Table 1. The initial panel of candidate tumor dependent pairs for lung adenocarcinoma (LADC), with fractions of the four differentially expressed patterns by the threshold 1.5-fold, screened from 668 collected synthetic lethal (SL) gene pairs.
| Tumor dependent pairs | Fractions of SL gene pairs computed from 83 Asian LADC versus non-cancerous tissues that were expressed 1.5-fold or higher | ||||||
|---|---|---|---|---|---|---|---|
| Gene 1 | Gene 2 | (up, up) pattern | (up, down) pattern | (down, up) pattern | (down, down) pattern | Permutation p-value |
q-value |
| FEN1 | RAD54B | 0.31a | 0.01 | 0.00 | 0.01 | 0.0001 | 0.0043 |
| BRCA1 | PARP1 | 0.18 | 0.00 | 0.00 | 0.00 | 0.0001 | 0.0043 |
| MSH2 | POLB | 0.14 | 0.01 | 0.02 | 0.00 | 0.0006 | 0.0156 |
| BCR | WNT5A | 0.11 | 0.01 | 0.01 | 0.00 | 0.0023 | 0.0473 |
| BRCA2 | PARP1 | 0.11 | 0.00 | 0.00 | 0.00 | 0.0022 | 0.0473 |
| TP53 | SGK2 | 0.06 | 0.00 | 0.00 | 0.00 | 0.0273 | 0.2367 |
| MYC | AURKB | 0.05 | 0.00 | 0.23 | 0.00 | 0.0001 | 0.0043 |
| ABL1 | WNT5A | 0.05 | 0.00 | 0.06 | 0.07 | 0.3871 | 0.5180 |
| TP53 | PAK3 | 0.02 | 0.06 | 0.02 | 0.01 | 0.2279 | 0.4757 |
| EGFR | SLEGFRb | 0.01~0.18 | 0.00 | 0.00 | 0.00 | 0.0001~0.4940 | 0.0043~0.5180 |
| EGFR | SLEGFRc | 0.00 | 0.01~0.20 | 0.00 | 0.00 | 0.0001~0.5084 | 0.0043~0.5180 |
| KRAS | SLKRASd | 0.01~0.07 | 0.00 | 0.00 | 0.00 | 0.0143~0.7506 | 0.1642~0.7506 |
| KRAS | SLKRASe | 0.00 | 0.01~0.07 | 0.00 | 0.00 | 0.0298~0.7410 | 0.2367~0.7448 |
a
The four fractions were computed from gene pairs that were 1.5-fold differentially expressed, thus they might not sum up to 100%.
b
22 verified EGFR SL pairs were identified in the (up, up) pattern.
c
30 verified EGFR SL pairs were identified in the (up, down) pattern.
d
168 verified KRAS SL pairs were identified in the (up, up) pattern.
e
121 verified KRAS SL pairs were identified in the (up, down) pattern.
The p-value for the highest fraction of the four patterns was computed by permutation test with 10,000 repeats, and the false discovery rate was estimated by q-value.