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Table 4 Identified 29 EDGs

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

EDGs Ai Ei pi B i \( {E}_i^{-} \) \( {E}_i^{+} \)
TP53 14 11 < e-06 both HNSC LGG SARC BLCA BRCA COAD GBM KIRC LIHC LUAD STAD
PTEN 14 1 0.00299 up   LGG
PIK3CA 11 2 0.00536 down BRCA STAD  
RB1 10 3 9e-05 up   BLCA LGG LUAD
ARID1A 10 2 0.00557 both STAD CESC
KRAS 8 4 4e-06 down COAD LUAD PAAD TGCT  
KMT2D 8 1 0.0265 down STAD  
NF1 6 1 0.00274 up   LGG
CTNNB1 5 1 0.00572 down LIHC  
†SETD2 5 0 0.00833 NA NA NA
BRAF 4 2 1.1e-05 down COAD THCA  
EGFR 4 2 5.3e-05 up   LGG LUAD
HRAS 4 3 7e-05 down HNSC PCPG THCA  
CIC 3 1 < e-06 down LGG  
IDH1 3 2 < e-06 both LGG GBM
RNF43 3 2 1e-06 down COAD STAD  
ATRX 3 2 2e-06 both LGG GBM
CDH1 3 2 7e-06 both BRCA STAD
NRAS 3 2 0.000199 up   TGCT THCA
KEAP1 3 1 0.000809 down LUAD  
ZBTB20 3 2 0.00119 down COAD STAD  
NOTCH1 3 2 0.00182 down HNSC LGG  
SMARCA4 3 1 0.0108 up   LUAD
GATA3 a 3 1 0.0138 down BRCA  
KMT2B 2 2 0.000317 down COAD STAD  
KIT 2 1 0.000889 down TGCT  
FUBP1 a 1 1 < e-06 down LGG  
SPOP a 1 1 < e-06 down PRAD  
NSD1 1 1 0.000432 up   HNSC
  1. Ai = number of tumor types in which EDG i is mutated in ≥ 5 samples with expression data;
  2. Ei = number of tumor types whose genome-wide expression levels are significantly associated with CDG i;
  3. \( {p}_i^{\prime }= \) p-value testing if CDG i is significantly associated with genome-wide expression changes across tumor types;
  4. Bi is the direction of change of expression levels associated with the mutation status of CDG i;
  5. \( {E}_i^{+}= \) tumor types that are up-regulated by CDG i, \( {E}_i^{-} \)= tumor types that are down-regulated by CDG i;
  6. a : genes that are not overlapping driver genes.
  7. †Note that SETD2 gene has a significant p-value \( {p}_i^{\prime } \) for testing association of genome-wide expression changes across multiple tumor types, but there is not a specific tumor type in which SETD2 mutation is significantly associated with genome-wide expression changes.