Table 1. Proteins identified only in cow milk or only sheep milk in the top 15 enriched biological process and molecular function GO terms shared by the two species.

Biological Process
GO Term	Unique to Sheep	Unique to Cow	Common
Acute inflammatory response (GO:0002526)	C1QA, C1QB, C1QC, C4B, C8A, CRP, KLKB1, KRT1, MASP2, TLR4, YWHAZ	APCS, CFI, IGF2, IL1B, IL6, INS, MBL2, ORM1	A2M, AHSG, B4GALT1, C1R, C1S, C2, C3, C4A, C4BPA, C5, C6, C7, C8B, C9, CFB, CFD, CFH, CLU, F2, FN1, ITIH4, LBP, MASP1, SAA1, SERPINA1, SERPINF2, SERPING1, TF
Response to wounding (GO:0009611)	ANXA1, AZU1, C1QA, C1QB, C1QC, C4B, C8A, CD9, CRP, ITGAL, KLKB1, KRT1, LAMB2, LMAN1, MASP2, NDST1, PRDX5, PROS1, PTX3, RAC1, TIMP3, TLR4, TNFAIP6, YWHAZ	ANXA5, AOX1, APCS, APOH, CD44, CFI, CXCL2, F11, F13B, FGF2, GNAQ, IGF1, IGF2, IGFBP1, IGFBP4, IL10, IL1B, IL6, INS, MBL2, MECOM, MYH10, MYH2, NFKB1, ORM1, PDGFA, PDGFB, PLAT, PPARD, PXK, S100A12, S100A8, S100A9, SERPIND1, TGFB1, TLR7, TNF	A2M, AHSG, AOC3, B4GALT1, C1R, C1S, C2, C3, C4A, C4BPA, C5, C6, C7, C8B, C9, CD14, CD36, CFB, CFD, CFH, CLU, CTSB, DSP, F2, F9, FGA, FGB, FGG, FN1, GSN, ITIH4, KNG1, LBP, MASP1, MIA3, PEBP1, PLG, PROC, SAA1, SERPINA1, SERPINA10, SERPINC1, SERPINF2, SERPING1, SPP1, TF, TGFB2, THBS1
Complement activation (GO:0006956)	C1QA, C1QB, C1QC, C4B, C8A, CRP, KRT1, MASP2	CFI, MBL2	C1R, C1S, C2, C3, C4A, C4BPA, C5, C6, C7, C8B, C9, CFB, CFD, CFH, CLU, MASP1, SERPING1
Humoral immune response (GO:0006959)	C1QA, C1QB, C1QC, C4B, C8A, CRP, KRT1, MASP2	CFI, IL6, MBL2, TNF	C1R, C1S, C2, C3, C4A, C4BPA, C5, C6, C7, C8B, C9, CFB, CFD, CFH, CLU, DMBT1, GPI, LTF, MASP1, SERPING1
Inflammatory response (GO:0006954)	ANXA1, AZU1, C1QA, C1QB, C1QC, C4B, C8A, CRP, ITGAL, KLKB1, KRT1, MASP2, NDST1, PRDX5, PTX3, RAC1, TLR4, TNFAIP6, YWHAZ	AOX1, APCS, CD44, CFI, CXCL2, IGF2, IGFBP4, IL10, IL1B, IL6, INS, MBL2, MECOM, NFKB1, ORM1, PXK, S100A12, S100A8, S100A9, TGFB1, TLR7, TNF	A2M, AHSG, AOC3, B4GALT1, C1R, C1S, C2, C3, C4A, C4BPA, C5, C6, C7, C8B, C9, CD14, CFB, CFD, CFH, CLU, F2, FN1, ITIH4, KNG1, LBP, MASP1, SAA1, SERPINA1, SERPINF2, SERPING1, SPP1, TF, THBS1
Defense response (GO:0006952)	ANXA1, AZU1, C1QA, C1QB, C1QC, C4B, C8A, CRP, CTSG, HLA-B, ITGAL, KLKB1, KRT1, LGALS3BP, MASP2, NDST1, PGLYRP2, PRDX1, PRDX5, PTX3, RAC1, TLR4, TNFAIP6, YWHAZ	AOX1, APCS, CD44, CD5L, CFI, COTL1, CXCL2, DEFB4A, IFIH1, IFNG, IGF2, IGFBP4, IL10, IL12A, IL1B, IL4, IL6, INS, MBL2, MECOM, NFKB1, NOS2, ORM1, PXK, S100A12, S100A8, S100A9, TGFB1, TLR7, TNF	A2M, AHSG, AOC3, APOA4, B4GALT1, C1R, C1S, C2, C3, C4A, C4BPA, C5, C6, C7, C8B, C9, CAMP, CD14, CFB, CFD, CFH, CLU, CST3, DMBT1, F2, FN1, HP, ITIH4, KNG1, LALBA, LBP, LTF, MASP1, MPO, PGLYRP1, SAA1, SERPINA1, SERPINF2, SERPING1, SFTPD, SPP1, TF, THBS1
