a question about figure on "Survival" based on mRNA expression

[Jun mei Hu Frisk]

Hi,

My name is Jun Mei Hu Frisk. I recently found your website, and it has been very helpful for my research.

Part of my research focuses on breast cancer, and in my current project I am studying how human chymase (CMA1) affects breast cancer in patients. Following your mRNA analysis tutorial, I divided the samples into two groups — CMA1-high and CMA1-low — based on mRNA expression levels. One of the most interesting findings so far is the survival data. Using the dataset “Breast Invasive Carcinoma (TCGA, Cell 2015),” I got a survival curve from your website (file attached). The y-axis is labelled “Probability of Overall Survival.”

When I check the original Cell paper (https://www.cell.com/cell/fulltext/S0092-8674(15)01195-2?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867415011952%3Fshowall%3Dtrue), their Figures 5D and 5E show survival statistics with the y-axis labelled “Percent survival.”

I am wondering how the survival plots on your website are generated. How is “Probability of Overall Survival” calculated, and how does it relate to the “Percent survival” shown in the original publication? Could you please help me understand the difference?

Your platform has the potential to become a very important resource for researchers. As a researcher, I need to fully understand the figures presented on your website, so any clarification you can provide would be greatly appreciated.

Best regards,
Jun Mei

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[JJ Gao]

Hi Jun Mei,

Thanks for reaching out to me. 

Both use the Kaplan–Meier method, a standard way to plot survival over time [1]. There is no difference in meaning or calculation. It’s just labeling: cBioPortal uses decimals (0 to 1), the Cell paper uses percentages (0% to 100%). 

[1] https://en.wikipedia.org/wiki/Kaplan%E2%80%93Meier_estimator

-JJ

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