Personal tools

Difference between revisions of "Template:F5samples"

From FANTOM5_SSTAR

Jump to: navigation, search
m
 
(450 intermediate revisions by 6 users not shown)
Line 1: Line 1:
{|style="background-color: #F5F5F5; width:25em; float: right;"  
+
{{Loading|loadingimage=sprites.gif}}<html>
! colspan="2" style="text-align: center; background-color: skyblue;" | [[id::{{{id}}}]]
+
<style type="text/css" title="currentStyle">
 +
@import "/5/sstar/rb_js/html5button/datatables.css";
 +
@import "/5/sstar/rb_js/datatables/extras/TableTools/media/css/TableTools.css";
 +
</style>
 +
<script type="text/javascript" src="/5/sstar/rb_js/jquery-1.7.1.min.js"></script>
 +
<script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.js"></script>
 +
<script type="text/javascript" src="/5/sstar/rb_js/custom/expoconvert.js"></script>
 +
<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>
 +
<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>{{#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],&nbsp;[{{{microRNAs_novel_srna}}} sRNA samples])</span><br/>Excluding candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_nonnovel_cage}}} CAGE samples],&nbsp;[{{{microRNAs_nonnovel_srna}}} sRNA samples])</span></td></tr>|<tr><th scope="row" align="right">MicroRNAs:</th><td>Including candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_novel_srna}}} sRNA samples])</span><br/>Excluding candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_nonnovel_srna}}} sRNA samples])</span></td></tr>}}
 +
|{{#ifexpr: {{#pos:{{{microRNAs_novel_cage}}}|ttp}}|<tr><th scope="row" align="right">MicroRNAs:</th><td>Including candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_novel_cage}}} CAGE samples])</span><br/>Excluding candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_nonnovel_cage}}} CAGE samples])</span></td></tr>|}}
 +
}}
 +
|}}
 +
{{#ifexpr: {{#pos:{{{refex}}}|ttp}}|
 +
<tr><th scope="row" align="right">RefEX:</th><td>[{{#replace:{{#replace:{{{refex}}}|[|%5b}}|]|%5d}} Specific genes]  </td></tr>|}}
 +
{{#ifexpr: {{#pos:{{{fantom_cat}}}|ttp}}|
 +
<tr><th scope="row" align="right">FANTOM CAT:</th><td>{{ #vardefine: i | 1 }}{{#arraymap:{{{fantom_cat}}}|;;|$|[$ {{ #var: i }}{{ #vardefine: i | {{ #expr: {{ #var: i }} + 1 }} }}]|,&#32;}}</td></tr>|}}
 +
{{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | <tr><th scope="row" align="right">CAGEd-oPOSSUM:</th><td>[http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/human/{{{id}}}/results.html link]  </td></tr> | }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | <tr><th scope="row" align="right">CAGEd-oPOSSUM:</th><td>[http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/mouse/{{{id}}}/results.html link] </td></tr> | }}</table>
 +
{|class="wikitable mw-collapsible mw-collapsed" style="width:auto"
 +
! Additional information
 
