Template:F5samples: Difference between revisions
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<style type="text/css" title="currentStyle"> | <style type="text/css" title="currentStyle"> | ||
@import "/5/sstar/rb_js/html5button/datatables.css"; | @import "/5/sstar/rb_js/html5button/datatables.css"; | ||
</style> | </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/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/html5button/datatables.js"></script> | ||
<script type="text/javascript" src="/5/sstar/rb_js/custom/expoconvert.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> | </html>{{#outerfile_existance: /5/sstar/sstar_img/f5samples/riken_cellimg/{{PAGENAME}}.jpg |<html> | ||
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{{#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}}} | | {{#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}} | ||
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}} | }} | ||
|}} | |}} | ||
--> | |||
{{#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 }} }}]|, }}</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 }} }}]|, }}</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 | ||
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<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}}| | ||
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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("!"); | ||
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}} | }} | ||
{{#vardefine:isHumanOrMouse|{{#switch:{{{sample_species}}}|Human (Homo sapiens)=1|Mouse (Mus musculus)=1|0}}}} | {{#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>[ | {{#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() { | $(document).ready(function() { | ||
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buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | ||
lengthMenu: [[10, 50, -1], [10, 50, "All"]], | lengthMenu: [[10, 50, -1], [10, 50, "All"]], | ||
columnDefs: [{ targets: [0], visible: true},{ targets: [0], visible: true}], | |||
columns:[ | |||
{title:"MCL coexpression id", visible:true}, | |||
{title:"Coexpression_dpi_cluster_scores_median_value", visible:true} | |||
], | |||
order: [[ 1, 'desc' ]] | order: [[ 1, 'desc' ]] | ||
}); | }); | ||
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|Mouse (Mus musculus)= | |Mouse (Mus musculus)= | ||
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | {{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | ||
|<h3>$</h3>{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]| | |<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> | ||
}}}} | }}}} | ||
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the median expression in the FANTOM5 collection is shown. Value is log10 | the median expression in the FANTOM5 collection is shown. Value is log10 | ||
transformed.<br><b>Analyst:</b>NA | transformed.<br><b>Analyst:</b>NA | ||
<br><br>link to dataset.<br>[ | <br><br>link to dataset.<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression data]}}}} | ||
{{#if: {{#pos:{{{repeat_enrich_byfamily}}}|,}} | | {{#if: {{#pos:{{{repeat_enrich_byfamily}}}|,}} | | ||
<html><script type="text/javascript"> | <html><script type="text/javascript"> | ||
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to the Z-score is taken as the resulting P-value. Lower P-value indicates | 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> | more (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br> | ||
<br><br>link to dataset.<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}}|&|$ | {{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | ||
|library id: $<span id="related_jaspar_table_export_tool"></span>{{#ask:[[jaspar_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]| | |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> | ||
}} | }} | ||
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{{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 | {{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> | 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>[ | <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}}|&|$ | {{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | ||
|library id: $<span id="related_novel_table_export_tool"></span>{{#ask:[[novel_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]| | |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> | ||
}} | }} | ||
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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"); | ||
} | } | ||
} | } | ||
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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"); | ||
} | } | ||
} | } | ||
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{{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 | {{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> | <br><br>link to source data<br> | ||
[ | [//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data] | ||
}}<br> | }}<br> | ||
{{#if: {{{ancestors_in_cell_lineage_facet}}} | | {{#if: {{{ancestors_in_cell_lineage_facet}}} | | ||
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{{Fontsize|3|Ancestor terms (development)}}{{#info:<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br> | {{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> | <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> | <br> | ||
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$(document).ready(function() { | $(document).ready(function() { | ||
if($('.homer-table')[0]){ | if($('.homer-table')[0]){ | ||
var | 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> | </script> | ||
</html> | </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