Table 3.

Gene set enrichment analysis for gene body DNA methylation in relation to four clinical endpoints of GC patients in TCGA

ID	Description	Number of genes	Number of unique genes	OS		DSS		PFI		DFI
				P-value	FDR	P-value	FDR	P-value	FDR	P-value	FDR
GOa
35267	NuA4 histone acetyltransferase complex	31	20	0.002	0.066	0.007	0.197	0.047	0.477	0.002	0.042
36019	Endolysosome	21	20	0.012	0.219	0.002	0.078	0.006	0.152	0.017	0.220
36020	Endolysosome membrane	14	14	0.007	0.154	0.001	0.036	0.003	0.106	0.036	0.364
43189	H4/H2A histone acetyltransferase complex	31	20	0.002	0.066	0.007	0.197	0.047	0.477	0.002	0.042
44346	Fibroblast apoptotic process	24	24	0.036	0.409	0.024	0.409	0.029	0.370	1.51 × 10−4	0.008
KEGG
04080	Neuroactive ligand-receptor interaction	272	272	1.24 × 10−16	2.64 × 10−14	2.32 × 10−16	4.95 × 10−14	3.44 × 10−10	7.34 × 10−8	1.000	1.000
04144	Endocytosis	201	201	0.005	0.324	0.026	0.923	0.027	0.645	0.194	0.858
04950	Maturity onset diabetes of the young	25	25	0.037	0.901	0.010	0.634	0.008	0.329	1.000	1.000
05217	Basal cell carcinoma	55	55	0.017	0.712	0.011	0.634	0.035	0.749	1.000	1.000

Abbreviations: GC gastric cancer, OS overall survival, DSS disease-specific survival, DFI disease-free interval, PFI progression-free interval, HRs hazard ratios, CI confidence interval, FDR false discovery rate

^aEach GO annotation includes an evidence code to indicate how the annotation to a particular term is supported. If a gene is linked to a GO annotation by two distinct evidence codes (e.g., Inferred from Direct Assay (IDA) and Inferred from Biological aspect of Ancestor (IBA)), it would be counted twice to the number of genes enriched in that gene set