Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties

Table 3

Biological process and molecular function GO terms associated with genes containing SNPs with polymorphic sites. False discovery rate (). Only the top 10 GO terms from biological process and molecular function were further discussed in this paper.

Reactome pathway name	Molecular function GO terms	Frequency of genes containing SNPs with polymorphic sites	Biological process GO terms	Frequency of genes containing SNPs with polymorphic sites
(1) Metabolism and regulation (R-OSA-2744345); (2) Secondary metabolite biosynthesis (R-OSA-2744341); (3) Hormone biosynthesis, signalling, and transport (R-OSA-2744341)	Binding (GO:0005488)	55	Cellular process (GO:0009987)	51
	Catalytic activity (GO:0003824)	52	Metabolic process (GO:0008152)	49
	Heterocyclic compound binding (GO:1901363)	43	Organic substance metabolic process (GO:0071704)	44
	Organic cyclic compound binding (GO:0097159)	43	Primary metabolic process (GO:0044238)	41
	Ion binding (GO:0043167)	38	Cellular metabolic process (GO:0044237)	41
	Small molecule binding (GO:0036094)	24	Nitrogen compound metabolic process (GO:0006807)	37
	Nucleotide binding (GO:0000166)	24	Macromolecule metabolic process (GO:0043170)	34
	Nucleoside phosphate binding (GO:1901265)	24	Cellular macromolecule metabolic process (GO:0044260)	29
	Purine nucleotide binding (GO:0017076)	23	Macromolecule modification (GO:0043412)	20
	Carbohydrate derivative binding (GO:0097367)	23	Cellular protein modification process (GO:0006464)	18