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| </style> | | </style> |
| <script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.js"></script> | | <script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.js"></script> |
| <script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
| |
|
| |
|
| </html>{{#outerfile_existance: /5/sstar/sstar_img/f5samples/riken_cellimg/{{PAGENAME}}.jpg |<html> | | </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}}}}}
| |
| <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>{{#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}}} | Gallus gallus ||<tr><th scope="row" align="right">Genomic View:</th><td>{{#ifexpr: {{#pos:{{{zenbu_config}}}|ttp}}|[{{{zenbu_config}}} zenbu] |}} {{#ifeq: {{{sample_species}}} | Human (Homo sapiens) |[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC]| }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) |[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> | }}</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}}}|{{{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|{{{hg38bam}}}|{{{hg38ctss}}}}}
| |
| |Mouse (Mus musculus) = {{FastaBamfileCTSS||Mm9|{{{mm9fasta}}}||{{{mm9bam}}}|{{{mm9ctss}}}|Mm10|{{{mm10bam}}}|{{{mm10ctss}}}}}
| |
| |
| |
| }}{{#if:{{#pos:{{{DRA_sample_Accession_HumanCAGEScan}}}|@|0}}|{{DRAAccessionNumbers|HumanCAGEScan|{{{DRA_sample_Accession_HumanCAGEScan}}}|{{{accession_numbers_HumanCAGEScan}}}|{{{cagescan_library_id}}}|{{{sample_species}}}}}|}}{{#ifexpr: {{#pos:{{{hg38bam_cs1}}}{{{mm10ctss_cs}}}|ttp}}|
| |
| {{#switch: {{{sample_species}}}
| |
| |Human (Homo sapiens) = {{FastaBamfileCTSS|HumanCAGEScan|Hg19|{{{hg19fasta_cs3prime}}}|{{{hg19fasta_cs5prime}}}|{{{hg19bam_cs}}}|{{{hg19ctss_cs}}}|Hg38|{{{hg38bam_cs}}}|{{{hg38ctss_cs}}}}}
| |
| |Mouse (Mus musculus) = {{FastaBamfileCTSS|HumanCAGEScan|Mm9|{{{mm9fasta_cs}}}||{{{mm9bam_cs}}}|{{{mm9ctss_cs}}}|Mm10|{{{mm10bam_cs}}}|{{{mm10ctss_cs}}}}}
| |
| |
| |
| }}
| |
| |}}{{#ifexpr:{{#pos:{{{HumanCAGEScanFiles}}}|ttp}}|{{FastaBamfileCTSSforCAGEScan|{{{HumanCAGEScanFiles}}}}}
| |
| |}}{{#if:{{#pos:{{{DRA_sample_Accession_RNASeq}}}|@|0}}|{{DRAAccessionNumbers|RNA-Seq|{{{DRA_sample_Accession_RNASeq}}}|{{{accession_numbers_RNASeq}}}|{{{rnaseq_library_id}}}|{{{sample_species}}}}}|}}
| |
| {{#ifexpr:{{#pos:{{{RNASeqFiles}}}|ttp}}|{{FastaBamfileCTSSforCAGEScan|{{{RNASeqFiles}}}}}
| |
| |}}<br/>
| |
| {{#if: {{#pos:{{{expression_enrichment_score}}}|chr}}| {{Fontsize|3|Relative expression to median (log10)}}
| |
| ----
| |
| {{Fontsize|3|Transcription factors with enriched expression in this sample}}{{nowrap|{{#info: Ranked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. }}}}
| |
| <html><!-- tf enrich table: start--> | | <html><!-- tf enrich table: start--> |
| <script type="text/javascript"> | | <script type="text/javascript"> |
| var species="</html>{{#var:species_temp}}<html>";
| |
| var mm_data = new Array();
| |
| var enrichment_scores_data = "</html>{{{expression_enrichment_score}}}<html>";
| |
| var sub_content = enrichment_scores_data.split(";;");
| |
|
| |
|
| $(document).ready(function() { | | $(document).ready(function() { |
|
| |
|
| 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 data = [ | | var data = [ |
| [ | | [ |
| Line 112: |
Line 36: |
| <table cellpadding="0" cellspacing="0" border="0" class="display" id="ffcp_tf_enrichscore"></table> | | <table cellpadding="0" cellspacing="0" border="0" class="display" id="ffcp_tf_enrichscore"></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]}}<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]]
| |
