From: The link between adjacent codon pairs and mRNA stability
(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 |