Innate immune response (GO:0045087)	C1QA, C1QB, C1QC, C4B, C8A, KRT1, MASP2, PGLYRP2, PRDX1, TLR4	CFI, IFIH1, MBL2, NOS2, TGFB1, TLR7	APOA4, C1R, C1S, C2, C3, C4A, C4BPA, C5, C6, C7, C8B, C9, CFB, CFD, CFH, CLU, DMBT1, LBP, MASP1, PGLYRP1, SERPING1, SFTPD
Positive regulation of immune system process (GO:0050778)	C1QA, C1QB, C1QC, C4B, C8A, CRP, KRT1, MASP2, TLR4, TNFSF13	CD5, CFI, IFNG, IL12A, IL1B, IL2, IL4, IL6, MBL2, NOS2, PNP, TGFB1, TLR7	ADAM10, B2M, C1R, C1S, C2, C3, C4A, C4BPA, C5, C6, C7, C8B, C9, CFB, CFD, CFH, CLU, HPX, LBP, MASP1, MIA3, PVRL2, SERPING1, TGFB2, THBS1
Protein maturation (GO:0051604)	C1QA, C1QB, C1QC, C4B, C8A, CPE, CRP, FURIN, KLKB1, KRT1, MASP2, SPCS3	APOH, CASP1, CFI, F11, LONP2, MBL2, NCLN, PTHLH	ATP6AP2, C1R, C1S, C2, C3, C4A, C4BPA, C5, C6, C7, C8B, C9, CALR, CFB, CFD, CFH, CLU, MASP1, SERPING1
Activation of immune response (GO:0002253)	C1QA, C1QB, C1QC, C4B, C8A, CRP, KRT1, MASP2, TLR4	CFI, MBL2, TLR7	C1R, C1S, C2, C3, C4A, C4BPA, C5, C6, C7, C8B, C9, CFB, CFD, CFH, CLU, MASP1, SERPING1
Positive regulation of response to stimulus (GO:0048584)	AGT, AZU1, C1QA, C1QB, C1QC, C4B, C8A, CRP, KRT1, MASP2, TLR4	CFI, EEF1E1, GHRH, IGF2, IL12A, IL1B, IL6, INS, MBL2, OSMR, PDGFB, TGFB1, TLR7, TNF	ADAM10, B2M, C1R, C1S, C2, C3, C4A, C4BPA, C5, C6, C7, C8B, C9, CFB, CFD, CFH, CLU, HPX, LBP, MASP1, PVRL2, SERPING1, TGFB2, THBS1
Response to organic substance (GO:0010033)	ACSL1, ANGPT1, ARSA, ASAH1, C1QB, CDH1, CFL1, ERO1L, HPRT1, HSPA1L, HSPA2, HSPA4, KRAS, KRT19, LEPR, LIFR, SMPD1, TGFBR3, TIMP3, TLR4	ADAM9, ADCY10, AFP, ALDOC, ANXA5, APCS, BCHE, BRCA2, CASP1, CD44, CFTR, CTSC, CTTNBP2, DGKD, DICER1, ENPP1, EPS8, FAS, GH1, GNRH1, IFNG, IGF2, IGFBP1, IGFBP2, IL10, IL12A, IL1B, IL6, INS, KDM3A, LEP, LONP2, OSMR, OXT, PDGFA, PDGFB, PRKDC, RYR1, SETD2, SLC34A2, SREBF2, TGFB1, TNF, TSHB	A2M, ACTC1, ADAM10, ADIPOQ, AHSG, ALPL, APOB, APOE, B2M, C1S, CD14, CFB, CYR61, DDR1, DNAJC3, FABP3, FBP1, GSN, HMGB2, HSP90AA1, HSP90AB1, HSPA1B, HSPA8, IDH1, LBP, LCAT, MFGE8, NME1-NME2, PEBP1, PLIN2, SDF4, SERPINA1, SERPINF2, SORT1, SPP1, TF, TGFB2, THBS1
Lymphocyte mediated immunity (GO:0002449)	C1QA, C1QB, C1QC, C4B, C8A, CRP, MASP2, PRDX1	CFI, FAS, MBL2	C1R, C1S, C2, C3, C4A, C4BPA, C5, C6, C7, C8B, C9, CLU, SERPING1
