Table 4.

ALIGATOR enrichment analyses of GO categories/KEGG pathways among association signals in EA and AA samples, showing significantly more enriched categories/pathways than expected by chance. Specific enriched categories representing potentially functional pathways are presented in the following two tables for the two analyses highlighted in bold in this table.

Note: Columns headed “N of cat” show the total numbers of categories significantly enriched at the p-value specified in the column head. “p-value” refers to the test of whether the number of enriched categories is higher than expected by chance.

The list of significant genes was defined as the 5% of genes with the most significant single-SNP p-values and analysis was restricted to categories containing at least 2 genes on this list. SNPs were assigned to genes if they lay within 20kb of that gene.

	Categories enriched at p<0.05				Categories enriched at p<0.01				Categories enriched at p<0.001
	EA		AA		EA		AA		EA		AA
Pruning of closely-overlapping categories	N of cat.	p-value	N of cat.	p-value	N of cat.	p-value	N of cat.	p-value	N of cat.	p-value	N of cat.	p-value
Unpruned (all categories analysed)	347	0.003	254	0.064	96	0.004	62	0.052	15	0.009	6	0.241
pruned (overlap <0.5)	234	0.001	180	0.040	58	0.005	46	0.034	13	0.001	5	0.200
pruned (overlap <0.2)	168	<0.001	127	0.040	50	<0.001	28	0.138	10	0.005	3	0.404