Table 1.
Details of response-differentially methylated regions (response-DMRs)
| Gene ID | Chr | Range (hg19) | Average Δβ (%)α | No. CpGs | Pβ | CpG Island % (Island/Shore) | RefSeq % (Promoter/Exon) | MCF7 ChromHMM % (Active/Bivalent/Polycomb/Quiescent)γ |
|---|---|---|---|---|---|---|---|---|
| TMEM176A/B | Chr7 | 150,497,065–150,498,205 | 27.2 | 14 | 2.04 × 10−9 | 100/0 | 90/10 | 0/0/0/100 |
| UNC5D | Chr8 | 3,509,283–35,093,411 | 28.2 | 10 | 2.35 × 10−4 | 100/0 | 93/7 | 0/0/100/0 |
| STAC2 | Chr17 | 37,381,830–37,382,301 | 14.9 | 7 | 3.73 × 10−4 | 100/0 | 72/28 | 0/0/0/100 |
| SDR42E1 | Chr16 | 82,044,738–82,045,297 | 23.8 | 10 | 1.13 × 10−3 | 80/20 | 90/10 | 100/0/0/0 |
| NELL1 | Chr11 | 20,690,682–20,691,429 | 22.8 | 12 | 1.49 × 10−3 | 100/0 | 83/17 | 0/0/100/0 |
| GRP | Chr18 | 56,887,002–56,887,785 | 20.3 | 11 | 2.97 × 10−3 | 73/27 | 73/27 | 0/0/100/0 |
| FOXG1 | Chr14 | 29,235,928–29,236,535 | 17.5 | 11 | 2.00 × 10−2 | 0/100 | 73/27 | 0/0/100/0 |
| CDH8 | Chr16 | 62,069,806–62,070,365 | 24.2 | 10 | 2.00 × 10−2 | 100/0 | 100/0 | 0/10/90/0 |
| GRIA4 | Chr11 | 105,480,979–105,481,322 | 15.4 | 7 | 2.26 × 10−1 | 86/14 | 86/14 | 0/0/100/0 |
αCalculated as Non-responders minus Complete responders
βFisher’s multiple comparison statistic
γData from ENCODE MCF7 Segmentation (Additional file 1)