|-
 
|-
! [[Property:name|name]]
+
|<div style="width:50%; float:left;">Sample information<table cellspacing="0" border="1">
| [[name::{{{name}}}]]
+
<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>
! [[Property:sample_species|species]]
+
<tr><th>dev stage</th><td>{{#switch:{{{sample_dev_stage}}}|,,,=NA| =NA |{{{sample_dev_stage}}}}}</td></tr>
| [[sample_species::{{{sample_species}}}]]{{#set:samplesp={{{sample_species}}}}}
+
<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>
! [[Property:profile_hcage|hCAGE]]
+
<tr><th>cell type</th><td>{{#switch:{{{sample_cell_type}}}|,,,=NA| =NA |{{{sample_cell_type}}}}}</td></tr>
| [[profile_hcage::{{{profile_hcage}}}]]
+
<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>
! [[Property:profile_rnaseq|RNA-seq]]
+
<tr><th>collaboration</th><td>{{#switch:{{{sample_collaboration}}}|,,,=NA| =NA |{{{sample_collaboration}}}}}</td></tr>
| [[profile_rnaseq::{{{profile_rnaseq}}}]]
+
{{#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;">
! [[Property:profile_srnaseq|smallRNA seq]]
+
RNA information<table cellspacing="0" border="1">
| [[profile_srnaseq::{{{profile_srnaseq}}}]]
+
<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>
! [[Property:profile_cagescan|nanoCAGEscan]]
+
<tr><th>sample type</th><td>{{#switch:{{{rna_sample_type}}}|,,,=NA| =NA |{{{rna_sample_type}}}}}</td></tr>
| [[profile_cagescan::{{{profile_cagescan}}}]]
+
<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-->
 +
<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( {
| colspan="2" style="text-align: center;  background-color: skyblue;" |sample detail
+
        data: mm_data,
|-
+
        dom: 'Blfrtip',
! [[Property:sample_strain|strain]]
+
        lengthMenu: [[10, 50, -1], [10, 50, "All"]],
| [[sample_strain::{{{sample_strain}}}]]
+
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
|-
+
        columnDefs: [{ targets: [1], visible: false}],
! [[Property:sample_tissue|tissue]]
+
        columns: [
| [[sample_tissue::{{{sample_tissue}}}]]
+
            { title: "CAGE peaks" ,
|-
+
              render: function ( data, type, row, meta ) {
! [[Property:sample_dev_stage|dev_stage]]
+
                var peak_loc = row[0];
| [[sample_dev_stage::{{{sample_dev_stage}}}]]
+
                var peak_name = row[1];
|-
+
return "<a href=\"/5/sstar/"+"FFCP_PHASE1:"+species+"::"+peak_loc +"\">"+peak_name+"</a>";
! [[Property:sample_sex|sex]]
+
              }
| [[sample_sex::{{{sample_sex}}}]]
+
            },
|-
+
            { title: "Log10(Relative expression over median)" },
! [[Property:sample_age|age]]
+
            { title: "TPM" },
| [[sample_age::{{{sample_age}}}]]
+
            { title: "TF." }
|-
+
        ],
! [[Property:sample_ethnicity|ethnicity]]
+
        order: [[ 2, 'desc' ]]
| [[sample_ethnicity::{{{sample_ethnicity}}}]]
+
    } );
|-
+
});
! [[Property:sample_cell_type|cell_type]]
+
</script>
| [[sample_cell_type::{{{sample_cell_type}}}]]
+
<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>
! [[Property:sample_cell_line|cell_line]]
+
</html>
| [[sample_cell_line::{{{sample_cell_line}}}]]
+
}}
|-
+
{{#vardefine:isHumanOrMouse|{{#switch:{{{sample_species}}}|Human (Homo sapiens)=1|Mouse (Mus musculus)=1|0}}}}
! [[Property:sample_collaboration|collaboration]]
+
{{#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>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters data]}}<html><script type="text/javascript">
| [[sample_collaboration::{{{sample_collaboration}}}]]
+
$(document).ready(function() {
|-
 
! [[Property:sample_experimental_condition|Experimental condition]]
 
| [[sample_experimental_condition::{{{sample_experimental_condition}}}]]
 
|-
 
! [[Property:sample_disease|disease]]
 
| [[sample_disease::{{{sample_disease}}}]]
 
  
|-
+
    if($('.relative-exp-of-coexp')[0]){
! [[Property:sample_cell_lot|cell_lot]]
+
        $('.relative-exp-of-coexp').DataTable({
| [[sample_cell_lot::{{{sample_cell_lot}}}]]
+
          dom: 'Blfrtip',
|-
+
          buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
! [[Property:sample_cell_catalog|cell_catalog]]
+
          lengthMenu: [[10, 50, -1], [10, 50, "All"]],
| [[sample_cell_catalog::{{{sample_cell_catalog}}}]]
+
          order: [[ 1, 'desc' ]]
|-
+
        });
! [[Property:sample_company|company]]
+
}
| [[sample_company::{{{sample_company}}}]]
+
});
|-
+
</script></html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?Coexpression_dpi_cluster_scores_median_value|intro=<table class="relative-exp-of-coexp stripe cell-border order-column compact"><html><thead></html><tr><th>Coexpression cluster</th><th>score</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table>|link=none|format=template|template=Coexpression_dpi_cluster_scores_median_in_ffsample|limit=5000|searchlabel=|default=No results for this sample}}
! [[Property:sample_donor(cell lot)|donor(cell lot)]]
+
|<br><br>}}
| [[sample_donor(cell lot)::{{{sample_donor(cell lot)}}}]]
+
|Mouse (Mus musculus)=
|-
+
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
! [[Property:sample_note|Note]]
+
|<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|searchlabel=}}
| [[sample_note::{{{sample_note}}}]]
+
|<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]]);
 +
}
 +
        $('#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>
| colspan="2" style="text-align: center;  background-color: skyblue;" |RNA info
+
|no result for this sample
|-
+
}}
! [[Property:sample_id|sample_id]]
 
| [[sample_id::{{{sample_id}}}]]
 
|-
 
! [[Property:rna_tube_id|tube_id]]
 
| [[rna_tube_id::{{{rna_tube_id}}}]]
 
|-
 
! [[Property:rna_box|box]]
 
| [[rna_box::{{{rna_box}}}]]
 
|-
 
! [[Property:rna_position|position]]
 
| [[rna_position::{{{rna_position}}}]]
 
|-
 
! [[Property:rna_lot_number|lot_number]]
 
| [[rna_lot_number::{{{rna_lot_number}}}]]
 
|-
 
! [[Property:rna_catalog_number|catalog_number]]
 
| [[rna_catalog_number::{{{rna_catalog_number}}}]]
 
