Of the 1,012 unique human mitochondrial genes described in MitoCarta [22], we analyzed 966 autosomal mitochondrial genes. This number was obtained after removing 13 genes encoded by the mitochondrial DNA and 31 mitochondrial genes that lie on the X and Y chromosomes, as they were not analyzed in the GWA studies and meta-analyses used in this work. Two autosomal genes were removed, as they were absent from the human gene list used for our analyses. For the DIAGRAM+ T2D meta-analysis, the effective gene set size of all mitochondrial genes was 885 genes, as 11 genes did not have any genotyped or imputed SNPs within their extended gene boundaries (110 kb upstream and 40 kb downstream to the most extreme transcript boundaries) and 70 genes were removed following physical proximity adjustment described in the GSEA section. There are 110,060 unique SNPs that fall within the gene regions of the 966 nuclear-encoded mitochondrial genes, based on the DIAGRAM+ meta-analysis (4.9% of all SNPs).
