Table 2. Differentially-methylated genes in 8p11-p12-amplified breast tumors.
| Gene symbol | Chromosome | Delta beta valuea | Gene expression (n=22)b | Gene expression (n=150)c | Cox coefficient (n=150)d | Cox P-value (n=150)d | DNA copy number 8p11-p12-amplified tumors (n=11)e amplification/loss/normal | DNA copy number 8p11-p12 nonamplified tumors (n=11)f amplification/loss/normal |
|---|---|---|---|---|---|---|---|---|
| BAMBI | 10p12.1 | Hypomethylated | Overexpressed | NS | 0/0/11 | 0/0/11 | ||
| CXCL12 | 10q11.21 | Hypermethylated | Underexpressed | −0.498 | 3.76E−05 | 0/0/11 | 0/0/11 | |
| HTRA1 | 10q26.13 | Hypermethylated | Underexpressed | −0.400 | 1.57E−04 | |||
| CRYAB;HSPB2 | 11q23.1 | Hypermethylated | Underexpressed | Underexpressed | NS | 0/4/7 | 0/0/11 | |
| PTHLH | 12p11.22 | Hypermethylated | Underexpressed | Underexpressed | NS | 1/0/10 | 0/0/11 | |
| HOXC13 | 12q13.13 | Hypermethylated | Overexpressed | 0.397 | 3.96E−04 | 0/1/10 | 0/0/11 | |
| PABPC3 | 13q12.13 | Hypermethylated | Overexpressed | 0.643 | 1.12E−06 | 0/4/7 | 0/0/11 | |
| TRAPPC6B | 14q21.1 | Hypermethylated | Overexpressed | 0.866 | 1.80E−05 | 0/2/9 | 0/0/11 | |
| BMP4 | 14q22.2 | Hypermethylated | Underexpressed | −0.379 | 0.001 | 0/3/8 | 0/0/11 | |
| BATF | 14q24.3 | Hypomethylated | Underexpressed | −0.502 | 0.002 | 0/4/7 | 0/0/11 | |
| ELL3 | 15q15.3 | Hypomethylated | Overexpressed | 0.432 | 0.009 | 0/0/11 | 0/0/11 | |
| SEPHS2 | 16p11.2 | Hypomethylated | Overexpressed | 0.495 | 0.003 | 0/0/11 | 0/0/11 | |
| SPN | 16p11.2 | Hypermethylated | Overexpressed | 0.254 | 0.064 | 0/0/11 | 0/0/11 | |
| SPAG9 | 17q21.33 | Hypermethylated | Overexpressed | Overexpressed | 0.628 | 0.000 | 1/0/10 | 0/0/11 |
| DHX40 | 17q23.1 | Hypermethylated | Overexpressed | 0.599 | 0.004 | 2/0/9 | 0/0/11 | |
| CCDC47 | 17q23.3 | Hypomethylated | Overexpressed | 0.671 | 0.001 | |||
| ICAM2 | 17q23.3 | Hypermethylated | Underexpressed | Underexpressed | −0.441 | 0.012 | 1/0/10 | 0/0/11 |
| CYGB | 17q25.1 | Hypermethylated | Underexpressed | −0.433 | 0.013 | 0/0/11 | 0/0/11 | |
| NFIX | 19p13.2 | Hypermethylated | Underexpressed | −0.289 | 0.023 | 0/0/11 | 0/0/11 | |
| NFIC | 19p13.3 | Hypermethylated | Underexpressed | NS | 0/1/10 | 0/0/11 | ||
| CACNG6 | 19q13.42 | Hypermethylated | Overexpressed | NS | 0/0/11 | 0/0/11 | ||
| PHGDH | 1p12 | Hypermethylated | Underexpressed | 0.313 | 0.002 | 0/0/11 | 0/0/11 | |
| CHI3L2 | 1p13.3 | Hypermethylated | Underexpressed | NS | 0/0/11 | 0/0/11 | ||
| COL11A1 | 1p21.1 | Hypermethylated | Overexpressed | NS | 0/1/10 | 0/0/11 | ||
| AGL | 1p21.2 | Hypomethylated | Overexpressed | Overexpressed | 0.337 | 0.013 | 0/1/10 | 0/0/11 |
