GSEA report, What does it mean gene sets are upregulated?

Question

[Amr]

What does it mean gene sets are upregulated in phenotype for example cancer ?

After performing GSEA for phenotypes normal vs cancer, the report has been obtained and in it:

35 / 50 gene sets are upregulated in phenotype cancer. I know the meaning of a gene is up regulated or down regulated but what does it mean gene sets are up regulated? does it mean that all genes inside the gene sets were up regulated ? or what ?

Thanks

Answer 1

[Rafael Soler]

Hello

GSEA is a tool that determines whether a set of genes defined a priori shows concordant and statistically significant differences between two biological states. For that reason, upregulated gene sets mean that the genes contained in these gene sets are (the vast majority) upregulated, so the program determines that this gene set is upregulated.

Best

[Amr]

Thank you for your explanation, ok then why I obtained enriched gene sets for normal phenotype? although it's normal so why there are differences in these genes? does it mean that this patient suffer from disease maybe diabetes or hypertension? I mean not cancer

[Rafael Soler]

The upregulated terms in the normal condition mean that these genes are downregulated or repressed in the cancer condition. In other words, these genes are repressed in cancer.

Best

[Amr]

Thanks genius :)