Finally, we conducted a pathway analysis using the ALLIGATOR software (13). In the pathway analyses, an SNP association P-value threshold of 0.005 gave the most significant over-representation of genes in pathways in the ‘age at first tooth’ GWAS (see Materials and Methods and Supplementary Material, Table S6a). The top 20 pathways (of the 2276 considered) from this analysis are shown in Table 3; 11 of these pathways had pathway association P-values <0.001 and the P-value associated with this degree of overrepresentation is 0.004 (Supplementary Material, Table S6A). However, none of the association P-value thresholds applied to the ‘number of teeth’ GWAS resulted in a significant over-representation of pathways (Supplementary Material, Table S6B). In Discussion, we focus on the results from the ‘age at first tooth’ GWAS. Table 3.Pathway analysisPathwayNumber of significant genes in pathwayTotal number of genes in pathwayExpected number of genes on listP-valueStudy-wide P-valueE hits/studySignalling events mediated by focal adhesion kinase7056747.11<10−40.0880.13Trail signalling pathway7159147.01<10−40.0880.13p53 pathway221609.24<10−40.0880.13Signalling events mediated by the hedgehog family13514.78<10−40.0880.13Class I PI3K signalling events6654443.8710−40.12850.19Syndecan-1-mediated signalling events7259749.572.0 × 10−40.170.26Glypican pathway9280868.24.0 × 10−40.24650.42Hedgehog signalling pathway (KEGG)11543.685.0 × 10−40.27950.51Signalling events mediated by
