Template:F5samples: Difference between revisions
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</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/custom/expoconvert.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> | <script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script> | ||
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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() { | $(document).ready(function() { | ||
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|Mouse (Mus musculus)= | |Mouse (Mus musculus)= | ||
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | {{#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|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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</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> | ||
</html> | </html> | ||
<br>|}}<!-- end of if(isHumanOrMouse) --> | <br>|}}<!-- end of if(isHumanOrMouse) --> | ||
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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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[[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_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> |
Revision as of 15:51, 16 January 2020
Name: | {{{name}}} |
---|---|
Species: | {{{sample_species}}} |
Library ID: | {{{library_id}}} |
Sample type: | {{{sample_category}}} |
Genomic View: |
Additional information | ||||||||||||||||||||||||||||
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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