Table 4 List of significant KEGG pathways (FDR<0.05) for PTSD and MDD among the top 100 CpG sites

Pathway	N	DE	FDR	Genes
PTSD
cGMP-PKG signaling pathway	167	5	0.000481	ADCY3;MEF2C;NFATC1;PIK3R2;CACNA1D
Oxytocin signaling pathway	158	5	0.000481	ADCY3;MEF2C;NFATC1;PIK3R2;CACNA1D
AGE-RAGE signaling pathway in diabetic complications	101	4	0.000917	FIGF;NFATC1;PIK3R2;TGFB3
MAPK signaling pathway	254	5	0.002	MEF2C;NFATC1;RPS6KA2;TGFB3;CACNA1D
Pantothenate and CoA biosynthesis	18	2	0.00771	PANK4;BCAT1
cAMP signaling pathway	200	4	0.00771	ADCY3;NFATC1;PIK3R2;CACNA1D
Focal adhesion	200	4	0.00771	COL9A3;FIGF;PIK3R2;TNXB
Progesterone-mediated oocyte maturation	89	3	0.00771	ADCY3;PIK3R2;RPS6KA2
Dilated cardiomyopathy	89	3	0.00868	ADCY3;TGFB3;CACNA1D
Osteoclast differentiation	125	3	0.00906	CTSK;NFATC1;PIK3R2
HTLV-I infection	255	4	0.00906	ADCY3;NFATC1;PIK3R2;TGFB3
Insulin resistance	109	3	0.00975	PIK3R2;RPS6KA2;OGT
Cholinergic synapse	111	3	0.015	ADCY3;PIK3R2;CACNA1D
Hepatitis B	135	3	0.0159	NFATC1;PIK3R2;TGFB3
PI3K-Akt signaling pathway	324	4	0.0176	COL9A3;FIGF;PIK3R2;TNXB
Adrenergic signaling in cardiomyocytes	148	3	0.0188	ADCY3;PIK3R2;CACNA1D
Carbohydrate digestion and absorption	41	2	0.0188	PIK3R2;CACNA1D
Inflammatory bowel disease (IBD)	63	2	0.033	NFATC1;TGFB3
Pathways in cancer	396	4	0.0354	ADCY3;FIGF;PIK3R2;TGFB3
Rap1 signaling pathway	212	3	0.0411	ADCY3;FIGF;PIK3R2
Rheumatoid arthritis	85	2	0.0411	CTSK;TGFB3
Protein digestion and absorption	84	2	0.0479	COL9A3;COL27A1
Hypertrophic cardiomyopathy (HCM)	83	2	0.0489	TGFB3;CACNA1D
MDD
Phosphatidylinositol signaling system	99	3	0.0425	INPP5D;DGKZ;MTMR2
Cell cycle	124	3	0.0425	MCM2;RAD21;TGFB3

Abbreviations: FDR, false discovery rate; MDD, major depressive disorder; PTSD, posttraumatic stress disorder. These pathways were also significant when we considered top 150 to 500 CpG sites (increment of 50 CpG sites). N is the size of the pathway, DE is the number of genes in our list overlapping with the pathway, Genes is the list of overlapping genes.

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