Hemostasis (GO:0007599)	CD9, KLKB1, LMAN1, PROS1	ANXA5, APOH, F11, F13B, GNAQ, IL6, PLAT, SERPIND1	C9, CD36, F2, F9, FGA, FGB, FGG, GPI, KNG1, PLG, PROC, SAA1, SERPINA1, SERPINC1, SERPING1
Adaptive immune response (GO:0002250)	C1QA, C1QB, C1QC, C4B, C8A, CRP, MASP2, TLR4	CFI, FAS, IL10, IL18BP, IL4, MBL2	C1R, C1S, C2, C3, C4A, C4BPA, C5, C6, C7, C8B, C9, CLU, SERPING1
Molecular Function
GO Term	Unique to Sheep	Unique to Cow	Common
Carbohydrate binding (GO:0030246)	AZU1, CANX, CLEC2D, ENPP2, GALNT1, GALNT3, GALNT5, ITGAM, KRT1, LGALS3, LMAN1, LMAN2, MAMDC2, MAN2A1, MANBA, MLEC, NOMO1, PGLYRP2, PRG3, PTX3, SERPINA5, SOD3, TGFBR3, THBS4, TINAGL1, TNFAIP6	APCS, APOH, BGN, CD44, ENPP1, ENPP3, F11, FGF1, FGF2, IL2, MBL2, MRC1, PYGL, SERPIND1, TALDO1, ZG16B	ALDOA, APOB, APOE, ATP6AP1, CALR, CD14, CLEC3B, CYR61, FBP1, FGFBP1, FN1, FUCA1, GALM, HRG, IGF2R, KNG1, LAMC2, LPL, MAN2A2, MAN2B1, PGLYRP1, SERPINC1, SFTPD, THBS1, VTN
Enzyme inhibitor activity (GO:0004857)	AGT, ANGPTL4, ANXA1, ANXA2, C4B, COL6A3, FURIN, GCHFR, HSPA5, ITIH3, PRDX5, PROS1, SERPINA5, SERPINB3, SERPINB4, TIMP3, YWHAG	A2ML1, ANXA5, APOC3, CABIN1, CD109, CSTB, FETUB, PDE6H, SERPIND1, SPINT1, TIMP2, TRIB3	A2M, AHSG, AMBP, C3, C4A, C5, CSN2, CST3, DNAJC3, HRG, ITIH1, ITIH2, ITIH4, KNG1, PEBP1, SERPINA1, SERPINA10, SERPINB1, SERPINC1, SERPINF1, SERPINF2, SERPING1
Glycosaminoglycan binding (GO:0005539)	AZU1, ITGAM, MAMDC2, PGLYRP2, SERPINA5, SOD3, TGFBR3, THBS4, TNFAIP6	APOH, BGN, CD44, F11, FGF1, FGF2, SERPIND1	APOB, APOE, ATP6AP1, CD14, CYR61, FGFBP1, FN1, HRG, KNG1, LAMC2, LPL, PGLYRP1, SERPINC1, THBS1, VTN
Heparin binding (GO:0008201)	AZU1, ITGAM, SERPINA5, SOD3, TGFBR3, THBS4	APOH, F11, FGF1, FGF2, SERPIND1	APOB, APOE, ATP6AP1, CYR61, FGFBP1, FN1, HRG, KNG1, LAMC2, LPL, SERPINC1, THBS1, VTN
Pattern binding (GO:0001871)	AZU1, ENPP2, ITGAM, MAMDC2, PGLYRP2, PTX3, SERPINA5, SOD3, TGFBR3, THBS4, TINAGL1, TNFAIP6	APOH, BGN, CD44, ENPP1, ENPP3, F11, FGF1, FGF2, SERPIND1	APOB, APOE, ATP6AP1, CD14, CYR61, FGFBP1, FN1, HRG, KNG1, LAMC2, LPL, PGLYRP1, SERPINC1, THBS1, VTN
Cell surface binding (GO:0043498)	ATP5B, CRP	ANXA5, APOH, MBL2, PDGFA, PDGFB	ADIPOQ, APOA4, FGA, FGB, FGG, LBP, THBS1
Peptidase activity (GO:0008233)	ACE, ACY1, ANPEP, AZU1, CNDP2, CPD, CPE, CPXM1, CPXM2, CTSG, DPP3, ERAP2, FURIN, HPN, KEL, KLKB1, LNPEP, MASP2, MMP2, PDIA3, PEPD, PM20D1, PRCP, PSMA5, PSMA8, SCPEP1, SPCS3, ST14, TINAGL1, TLL1	ADAM9, ADAMTS7, AGBL3, AQPEP, CASP1, CFI, CTSA, CTSC, CTSF, CTSZ, F11, HTRA1, LGMN, LONP1, LONP2, MMP8, MMP9, PLAT, PRSS1, SPPL2A, USP24, USP28, USP34, ZFYVE9	ADAM10, C1R, C1S, C2, CFB, CFD, CPB2, CTSB, CTSD, ENO1, ERAP1, F2, F9, HP, LAP3, LTF, MASP1, PLG, PROC, PRSS22, PRTN3, PSMB1, SERPINA1, TPP1
