Personal tools

Template:F5samples: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(52 intermediate revisions by the same user not shown)
Line 18: Line 18:
{{#ifexpr: {{#pos:{{{cagescan_library_id}}}|Cig}}|<tr><th scope="row" align="right">CAGEScan Library ID:</th><td>{{#replace:{{{cagescan_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>
<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>}}
{{#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_cage}}}{{{microRNAs_novel_srna}}}|ttp}}|
{{#ifexpr: {{#pos:{{{microRNAs_novel_srna}}}|ttp}}
{{#ifexpr: {{#pos:{{{microRNAs_novel_srna}}}|ttp}}
Line 25: Line 26:
}}
}}
|}}
|}}
-->
{{#ifexpr: {{#pos:{{{refex}}}|ttp}}|
{{#ifexpr: {{#pos:{{{refex}}}|ttp}}|
<tr><th scope="row" align="right">RefEX:</th><td>[{{#replace:{{#replace:{{{refex}}}|[|%5b}}|]|%5d}} Specific genes]  </td></tr>|}}
<tr><th scope="row" align="right">RefEX:</th><td>[{{#replace:{{#replace:{{{refex}}}|[|%5b}}|]|%5d}} Specific genes]  </td></tr>|}}
{{#ifexpr: {{#pos:{{{fantom_cat}}}|ttp}}|
{{#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>|}}
<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>
{{#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"
{|class="wikitable mw-collapsible mw-collapsed" style="width:auto"
! Additional information
! Additional information
Line 50: Line 52:
<tr><th>sample type</th><td>{{#switch:{{{rna_sample_type}}}|,,,=NA| =NA |{{{rna_sample_type}}}}}</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>
<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}}}
|}{{#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|{{{hg38bam}}}|{{{hg38ctss}}}}}
|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|{{{mm10bam}}}|{{{mm10ctss}}}}}
|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}}|
}}{{#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}}|
Line 77: Line 79:


for(i=0;i<sub_content.length;i++){
for(i=0;i<sub_content.length;i++){
var temp =sub_content[i];
var temp=sub_content[i];
if(temp != null){
if(temp!= null){
if(temp.length>2){
if(temp.length>2){
var sub_sub_content=sub_content[i].split("!");
var sub_sub_content=sub_content[i].split("!");
Line 123: Line 125:
           buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
           buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
           lengthMenu: [[10, 50, -1], [10, 50, "All"]],
           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' ]]
           order: [[ 1, 'desc' ]]
         });
         });
Line 131: Line 138:
|Mouse (Mus musculus)=
|Mouse (Mus musculus)=
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
{{#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|searchlabel=}}
|<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>
}}}}
}}}}
Line 233: Line 240:
               render: function ( data, type, row, meta ) {
               render: function ( data, type, row, meta ) {
                 var num=row[2];
                 var num=row[2];
return exp_converter(num,2,"e") ;
return exp_converter(num,2,"e");
               }
               }
             }
             }
Line 268: Line 275:
               render: function ( data, type, row, meta ) {
               render: function ( data, type, row, meta ) {
                 var num=row[2];
                 var num=row[2];
return exp_converter(num,2,"e") ;
return exp_converter(num,2,"e");
               }
               }
             }
             }

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
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)<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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Template:F5samples&oldid=4578816"