We next tested empirically the performance of MAGENTA on LDL cholesterol, HDL cholesterol and triglyceride blood levels. The molecular pathways involved in lipid and lipoprotein metabolism are relatively well known, and many of the genes that lie near the 30 SNPs so far reported to be associated with one or more of these traits function in known processes related to lipid or lipoprotein metabolism [34]. MAGENTA was applied to three GWA meta-analyses [34], whose sample size (19,840 individuals) is on the same order of magnitude as that of the largest available T2D meta-analysis (DIAGRAM+) used below to test for mitochondria-related associations with T2D. A total of 51 (partially overlapping) gene sets related to lipid, lipoprotein and fatty acid metabolism were tested (defined by PANTHER [42] and Gene Ontology [43] databases; see Materials and Methods). Of these gene sets, we found biological processes related to lipid, lipoprotein and fatty acid metabolism, binding and transport activities, and triglyceride metabolism to be significantly enriched for LDL cholesterol, HDL cholesterol and/or triglyceride associations after Bonferroni correction (top gene sets are listed in Table 2;
