Calculate weighted mutation score (analysis)

Analysis title

Calculate weighted mutation score

Provider

Biosoft

Class

MutatedGenesGERankCalculator

Plugin

biouml.plugins.genomeenhancer (Genome Enhancer)

Description

This method is applied to the result of "Mutations to genes with weights" analysis, that converts mutation track to gene set and calculates weights based on mutation positions.

This method calculates the weighted mutation score using the following formula:

Weighted score = In_disease * In_transpath * Gene mutation weight, where

• In_disease = 2.0 for genes assigned to selected diseases,
• In_transpath = 1.5 for genes mapped to Transpath pathways,
• and In_disease = In_transpath = 1.0 in all other cases.

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:

W = 1.0 * (Count_total - Count_in_promoters - Count_in_exons) + 1.3 * Count_in_promoters + 0.7 * Count_in_exons

Parameters:

• Input table – Input table
• Use simple weight – Use weight from selected column, omit mutation weight calculation by counts
• Column with total count or weight – Column with total count or weight
• Column with exone count – Column with exone count
• Column with promoter count – Column with promoter count
• Species – Species
• Diseases list – Diseases list
• Result table – Result table