In GSEA, What does it mean enriched gene sets at nominal p-value <1%? and what does it mean also regarding specific phenotype for example (cancer in cancer vs Normal samples)

Hello

The P-value, or calculated probability, is the probability of finding the observed, or more extreme, results when the null hypothesis of a study question is true. Having a p-value <1% means that is very likely that we will reject the null hypothesis, in your case, that these enriched gene sets are not statistically different between the cancer and the normal samples. In other words, you can say that your enriched gene sets are statistically different between the cancer and the normal samples.

You can watch this video if you have more doubts [StatQuest: P Values, clearly explained][1]

Best


  [1]: https://www.youtube.com/watch?v=5Z9OIYA8He8