Table 2.
An example illustrating that one can obtain more accurate allele-specific expression estimates at RNA-isoform level. Assume this gene has two isoforms. Isoform 1 includes exons 1 and 3, and isoform 2 includes exons 1, 2, and 3. The columns Exon1, Exon2, and Exon3 show the number of reads mapped to the corresponding exons. Columns FPKMisoform and FPKMgene show FPKM estimates at isoform and gene level, respectively
| Allele | Isoform | Exon 1 | Exon 2 | Exon 3 | FPKMisoform | FPKMgene |
|---|---|---|---|---|---|---|
| Both | isoform 1 | 100 | 0 | 100 | 1 | 1.67/2 |
| isoform 2 | 100 | 100 | 100 | 1 | ||
| Paternal allele | isoform 1 | 30 | 0 | 30 | 0.3 | 0.90/1 |
| isoform 2 | 70 | 70 | 70 | 0.7 | ||
| Maternal allele | isoform 1 | 70 | 0 | 70 | 0.7 | 0.77/1 |
| isoform 2 | 30 | 30 | 30 | 0.3 |