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Table 5 Patterns of target genes’ promoter regions methylation and expression changes by mutations of the overlapping driver genes across tumor types

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

Overlapping driver
genes
Ti Ei Ti ∩ Ei DM DE \( \frac{\mid DM\cap DE\mid }{\mid DE\mid } \) (%) p(DM ∙ DE) p(−−) p(+−) p(−+) p(++) p.methyl p.exp
TP53 8 11 7 10389 10066 52 2.8e-32 1 9.7e-95 7.1e-65 1 0 0
PTEN 3 1 1 12259 10293 61 0.014 1 1e-15 1e-15 1 2.98e-10 0
RB1 2 3 1 9049 8062 46 0.0066 0.81 0.05 1e-15 1 0 0
PIK3CA 1 2 1 13933 5822 73 5e-12 1 1e-15 5.4e-05 1 1.93e-11 0
ARID1A 1 2 1 9487 8573 53 1e-15 0.98 1e-15 0.29 1 0 0
KRAS 1 4 1 15041 8427 73 1 1 7.5e-12 1 0.87 0 0
KMT2D 2 1 1 9802 8485 52 4.3e-14 1 1e-15 0.014 1 7.37e-10 0
NF1 2 1 1 10288 7435 53 9e-07 1 1e-15 1e-15 1 0 0
CTNNB1 2 1 1 7583 7591 37 0.64 1 1e-15 1 1 0 0
EGFR 1 2 1 13156 10606 66 0.0096 1 1e-15 1e-15 1 7.63e-07 0
HRAS 2 3 2 8758 6300 47 3.7e-19 0.97 7e-29 8.1e-20 1 0 0
BRAF 2 2 2 9120 10092 47 1.3e-06 0.96 1.3e-14 7e-29 1 0 9.99e-16
IDH1 2 2 2 10596 10134 55 6.6e-16 1 7e-29 7e-29 1 0 0
CIC 1 1 1 14066 12718 71 1.2e-08 1 1e-15 1e-15 1 0 0
NRAS 2 2 1 8413 10581 43 5.6e-06 1 1e-15 1e-15 1 0 0
RNF43 2 2 2 9978 9292 51 4.9e-08 1 3.9e-29 2e-14 1 0 0
ATRX 1 2 1 11646 12114 60 2.2e-16 1 1e-15 1e-15 1 0 0
ZBTB20 2 2 2 8415 6667 43 1.1e-10 0.94 8.6e-19 2.1e-09 1 0 0
NOTCH1 1 2 1 10225 7849 55 1e-15 1 1e-15 1e-15 1 0 0
CDH1 2 2 2 8634 8254 45 3.6e-16 1 1.1e-23 3.5e-26 1 0 0
KEAP1 1 1 1 10060 10030 50 0.4 1 1e-15 0.017 1 1.25e-12 0
SMARCA4 1 1 1 6118 6234 30 0.86 1 1e-15 0.93 1 1.11e-16 3.56e-11
KIT 1 1 1 15035 10164 74 0.87 1 4.4e-16 0.029 0.95 2.54e-09 1.07e-06
KMT2B 2 2 2 8066 6649 44 1.7e-24 1 7e-29 2.3e-24 1 0 0
NSD1 1 1 1 13052 8233 67 1.2e-10 0.55 1.9e-14 3.1e-10 1 NA NA
  1. |DM|: number of differentially methylated genes averaged across Ti ∩ Ei tumor types;
  2. |DE|: number of differentially expressed genes averaged across Ti ∩ Ei tumor types;
  3. \( \frac{\mid DM\cap DE\mid }{\mid DE\mid } \) (%): percent of differentially methylated target genes out of differentially expressed target genes, averaged across tumor types Ti ∩ Ei
  4. p(DM ∙ DE): p-value testing if number of target genes that are differentially methylated and expression is larger than expected using a hypergeometric distribution combined across tumor types Ti ∩ Eiusing the Fisher’s method.
  5. p(−−), p(+−), p(−+), p(++): p-values that test if number of target genes with “--”,“+-”,“-+”,“++” pattern of methylation and expression changes is larger than expected a using hypergeometric distribution combined across tumor types using the Fisher’s method.
  6. p.methyl: median p-value from testing if the number of overlapping target genes that are differentially methylated by the mutation of the CDG between any pair of two tumor types is larger than expected using a hypergeometric distribution.
  7. p.exp: median p-value from testing if the number of overlapping target genes that are differentially expressed by the mutation of the CDG between any pair of two tumor types is larger than expected using a hypergeometric distribution.