Question: PathScan: How to control for gene-specific differences in background mutation rates?
1
gravatar for Christian
4.7 years ago by
Christian2.8k
Cambridge, US
Christian2.8k wrote:

I am wondering about the proper way to control for gene-specific differences in the background mutation rate when using Genome MuSiC PathScan.

From what I understand from the documentation, PathScan assumes a uniform background mutation rate for all genes that enter the analysis. I think this assumption is wrong and I am thus worried about its consequences in terms of pathways that are erroneously identified as significantly mutated.

Is there any way to deal with this? Is it for example a viable strategy to first identify significantly mutated genes with Genome MuSiC SMG  (which considers gene-specific differences in the background mutation rate) and let only the significantly mutated genes enter the pathway analysis? But I assume that this would result in a loss of power, because we are no longer looking at all mutations affecting a particular pathway at once.

Are there maybe alternative tools that consider gene-specific mutation rates for pathway enrichment analysis in cancer?

ADD COMMENTlink modified 4.6 years ago by Biostar ♦♦ 20 • written 4.7 years ago by Christian2.8k

Good question. The assumption of uniform background rates is completely inappropriate. I'm trying to deal with the same issue using hierarchical models, but it's a bit tricky; so I'd be very interested to know of any other tools

ADD REPLYlink written 4.7 years ago by russhh4.7k
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