Table 3

T1D vs. NGT
SwissProt	Symbol	T-test	Wilcoxon	SAM	LIMMA	ROTS	Koo et al. [29]
P84103	SFRS3	*0,042*	0,262	*0,000*	0,141	*0,000*	0
O43854	EDIL3	*0,038*	0,146	*0,000*	0,140	*0,000*	1
Q9BZB8	CPEB1	*0,031*	0,213	*0,000*	0,140	*0,000*	1
P40394	ADH7	0,586	0,278	*0,000*	0,141	*0,000*	1
Q96JZ2	HSH2D	0,096	0,199	*0,000*	0,141	*0,000*	1
Q6PIH6	IGKV1-5	0,128	0,395	*0,000*	0,249	*0,050*	1
P68104	EEF1A1	0,060	0,146	*0,000*	0,140	*0,000*	1
P17813	ENG	0,173	0,262	*0,000*	0,141	*0,000*	1
P09210	GSTA2	*0,043*	0,146	1,000	0,141	*0,000*	0
Q8NB37	PDDC1	*0,022*	0,393	*0,000*	0,231	0,056	1
NA	NA	*0,041*	0,395	*0,051*	0,389	0,125	0
T1D vs. NGT+T2D
SwissProt	Symbol	T-test	Wilcoxon	SAM	LIMMA	ROTS	Koo et al. [29]
P68104	EEF1A1	*0,038*	0,251	*0,000*	*0,025*	*0,000*	1
O43854	EDIL3	0,058	0,359	*0,000*	0,237	*0,000*	1
T1D vs. T2D
SwissProt	Symbol	T-test	Wilcoxon	SAM	LIMMA	ROTS	Koo et al. [29]
NA	NA	0,281	0,186	*0,000*	0,069	*0,000*	0
Q969W0	C14orf147	0,654	0,241	*0,088*	0,354	*0,000*	0
Q5R7J7	C16orf69	0,839	0,146	*0,000*	0,257	*0,000*	0
P12074	COX6A1	0,435	0,168	*0,000*	0,354	*0,000*	0
Q96IY1	NSL1	0,907	0,112	*0,000*	0,354	*0,000*	0

Table 3: Differential expression detections made with at least two methods excluding Rank Product (FDR<0.05). Significant detections with FDR<0.05 are highlighted in bold text. The first two columns are the detected proteins and the next five columns show their corresponding FDR values from the different tests. The last column indicates whether our detections were found in the original study of Koo et al. [29]: “1” means “detected” and “0” means “not detected”.