Table 3.

Proteins selected by randomised LASSO stability selection analyses when regressed on raw M values or on the M value residuals after regressing out clinical predictors of insulin sensitivity

Covariates regressed out of M value	None	Centre*-Age	Centre*-Age-Sex*	Centre*-Age-Sex*-BMI	Centre*-Age-Sex*-BMI-Lipids-SBP	BMI-Lipids-SBP
Protein selected in RISC
ADGRG2_Q8IZP9_metabo	x	x
CD300LG_Q6UXG3_develo				x
FABP2_P12104_cardio_ii			x
FABP4_P15090_cardio_iii	x	x	x
IGFBP_1_P08833_cardio_iii	x	x	x
IGFBP_2_P18065_cardio_iii	x	x	x	x	x	x
INHBC_P55103_develo	x	x	x
LEP_P41159_cardio_ii	x	x	x
RTN4R_Q9BZR6_metabo	x	x	x
SCGB3A2_Q96PL1_cardio_iii	x	x	x	x	x	x
Protein selected in ULSAM
ADGRG1_Q9Y653_organ_damage	x	x	N/A
FABP4_P15090_cardio_iii	x		N/A
IGFBP_2_P18065_cardio_iii	x	x	N/A	x	x	x
ITGAV_P06756_oncolo_ii	x	x	N/A	x	x	x
LEP_P41159_cardio_ii	x	x	N/A
LPL_P06858_cardio_ii	x	x	N/A	x
RTN4R_Q9BZR6_metabo		x	N/A
Variance (R2) explained by proteins selected (95% CI)
RISC → RISC	0.366	0.363	0.381	0.338	0.362	0.352
	(0.281–0.452)	(0.278–0.448)	(0.297–0.465)	(0.253–0.425)	(0.277–0.448)	(0.266–0.439)
ULSAM → RISC	0.348					0.345
	(0.300–0.396)					(0.296–0.393)
ULSAM → ULSAM	0.582	0.587		0.472	0.495	0.495
	(0.502–0.663)	(0.507–0.667)		(0.380–0.565)	(0.406–0.586)	(0.404–0.585)
RISC → ULSAM	0.524					0.444
	(0.475–0.573)					(0.391–0.497)

^*Variable not applicable in ULSAM cohort.

Protein label includes name, UniProt ID, panel

R² = variance explained of M value of selected proteins and covariates in the testing dataset. Numbers in parentheses provide 95% confidence intervals for given R².

N/A, not applicable as ULSAM included only male participants.

RISC → RISC, models trained in RISC and tested in RISC; ULSAM → ULSAM, models trained in ULSAM and tested in ULSAM; RISC → ULSAM, models trained in RISC and tested in ULSAM; ULSAM → RISC, models trained in ULSAM and tested in RISC