Finding biomarkers between tumor and normal samples
Hello everyone,
I have a total RNASeq data of 10 PDAC tumors and Normal samples. The DE analysis was performed by DESeq2, and I have a list of all the differentially expressed genes in the dataset.
1) How am I suppose to find biomarker genes which are significantly enriched in the Tumor condition as compared to the normal? 2) And can we find likewise significant biomarkers for every tumor sample?
Thank you in advance.
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First for biomarkers you need to specify what kind of biomarker you are looking for. As you may know, there is three main biomarkers in cancer studies: diagnostics, prognostics, and predictive. Your study design largely defines what kind of biomarker you likely find ain a study. You may be able to find a candidate gene as a biomarker in a study, but it needs to be validated in other independent studies. My answer to your second question: NO.