Pathway enrichment for Copy Number Alterations (CNA)

Question

[Chirag Nepal]

Hi all,

I used genome music to determine enriched pathways in SNV. Are there any tools to do enriched pathways analysis in CNA.

Thanks!

Answer 1

[Chris Miller]

It's a difficult problem, because a typical arm-level CNA can encompass hundreds or thousands of genes. If you have a cohort, you might try running something like GISTIC to identify the focal peaks of CN, and then run that much smaller set of genes through enrichment analysis.

[Chirag Nepal]

Thanks Chris !

I have done the same. I wanted to know if there were some better ways to do.