Top GSEA results for lipid-related pathways using LDL cholesterol, HDL cholesterol, and triglyceride GWA meta-analyses.

The most significant lipid-related biological gene sets with a gene set enrichment p-value of <0.015 are presented using GWA meta-analyses of LDL cholesterol, HDL cholesterol and triglyceride blood levels across a total of 19,840 individuals. Complete results for all 51 lipoprotein and lipid related pathways are presented in Tables S5, S6, S7. GSEA p-values marked with an asterisk are significant under a conservative Bonferroni correction (each database was corrected separately due to considerable overlap between gene sets across the different databases). The number of genes per gene set analyzed with MAGENTA in column three is after removing genes without SNPs in their extended gene boundaries and after adjusting for chromosomal proximity between subsets of genes in a gene set (see Materials and Methods). The fifth column contains GSEA p-values following exclusion of genes near validated SNPs for the relevant lipid trait (19 genes for LDL cholesterol, 20 genes for HDL cholesterol and 19 genes for triglyceride levels; taken from Table 2 in [34]). The sixth column lists all genes near validated lipid SNPs (as of [34]) that fall in a given gene set, including the genes removed due to adjustment for physical proximity in the genome. GO stands for Gene Ontology, BP for Biological Process, and MF for Molecular Function.