Mutations to genes with weights (analysis)

Analysis title

Mutations to genes with weights

Provider

Biosoft

Class

MutationWeightGECalculator

Plugin

biouml.plugins.genomeenhancer (Genome Enhancer)

Description

Convert mutations to genes and calculates specific mutation weight (w) for each variation depending on it’s location in gene body and gene flanking regions (5' region size upstream and 3' region size downstream of the gene body).

• w = 0.7 for variations in exon area
• w = 1.3 for variations in promoter region (-1000bp upstream and 100bp downstream of TSS),
• w = 1.0 for variations in other locations.

Parameters:

• Input track – Track with mutations
• Species – Species to which analysis should be confined
• 5' region size – Include 5' region (promoter) of given size in bp
• 3' region size – Include 3' region of given size in bp
• Promoter from – Promoter from
• Promoter to – Promoter to
• Types of resulting column – Types of resulting column in gene set
• Output track – Track with mutations and weight column
• Output table – Output table with genes mapped from mutations