Survival analysis based on gene signature
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9 weeks ago
Sy80 ▴ 10

Hi all

Does anyone have any advice on how to create a KM plot (in R) based on the expression of a set of genes (hi vs low)?

I am able to test the genes individually (and generate survival curves for each gene) but would like to assess whether the signature has a prognostic effect in the TCGA datasets.

Any help is much appreciated - thank you!

signature survival gene TCGA • 306 views
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In such cases, I would suggest first doing a single-sample gene set enrichment analysis (like GSVA, ssGSEA) and then doing a survival analysis based on scores from interested pathways.

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Great idea. I will give this a try. Thank you!

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The Cox regression is an option for multivariate survival analysis

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I will try Cox regression with single sample enrichment scores as a continuous variable as per suggestions. Thank you!

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