | |||
$('.novel_motif_pval').DataTable({ | |||
dom: 'Blfrtip', | |||
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | |||
lengthMenu: [[5, 50, -1], [5, 50, "All"]], | |||
columnDefs: [ | |||
{ targets: 0, orderable: false}, | |||
{ targets: 1, orderable: false, width: "50pt", className: "bgwhite"} | |||
], | |||
columns: [ | |||
< | { title: "Novel motif" }, | ||
{ title: "Logo", | |||
render: function ( data, type, row, meta ) { | |||
return "<img src=\"/5/sstar/seqlogo/novel/" + $(row[0]).text() + ".png\" width =\"80\" height = \"20\">"; | |||
} | |||
}, | |||
{ title: "p-value", | |||
render: function ( data, type, row, meta ) { | |||
var num=row[2]; | |||
return exp_converter(num,2,"e"); | |||
} | |||
} | |||
], | |||
order: [[ 2, 'asc' ]] | |||
}); | |||
} | |||
}); | |||
</script> | |||
</html> | |||
</ | |||
<html> | |||
<style type="text/css"> | |||
.white { background-color: white} | |||
table.homer-table td { padding: 1px } | |||
</style> | |||
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/media/js/dataTables.Percentage.js"></script> | |||
</html> | |||
<br>|}}<!-- end of if(isHumanOrMouse) --> | |||
{{Fontsize|3|FANTOM5 (FF) ontology }} | |||
---- | |||
{{Fontsize|3|Direct parent terms}} | |||
{{#if: {{{is_a}}} | | |||
<div style="width:25%; float:left;"> | |||
'''is_a relathionship'''<br>{{#arraymap:{{{is_a}}}|;;|$| | |||
{{#set:is_a=$}}{{#ifexist:$|[[$|$ {{#show:$|?name}}]]|$}}|<br>}} | |||
</div> | |||
|}} | |||
{{#if: {{{part_of}}} | | |||
<div style="width:25%; float:left;"> | |||
'''part_of relathionship'''<br>{{#arraymap:{{{part_of}}}|;;|$| | |||
{{#set:part_of=$}}{{#ifexist:$|[[$|$ {{#show:$|?name}}]]|$}}|<br>}} | |||
</div> | |||
|}} | |||
{{#if: {{{has_quality}}} | | |||
<div style="width:25%; float:left;"> | |||
'''has_quality relathionship'''<br>{{#arraymap:{{{has_quality}}}|;;|$| | |||
{{#set:has_quality=$}}{{#ifexist:$|[[$|$ {{#show:$|?name}}]]|$}}|<br>}} | |||
</div> | |||
|}} | |||
<div style="clear:both;"></div> | |||
{{Fontsize|3|Ancestor terms (non development)}}{{#info:<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji | |||
< | <br><br>link to source data<br> | ||
{{#if: {{{ancestors_in_cell_lineage_facet}}} | | [//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data] | ||
{{#set:ancestors_in_cell_lineage_facet=$}} | }}<br> | ||
{{#if: {{{ancestors_in_disease_facet}}} |< | {{#if: {{{ancestors_in_cell_lineage_facet}}} | | ||
{{#set:ancestors_in_disease_facet=$}} | <div style="width:25%; float:left;"> | ||
{{#if: {{{ancestors_in_anatomy_facet}}} |< | <b>CL: Cell type</b><br> | ||
{{#set:ancestors_in_anatomy_facet=$}} | {{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ancestors_in_cell_lineage_facet}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ancestors_in_cell_lineage_facet}}}|,|$|{{#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::$]]|?name=|format=list}}|<br>}} }} | ||
{{# | |||
{{#arraymap:{{{ | |||
</div> | |||
}} | |||
<div style="clear:both;"></div> | |||
{{Fontsize|3|Ancestor terms (development)}}{{#info:<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br> | |||
<b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br> | |||
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data] | |||
}} | |||
<br> | |||
{{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ffid_belonging_in_development}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ffid_belonging_in_development}}}|,|$|{{#ifexist:$|{{#set:ffid_belonging_in_development=$}}[[$]] ({{#show:$|?name}})}}|<br>}} }} | |||
<br><br> | |||
{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}| | |||
{{#set:sample_category={{{sample_category}}}}} | |||
{{#arraymap:{{{library_id}}}|!|$ | |||
|{{#set:Library accession number=$}} | |||
}} | |||
{{#arraydefine:accession_numbers_array|{{{accession_numbers}}}|!}}{{#loop: k | |||
| 0 | |||
| {{#arraysize:accession_numbers_array}} | |||
| <nowiki/> | |||
{{#vardefine:exp_met|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|0}}}} | |||
