Table 1.
The significance level of covariates in 11 cancer datasets
| Predictors | BLCA | BRCA | COAD | HNSC | KIRC | LUAD | LUSC | OV | SKCM | STAD | UCEC |
|---|---|---|---|---|---|---|---|---|---|---|---|
| RegionLength | 0.23 (0) | 0.27 (0) | 0.23 (0) | 0.27 (0) | 0.21 (0) | 0.29 (0) | 0.26 (0) | 0.21 (0) | 0.29 (0) | 0.24 (0) | 0.24 (0) |
| SynonymousVariant | 0.31 (1.37E-247) | 0.43 (0) | 0.35 (3.65E-225) | 0.47 (0) | 0.31 (1.13E-264) | 0.65 (0) | 0.53 (0) | 0.33 (8.95E-230) | 0.73 (0) | 0.43 (0) | 0.34 (7.49E-265) |
| TissueExpression | 0.04 (7.09E-05) | 0.06 (1.92E-11) | -0.08 (6.78E-09) | -0.05 (8.97E-07) | 0.07 (4.02E-11) | -0.21 (1.16E-99) | -0.17 (1.42E-52) | -0.02 (0.10) | -0.36 (6.06E-166) | -0.09 (2.35E-14) | 0.07 (4.16E-13) |
| CellLineExpression | -0.07 (2.52E-14) | -0.12 (4.12E-40) | -0.20 (2.94E-79) | -0.21 (2.49E-137) | -0.04 (1.15E-05) | -0.32 (0) | -0.28 (3.95E-235) | -0.08 (9.26E-17) | -0.28 (2.97E-206) | -0.23 (1.43E-154) | -0.11 (4.79E-33) |
| ReplicationTiming | 0.10 (9.00E-19) | 0.16 (5.05E-56) | 0.25 (1.90E-90) | 0.28 (1.89E-172) | 0.04 (1.37E-04) | 0.43 (0) | 0.37 (2.63E-295) | 0.13 (1.99E-29) | 0.39 (2.92E-283) | 0.30 (1.51E-177) | 0.12 (6.69E-26) |
| CNV | 0.01 (0.16) | 0.02 (1.95E-04) | -5.25E-03 (0.30) | 0.04 (8.51E-10) | -0.04 (3.44E-14) | 0.07 (9.71E-20) | 0.07 (7.16E-18) | -8.85E-03 (0.48) | NA | 0.02 (1.35E-03) | 9.71E-03 (0.04) |
| HiC | -0.08 (7.05E-18) | -0.13 (5.99E-43) | -0.19 (4.53E-59) | -0.23 (1.16E-127) | -0.02 (0.03) | -0.34 (0) | -0.30 (3.16E-213) | -0.10 (1.47E-20) | -0.30 (2.05E-233) | -0.24 (3.87E-129) | -0.07 (1.42E-14) |
| ConstraintScore | 0.02 (0.02) | 0.05 (5.10E-11) | 0.02 (0.02) | -8.64E-03 (0.26) | 0.04 (2.63E-06) | -0.05 (1.23E-12) | -0.07 (8.70E-17) | 9.34E-03 (0.31) | -0.09 (6.37E-31) | -0.01 (0.07) | 0.11 (5.25E-39) |
| ATACSeq | -9.23E-03 (0.02) | -0.02 (2.66E-11) | -0.02 (1.56E-06) | -0.03 (1.27E-13) | 1.65E-03 (0.67) | -0.06 (7.49E-47) | -0.04 (1.59E-21) | NA | -0.05 (2.13E-24) | -0.03 (1.67E-11) | -5.32E-03 (0.13) |
| Methylation | -2.27E-04 (8.63E-03) | -3.35E-04 (1.08E-06) | 4.04E-05 (0.67) | 2.74E-05 (0.73) | -4.26E-04 (1.57E-09) | 2.55E-04 (0.02) | -6.81E-05 (0.34) | -3.05E-04 (7.06E-04) | -1.83E-04 (2.49E-03) | 9.46E-05 (0.41) | -2.14E-04 (0.01) |
Note: The coefficients are derived under the ZTNB model. The predictors are centered at median and scaled by median absolute deviation for standardization. The values in the brackets are P-values for the significance of the coefficients calculated by Wald test. The full names of cancers are in Supplementary Table S1.