How to verify concurrent copy number aberration with gene expression?

Question

[Avro]

Hi everyone,

I have used GITIC2.0 to identify potentially amplified genes in a cohort of breast tumors. However, before I verify protein levels, I would like to verify gene expression levels. I am reading about gene expression analysis. Usually, you verify gene expression between two states. I was thinking about two strategies:

1. Separate patients based on GISTIC2.0 call (gene amplified or not) and perform a t-test on each single gene of interest?
2. Separate patients based on GISTIC2.0 call and plot whisker plots (CNA and mRNA) to see if there is overlap or not?

Are these good strategies?

Thank you very much for your time.

Answer 1

[Pascal]

Hi Avro,

I am doing a similar thing. I think performing differential expression tests between single gene is a possibility. You could also calculate the correlation between CNV and gene expression.