https://wiki.biouml.org/index.php?action=history&feed=atom&title=Calculate_weighted_mutation_score_%28analysis%29 2026-04-13T07:59:52Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Calculate_weighted_mutation_score_(analysis)&diff=8871&oldid=prev 2020-12-09T11:15:01Z

<p>Protected &quot;<a href="/index.php/Calculate_weighted_mutation_score_(analysis)" title="Calculate weighted mutation score (analysis)">Calculate weighted mutation score (analysis)</a>&quot;: Autogenerated page (‎[edit=sysop] (indefinite))</p> <table class='diff diff-contentalign-left'> <tr style='vertical-align: top;'> <td colspan='1' style="background-color: white; color:black;">← Older revision</td> <td colspan='1' style="background-color: white; color:black;">Revision as of 11:15, 9 December 2020</td> </tr></table>

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<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;Analysis title<br /> :[[File:Default-analysis-icon.png]] Calculate weighted mutation score<br /> ;Provider<br /> :[[Biosoft]]<br /> ;Class<br /> :{{Class|biouml.plugins.genomeenhancer.analysis.MutatedGenesGERankCalculator}}<br /> ;Plugin<br /> :[[Biouml.plugins.genomeenhancer (plugin)|biouml.plugins.genomeenhancer (Genome Enhancer)]]<br /> <br /> ==== Description ====<br /> This method is applied to the result of &quot;[[Mutations to genes with weights (analysis)|Mutations to genes with weights]]&quot; analysis, that converts mutation track to gene set and calculates weights based on mutation positions.<br /> <br /> This method calculates the weighted mutation score using the following formula:<br /> <br /> Weighted score = In_disease * In_transpath * Gene mutation weight, where<br /> <br /> * In_disease = 2.0 for genes assigned to selected diseases,<br /> * In_transpath = 1.5 for genes mapped to Transpath pathways,<br /> * and In_disease = In_transpath = 1.0 in all other cases.<br /> <br /> Gene mutation weight is taken from ''Column with total count or weight'' in case of ''Use simple weigth'' is checked. Otherwise it is calculated as follows:<br /> <br /> W = 1.0 * (Count_total - Count_in_promoters - Count_in_exons) + 1.3 * Count_in_promoters + 0.7 * Count_in_exons<br /> <br /> ==== Parameters: ====<br /> <br /> * '''Input table''' – Input table<br /> * '''Use simple weight''' – Use weight from selected column, omit mutation weight calculation by counts<br /> * '''Column with total count or weight''' – Column with total count or weight<br /> * '''Column with exone count''' – Column with exone count<br /> * '''Column with promoter count''' – Column with promoter count<br /> * '''Species''' – Species<br /> * '''Diseases list''' – Diseases list<br /> * '''Result table''' – Result table<br /> <br /> [[Category:Analyses]]<br /> [[Category:Genome enhancer (analyses group)]]<br /> [[Category:Biosoft analyses]]<br /> [[Category:Autogenerated pages]]</div>

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