Gene | ACGC (n = 2145) | ACGC+SSC+ASC (n = 6107) | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Phase-I | Phase-II | All | CH model | denovolyzeR | LGD | MIS | All | CH model | denovolyzeR | ||||||||
LGD | MIS | LGD | MIS | LGD | MIS | LGD_q | prot_q | LGD_q | prot_q | LGD_q | prot_q | LGD_q | prot_q | ||||
SCN2A † | 6 | 4 | 5 | 9 | 11 | 13 | 3.68E−25 | 1.23E−40 | 4.21E−18 | 1.05E−29 | 15 | 21 | 36 | 7.77E−28 | 2.23E−49 | 3.52E-22 | 3.35E-42 |
CHD8 † | 3 | 1 | 2 | 1 | 5 | 2 | 3.18E−09 | 7.56E−08 | 5.40E−07 | 1.68E−04 | 14 | 4 | 18 | 7.49E−25 | 7.45E−18 | 3.52E−22 | 1.19E−13 |
MECP2 † | 1 | 3 | 2 | 1 | 3 | 4 | 1.00E−06 | 1.12E−11 | 1.78E−05 | 4.12E−08 | 3 | 5 | 8 | 6.26E−04 | 1.33E−08 | 1.78E−03 | 1.42E−06 |
DYRK1A † | 1 | 1 | 2 | 0 | 3 | 1 | 1.51E−05 | 2.78E−04 | 5.92E−05 | 2.75E−03 | 8 | 1 | 9 | 3.78E−13 | 2.51E−07 | 1.31E−13 | 4.23E−07 |
ASXL3 † | 0 | 1 | 3 | 1 | 3 | 2 | 7.28E−04 | 5.62E−03 | 1.82E−04 | 4.29E−03 | 5 | 2 | 7 | 6.33E−04 | 0.894 | 6.03E−06 | 0.0200 |
WAC † | 0 | 0 | 2 | 0 | 2 | 0 | 9.05E−04 | 0.0311 | 5.14E−03 | 0.2322 | 4 | 0 | 4 | 2.12E−05 | 0.0532 | 6.57E−05 | 0.1384 |
FOXP1 † | 0 | 0 | 2 | 1 | 2 | 1 | 1.04E−03 | 3.46E−03 | 0.0103 | 0.0285 | 4 | 1 | 5 | 3.36E−05 | 0.014 | 3.81E−04 | 0.0235 |
CTTNBP2 | 0 | 1 | 2 | 0 | 2 | 1 | 4.69E−03 | 0.0189 | 0.0226 | 0.2162 | 3 | 1 | 4 | 0.0331 | 1 | 0.1072 | 1 |
TNRC6B † | 0 | 0 | 2 | 0 | 2 | 0 | 7.00E−03 | 0.2549 | 0.0158 | 0.5818 | 4 | 0 | 4 | 1.97E−03 | 1 | 1.17E−03 | 1 |
MED13L † | 1 | 0 | 1 | 0 | 2 | 0 | 7.00E−03 | 0.2549 | 0.0386 | 0.9485 | 4 | 1 | 5 | 1.97E−03 | 0.9197 | 9.40E−03 | 1 |
CDKL5 † | 1 | 0 | 1 | 0 | 2 | 0 | 8.26E−03 | 0.2732 | 7.14E−03 | 0.3409 | 2 | 1 | 3 | 1 | 1 | 0.5527 | 1 |
DSCAM † | 2 | 0 | 0 | 1 | 2 | 1 | 0.0130 | 0.0770 | 0.0226 | 0.3035 | 6 | 2 | 8 | 1.03E−05 | 0.0272 | 1.55E−06 | 0.0135 |
ZNF292 | 1 | 0 | 1 | 0 | 2 | 0 | 0.0139 | 0.6051 | 0.0158 | 0.8299 | 3 | 2 | 5 | 0.2763 | 1 | 0.0508 | 1 |
POGZ † | 1 | 1 | 0 | 0 | 1 | 1 | 0.0507 | 0.0153 | 0.3864 | 0.5818 | 4 | 4 | 8 | 2.40E−06 | 1.84E−09 | 3.48E−03 | 7.13E−04 |
WDFY3 | 1 | 1 | 0 | 2 | 1 | 3 | 0.2966 | 0.0153 | 0.7292 | 0.2736 | 3 | 7 | 10 | 0.2778 | 7.21E−04 | 1 | 5.44E−03 |
NAA15 † | 0 | 0 | 1 | 1 | 1 | 1 | 0.0851 | 0.0228 | 0.3452 | 0.3025 | 2 | 2 | 4 | 0.1747 | 0.0287 | 1 | 0.4185 |
