Table 1.
Summary table of Polycomb/Trithorax analysis
| Factors | #(overlapped)/#total (percentage) | P-value | |||||
|---|---|---|---|---|---|---|---|
| Perm | Indep | Hai | Hyb | ||||
| TF1 | TF2 | TF1 | TF2 | Test | Res | FL | Mtd |
| Dsp1 | GAF | 1329/1982 (67%) | 1266/3019 (41.9%) | <0.001 | ~1 | <2e-04 | <2e-04 |
| Dsp1 | Me3K27 | 193/1982 (9.74%) | 242/2480 (9.76%) | <0.001 | ~1 | ~1 | ~1 |
| Dsp1 | Me3K4 | 1225/1982 (61.8%) | 1158/4893 (23.7%) | <0.001 | ~1 | < 2e-04 | ~1 |
| Dsp1 | Pc | 309/1982 (15.6%) | 279/2110 (13.2%) | <0.001 | ~1 | ~1 | ~1 |
| Dsp1 | Ph | 234/1982 (11.8%) | 223/441 (50.6%) | <0.001 | ~1 | < 2e-04 | ~1 |
| Dsp1 | Pho | 1272/1982 (64.2%) | 1281/3152 (40.6%) | <0.001 | ~1 | <2e-04 | <2e-04 |
| Dsp1 | Phol | 1034/1982 (52.2%) | 1085/2951 (36.8%) | <0.001 | ~1 | < 2e-04 | ~1 |
| Dsp1 | TrxC | 123/1982 (6.2%) | 126/167 (75.4%) | <0.001 | ~1 | < 2e-04 | ~1 |
| Dsp1 | TrxN | 1255/1982 (63.3%) | 1297/4868 (26.6%) | <0.001 | ~1 | < 2e-04 | ~1 |
| GAF | Me3K27 | 253/3019 (8.38%) | 297/2480 (12.0%) | <0.001 | ~1 | ~1 | ~1 |
| GAF | Me3K4 | 1539/3019 (51%) | 1528/4893 (31.2%) | <0.001 | ~1 | 0.11 | ~1 |
| GAF | Pc | 399/3019 (13.2%) | 369/2110 (17.5%) | <0.001 | ~1 | ~1 | ~1 |
| GAF | Ph | 234/3019 (7.75%) | 231/441 (52.4%) | <0.001 | ~1 | < 2e-04 | ~1 |
| GAF | Pho | 1147/3019 (38%) | 1204/3152 (38.2%) | <0.001 | ~1 | < 2e-04 | ~1 |
| GAF | Phol | 993/3019 (32.9%) | 1067/2951 (36.2%) | <0.001 | ~1 | < 2e-04 | ~1 |
| GAF | TrxC | 110/3019 (3.64%) | 114/167 (68.3%) | <0.001 | ~1 | < 2e-04 | ~1 |
| GAF | TrxN | 1294/3019 (42.9%) | 1371/4868 (28.2%) | <0.001 | ~1 | ~1 | ~1 |
| Me3K27 | Me3K4 | 174/2480 (7.02%) | 155/4893 (3.17%) | <0.001 | ~1 | ~1 | ~1 |
| Me3K27 | Pc | 1914/2480 (77.2%) | 1591/2110 (75.4%) | <0.001 | ~0.73 | <2e-04 | <2e-04 |
| Me3K27 | Ph | 433/2480 (17.5%) | 364/441 (82.5%) | <0.001 | ~0.76 | <2e-04 | <2e-04 |
| Me3K27 | Pho | 641/2480 (25.8%) | 629/3152 (20.0%) | <0.001 | ~1 | 0.91 | ~1 |
| Me3K27 | Phol | 80/2480 (3.23%) | 69/2951 (2.34%) | <0.001 | ~1 | ~1 | ~1 |
| Me3K27 | TrxC | 116/2480 (4.68%) | 98/167 (58.7%) | <0.001 | ~1 | < 2e-04 | ~1 |
| Me3K27 | TrxN | 141/2480 (5.69%) | 126/4868 (2.59%) | <0.001 | ~1 | ~1 | ~1 |
| Me3K4 | Pc | 264/4893 (5.4%) | 263/2110 (12.5%) | <0.001 | ~1 | ~1 | ~1 |
| Me3K4 | Ph | 84/4893 (1.72%) | 83/441 (18.8%) | <0.001 | ~1 | ~1 | ~1 |
| Me3K4 | Pho | 1921/4893 (39.3%) | 2027/3152 (64.3%) | <0.001 | ~1 | <2e-04 | <2e-04 |
| Me3K4 | Phol | 2396/4893 (49%) | 2559/2951 (86.7%) | <0.001 | ~1 | <2e-04 | <2e-04 |
| Me3K4 | TrxC | 31/4893 (0.634%) | 31/167 (18.6%) | <0.001 | ~1 | ~1 | ~1 |
| Me3K4 | TrxN | 3179/4893 (65%) | 3500/4868 (71.9%) | <0.001 | ~1 | <2e-04 | <2e-04 |
| Pc | Ph | 347/2110 (16.4%) | 437/441 (99%) | <0.001 | ~1 | <2e-04 | <2e-04 |
| Pc | Pho | 587/2110 (27.8%) | 793/3152 (25.2%) | <0.001 | ~1 | 2e-04 | ~1 |
| Pc | Phol | 153/2110 (7.25%) | 169/2951 (5.73%) | <0.001 | ~1 | ~1 | ~1 |
| Pc | TrxC | 122/2110 (5.78%) | 135/167 (80.8%) | <0.001 | ~1 | < 2e-04 | ~1 |
| Pc | TrxN | 238/2110 (11.3%) | 269/4868 (5.53%) | <0.001 | ~1 | ~1 | ~1 |
| Ph | Pho | 417/441 (94.6%) | 412/3152 (13.1%) | <0.001 | ~1 | <2e-04 | <2e-04 |
| Ph | Phol | 90/441 (20.4%) | 97/2951 (3.29%) | <0.001 | ~1 | ~1 | ~1 |
| Ph | TrxC | 124/441 (28.1%) | 130/167 (77.8%) | <0.001 | ~1 | < 2e-04 | ~0.059 |
| Ph | TrxN | 114/441 (25.9%) | 127/4868 (2.61%) | <0.001 | ~1 | ~1 | ~1 |
| Pho | Phol | 1813/3152 (57.5%) | 1852/2951 (62.8%) | <0.001 | ~1 | <2e-04 | <2e-04 |
| Pho | TrxC | 131/3152 (4.16%) | 139/167 (83.2%) | <0.001 | ~1 | < 2e-04 | ~1 |
| Pho | TrxN | 2060/3152 (65.4%) | 2069/4868 (42.5%) | <0.001 | ~1 | <2e-04 | <2e-04 |
| Phol | TrxC | 61/2951 (2.07%) | 61/167 (36.5%) | <0.001 | ~1 | 0.15 | ~1 |
| Phol | TrxN | 2540/2951 (86%) | 2510/4868 (51.6%) | <0.001 | ~1 | <2e-04 | <2e-04 |
| TrxC | TrxN | 93/167 (55.7%) | 94/4868 (1.93%) | <0.001 | ~1 | 0.25 | ~1 |
Pilot runs of 100 resamplings were performed to filter out clearly non-co-occurring pairs. Thereafter, 5000 resamplings were used for candidate pairs when testing the hybrid method. Tests using the permutation test approach were restricted to 1000 resamplings. Pairs with significant p-values by the hybrid method are indicated in bold(p-value ≤ 0.05) and italics(p-value ≤ 0.1).