Question: How to perform GSEA analysis with survival phenotype?
2
gravatar for blairzxy
2.5 years ago by
blairzxy30
blairzxy30 wrote:

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!

survival gsea • 1.0k views
ADD COMMENTlink modified 2.5 years ago by Sean Davis25k • written 2.5 years ago by blairzxy30
2
gravatar for Sean Davis
2.5 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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.

ADD COMMENTlink written 2.5 years ago by Sean Davis25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1976 users visited in the last hour