Table 5.
Test for associations of codon optimality with mRNA decay rate, protein per mRNA, and ribosome occupancy
| (A) Correlation | ||||||
| Spearman | Kendall | |||||
| ρ | P value | Permutation P value |
τ | P value | Permutation P value |
|
| mRNA decay rate (Cramer 1) | −0.59 | 0.0E + 00 | 1.0E-04 | −0.42 | 0.0E + 00 | 1.0E-04 |
| mRNA decay rate (Cramer 2) | −0.45 | 7.5E-185 | 1.0E-04 | −0.31 | 4.6E-176 | 1.0E-04 |
| mRNA decay rate (Gresham) | −0.24 | 7.4E-56 | 1.0E-04 | −0.17 | 1.2E-56 | 1.0E-04 |
| mRNA decay rate (Coller) | −0.29 | 1.9E-71 | 1.0E-04 | −0.19 | 9.7E-70 | 1.0E-04 |
| Protein per mRNA | 0.56 | 1.6E-246 | 1.0E-04 | 0.39 | 0.0E + 00 | 1.0E-04 |
| Ribosome occupancy | 0.45 | 5.6E-224 | 1.0E-04 | 0.32 | 0.0E + 00 | 1.0E-04 |
| (B) Partial correlation controlled for the fraction of the inhibitory codon pairs | ||||||
| Spearman | Kendall | |||||
| ρ | P value | Permutation P value |
τ | P value | Permutation P value |
|
| mRNA decay rate (Cramer 1) | −0.49 | 9.7E-243 | 1.0E-04 | −0.34 | 1.6E-233 | 1.0E-04 |
| mRNA decay rate (Cramer 2) | −0.37 | 1.9E-125 | 1.0E-04 | −0.25 | 7.0E-117 | 1.0E-04 |
| mRNA decay rate (Gresham) | −0.19 | 6.3E-35 | 1.0E-04 | −0.11 | 2.9E-27 | 1.0E-04 |
| mRNA decay rate (Coller) | −0.23 | 6.1E-47 | 1.0E-04 | −0.16 | 5.2E-47 | 1.0E-04 |
| Protein per mRNA | 0.49 | 4.2E-181 | 1.0E-04 | 0.33 | 2.3E-167 | 1.0E-04 |
| Ribosome occupancy | 0.46 | 1.4E-230 | 1.0E-04 | 0.27 | 2.5E-165 | 1.0E-04 |
| (C) Partial correlation controlled for the presence/absence of the inhibitory codon pairs | ||||||
| Spearman | Kendall | |||||
| ρ | P value | Permutation P value |
τ | P value | Permutation P value |
|
| mRNA decay rate (Cramer 1) | −0.50 | 9.4E-254 | 1.0E-04 | −0.34 | 3.3E-234 | 1.0E-04 |
| mRNA decay rate (Cramer 2) | −0.38 | 7.4E-132 | 1.0E-04 | −0.25 | 3.1E-114 | 1.0E-04 |
| mRNA decay rate (Gresham) | −0.20 | 4.2E-37 | 1.0E-04 | −0.11 | 2.5E-25 | 1.0E-04 |
| mRNA decay rate (Coller) | −0.24 | 1.7E-51 | 1.0E-04 | −0.16 | 6.7E-49 | 1.0E-04 |
| Protein per mRNA | 0.49 | 4.2E-186 | 1.0E-04 | 0.33 | 1.4E-164 | 1.0E-04 |
| Ribosome occupancy | 0.46 | 2.2E-235 | 1.0E-04 | 0.27 | 1.9E-158 | 1.0E-04 |
(A) Spearman’s and Kendall’s correlation coefficients to assess an association between codon optimality and various gene expression variables. P values obtained according to Kim [16] and those based on permutation tests are shown. (B) Same as (A) but for partial correlation coefficients controlled for GC content, the fraction of the inhibitory codon pairs, dipeptide content, and coding length. (C) Same as (A) but for partial correlation coefficients controlled for GC content, the presence/absence of the inhibitory codon pairs, dipeptide content, and coding length