Table 2.

CSF Markers selected for each of the specific diagnostic panels after 10 fold-cross validation

AD vs. CON panel (n=425)						AD vs. Non-AD dem panel (n=552)
Protein	Effect	fold-change	FDR adjusted p- value	Frecuency 10- fold CV (%)	Overlapped groups	Protein	Effect	fold-change	FDR adjusted p- value	Frecuency 10- fold CV (%)	Overlapped groups
ABL1	0.445	1.361	6.57E-23	100	MCI(Aβ+) and AD	ABL1	0.304	1.235	3.05E-29	100	MCI(Aβ+) and AD
SDC4	0.454	1.370	1.18E-19	100	MCI(Aβ+) and AD	THOP1	0.306	1.236	4.27E-21	100	MCI(Aβ+) and AD
MMP-10	0.616	1.532	1.18E-19	100	AD only	ENO2	0.230	1.173	4.27E-21	100	MCI(Aβ+) and AD
ITGB2	0.639	1.557	5.97E-19	100	AD only	GZMB	−0.109	0.927	9.05E-05	100	n.a.
CLEC5A	0.683	1.605	3.06E-15	100	MCI(Aβ+) and AD	DDC	−0.143	0.906	2.92E-04	100	MCI(Aβ+) and AD
TREM1	0.361	1.285	1.11E-11	100	AD only	MMP7	−0.150	0.901	1.32E-02	80	n.a.
THBD	−0.160	0.895	4.15E-02	100	General dem.	VEGFR-3	−0.013	0.991	5.40E-01	80	n.a.
SPON2	−0.055	0.963	1.90E-01	50	n.a.	ITGB2	0.315	1.244	2.02E-17	70	AD only
						PTK7	−0.015	0.990	5.84E-01	70	MCI(Aβ+) only

Table shows the effect (beta coefficient), p- and q- values after applying two-sided nested F-test analysis and FDR post-hoc correction to compare CSF protein abundance between AD and CON or non-AD dementias in the discovery cohort. Only those CSF markers selected within the specific diagnostic panels are included.

The frecuency indicates the fold-based selection proportions for each marker after performing penalized generalized linear modeling (GLM) with an elastic net penalty (see methods).

Overlapped groups indicates whether the proteins were dysregulated in MCI(Aβ+) but not in AD (MCI(Aβ+) only); proteins dysregulated in both MCI(Aβ+) and AD; proteins dysregulated in AD only; or proteins dysregulated in both MCI(Aβ+) and AD or AD only, but not between AD and non AD dementias (general dem) based on the Upset plot (figure 2a). N.a, not applicable as marker was not differentially regulated between AD and controls.