*4.8. Gene Set Enrichment Analysis (GSEA) and Gene Ontology Enrichment Analysis (GOEA)*

To test whether the differentially expressed genes identified by our cutoff criteria (fold change > 1.5, adjusted *p*-value (adjp) < 0.05) are associated with specific biological functions we performed gene ontology enrichment analysis (GOEA http://bioinformatics. sdstate.edu/go/) (accessed on 25 November 2020) [26] and gene set enrichment analysis (GSEA, Broad Institute http://www.gsea-msigdb.org/gsea) [27] accessed on 26 December 2020) [28]. For GOEA annotation Fisher's exact test is used to determine if different annotation terms are enriched among the differentially expressed genes. Gene ontology (GO) terms showing a Fisher's exact *p*-value < 0.05 were considered significantly enriched. To calculate GSEA we used the Molecular Signature Database (MSigDB) to investigate the overlap between our gene lists and known annotated gene sets. Gene sets showing a false discovery rate (FDR) <0.05 were considered as significantly enriched among differentially expressed genes. We considered the biological processes associated with significantly enriched GO terms or MSigDB gene sets as being potentially relevant for endometriosis.