  
|-
+
<br>
! [[Property:rna_rin|RIN]]
+
{{Fontsize|3|TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample}}
| [[rna_rin::{{{rna_rin}}}]]
+
----
|-
+
{{Fontsize|3|JASPAR motifs}}{{#info:<b>Summary:</b>Association of JASPAR motif to the promoter expression in this
! [[Property:rna_od260/230|OD260/230]]
+
sample. Pearson's correlation between the number of TFBSs estimated by
| [[rna_od260/230::{{{rna_od260/230}}}]]
+
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
! [[Property:rna_od260/280|OD260/280]]
+
matrix, and the tail probability of the normal distribution corresponding
| [[rna_od260/280::{{{rna_od260/280}}}]]
+
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>
! [[Property:rna_sample_type|sample_type]]
+
<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>
| [[rna_sample_type::{{{rna_sample_type}}}]]
+
{{#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}}
! [[Property:rna_extraction_protocol|extraction_protocol]]
+
|<br>
| [[rna_extraction_protocol::{{{rna_extraction_protocol}}}]]
+
}}
|-
+
<br><br>
! [[Property:rna_weight_ug|weight_ug]]
+
{{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
| [[rna_weight_ug::{{{rna_weight_ug}}}]]
+
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>
! [[Property:rna_concentration|concentration]]
+
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
| [[rna_concentration::{{{rna_concentration}}}]]
+
|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]){
  
{{{name}}}. Its transcriptome profile can be found in Genome Browsers ( [https://fantom5-collaboration.gsc.riken.jp/zenbu/dex/#section=Experiments;search={{#replace:{{{id}}}|FF:|}} zenbu] and  [https://fantom5-collaboration.gsc.riken.jp/ucsc/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] )
+
$('.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>
 +
[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}}} |
|style="background-color: #F0F0F0" |
+
<div style="width:25%; float:left;">
Specific TFs
+
<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>}} }}
*...
 
*...
 
|style="background-color: #F0F0F0" |  
 
Specific genes
 
*...
 
*...
 
*...
 
|style="background-color: #F0F0F0" |  
 
Specific TSS regions
 
*...
 
*...
 
*...
 
|style="background-color: #F0F0F0" |  
 
Specific motifs
 
*...
 
*...
 
*...
 
|style="background-color: #F0F0F0" |
 
De-novo motifs
 
*...
 
*...
 
*...
 
|}
 
  
== Parent Ontologies ==
+
</div>
{{#if: {{{ancestors_in_cell_lineage_facet}}} | yes}}
+
}}
{{#if: {{{ancestors_in_disease_facet}}} | yes | no}}
+
<div style="clear:both;"></div>
{{#if: {{{ancestors_in_anatomy_facet}}} | {{#show:{{PAGENAME}}}} |}}
 
  
{{#arraymap:{{{ancestors_in_cell_lineage_facet|}}}|,|x|{{#set:ancestors_in_cell_lineage_facet=x}}}}
+
{{Fontsize|3|Ancestor terms (development)}}{{#info:<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br>
{{#arraymap:{{{ancestors_in_disease_facet|}}}|,|x|{{#set:ancestors_in_disease_facet=x}}}}
+
<b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>
{{#arraymap:{{{ancestors_in_anatomy_facet|}}}|,|x|{{#set:ancestors_in_anatomy_facet=x}}}}
+
[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=$}}
 +
}}
  
{{FULLPAGENAME}}
+
{{#arraydefine:accession_numbers_array|{{{accession_numbers}}}|!}}{{#loop: k
{{PAGENAME}}
+
  | 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}}}}|}}
 +
}}
 +
|}}
  
{{#show:{{FULLPAGENAME}}}}
 
{{#ask:[[id::{{{id}}}]]|?Ancestors in anatomy facet}}
 
  
<div>
+
{{#set:sample_category={{{sample_category}}}}}
{{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | http://upload.wikimedia.org/wikipedia/commons/thumb/1/11/Uomo_Vitruviano.jpg/86px-Uomo_Vitruviano.jpg | }}
+
{{#set:profile_hcage={{{profile_hcage}}}}}
{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | http://genome.ucsc.edu/images/Mus_musculus.jpg | }}
+
{{#set:profile_rnaseq={{{profile_rnaseq}}}}}
{{#ifeq: {{{sample_species}}} | Rat (Rattus rattus) |  http://genome.ucsc.edu/images/Rattus_norvegicus.jpg | }}
+
{{#set:profile_srnaseq={{{profile_srnaseq}}}}}
{{#ifeq: {{{sample_species}}} | Dog (Canis lupus familaris) | http://genome.ucsc.edu/images/Canis_familiaris.jpg | }}
+
{{#set:profile_cagescan={{{profile_cagescan}}}}}
{{#ifeq: {{{sample_species}}} | Chicken (Gallus gallus) | http://genome.ucsc.edu/images/Gallus_gallus.jpg | }}
+
{{#set:sample_strain={{{sample_strain}}}}}
</div>
+
{{#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]]
 +
 +
<html>
 +
<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>

Latest revision as of 07:52, 23 May 2019


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



FANTOM5 (FF) ontology


Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

Ancestor terms (non development)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