Table 3.

The 16 top-ranked biological processes that were significantly overrepresented among the 571 genes containing highly differentiated SNPs in the five studied populations of Arabidopsis halleri

GO term	Biological process	Annotated*	Significant†	Expected‡	Fisher's test§
GO:0042742	Defence response to bacterium	211	13	4.95	0.0015
GO:0007568	Ageing	99	8	2.32	0.0023
GO:0007166	Cell surface receptor signalling pathway	149	10	3.49	0.0028
GO:0010214	Seed coat development	14	3	0.33	0.0038
GO:0046777	Protein autophosphorylation	86	7	2.02	0.0041
GO:0006820	Anion transport	86	7	2.02	0.0041
GO:0009863	Salicylic acid mediated signalling pathway	30	4	0.7	0.005
GO:0055085	Transmembrane transport	459	20	10.76	0.0062
GO:0051187	Cofactor catabolic process	32	4	0.75	0.0064
GO:0016568	Chromatin modification	95	7	2.23	0.007
GO:0048544	Recognition of pollen	33	4	0.77	0.0071
GO:0009740	Gibberellic acid mediated signalling pathway	35	4	0.82	0.0088
GO:0006306	DNA methylation	35	4	0.82	0.0088
GO:0006342	Chromatin silencing	19	3	0.45	0.0094
GO:2000280	Regulation of root development	19	3	0.45	0.0094
GO:0006487	Protein N-linked glycosylation	19	3	0.45	0.0094

^*Number of genes within the background list which contain a specific GO term.

^†Number of genes in the candidate list which have a specific GO term.

^‡Expected frequency (number of genes) of a given GO term based on the size of the candidate gene list.

^§p-value of the Fisher's exact test.