| PODN | 1p32.3 | Hypermethylated | Underexpressed | −0.366 | 0.001 | 0/2/9 | 0/0/11 | |
| MMP23A;MMP23B | 1p36.33 | Hypermethylated | Underexpressed | −0.415 | 0.003 | 0/1/10 | 0/0/11 | |
| MMP23B | 1p36.33 | Hypermethylated | Underexpressed | −0.415 | 0.003 | 0/1/10 | 0/0/11 | |
| EXOC8 | 1q42.2 | Hypomethylated | Overexpressed | Overexpressed | 0.734 | 2.58E−05 | 1/1/9 | 0/0/11 |
| SYCP2 | 20q13.33 | Hypomethylated | Overexpressed | Overexpressed | 0.447 | 3.15E−05 | 2/0/9 | 0/0/11 |
| GREB1 | 2p25.1 | Hypomethylated | Overexpressed | −0.268 | 0.050 | 0/2/9 | 0/1/10 | |
| C2orf40 | 2q12.2 | Hypermethylated | Underexpressed | Underexpressed | −0.268 | 0.005 | ||
| SATB2 | 2q33.1 | Hypermethylated | Overexpressed | NS | 0/0/11 | 0/0/11 | ||
| KIF1A | 2q37.3 | Hypermethylated | Overexpressed | NS | 0/0/11 | 0/0/11 | ||
| TF | 3q22.1 | Hypermethylated | Underexpressed | NS | 0/1/10 | 0/0/11 | ||
| TAPT1 | 4p15.32 | Hypomethylated | Overexpressed | NS | ||||
| SORBS2 | 4q35.1 | Hypomethylated | Underexpressed | Underexpressed | −0.326 | 0.004 | ||
| PIK3R1 | 5q13.1 | Hypermethylated | Overexpressed | 0.536 | 3.96E−04 | 0/0/11 | 0/0/11 | |
| CARTPT | 5q13.2 | Hypermethylated | Underexpressed | NS | ||||
| PCSK1 | 5q15 | Hypermethylated | Underexpressed | −0.326 | 0.002 | 0/1/10 | 0/0/11 | |
| PAM | 5q21.1 | Hypermethylated | Underexpressed | Underexpressed | −0.340 | 0.024 | 0/0/11 | 0/0/11 |
| DMXL1 | 5q23.1 | Hypermethylated | Overexpressed | Overexpressed | 0.620 | 9.99E−06 | 0/0/11 | 0/0/11 |
| H2AFY | 5q31.1 | Hypermethylated | Overexpressed | Overexpressed | 0.831 | 3.15E−07 | 0/0/11 | 0/0/11 |
| DOCK2 | 5q35.1 | Hypomethylated | Underexpressed | NS | 0/0/11 | 0/0/11 | ||
| SCGB3A1 | 5q35.3 | Hypermethylated | Underexpressed | −0.240 | 0.001 | 0/0/11 | 0/0/11 | |
| USP49 | 6p21.1 | Hypermethylated | Overexpressed | 0.310 | 0.031 | 1/0/10 | 0/0/11 | |
| SCAND3 | 6p22.1 | Hypermethylated | Overexpressed | 0.492 | 0.015 | |||
| ID4 | 6p22.3 | Hypermethylated | Overexpressed | 0.492 | 1.95E−05 | 0/0/11 | 0/0/11 | |
| RARS2;ORC3L | 6q15 | Hypomethylated | Overexpressed | 0.822 | 1.85E−05 | 2/1/8 | 0/0/11 | |
| LRP11 | 6q25.1 | Hypomethylated | Overexpressed | 0.638 | 3.05E−04 | 0/1/10 | 0/0/11 | |
| C7orf28A | 7p22.1 | Hypomethylated | Overexpressed | 0.775 | 1.85E−05 | 0/0/11 | 0/0/11 | |
| LFNG | 7p22.3 | Hypermethylated | Underexpressed | −0.668 | 4.55E−06 | 0/0/11 | 0/0/11 | |
| PON3 | 7q21.3 | Hypermethylated | Underexpressed | Underexpressed | −0.305 | 3.19E−05 | 1/0/10 | 0/0/11 |
| NRCAM | 7q31.1 | Hypomethylated | Overexpressed | 0.336 | 0.024 | 0/0/11 | 0/0/11 | |
| NDUFA5 | 7q31.32 | Hypermethylated | Overexpressed | 0.771 | 1.48E−04 | 0/1/10 | 0/0/11 | |
