A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Table 3 Chromatin regulators are enriched in genes that physically interact with MDGs

MDGs	\|T_i\|	N₄ (# of physically interacting genes)	N₅ (# of physically interacting genes in list A)	Enrichment Pvalue_Aⁱ
TP53	8	923	192	0
PTEN	3	224	19	0.00035
RB1	2	250	64	0
NF1	2	29	3	0.079
CTNNB1	2	364	63	0
HRAS	2	86	6	0.08
BRAF	2	54	8	0.00053
IDH1	2	49	7	0.0015
NRAS	2	36	3	0.13
RNF43	2	18	7	1.4e-06
ZBTB20	2	17	1	0.45
CDH1	2	144	18	2.9e-06

|Ti|: number of tumor types whose genome-wide methylation levels are significantly associated with the mutation status of CDG i;
N₄: number of genes physically interact with MDG i;
N₅: number of genes physically interact with MDG i that are also in list A;
Enrichment Pvalue_Aⁱ is calculated using a hypergeometric distribution testing if genes in list A are enriched among selected physically interacting genes.

ISSN: 1755-8794