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

From: 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

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