quering publicaly available data sets of RNA-seq and constructing a Kaplan Meier plot

Question

[moutazhatem.mh]

Hi all, I often see in publications querying big data repositories using a gene of interest or genes signatures and showing the results as a Kaplan Meier plot comparing between patients with high expression and patient with low expression.

my question is how can I do such analysis?

[lieven.sterck]

A good starting point would be to check the publications you refer to and look in detail in them on how they created those plots.

(not saying it is the only way, or even that that info will be available from those publications, but it is a good starting point nonetheless :) )

Answer 1

[GenoMax]

Kevin Blighe has a tutorial available: Survival analysis with gene expression

Answer 2

[EagleEye]

Hi,

For quick overview of your gene-of-interest, protein atlas (in pathology section) includes Kaplan Meier plots for individuals cancer types.

Example: Status of BRCA1 gene in breast cancer (higher expression of BRCA1 shows poor survival in patients).

https://www.proteinatlas.org/ENSG00000012048-BRCA1/pathology/breast+cancer