PAN - TCGA survival analysis

Question

[rt.cgen]

I am trying to run survival analysis (KM plot) for a set of genes on PAN-TCGA dataset, I am aware of tools like RTCGAToolBox that can help in downloading and running these analysis for a cancer type at a time. I have also tried cbioportals' web-API and R package ("cgdsR"). I finally resorted to using R package "survival" but that isn't helpful either. There are easy ways to run survival analysis for one cancer type but so far I haven't found anything that computes survival analysis for many cancer type for a set of genes.

TL;DR - Survival analysis for cumulative TCGA dataset (spanning a few TCGA dataset) for a set of genes.

Any help would be greatly appreciated. TIA

I am reposting this question since I did not get any response earlier.

Answer 1

[Jordan Anaya]

I'm not quite sure what type of plot you want to make. If you want to look at several genes in a single cancer I can understand that. For example, you can compare patients with high expression of both genes X and Y vs. low expression of both X and Y. To perform a pan-cancer Kaplan plot are you just planning on merging all of the patients together?

If that is what you are looking to do you could download the data from OncoLnc: http://www.oncolnc.org/ for each cancer and gene and then make your plot with whatever software you want. One concern that I would have is the RSEM values are normalized by the TCGA per cancer so I don't know how appropriate it is to compare the RSEM values in one cancer to the RSEM values in another cancer.

[rt.cgen]

I am trying to make KM plots for a set of genes in multiple cancer types at the same time. I am planning on merging clinical data set for PAN TCGA to make pan-cancer KM plots but I am not sure if that's correct approach, because I would need to merge mutation data for all cancers as well.