Table 2.

Pathway enrichment of within-species sequence variation

Name	MK enrichment*	P†	Annotation
GO:0007124	6.0	9 × 10−5	Pseudohyphal growth
GO:0006950	2.2	0.0005	Response to stress
GO:0006259	2.1	0.006	DNA metabolic process
GO:0007126	2.5	0.03	Meiosis

Listed are the top-scoring pathways in a test for enrichment among genes with evidence for protein coding variation within S. cerevisiae according to the McDonald–Kreitman test. Results for all pathways are given in Table S5. Gene groups were defined as the Biological Process categories from Gene Ontology, with 1.2 false-positive groups expected.

*The ratio between the number of genes in the pathway scored as significant in the McDonald–Kreitman test and the number of genes in all pathways scored as significant, divided by the analogous ratio for all tested genes regardless of significance.

^†Hypergeometric P value for pathway enrichment of genes significant in the McDonald–Kreitman test.