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Table 1 The identified 32 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 |Ai| |Ti| Pi Di T-i T+i
TP53 15 8 < e-06 botha BLCA BRCA HNSC LIHC
LUAD STAD UCEC
LGGa
PTEN 14 3 0.00147 both LGG STAD UCEC
RB1 11 2 0.00861 both LGG BLCA
PIK3CA 11 1 0.0277 hyper   STAD
ARID1A 10 1 0.0401 hyper   STAD
KRAS 8 1 1.2e-05 hypo TGCT  
KMT2D 8 2 0.00575 both BLCA STAD
NF1 6 2 0.000227 hypo LGG PCPG  
CTNNB1 6 2 0.00185 hypo LIHC UCEC  
SETD2 5 2 0.00351 hyper   KIRC KIRP
KMT2C b 5 1 0.00681 hyper   STAD
EGFR 4 1 9.5e-05 hypo LGG  
HRAS 4 2 0.000266 both PCPG HNSC
BRAF 4 2 0.00474 both THCA COAD
IDH1 3 2 < e-06 hyper   GBM LGG
CIC 3 1 1.3e-05 hyper   LGG
NRAS 3 2 1.4e-05 both TGCT THCA
RNF43 3 2 5.1e-05 both STAD COAD
ATRX 3 1 0.000487 hypera   LGGa
ZBTB20 3 2 0.00151 hyper   COAD STAD
NOTCH1 3 1 0.00189 hyper   LGG
CDH1 3 2 0.00213 hyper   BRCA STAD
KEAP1 3 1 0.00578 hypo LUAD  
SMARCA4 3 1 0.00687 hypo LUAD  
FOXA1 b 3 1 0.00953 hypo PRAD  
EPHA2 b 3 1 0.0104 hyper   STAD
KIT 2 1 < e-06 hypo TGCT  
KMT2B 2 2 0.000511 both STAD COAD
FGFR3 b 2 1 0.000697 hypo BLCA  
STK11 b 2 1 0.00193 hypo LUAD  
NSD1 1 1 < e-06 hypo HNSC  
BAP1 b 1 1 0.000142 hyper   LIHC
  1. |Ai|: number of tumor types in which CDG i is mutated in ≥ 5 samples with available methylation data;
  2. |Ti|: number of tumor types whose genome-wide methylation levels are significantly associated with the mutation status of CDG i;
  3. pi: p-value testing if CDG i is significantly associated with genome-wide methylation changes across tumor types;
  4. Di: direction of methylation changes associated with mutation status of CDG i;
  5. T+i: tumor types that are hyper-methylated by CDG i;
  6. T-i: tumor types that are hypo-methylated by CDG i;
  7. a: Further stratified analysis by IDH1 mutation status in LGG tumor samples suggests an opposite direction from hyper- to hypo-methylation;
  8. b: genes that are not overlapping driver genes
  9. __ : genes that are identified as associated with genome-wide patterns of aberrant methylation by Chen et al. [5]