Entorhinal cortex epigenome-wide association study highlights four novel loci showing differential methylation in Alzheimer’s disease

Table 5 Experiment-wide significant Spearman rank correlations between CpG DNAm and gene expression levels

CpG	Gene	Spearman’s ρ	P_Spearman	β_{Case / Control}	P_{Case / Control}	β_Braak	P_Braak	Location of CpG
cg04520340	PRKCZ	-0.28	5.59E-03	-0.49	2.83E-11	-0.98	2.83E-11	gene body
cg05066959	ANK1	-0.23	2.28E-02	-0.39	6.07E-07	-0.76	1.30E-06	gene body island
cg05228284	DIRAS1	0.24	1.76E-02	-0.51	7.54E-12	-1.10	5.85E-13	5’-UTR CGI
cg05417607	MYO1C	0.26	1.17E-02	0.49	2.93E-12	0.93	2.83E-11	gene body
cg20618448	FLT3LG	0.20	4.29E-02	0.36	1.67E-07	0.75	3.64E-08	Intergenic
cg20648333	PALD1	0.22	2.97E-02	0.17	0.025071	0.35	0.015889	gene body
cg20648333	PRF1	0.22	3.03E-02	0.36	3.90E-06	0.60	0.000114	Intergenic
cg22090150	CYB5D2	-0.35	3.9E-04	-0.28	0.000609	-0.56	0.000512	Intergenic
cg22090150	ANKFY1	0.24	1.76E-02	0.46	4.68E-09	0.88	2.03E-08	gene body
cg22388948	TENT5A	-0.28	5.59E-03	0.42	1.67E-07	0.79	6.69E-07	gene body

Experiment-wide significant Spearman rank correlations between CpG DNAm and gene expression levels. Β Effect sizes of gene expression association with AD case–control status / Braak stage, P P-value of gene expression association with AD case–control status / Braak stage after multiple testing adjustment with the Benjamini Hochberg method; Location: Location of the CpG in the genome with respect to the correlated gene; Results of all 39 tested DNAm-mRNA pairs can be found in Supplementary Tables 8, 9, and 10. One additional CpG-mRNA pair was found to significantly correlate in human brain samples by de Witte et al., 2021 [38]; in our data, this pair showed a borderline significant correlation in the same direction as described by ref. [38] (see Supplementary Table 8). CpGs are ordered alphabetically. For some loci more than one gene was annotated to specific CpGs; in these instances, multiple DNAm-mRNA correlation results were computed for the same CpG

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