Table 1.
Glossary of abbreviations
| Abbreviation | Explanation |
|---|---|
| APE | AUG proximal element: control sequences that flank the iAUG |
| dAPE | Downstream APE: that part of the APE located downstream (3′) of the iAUG |
| uAPE | Upstream APE: that part of the APE located upstream (5′) of the iAUG |
| 5′ofAPE | The 5′UTR sequences that lie 5′ of the APE |
| iAUG | Initiating AUG: the AUG codon at the 5′ end of the CDS |
| uAUG | Upstream AUG: an AUG codon in the 5′ UTR, i.e., an AUG at the 5′ end of an uORF |
| BIC | Bayesian Information Criteria: a method to select an efficient set of model features |
| 5′ cap | The 5′ most nucleotide of the mRNA |
| CDS | Coding sequence: the protein coding portion of the mRNA |
| CDS 3′ofAPE | That part of the CDS that lies 3′ of the APE |
| MFE | Minimum free energy: the Gibbs free energy of folding for a defined segment of RNA |
| uORF | Upstream open reading frame: an uAUG containing open reading frame in the 5′UTR |
| PWM | Position Weight Matrix: the fraction of A, U, G, and Cs at each nucleotide position |
| 5′region | The region spanning the 5′UTR and the 5′ most ~ 30 nucleotides of the CDS |
| 5′UTR | 5′ Untranslated region: all mRNA nucleotides 5′ of the CDS |
| TR | Translation rate: rate of translation per mRNA molecule at steady state |
| high TR | A cohort of genes with the highest translation rates |
| low TR | A cohort of genes with the lowest translation rates |