Table 1.
Relationship between allele-specific expression results and linkage analysis results
| Type of self-linker | Type of allele-specific expression | Number of self-linkers/Total | Enrichment (or deficiency) P-value | |
|---|---|---|---|---|
| Self-link FDR ≤ 0.05 Allele-specific expression P ≤ 0.006 | BY allele upregulated | ASE-BY | 21/59 = 36% | 0.001 |
| All non-ASE-BY | 102/565 = 18% | (enrichment) | ||
| RM allele upregulated | ASE-BY | 2/59 = 3% | 0.008 | |
| All non-ASE-BY | 78/565 = 14% | (deficiency) | ||
| BY allele upregulated | ASE-RM | 0/11 = 0% | 0.10 | |
| All non-ASE-RM | 111/586 = 19% | (deficiency) | ||
| RM allele upregulated | ASE-RM | 3/11 = 27% | 0.16 | |
| All non-ASE-RM | 75/586 = 13% | (enrichment) | ||
| Self-link p ≤ 0.05 Allele-specific expression P ≤ 0.05
|
BY allele upregulated | ASE-BY | 59/159 = 37% | 4e-6 |
| All non-ASE-BY | 108/505 = 21% | (enrichment) | ||
| RM allele upregulated | ASE-BY | 15/159 = 9% | 2e-4 | |
| All non-ASE-BY | 101/505 = 20% | (deficiency) | ||
| BY allele upregulated | ASE-RM | 6/55 = 11% | 0.005 | |
| All non-ASE-RM | 145/555 = 26% | (deficiency) | ||
| RM allele upregulated
|
ASE-RM | 21/55 = 38% | 1e-4 | |
| All non-ASE-RM | 92/555 = 17% | (enrichment) |
Each cell shows the count of self-linking ORFs associated with higher expression of the BY allele (BY allele up-regulated) or higher expression of the RM allele (RM allele up-regulated), divided by the total number of ORFs showing evidence for (or against) allele-specific expression of the BY (ASE-BY) or RM allele (ASE-RM). P-values are for one-tailed tests of the hypothesis that ORFs showing allele-specific expression are enriched for self-linkages associated with higher expression of that same allele and deficient for self-linkages associated with higher expression of the other allele. Note the total number of ORFs in the denominator varies from test to test. Because a given ORF may contain multiple marker probes, each ORF is counted once as showing allele-specific expression if any of its marker probes fulfill the criterion for allele-specific expression, and once as not showing allele-specific expression if any of its marker probes fail to meet the criterion. Forming the table in this way is conservative, because unless all probes interrogating the same ORF uniformly show evidence for (or against) allele-specific expression, that ORF will contribute one count to both the rate of self-linkers (or non-self-linkers) in the allele-specific expression and the nonallele-specific expression sets, tending to make the two rates appear similar.