The most significantly overrepresented gene ontology processes.

The 589 genes identified as having GWAS SNP signals p<0.001 were used: APOE was included in the gene list. In this analysis one SNP was not allowed to add more than one gene to any gene ontology category. “Study-wide p-value” is the probability of obtaining by chance at least one GO category with a category-specific enrichment p-value at least as significant as that observed. . There are genes in the pathways that are in close proximity and that are both included because of the same significant SNP in both genes, as genes were associated with a SNP if it mapped within 20kb of a given gene: details of these genes are in Tables 5 and 6. If CR2, IL18RAP and IL18R1 are removed (effectively counting CR1/CR2 as one signal and IL1RL1/IL18RAP/IL18R1 as one signal) the GO analysis yields GO:0006958 and GO:0002455: 27 genes, 5 significant (0.60 expected) p = 0.0002, GO:0006956: 36 genes, 5 significant (0.79 expected) p = 0.0004, GO:0002541: 37 genes, 5 significant (0.81 expected) p = 0.0004 and GO:0045087: 117 genes, 8 significant (2.58 expected) p = 0.0044. Only processes are presented. The full data are available in Table S1.