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Table 2 MDGs dysregulate expression levels of chromatin regulators

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| N1 (# of dysregulated genes) N2 (# of
dysregulated
genes in list A)
Enrichment PvalueA N3 (# of
dysregulated
genes in list B)
Enrichment PvalueB Genes in list B that are dysregulateda Genes in list B that are
differentially methylatedb
TP53 8 233 19 0.00056 5 3.2e-06 CBX7 RAD54L TTF2 KDM1A SUV39H2  
PTEN 3 1,534 81 0.00012 9 9.1e-06 DNMT1 DNMT3A SETBP1 PRDM5 CBX7 RAD54L EZH2 PCNA HDAC1 DNMT3A PRDM5 HDAC1
RB1 2 1,447 83 5.2e-06 4 0.056 DNMT1 EYA4 EZH2 PCNA PCNA
NF1 2 766 36 0.044 0 1   
CTNNB1 2 5,515 207 0.12 12 0.0033 DNMT1 SETBP1 PRDM2 PRDM5 CBX7 KAT2B RAD54L WHSC1 EZH2 UHRF1 TDG TET3 PRDM2 CBX7
HRAS 2 1,137 63 2.0e-04 3 0.11 PRDM2 RAD54L HDAC1 PRDM2
BRAF 2 3,128 133 0.008 8 0.0091 DNMT1 DNMT3A DNMT3B KAT2B WHSC1 EZH2 UHRF1 KDM1A DNMT3A UHRF1
IDH1 2 3,560 208 2.8e-15 2 0.9 SUV39H2 TET3  
NRAS 2 1,609 87 2.8e-05 1 0.82 HDAC1  
RNF43 2 3,212 157 4.4e-06 8 0.011 DNMT3A DNMT3B PRDM2 RAD54L WHSC1 UHRF1 HDAC1 TET3 DNMT3A DNMT3B PRDM2 WHSC1
ZBTB20 2 1,563 78 0.00088 6 0.0039 DNMT3A RAD54L WHSC1 UHRF1 TTF2 HDAC1 DNMT3A WHSC1 UHRF11
CDH1 2 2,792 136 2.7e-05 14 3.3e-08 DNMT3B SETBP1 PRDM2 CBX7 DUSP1 RAD54L WHSC1 EZH2 PCNA KDM1A SUV39H2 HDAC1 TDG TET3 PRDM2 CBX7 WHSC1 KDM1A
  1. |Ti|: number of tumor types whose genome-wide methylation levels are significantly associated with the mutation status of CDG i;
  2. N1: number of genes whose expression levels are dysregulated by MDG i in all |Ti| tumor types;
  3. N2: number of genes in list A that are dysregulated in all |Ti| tumor types;
  4. N3: number of genes in list B that are dysregulated in all |Ti| tumor types;
  5. Enrichment PvalueA, and PvalueB are calculated using hypergeometric distributions testing if genes in lists A and B are enriched among genome-wide differentially expressed target genes;
  6. aGenes in list B that are dysregulated in all |Ti| tumor types;
  7. bGenes in list B that are differentially methylated in all |Ti| tumor types.