We used an R package gProfileR (https://biit.cs.ut.ee/gprofiler/gost) for running gene ontology analysis, as it allows a ranked gene list, which resembles Gene Set Enrichment Analysis (GSEA). Because it does not require a P-value threshold to select significantly associated genes, it allows comparing gene ontologies for differently powered GWAS in a non-bias fashion. After ranking genes based on Z-scores generated by H-MAGMA, we ran gene ontology analysis using this command line: gprofiler(<Ranked gene list>, organism=“hsapiens”, ordered_query=T, significant=T, max_p_value=0.05, min_set_size=15, max_set_size=600, min_isect_size=5, correction_method=“fdr”, hier_filtering=“moderate”, custom_bg=background gene set, include_graph=T, src_filter=“GO”)
