Table 2. Associations between mutated driver genes and HyperZ and HypoZ indices or site–specific methylation alterations.
| Cancer type | Driver genes associated with HyperZ and HypoZ (in alphabetical order)a | # driver genes associated with any probeb | ||
|---|---|---|---|---|
| HyperZ | HypoZ | Total | ||
| BLCA | STAG2 | NA | 1 | 0 |
| BRCA | FOXA1 | CDH1 | 2 | 50 |
| COAD | ADORA3,AKAP9,ARAP3,ATG2B, BCL9,BRAF,BRD8,CAB39L,CCDC88A, CD58,CDK12,CEL,CHD3,CYLC1, DAXX,DNAH17,DOCK1,DSG4,EGR1, ERCC3,FBN2,FHOD3,FMN2,GIGYF2, GPATCH8,GPR112,HEATR4,HIPK2, HIST1H1E,IGF2R,INADL,IQSEC2, KAT2B,KBTBD4,KCTD3,KLKB1, LATS1,LEPRE1,MACF1,MBD6,MGA, MTA2,MTTP,NOVA1,OR4M2,OVCH1, PCDHGA11,PLAGL2,PLEKHA6, PLXNA3,PREX2,PSD,PTCH1,RNF43, SPEN,SVIL,TET3,TNRC6C,UBQLN2, UBR4,USP34,XYLT2,ZBTB20,ZFYVE26 |
C14orf39,CNTNAP5,FBN2, MEPE,SPEN |
67 | 189 |
| GBM | IDH1,PDGFRA,STAG2 | PDGFRA,STAG2 | 3 | 16 |
| HNSC | CASP8 | NSD1 | 2 | 34 |
| KIRC | BAP1,PBRM1,SETD2 | ARID1A | 4 | 14 |
| KIRP | NF2,SETD2 | 2 | 10 | |
| LIHC | CTNNB1,TP53 | 2 | 11 | |
| LUAD | STK11 | KEAP1,LTBP1,STK11,TP53 | 4 | 80 |
| LUSC | TP53 | 1 | 0 | |
| PAAD | 0 | 7 | ||
| PRAD | SPOP | TP53 | 2 | 12 |
| READ | 0 | 0 | ||
| SKCM | 0 | 43 | ||
| STAD | ADNP2,ALG10,ARID1A,BCL9L,BCOR, C5orf42,EIF5B,EPHA2,FHOD3,GLI1, GON4L,IRS4,KIAA0195,PFKP,PIK3CA, RALGAPB,RNF43,STAB1,TBX4,TLE2, TP53,TP53BP2,WASF3,WDR7,WNT16, XYLT2,ZBTB20,ZFHX4,ZNF608 |
FRMD4A,TP53,ZFHX4 | 30 | 357 |
| TGCT | NAc | NAc | NAc | 25 |
| THCA | BRAF,HRAS,NRAS | BRAF,EIF1AX,HRAS,NRAS | 4 | 5 |
| UCEC | CUX1,PIK3R1,PTEN | TP53 | 4 | 53 |
a Negatively associated genes are shown in bold; positively associated genes are shown in normal font.
b See S2 Table for driver genes associated with site-specific methylation alterations
c Normal tissue samples were not available to calculate HyperZ/HypoZ indices