Table 2.
Results of quantitative PCR experiments analyzing allele-specific expression
| ORF name | Predicted ASE direction | Self-linkage p-value | Estimated proportion of BY allele based on linkage data | Estimated proportion of BY allele from Q-PCR experiments | P-value for allele-specific expression from Q-PCR experiments |
|---|---|---|---|---|---|
| CIS3* | ASE-BY | 1e-6 | 0.55 | 0.55 | 0.007 |
| HSPI50* | ASE-BY | 9e-7 | 0.55 | 0.54 | 0.02 |
| MOG1* | ASE-BY | 4e-6 | 0.54 | 0.53 | 0.004 |
| TIP1* | ASE-BY | 4e-10 | 0.70 | 0.79 | 0.004 |
| YHR032W* | ASE-BY | 0.03 | 0.48 | 0.44 | 0.05 |
| ERD2 | ASE-BY | 4e-7 | 0.53 | 0.50 | 0.76 |
| ITR1 | ASE-BY | 5e-5 | 0.54 | 0.50 | 0.91 |
| OPI3 | ASE-BY | 2e-5 | 0.56 | 0.50 | 1.0 |
| SOD1 | ASE-BY | 3e-6 | 0.54 | 0.49 | 0.32 |
| SEC53 | ASE-BY | 0.27 | 0.50 | 0.51 | 0.15 |
| CHO2 | ASE-BY | 0.04 | 0.52 | 0.48 | 0.01 |
The allele predicted to show preferential expression based on the microarray analysis is shown in column 2. We calculated self-linkage p-values as described previously (Brem et al. 2002). The predicted amount of BY allele expressed based in the linkage data was determined by comparing the mean expression level in segregants bearing the BY genotype at the ORF in question to the segregants bearing the RM genotype at this locus. Single astericks indicate ORFs that showed significant allele-specific expression according to quantitative PCR in the direction predicted, thus confirming the array-based detection.