Table 2.

The Strongest Associations of Proteins and Nutrients (or indicators of acute phase response) Observed in Our Experiments^a

N/I	accession	protein	n	ME	MP	SS
Crp	gi55770842	C-reactive protein	357	0.86	0.74	0.71
ret	gi55743122	retinol-binding protein 4	406	0.74	0.47	0.50
agP	gi116256481	TNFAIP3-interacting protein 1	301	0.60	0.46	0.42
agP	gi115298645	mitogen-activated protein kinase kinase kinase	259	0.58	0.40	0.38
agP	gi167857790	orosomucoid 1	406	0.55	0.41	0.37
crp	gi40316912	serum amyloid A protein preproprotein	399	0.51	0.44	0.39
agP	gi4826762	haptoglobin isoform 1 preproprotein	266	0.50	0.33	0.31
crp	gi16418467	leucine-rich α-2-glycoprotein 1	406	0.50	0.39	0.37
crp	gi31652249	lipopolysaccharide-binding protein	406	0.48	0.40	0.36
ret	gi4507725	transthyretin	406	0.45	0.22	0.23
agP	gi16418467	leucine-rich α-2-glycoprotein 1	406	0.44	0.31	0.28
agP	gi4505529	orosomucoid 2	406	0.43	0.29	0.26
crp	gi116256481	TNFAIP3-interacting protein 1	301	0.41	0.32	0.28
crp	gi115298645	mitogen-activated protein kinase kinase kinase	259	0.41	0.28	0.27
crp	gi4502133	serum amyloid P component	406	0.41	0.29	0.30

^aThe nutrients/indicators (N/I) are the C-reactive protein (crp), plasma retinol (ret), and the α(1)-acid glycoprotein (agp). The statistical inference is based on three different approaches. SS: estimates of relative protein abundance from different experiments were combined using the median sweep (Figure 1), and the estimates from each experiment were simply stacked, ignoring among-experiments variability. MP: the masterpool approach, using a reference sample for relative abundance estimation, and combining estimates among experiments. ME: using linear mixed effects models (eq 5) to account for among-experiments variability, with median sweep-derived relative abundance estimates. The total number of observed protein–outcome pairs (n) ranged from 259 (37 experiments with 7 biological samples each) to 406 (observed in all samples of the 58 experiments).