Table 1.
Epi‐LumB specific CpG methylation events (significant at the <1% FDR in both the PEBC and TCGA cohorts) were found to affect a subset of previously known tumor suppressor genes (based on the catalogue of 716 TSG's). The statistics shown describe the relation between CpG methylation and expression over Epi‐LumB‐associated TSG's in the TCGA cohort where data was available on both CpG methylation and expression (by RNA sequencing) for 731 tumors and 82 normal breast tissue samples. Statistically significant hits are shown (including a minimum threshold of R2 > 0.10 and fold change > 2).
| TargetID | Gene symbol | R2 | Fold change in expression (Unmethylated/Methylated) | P‐value (adjusted) |
|---|---|---|---|---|
| cg14352983 | L3MBTL4 | 0.264 | 2.667 | 4.96E‐55 |
| cg08336641 | L3MBTL4 | 0.259 | 3.004 | 1.12E‐53 |
| cg14155416 | L3MBTL4 | 0.255 | 2.621 | 7.90E‐53 |
| cg12924825 | L3MBTL4 | 0.253 | 2.902 | 2.17E‐52 |
| cg18556788 | L3MBTL4 | 0.245 | 2.652 | 2.02E‐50 |
| cg17688525 | L3MBTL4 | 0.241 | 2.710 | 1.43E‐49 |
| cg03715143 | ID4 | 0.238 | 2.850 | 8.89E‐49 |
| cg09232937 | IRX1 | 0.191 | 6.137 | 2.08E‐38 |
| cg05724871 | L3MBTL4 | 0.177 | 2.625 | 1.99E‐35 |
| cg14271531 | ID4 | 0.147 | 2.676 | 5.32E‐29 |
| cg21167628 | PTCH2 | 0.116 | 2.028 | 7.70E‐23 |
| cg20918243 | RASSF10 | 0.109 | 9.006 | 2.33E‐21 |
| cg10530883 | IRX1 | 0.106 | 5.251 | 8.22E‐21 |