How to perform GSEA analysis with survival phenotype?

Question

[blairzxy]

I want to use GSEA to do enrichment analysis with continuous survival days along with the survival status.

The problem for traditional GSEA is that it only allow me to input one column of phentype and I couldn't specify it to perform cox regression analysis. To solve this, I tried to perform cox regression first and input the gene list into GSEA website to get the enriched pathways. However, I'm not sure if it's the right way to do. It would be great if someone familiar with this type of questions could help me out.

Thanks so much!

Answer 1

[Sean Davis]

Your approach of using cox regression to get an ordered list of genes is fine. From there, you can proceed to threshold based on some cutoff for significance or use a rank-based GSEA approach.