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Table 1 Summary table of Polycomb/Trithorax analysis

From: On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence

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
  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).