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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).