Table 1.
Initial panel of candidate TD pairs for CRC, showing the percentages of the four gene expression patterns.
| TD pairs |
Percentages of gene pairs from 70 Asian CRC versus 12 non-cancerous tissues that were expressed 2-fold or more |
||||||
|---|---|---|---|---|---|---|---|
| Gene 1 | Gene 2 | (up, up) pattern | (up, down) pattern | (down, up) pattern | (down, down) pattern | Permutation P value* | FDR† |
| FEN1 | RAD54B | 0.67‡ | 0.00 | 0.00 | 0.00 | 0.0001 | 1×10- 5 |
| BRCA2 | PARP1 | 0.34 | 0.00 | 0.00 | 0.00 | 0.0001 | 1×10- 5 |
| MSH2 | POLB | 0.33 | 0.00 | 0.00 | 0.00 | 0.0001 | 1×10- 5 |
| BRCA1 | PARP1 | 0.26 | 0.00 | 0.00 | 0.00 | 0.0001 | 1×10- 5 |
| MYC | AURKB | 0.17 | 0.00 | 0.00 | 0.00 | 0.0001 | 1×10- 5 |
| RB1 | SKP2 | 0.06 | 0.00 | 0.00 | 0.00 | 0.0002 | 2×10- 5 |
| CSNK1E | CTNNB1 | 0.03 | 0.00 | 0.00 | 0.00 | 0.0001 | 1×10- 5 |
| BCR | WNT5A | 0.03 | 0.01 | 0.00 | 0.00 | 0.0001 | 1×10- 5 |
| KRAS | SLKRAS§ | 0.01 | 0.00 | 0.00 | 0.00 | 0.0001 ~ 0.7200 | 1×10- 5 ~ 0.0303 |
| TP53 | SGK2 | 0.00 | 0.33 | 0.00 | 0.20 | 0.0004 | 3×10- 5 |
| KRAS | SLKRAS¶ | 0.00 | 0.01 | 0.00 | 0.00 | 0.0001 ~ 0.8540 | 1×10- 5 ~ 0.0351 |
| PTEN | PARP1 | 0.00 | 0.00 | 0.01 | 0.00 | 0.0001 | 1×10- 5 |
| ABL1 | WNT5A | 0.00 | 0.00 | 0.01 | 0.00 | 0.0043 | 0.0003 |
*
This P value was for the highest percentage of the four patterns computed by permutation test with 10,000 repeats.
†
FDR was estimated by q-value.
‡
The four fractions are computed from gene pairs that were 2-fold differentially expressed, thus they might not sum up to 100%.
§
57 verified KRAS SL pairs were identified in the (up, up) pattern.
¶
19 verified KRAS SL pairs were identified in the (up, down) pattern.