Table 1.
Spearman rank correlations between TR rate and various variables
| Variables | Rho | P-value | Rho* | P-value* |
|---|---|---|---|---|
| GC CDS | 0.297 | 0.0 | −0.317 | 0.0 |
| Gene length | −0.356 | 0.0 | 0.429 | 0.0 |
| mRNA stability | 0.308 | 0.0 | −0.304 | 0.0 |
| Gene expression | 0.619 | 0.0 | −0.848 | 0.0 |
| CAI CDS | 0.563 | 0.0 | −0.79 | 0.0 |
| CAI end | 0.43 | 0.0 | −0.652 | 0.0 |
| Translational efficiency | 0.496 | 0.0 | −0.35 | 0.0 |
Data for columns with asterisk (*) indicate that the non-leaky set is excluded (contains only proteins from leaky and semi-leaky sets). mRNA stability is measured as minimum free energy. Gene expression is calculated as Transcript Per Million (TPM). CAI stands for Codon Adaptation Index—a parameter for estimating codon usage. CAI CDS is for the CDS, whereas CAI end includes only the last 30 nucleotides (see Materials and Methods).