Table 4. CuffDiff results for the four known AIR genes in the rat pineal gland, using the full annotation.
| Output file | Gene symbol | # Tests for gene | Experiments (full annotation) | |||
|---|---|---|---|---|---|---|
| Ctrl day/night | Sham day/night | CN versus NE | CN versus DBcAMP | |||
| Splicing.diff | Atp7b | 4 | 1 | 1 | 1 | 1 |
| Crem | 9 | 0.99991 | 0.99991 | 0.99991 | 0.9999 | |
| Pde4b | 30 | 0.99991 | 0.99991 | 0.99991 | 0.1444 | |
| Slc15a1 | 3 | 1 | 1 | 1 | 1 | |
| Promoters.diff | Atp7b | 1 | 0.13110 | 1 | 1 | 1 |
| Crem | 1 | 0.99991 | 0.99991 | 0.99991 | 0.99991 | |
| Pde4b | 1 | 1 | 0.99991 | 1 | 1 | |
| Slc15a1 | 1 | 1 | 1 | 1 | 1 | |
| cds.diff | Atp7b | 1 | 1 | 1 | 1 | 1 |
| Crem | 1 | 0.99808 | 0.99862 | 0.99988 | 0.99896 | |
| Pde4b | 1 | 0.99808 | 0.99862 | 0.99988 | 0.99896 | |
| Slc15a1 | 1 | 1 | 1 | 1 | 1 | |
The CuffDiff analysis design differs somewhat from that of DEXSeq or JunctionSeq. CuffDiff peforms separate analyses testing for isoform switching (splicing.diff), differences in CDS expression (cds.diff), and differential promoter usage (promoters.diff), producing several tests for each gene. The results for the four known-AIR genes are shown below. When an analysis file contained multiple tests for a given gene, the most significant adjusted P-value is shown. (Note: CuffDiff was not tested on the incomplete annotation set.)