What is the cutoff used for define high or low expression level of gene for survival analysis

Hi everyone

In RNA-seq analysis, we need to separate samples into two groups for survival analysis. How can I define high level or low level for a gene according to counts or FPKM. Use median? average or quantile?

In TCGA or Oncomine, how are they define the cutoff for a gene ?

Thanks.

There’s no definitive answer to your question. I would not advise going by the median or average. Quantile is a reasonable idea, or tertiles, with the higher third being regarded as “high expression”.

An even better idea would be to convert your data to the Z scale, i.e., standard deviations from the mean, and then choose absolute 3, 4, 5, or 6 (3, 4, 5, or 6 standard deviations from the mean) as potential cut-offs. I trust that you have QC’d your data already and that low count transcripts have been removed.