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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";
@import "/5/sstar/rb_js/datatables/extras/TableTools/media/css/TableTools.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/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>
<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>{{#outerfile_existance: /5/sstar/sstar_img/f5samples/riken_cellimg/{{PAGENAME}}.jpg |<html>
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               }
               }
             },
             },
            { title: "" },
             { title: "Log10(Relative expression over median)" },
             { title: "Log10(Relative expression over median)" },
             { title: "TPM" },
             { title: "TPM" },
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</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">
{{#vardefine:isHumanOrMouse|{{#switch:{{{sample_species}}}|Human (Homo sapiens)=1|Mouse (Mus musculus)=1|0}}}}
{{#ifeq:{{#var:isHumanOrMouse}}|1|<br><br>{{Fontsize|3|Co-expression clusters with enriched expression in this sample}}{{#info:Ranked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters data]}}<html><script type="text/javascript">
$(document).ready(function() {
$(document).ready(function() {


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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|}}]]|mainlabel=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|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>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression data]}}}}
<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>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression data]}}<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|_}}]]|mainlabel=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}}
|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>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression data]}}<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|_}}]]|mainlabel=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}}
|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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</style>
</style>
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/media/js/dataTables.Percentage.js"></script>
<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>
</html>
<br>
<br>|}}<!-- end of if(isHumanOrMouse) -->
{{Fontsize|3|FANTOM5 (FF) ontology }}
{{Fontsize|3|FANTOM5 (FF) ontology }}
----
----
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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>
[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data]
[//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>
[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data]
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data]
}}
}}
<br>
<br>
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[[Category:FF_Ontology]]
[[Category:FF_Ontology]]
[[Category:FF_Samples]]
[[Category:FF_Samples]]
<html>
<script type="text/javascript">
$(document).ready(function() {
    if($('.homer-table')[0]){
        var homer_denovo_table2 = $('.homer-table').DataTable({
                        dom: 'Blfrtip',
                        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
                        lengthMenu: [[5, 50, -1], [5, 50, "All"]],
scrollCollapse: true,
                        columnDefs: [
                            { targets: 0, orderable: false},
                            { targets: 1, orderable: false},
                            { targets: 2, width: "100pt", "type": "numeric"},
                            { targets: 3, orderable: false, type: "percent"},
                            { targets: 4, orderable: false, type: "percent"},
                            { targets: 5, orderable: false}
                        ]
        });
    }
});
</script>
</html>

Revision as of 14:25, 29 May 2020


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)<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

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