Table 2. DNA methylation frequencies in tumor-adjacent normal lung, primary lung tumors and distant metastases.
| ID | Normal Lung |
Lung Tumor |
Metastases |
P | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Methylation Level |
Methylation Level |
Methylation Level |
||||||||||||||
| 0–1% n (%) | 1–10% n (%) | 10–50% n (%) | 50–100% n (%) | N (%) | 0–1% n (%) | 1–10% n (%) | 10–50% n (%) | 50–100% n (%) | N (%) | 0–1% n (%) | 1–10% n (%) | 10–50% n (%) | 50–100% n (%) | N(%) | Tumor vs. Normal | |
| OTX2 | 31 (100) | 0 (0) | 0 (0) | 0 (0) | 31 (100) | 25 (49.0) | 26 (51.0) | 0 (0) | 0 (0) | 51 (100) | 1 (4.4) | 14 (60.8) | 7 (30.4) | 1 (4.4) | 23 (100) | <0.0001 |
| HOXD3 | 23 (74.2) | 7 (22.6) | 1 (3.2) | 0 (0) | 31 (100) | 0 (0) | 7 (14.0) | 34 (68.0) | 9 (18.0) | 50 (100) | 0 (0) | 0 (0) | 13 (56.5) | 10 (43.5) | 23 (100) | <0.0001 |
| HOXB3/HOXB4 | 31 (100) | 0 (0) | 0 (0) | 0 (0) | 31 (100) | 12 (25.0) | 16 (33.3) | 19 (39.6) | 1 (2.1) | 48 (100) | 3 (13.0) | 2 (8.7) | 13 (56.5) | 5 (21.8) | 23 (100) | <0.0001 |
| HOXD10 | 26 (81.3) | 6 (18.7) | 0 (0) | 0 (0) | 32 (100) | 5 (9.8) | 27 (52.9) | 18 (35.3) | 1 (2.0) | 51 (100) | 2 (8.3) | 10 (41.7) | 11 (45.8) | 1 (4.2) | 24 (100) | <0.0001 |
| Chr1(q21.1).A | 15 (50.0) | 15 (50.0) | 0 (0) | 0 (0) | 30 (100) | 0 (0) | 10 (20.8) | 32 (66.7) | 6 (12.5) | 48 (100) | 0 (0) | 2 (8.7) | 12 (52.2) | 9 (39.1) | 23 (100) | <0.0001 |
| HIST1H3G/HIST1H2BI | 32 (100) | 0 (0) | 0 (0) | 0 (0) | 32 (100) | 19 (36.5) | 27 (51.9) | 6 (11.6) | 0 (0) | 52 (100) | 8 (34.8) | 6 (26.1) | 9 (39.1) | 0 (0) | 23 (100) | <0.0001 |
| GHSR | 11 (35.5) | 19 (61.3) | 1 (3.2) | 0 (0) | 31 (100) | 2 (4.2) | 6 (12.5) | 29 (60.4) | 11 (22.9) | 48 (100) | 1 (4.4) | 2 (8.7) | 11 (47.8) | 9 (39.1) | 23 (100) | <0.0001 |
| SIM1 | 28 (90.3) | 3 (9.7) | 0 (0) | 0 (0) | 31 (100) | 4 (8.2) | 22 (44.9) | 21 (42.8) | 2 (4.1) | 49 (100) | 1(4.6) | 3 (13.6) | 14 (63.6) | 4 (18.2) | 22 (100) | <0.0001 |
| OSR1 | 30 (96.8) | 1 (3.2) | 0 (0) | 0 (0) | 31 (100) | 1 (2.1) | 12 (25.0) | 30 (62.5) | 5 (10.4) | 48 (100) | 3 (13.6) | 1 (4.6) | 9 (40.9) | 9 (40.9) | 22 (100) | <0.0001 |
| FRG1BP | 0 (0) | 0 (0) | 32 (100) | 0 (0) | 32 (100) | 0 (0) | 4 (7.7) | 48 (92.3) | 0 (0) | 52 (100) | 0 (0) | 4 (17.4) | 17 (73.9) | 2 (8.7) | 23 (100) | 0.159 |
| Chr6(p22.1) | 32 (100) | 0 (0) | 0 (0) | 0 (0) | 32 (100) | 16 (32.6) | 13 (26.6) | 16 (32.6) | 4 (8.2) | 49 (100) | 5 (21.7) | 2 (8.7) | 12 (52.2) | 4 (17.4) | 23 (100) | <0.0001 |
| HOXA3 | 0 (0) | 14 (48.3) | 15 (51.7) | 0 (0) | 29 (100) | 0 (0) | 3 (6.0) | 40 (80.0) | 7 (14.0) | 50 (100) | 0 (0) | 6 (26.1) | 10 (43.5) | 7 (30.4) | 23 (100) | <0.0001 |
| LY75-CD302 | 30 (96.8) | 1 (3.2) | 0 (0) | 0 (0) | 31 (100) | 47 (97.9) | 1 (2.1) | 0 (0) | 0 (0) | 48 (100) | 22 (100) | 0 (0) | 0 (0) | 0 (0) | 22 (100) | >0.999 |
| CTAGE15 | 0 (0) | 0 (0) | 0 (0) | 32 (100) | 32 (100) | 0 (0) | 0 (0) | 0 (0) | 52 (100) | 52 (100) | 0 (0) | 0 (0) | 1 (4.4) | 22 (95.6) | 23 (100) | >0.999 |
| LOC648987 | 29 (100) | 0 (0) | 0 (0) | 0 (0) | 29 (100) | 34 (75.5) | 7 (15.6) | 4 (8.9) | 0 (0) | 45 (100) | 12 (57.1) | 4 (19.1) | 5 (23.8) | 0 (0) | 21 (100) | 0.005 |
| HIST1H2AJ/HIST1H2BM | 32 (100) | 0 (0) | 0 (0) | 0 (0) | 32 (100) | 40 (78.4) | 11 (21.6) | 0 (0) | 0 (0) | 51 (100) | 19 (82.6) | 3 (13.0) | 1 (4.4) | 0 (0) | 23 (100) | 0.005 |
| HOXA5 | 0 (0) | 11 (35.5) | 20 (64.5) | 0 (0) | 31 (100) | 0 (0) | 10 (19.2) | 36 (69.2) | 6 (11.6) | 52 (100) | 0 (0) | 5 (21.7) | 8 (34.8) | 10 (43.5) | 23 (100) | 0.035 |
| HIST1H3E | 0 (0) | 0 (0) | 29 (90.6) | 3 (9.4) | 32 (100) | 0 (0) | 0 (0) | 5 (10.0) | 45 (90.0) | 50 (100) | 0 (0) | 0 (0) | 1 (4.4) | 22 (95.6) | 23 (100) | <0.0001 |