CUL3 | 1 | 0 | 0 | 1 | 1 | 1 | 0.1056 | 0.0446 | 0.3825 | 0.3035 | 2 | 1 | 3 | 0.2778 | 1 | 1 | 1 |
STXBP1 † | 1 | 0 | 0 | 0 | 1 | 0 | 0.1056 | 0.6051 | 0.3267 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 1 |
ADNP † | 1 | 0 | 0 | 0 | 1 | 0 | 0.1314 | 0.9222 | 0.2294 | 1 | 5 | 0 | 5 | 2.40E−06 | 0.0764 | 4.55E−07 | 0.0669 |
DDX3X † | 0 | 1 | 1 | 0 | 1 | 1 | 0.1335 | 0.0871 | 0.2367 | 0.2989 | 2 | 1 | 3 | 0.7186 | 1 | 0.4989 | 1 |
RALGAPB | 0 | 0 | 1 | 1 | 1 | 1 | 0.1335 | 0.0815 | 0.3267 | 0.5816 | 2 | 1 | 3 | 0.6237 | 1 | 1 | 1 |
GIGYF2 | 1 | 1 | 0 | 0 | 1 | 1 | 0.1335 | 0.0770 | 0.6428 | 0.5818 | 2 | 3 | 5 | 0.7186 | 0.0363 | 1 | 0.5211 |
NCKAP1 | 1 | 0 | 0 | 0 | 1 | 0 | 0.1335 | 0.9135 | 0.5383 | 1 | 3 | 0 | 3 | 0.0206 | 1 | 0.4100 | 1 |
GRIN2B † | 1 | 0 | 0 | 0 | 1 | 0 | 0.1359 | 1 | 0.2367 | 1 | 4 | 0 | 4 | 4.61E−04 | 1 | 1.17E−04 | 1 |
MYT1L † | 1 | 0 | 0 | 0 | 1 | 0 | 0.1717 | 1 | 0.2294 | 1 | 2 | 2 | 4 | 1 | 1 | 0.4100 | 1 |
SHANK2 | 0 | 0 | 1 | 0 | 1 | 0 | 0.2017 | 1 | 0.3267 | 1 | 2 | 1 | 3 | 1 | 1 | 1 | 1 |
SYNGAP1 † | 1 | 0 | 0 | 0 | 1 | 0 | 0.2966 | 1 | 0.3154 | 1 | 6 | 3 | 9 | 1.84E−05 | 0.0168 | 8.04E−08 | 8.79E−05 |
PHIP † | 1 | 0 | 0 | 0 | 1 | 0 | 0.2966 | 1 | 0.5095 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 1 |
CHD2 † | 0 | 0 | 1 | 1 | 1 | 1 | 0.3536 | 0.9217 | 0.5095 | 0.7736 | 4 | 4 | 8 | 0.0331 | 0.5391 | 0.0125 | 3.31E−03 |
SHANK1 | 1 | 0 | 0 | 0 | 1 | 0 | 0.3536 | 1 | 0.3267 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 1 |
DOCK8 | 1 | 0 | 0 | 0 | 1 | 0 | 0.4837 | 1 | 0.3267 | 1 | 2 | 0 | 2 | 1 | 1 | 1 | 1 |
ANK2 | 0 | 1 | 1 | 0 | 1 | 1 | 0.7356 | 1 | 0.6639 | 1 | 5 | 4 | 9 | 0.0587 | 1 | 2.54E−03 | 0.0396 |
ASH1L † | 0 | 1 | 0 | 1 | 0 | 2 | 1 | 0.2732 | 1 | 1 | 3 | 2 | 5 | 0.0825 | 1 | 0.5350 | 1 |
RIMS1 | 0 | 0 | 0 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 2 | 1 | 3 | 0.7186 | 1 | 1 | 1 |
TSC2 † | 0 | 1 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 4 | 4 | 1 | 1 | 1 | 1 |
KMT2C | 0 | 1 | 0 | 1 | 0 | 2 | 1 | 1 | 1 | 1 | 1 | 4 | 5 | 1 | 1 | 1 | 1 |
ITPR1 | 0 | 1 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 3 | 3 | 1 | 1 | 1 | 1 |
WHSC1 | 0 | 0 | 0 | 1 | 0 | 1 | 1 | 0.9499 | 1 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 1 |