| LEP | 7q32.1 | Hypermethylated | Overexpressed | 0.357 | 0.003 | 0/0/11 | 0/0/11 | |
| RARRES2 | 7q36.1 | Hypermethylated | Underexpressed | −0.272 | 0.020 | 0/0/11 | 0/0/11 | |
| BRF2 | 8p11.23 | Hypermethylated | Overexpressed | Overexpressed | NS | 7/2/2 | 0/0/11 | |
| IMPAD1 | 8q12.1 | Hypomethylated | Overexpressed | Overexpressed | 1.067 | 2.70E−07 | ||
| FABP5 | 8q21.13 | Hypermethylated | Overexpressed | NS | 1/0/10 | 0/0/11 | ||
| PLEKHF2 | 8q22.1 | Hypomethylated | Overexpressed | Overexpressed | 0.393 | 4.47E−04 | 3/0/8 | 0/0/11 |
| VPS13B | 8q22.2 | Hypomethylated | Overexpressed | 0.878 | 7.06E−06 | |||
| RRM2B | 8q22.3 | Hypomethylated | Overexpressed | Overexpressed | 0.452 | 0.001 | 3/0/8 | 0/0/11 |
| TRPS1 | 8q23.3 | Hypermethylated | Overexpressed | Overexpressed | 0.320 | 0.008 | 6/0/5 | 0/0/11 |
| TRPS1 | 8q23.3 | Hypomethylated | Overexpressed | Overexpressed | 0.320 | 0.008 | 6/0/5 | 0/0/11 |
| ENPP2 | 8q24.12 | Hypermethylated | Underexpressed | Underexpressed | −0.258 | 0.017 | 2/0/9 | 0/0/11 |
| TAF2 | 8q24.12 | Hypomethylated | Overexpressed | 1.164 | 1.34E−06 | 2/0/9 | 0/0/11 | |
| SQLE | 8q24.13 | Hypomethylated | Overexpressed | Overexpressed | 0.566 | 2.95E−07 | 2/0/9 | 0/0/11 |
| TATDN1 | 8q24.13 | Hypomethylated | Overexpressed | Overexpressed | 0.783 | 2.89E−06 | 5/0/6 | 0/0/11 |
| NDRG1 | 8q24.22 | Hypomethylated | Overexpressed | 0.843 | 5.03E−11 | 2/1/8 | 0/0/11 | |
| WDR44 | Xq24 | Hypomethylated | Overexpressed | 0.937 | 4.75E−06 | 3/0/8 | 0/0/11 |
Abbreviation: NS, not statistically significant.
Genes not correlating between DNA methylation and transcriptional patterns are shown in bold text.
a
Delta beta value (8p11-p12-amplified tumors versus nonamplified tumors) >0.14 are indicated by hypermethylation and <−0.14 are indicated by hypomethylation; Bonferroni adjusted P-value P<0.05.
b
Gene expression microarray log2 ratio for the 22 tumors (8p11–p12-amplified tumors versus nonamplified tumors) >0.58 are indicated by overexpression and <−0.58 are indicated by underexpression.
c
Gene expression microarray log2 ratio for the 150 tumors (8p11-p12-amplified tumors versus nonamplified tumors) > 0.58 are indicated by overexpression and < −0.58 are indicated by underexpression.
d
Univariate Cox proportional hazard regression models using the gene expression data for the 150 tumors and overall survival rates.
e
Array-CGH log2 ratio thresholds set at ⩾+0.5, −0.2 and between +0.5 and −0.2 for amplification, loss and normal copy number, respectively.
f
Array-CGH log2 ratio thresholds set at ⩾+0.5, –0.2 and between +0.5 and −0.2 for amplification, loss and normal copy number, respectively.