Hello,

I have association study results between proteins from SomaSCAN assay and cognitive ability. I want to perform enrichment and I am bit uncertain which to use as background. I have about 800 hits after bonferroni correction out of the 7200 total proteins which I have. When I set background to the total number of proteins (including the significant hits) which I used in the assay after filtering proteins out for quality control (e.g. mouse proteins, spuriomers), there is no enrichment after adjustment for bonferroni correction, however there are plenty <0.05 with no correction for multiple testing. When I do not set a background set of genes, I have a lot of enrichment after correction for multiple testing, and the biological processes which are enriched are similar to the ones I have when I do set the background to the proteins in my assay (but which do not survive multiple testing correction). I would appreciate any advice.

example of code

go_enrich <- enrichGO(gene=candidate_genes_map$UNIPROT, 
                      universe=background_genes_map$UNIPROT,
                      OrgDb = org.Hs.eg.db,    # Using human gene annotations
                      keyType = "UNIPROT",    # Gene ID type (Entrez)
                      ont = "BP",              # Biological Processes
                      pvalueCutoff = 0.05,    # Set p-value cutoff for significance
                      pAdjustMethod = "BH")

Many thanks!