Table 3.
Observed p-values of causal genes in each tested approach and, when applicable, the genetic variant detected
| Gene | A | B | C | D | E | F | G | H |
|---|---|---|---|---|---|---|---|---|
| AKT3 | 0.52, NA −0.74 (0.16) |
0.52, NA −0.74 (0.16) |
NCV |
NCV |
NCV |
NCV |
1, NA NC (0.16) |
1, NA NC (0.16) |
| BCL2L11 | 0.53, NA −0.21 (0.22) |
0.96, NA −0.02 (0.22) |
0.74, NA −0.03 (0.27) |
0.43, C2S2309 0.17 (0.27) |
1, NA NC (0.27) |
1, NA NC (0.27) |
1, NA NC (0.27) |
1, NA NC (0.27) |
| ELAVL4 | 0.01*, NA −0.76 (0.21) |
0.98, NA −0.02 (0.21) |
0.28, NA −0.12 (0.30) |
0.01, C1S3201 0.46 (0.30) |
1, NA NC (0.30) |
1, NA NC (0.30) |
1, NA NC (0.30) |
1, NA NC (0.30) |
| HSP90AA1 | 0.09, NA −0.30 (0.04) |
0.32, NA −0.41 (0.04) |
0.63, NA −0.06 (0.04) |
0.008, C14S3706 0.20 (0.04) |
0.29, C14S3706 −0.03 (0.04) |
0.21, C14S3706 −0.15 (0.04) |
1, NA NC (0.04) |
1, NA 0.14 (0.04) |
| NRAS | 1, NA 0.00 (0.18) |
1, NA 0.00 (0.18) |
NCV | NCV | NCV | NCV | 1, NA NC (0.18) |
1, NA NC (0.18) |
| PIK3C2B | 0.61, NA 0.05 (0.18) |
0.69, NA −0.06 (0.18) |
0.45, NA 0.12 (0.30) |
0.0006, C1S9210 1.47 (0.30) |
1, NA NC (0.30) |
1, NA NC (0.30) |
0.01, C1S9183 0.13 (0.30) |
0.04, C1S9183 0.11 (0.30) |
| PIK3C3 | 1, NA 0.00 (0.28) |
1, NA 0.00 (0.28) |
0.23, NA −0.63 (0.34) |
0.27, C18S2479 0.02 (0.34) |
1, NA NC (0.34) |
1, NA NC (0.34) |
1, NA NC (0.34) |
1, NA NC (0.34) |
| PIK3R3 | 0.12, NA 5.16 (0.17) |
1, NA 0.00 (0.17) |
0.23, NA −0.11 (0.17) |
0.08, C1S2903 0.30 (0.17) |
0.005, C1S2903 0.02 (0.17) |
0.005, C1S2903 0.02 (0.17) |
0.003, C1S2864 0.15 (0.17) |
0.003, C1S2864 0.15 (0.17) |
| PRKCA | 0.82, NA −0.21 (0.10) |
1, NA 0.00 (0.10) |
0.24, NA 0.11 (0.17) |
0.035, C17S3578 0.64 (0.17) |
0.15, C17S4567 0.04 (0.17) |
0.15, C17S4567 0.04 (0.17) |
1, NA NC (0.17) |
1, NA NC (0.17) |
| PRKCB1 | 0.47, NA 0.15 (0.23) |
0.62, NA 0.27 (0.23) |
0.75, NA 0.02 (0.23) |
0.11, C16S1808 0.29 (0.23) |
1, NA NC (0.23) |
1, NA NC (0.23) |
1, NA NC (0.23) |
1, NA NC (0.23) |
| PTK2 | 0.04, NA −1.62 (0.03) |
0.04, NA 0.27 (0.03) |
0.17, NA −0.28 (0.03) |
0.029, C8S4830 0.26 (0.03) |
1, NA NC (0.03) |
1, NA NC (0.03) |
1, NA NC (0.03) |
1, NA NC (0.03) |
| PTK2B | 0.89, NA 0.08 (0.13) |
1, NA 0.00 (0.13) |
0.003, NA −0.22 (0.20) |
0.01, C8S911 −0.14 (0.20) |
0.001, C8S911 0.05 (0.20) |
0.001, C8S911 0.05 (0.20) |
1, NA NC (0.20) |
1, NA NC (0.20) |
| RRAS | 0.41, NA −0.19 (0.17) |
0.61, NA −0.42 (0.17) |
0.33, NA 0.10 (0.20) |
0.08, C19S4940 0.07 (0.20) |
1, NA NC (0.20) |
1, NA NC (0.20) |
1, NA NC (0.20) |
1, NA NC (0.20) |
| SHC1 | 0.71, NA −0.35 (0.09) |
1, NA 0.00 (0.09) |
0.15, NA −0.17 (0.09) |
0.03, C1S7055 0.00 (0.09) |
1, NA NC (0.09) |
1, NA NC (0.09) |
1, NA NC (0.09) |
1, NA NC (0.09) |
| SOS2 | 1, NA 0.00 (0.25) |
1, NA 0.00 (0.25) |
0.008, NA −0.26 (0.28) |
0.009, C14136 −0.21 (0.28) |
1, NA NC (0.28) |
1, NA NC (0.28) |
1, NA NC (0.28) |
1, NA NC (0.28) |
Each cell gives four pieces of information: In the top line, the p-value and the associated genetic variant resulting from a nonconvergent model (or NA if it was not applicable) are given. An asterisk next to the p-value indicates that the gene was significant but enhanced the trait’s heritability. In the second line of each cell, the regression β value obtained in each analysis and the β value used by the GAW17 organization in the data simulation (in parentheses) are given; NC indicates genes not presenting a convergent QTDT model. NCV (no common variants) in a cell indicates that the gene did not present any common variants. Columns A and B were compared to the mean value of β of the simulated SNPs, and columns C–H were compared to the top β among simulated SNPs. The tested approaches A–H are defined in Table 2.