Table 5.

The gene ontology (GO) terms of biological processes enriched in genes significantly associated with residual feed intake phenotypes (GSA_phenotype) and GEBV (GSA_GEBV) repeatedly in different analyses

GO term	GO definition	Analysis (No. of genes)	Common genes1
GO:0006412	Translation	Angus liver, GEBV (32); Angus muscle, GEBV (27); Angus muscle, phenotype (38); Holstein blood, phenotype (142)	58
GO:0019941	Modification-dependent protein catabolic process	Angus liver, GEBV (24); Angus muscle, GEBV (19); Angus muscle, phenotype (22); Holstein blood, phenotype (81)	32
GO:0043632	Modification-dependent macromolecule catabolic process	Angus liver, GEBV (24); Angus muscle, GEBV (19); Angus muscle, phenotype (22); Holstein blood, phenotype (81)	32
GO:0006508	Proteolysis	Angus liver, GEBV (42); Angus muscle, GEBV (41); Angus muscle, phenotype (38)	32
GO:0030163	Protein catabolic process	Angus liver, GEBV (30); Angus muscle, GEBV (23); Holstein blood, phenotype (96)	25
GO:0044257	Cellular protein catabolic process	Angus liver, GEBV (28); Angus muscle, GEBV (21); Holstein blood, phenotype (88)	22
GO:0055114	Oxidation reduction	Angus liver, GEBV (54); Angus liver, phenotype (36); Holstein liver, phenotype (20)	29
GO:0006325	Chromatin organization	Angus muscle, phenotype (15); Holstein blood, phenotype (59)	8
GO:0006396	RNA processing	Angus muscle, phenotype (26); Holstein blood, phenotype (113)	10
GO:0007049	Cell cycle	Angus liver, phenotype (19); Holstein blood, phenotype (92)	7
GO:0007166	Cell surface receptor linked signal transduction	Angus muscle, GEBV (29); Holstein blood, GEBV (7)	1
GO:0009057	Macromolecule catabolic process	Angus liver, GEBV (35); Holstein blood, phenotype (115)	14
GO:0009063	Cellular AA catabolic process	Angus muscle, GEBV (5); Holstein liver, phenotype (5)	2
GO:0016071	mRNA metabolic process	Angus muscle, phenotype (16); Holstein blood, phenotype (71)	6
GO:0016568	Chromatin modification	Angus muscle, phenotype (11); Holstein blood, phenotype (42)	7
GO:0032313	Regulation of Rab GTPase activity	Angus liver, phenotype (6); Holstein blood, phenotype (16)	3
GO:0032318	Regulation of Ras GTPase activity	Angus liver, phenotype (7); Holstein blood, phenotype (23)	4
GO:0032483	Regulation of Rab protein signal transduction	Angus liver, phenotype (6); Holstein blood, phenotype (16)	3
GO:0034621	Cellular macromolecular complex subunit organization	Holstein blood, phenotype (60); Holstein liver, GEBV (10)	3
GO:0044265	Cellular macromolecule catabolic process	Angus liver, GEBV (32); Angus muscle, phenotype (26)	4
GO:0045449	Regulation of transcription	Angus muscle, phenotype (67); Holstein blood, phenotype (319)	29
GO:0045597	Positive regulation of cell differentiation	Angus liver, phenotype (9); Angus muscle, phenotype (9)	1
GO:0046578	Regulation of Ras protein signal transduction	Angus liver, phenotype (13); Holstein liver, GEBV (11)	1
GO:0050870	Positive regulation of T cell activation	Angus muscle, phenotype (6); Holstein blood, phenotype (22)	3
GO:0051056	Regulation of small GTPase mediated signal transduction	Angus liver, phenotype (14); Holstein liver, GEBV (12)	1
GO:0051094	Positive regulation of developmental process	Angus liver, phenotype (10); Angus muscle, phenotype (11)	1
GO:0051276	Chromosome organization	Angus muscle, phenotype (19); Holstein blood, phenotype (76)	10
GO:0051603	Proteolysis involved in cellular protein catabolic process	Angus liver, GEBV (28); Holstein blood, phenotype (88)	12
GO:0070647	Protein modification by small protein conjugation or removal	Angus liver, GEBV (11); Holstein blood, phenotype (33)	6

¹Number of genes that were significantly associated with residual feed intake in more than 1 data set.