Today we present to you a way to explore the effect of CNAs on gene expression on a cohort of cancer samples with the help of Gitools. To do this you first need to prepare a multi-dimensional genomic data matrix containing both CNA and expression values. We have described before how it can be loaded into Gitools – see our case study six: Studying multi-dimensional cancer data with Gitools, and our previous blog post: Exploring multiple cancer genomic alterations with Gitools.
Once you have the genomic alterations and expression data in Gitools you can see if the samples with a particular type of genomic alteration (eg. gain) have different expression values than those without this alteration. In some cases this can be easily viewed in the heatmaps (see figure above), however if we want to corroborate this observation statistically we can also use the new Group Comparisons analysis, which we have added in our 1.6.0 release of Gitools, to test if the expression values in the samples with the genomic alteration are different than in those samples without this alteration.
The guide on how to explore the effect of alteration on expression can be found as a new chapter of this case study where it is explained step by step – and it also contains the following video: