|
SNP and haplotype-based cis sequence effects on gene expression* |
||||
| Gene |
N SNPs analyzed SNP-wise |
SAM model analysis, single P |
SNP-wise regression, best P** |
TreeScan, best Ppermuted |
|
|
||||
| ALDH2 |
2 |
0.482 |
0.577 |
0.796 |
| BCL2L1 |
2 |
0.283 |
0.488 |
0.191 |
| BIC |
9 |
0.010 |
0.016 |
0.056 |
| BIRC3 |
2 |
0.110 |
0.550 |
0.092 |
| BLM |
9 |
0.941 |
0.266 |
0.882 |
| CCNA2 |
3 |
0.142 |
0.085 |
0.635 |
| CCND3 |
4 |
0.601 |
0.519 |
0.819 |
| CDKN1B |
3 |
0.142 |
0.059 |
0.259 |
| CHEK1 |
2 |
0.542 |
0.290 |
0.577 |
| CYP1B1 |
14 |
did not compute |
0.032 |
0.438 |
| FCGR2B |
6 |
0.011 |
0.003 |
0.024 |
| IFNGR1 |
2 |
0.981 |
0.854 |
0.902 |
| IFNGR2 |
2 |
0.175 |
0.096 |
0.374 |
| IRF1 |
1 |
0.160 |
0.282 |
Na |
| JAK1 |
5 |
0.194 |
0.375 |
0.123 |
| LMO2 |
8 |
0.830 |
0.181 |
0.024 |
| LTA |
103 |
0.785 |
0.380 |
0.992 |
| MGMT |
4 |
0.330 |
0.064 |
0.329 |
| MSH2 |
1 |
0.388 |
0.409 |
Na |
| MYBL2 |
8 |
0.105 |
0.008 |
0.095 |
| MYC |
1 |
0.303 |
0.409 |
Na |
| NBS1 |
4 |
0.005 |
0.000 |
0.197 |
| OAS1 |
1 |
0.186 |
0.206 |
Na |
| PCNA |
2 |
0.138 |
0.064 |
0.006 |
| PHB |
3 |
0.902 |
0.651 |
0.937 |
| PIM1 |
2 |
0.689 |
0.419 |
0.721 |
| PTEN |
3 |
0.257 |
0.236 |
0.569 |
| TNF |
103 |
0.619 |
0.394 |
0.756 |
| TP73L |
9 |
0.305 |
0.024 |
0.563 |
| TYMS |
4 |
0.127 |
0.100 |
0.185 |
|
*Statistically significant results are bolded. **See Additional file 3 for SNP details. | ||||
Bergen et al. BMC Genomics 2007 8:296 doi:10.1186/1471-2164-8-296 |
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