Question: Pathway enrichment for Copy Number Alterations (CNA)
1
gravatar for Chirag Nepal
3.8 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

Hi all,

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

 

thanks !

cnv genome music cna • 1.2k views
ADD COMMENTlink modified 3.7 years ago by Chris Miller21k • written 3.8 years ago by Chirag Nepal2.2k
0
gravatar for Chris Miller
3.7 years ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:

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.

ADD COMMENTlink written 3.7 years ago by Chris Miller21k

Thanks Chris !

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

ADD REPLYlink written 3.7 years ago by Chirag Nepal2.2k
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