Question: How to make a survival plot for a gene between High expression and low expression samples?
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12 months ago by
Biologist150 wrote:


I have downloaded TCGA data for lung cancer. It is counts data. I want to make survival plot for a specific gene between high expression and low expression samples. I want to make both Overall survival and Disease free survival plots. It should look something like this Kaplan-Meier survival analysis of OS (P < 0.001, log-rank) and DFS (P < 0.001, log-rank) rate in 144 patients based on the expression level of SNHG20 expression

How to divide the samples into high and low expression samples based on expression of single gene? I have counts data. Is there any cutoff for that?

plot survival rna-seq tcga R • 601 views
ADD COMMENTlink written 12 months ago by Biologist150

You could plot the data and see how it spreads and use this do define the cutoff (e.g. if you notice there is clear separation into 2 groups). Another approach might be to use z-score and take +-1-2 score as high and low..

ADD REPLYlink written 12 months ago by roy.granit800

Based on z-score, so +1 and +2 are high, -1 and -2 are low? And for this survival do I also need to consider normal samples? or only tumor samples?

ADD REPLYlink written 12 months ago by Biologist150

Yes, you can try a cutoff on 1 or 2 and see how it looks like ( for a two sided distribution the critical Z score values when using a 95% confidence level are -1.96 and +1.96). This task could be easily accomplished using

I would plot cancer and normal on different charts (not sure there is point in showing a survival chart for normal individuals).

ADD REPLYlink modified 12 months ago • written 12 months ago by roy.granit800

Ok. Thankyou. then I will convert counts data to logCPM and then to Z-score. From that samples with values less than -1.96 are low and samples with more than +1.96 are high and then make a survival plot for that.

ADD REPLYlink written 12 months ago by Biologist150
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