Identical protein binding (GO:0042802)	C1QB, GLA, GPD1L, HPRT1, LMAN1, MYH9, PAK2, PCMT1, PLOD1, PON1, SHBG, TPD52L1	ACTN4, CASP8AP2, CCDC88A, CENPF, CLIP1, CTSC, DGKD, DVL1, E2F8, ENPP1, FAS, FLT1, GCC2, MYCBP2, MYO18A, NFKB1, NOS2, PDGFA, PDGFB, PYGL, ROCK1, S100B, SHMT1, TARS, TGFB1, TNF, TOP2A, TP63, TTN, WRN, ZNHIT6	ABCG2, ACTG1, ADAM10, ADIPOQ, ALDOA, AMBP, AOC3, APOA1, APOA4, APOE, ARHGDIA, B4GALT1, FBP1, FLNA, HSP90AA1, LCP1, LDHB, MASP1, NME1-NME2, PDXK, PVRL2, SDF4, SDS, TGFB2, THBS1
Calcium ion binding (GO:0005509)	ANXA1, ANXA2, ARSA, ATP5B, CACHD1, CALM1, CALU, CANT1, CANX, CDH1, CLSTN1, CRP, DCHS1, DSG1, DSG2, EDEM2, EHD4, FAM20C, FAT2, FBLN1, FURIN, GALNT1, GALNT3, GALNT5, GAS6, HSPA5, ITGAL, ITGAM, LMAN2, LTBP1, MAN1A1, MASP2, MMP2, NID1, PCDH1, PCDHB14, PCDHB7, PCDHB8, PCDHGA10, PCDHGA11, PCDHGA2, PCDHGA3, PCDHGA8, PCDHGB3, PCDHGB5, PCDHGB7, PCDHGC3, PROS1, PXDN, SULF2, THBS4, TLL1	ACTN4, AMY2B, ANO1, ANXA5, APCS, CELSR2, CRTAC1, DSC2, DST, EFHD2, EGF, FAT3, FAT4, HPSE, IDS, ITGA8, ITPR1, ITPR3, ITSN1, LRP1, MACF1, MAN1B1, MBL2, MMP8, MMP9, MRC1, NELL2, NOS2, PKDREJ, PLCB1, PLCB3, PRSS1, PTHLH, RET, RPTN, RYR1, RYR3, S100A12, S100A8, S100A9, S100B, SCUBE3, SLIT1, SPTA1, TRPC5, TTN, UTRN	AOC3, C1R, C1S, CALR, CIB1, CSN2, DAG1, F2, F9, FGG, GSN, HSP90B1, ITIH1, LALBA, LCP1, LPO, LRP2, MASP1, MPO, NUCB1, NUCB2, PDIA4, PLG, PRKCSH, PROC, SDF4, SFTPD, THBS1, TKT
Unfolded protein binding (GO:0051082)	CANX, CCT8, DNAJB11, HSPA2, HSPA5, HSPA9, LMAN1, PPIC	APCS, DNAJB9	CALR, HSP90AA1, HSP90AB1, HSP90B1, HSPA1B, HSPA8, PPIA, PPIB, SIL1
Antioxidant activity (GO:0016209)	GPX3, PRDX1, PRDX4, PRDX5, PXDN, SEP15, SOD3	N/A	ALB, APOA4, APOE, LPO, MPO, PRDX6
Cholesterol transporter activity (GO:0017127)	N/A	N/A	APOA1, APOA4, APOB, APOE
Beta-amyloid binding (GO:0001540)	N/A	BCHE	APOA1, APOE, CST3, TGFB2
Lipid binding (GO:0008289)	ALDH1A1, ANXA1, ANXA2, APOF, PITPNA, PLTP, PON1, RBP1, SHBG	ACBD3, ANXA5, APOC3, APOH, CCDC88A, CIT, DGKD, IL2, ITPR1, ITPR3, NPC2, PPARD, PREX1, PRKD3, PXK, PYGL, ROCK1	ALB, APOA1, APOA4, APOB, APOE, AZGP1, CD36, FABP3, GC, LBP, LPL, MFGE8, PEBP1, PITPNB, PSAP, PTGDS, SCGB2A2
Lipoprotein receptor binding (GO:0070325)	N/A	APOC3, LRP1	APOA1, APOB, APOE, HSP90B1