{{#if:{{#var:exp_met}}|{{#set:Experiment method={{#var:exp_met}}}}|}} | |||
{{#vardefine:lib_exp|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|1}}}} | |||
{{#if:{{#var:lib_exp}}|{{#set:Experiment accession number={{#var:lib_exp}}}}|}} | |||
{{#vardefine:lib_run|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|2}}}} | |||
{{#if:{{#var:lib_run}}|{{#set:Run accession number={{#var:lib_run}}}}|}} | |||
{{#vardefine:lib_bam|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|3}}}} | |||
{{#if:{{#var:lib_bam}}|{{#set:Bam accession number={{#var:lib_bam}}|BAM}}|}} | |||
{{#vardefine:lib_ctss|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|4}}}} | |||
{{#if:{{#var:lib_ctss}}|{{#set:CTSS accession number={{#var:lib_ctss}}}}|}} | |||
}} | |||
|}} | |||
{{#set:sample_category={{{sample_category}}}}} | |||
{{#set:profile_hcage={{{profile_hcage}}}}} | |||
{{# | {{#set:profile_rnaseq={{{profile_rnaseq}}}}} | ||
{{# | {{#set:profile_srnaseq={{{profile_srnaseq}}}}} | ||
{{# | {{#set:profile_cagescan={{{profile_cagescan}}}}} | ||
{{# | {{#set:sample_strain={{{sample_strain}}}}} | ||
{{# | {{#set:sample_tissue={{{sample_tissue}}}}} | ||
{{#set:sample_dev_stage={{{sample_dev_stage}}}}} | |||
{{#set:sample_sex={{{sample_sex}}}}} | |||
{{#set:sample_age={{{sample_age}}}}} | |||
{{#set:sample_ethnicity={{{sample_ethnicity}}}}} | |||
{{#set:sample_cell_type={{{sample_cell_type}}}}} | |||
{{#set:sample_cell_line={{{sample_cell_line}}}}} | |||
{{#set:sample_collaboration={{{sample_collaboration}}}}} | |||
{{#set:sample_experimental_condition={{{sample_experimental_condition}}}}} | |||
{{#set:sample_disease={{{sample_disease}}}}} | |||
{{#set:sample_cell_lot={{{sample_cell_lot}}}}} | |||
{{#set:sample_cell_catalog={{{sample_cell_catalog}}}}} | |||
{{#set:sample_company={{{sample_company}}}}} | |||
{{#set:sample_donor(cell lot)={{{sample_donor(cell lot)}}}}} | |||
{{#set:sample_note={{{sample_note}}}}} | |||
{{#set:sample_id={{{sample_id}}}}} | |||
{{#set:rna_tube_id={{{rna_tube_id}}}}} | |||
{{#set:rna_box={{{rna_box}}}}} | |||
{{#set:rna_position={{{rna_position}}}}} | |||
{{#set:rna_lot_number={{{rna_lot_number}}}}} | |||
{{#set:rna_catalog_number={{{rna_catalog_number}}}}} | |||
{{#set:rna_rin={{{rna_rin}}}}} | |||
{{#set:rna_od260/230={{{rna_od260/230}}}}} | |||
{{#set:rna_od260/280={{{rna_od260/280}}}}} | |||
{{#set:rna_sample_type={{{rna_sample_type}}}}} | |||
{{#set:rna_extraction_protocol={{{rna_extraction_protocol}}}}} | |||
{{#set:rna_weight_ug={{{rna_weight_ug}}}}} | |||
{{#set:rna_concentration={{{rna_concentration}}}}} | |||
{{#if:{{{timecourse}}}|{{#arraymap:{{{timecourse|}}}|,|$| {{#set:timecourse=$}}}}|}} | |||
{{#set:donor={{{donor}}}}} | |||
{{#set:time={{{time}}}}} | |||
{{#switch:{{{datafreeze_phase}}}|1={{#set:datafreeze_phase=1}}|2={{#set:datafreeze_phase=2}}|{{#set:datafreeze_phase=-1}}}} | |||
{{#arraymap:{{#explode:{{{profile_hcage|}}}|,|0}}|&|$ | |||
|{{#set:sample_seq_library_id=$}} | |||
}} | |||
{{#set:sample_timecourse={{{sample_timecourse|}}}}} | |||
[[Category:FF_Ontology]] | [[Category:FF_Ontology]] | ||
[[Category:FF_Samples]] | [[Category:FF_Samples]] | ||
<html> | |||
<script type="text/javascript"> | |||
$(document).ready(function() { | |||
if($('.homer-table')[0]){ | |||
var homer_denovo_table2 = $('.homer-table').DataTable({ | |||
dom: 'Blfrtip', | |||
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | |||
lengthMenu: [[5, 50, -1], [5, 50, "All"]], | |||
scrollCollapse: true, | |||
columnDefs: [ | |||
{ targets: 0, orderable: false}, | |||
{ targets: 1, orderable: false}, | |||
{ targets: 2, width: "100pt", "type": "numeric"}, | |||
{ targets: 3, orderable: false, type: "percent"}, | |||
{ targets: 4, orderable: false, type: "percent"}, | |||
{ targets: 5, orderable: false} | |||
] | |||
}); | |||
} | |||
}); | |||
</script> | |||
</html> | |||
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
RNA information
|
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
