From: The link between adjacent codon pairs and mRNA stability
(A) Correlation based on the fraction of the inhibitory codon pairs | ||||||
Spearman | Kendall | |||||
ρ | P value | Permutation P value | τ | P value | Permutation P value | |
mRNA synthesis rate (Cramer 1) | −0.23 | 5.1E-51 | 1.0E-04 | −0.18 | 9.7E-51 | 1.0E-04 |
mRNA synthesis rate (Cramer 2) | −0.20 | 1.6E-36 | 1.0E-04 | −0.15 | 3.6E-36 | 1.0E-04 |
mRNA synthesis rate (Gresham) | −0.22 | 1.6E-50 | 1.0E-04 | −0.17 | 5.6E-52 | 1.0E-04 |
mRNA synthesis rate (Coller) | −0.28 | 5.5E-68 | 1.0E-04 | −0.21 | 2.1E-63 | 1.0E-04 |
mRNA decay rate (Cramer 1) | 0.37 | 1.3E-133 | 1.0E-04 | 0.29 | 0.0E + 00 | 1.0E-04 |
mRNA decay rate (Cramer 2) | 0.35 | 1.2E-109 | 1.0E-04 | 0.26 | 0.0E + 00 | 1.0E-04 |
mRNA decay rate (Gresham) | 0.25 | 2.9E-59 | 1.0E-04 | 0.19 | 0.0E + 00 | 1.0E-04 |
mRNA decay rate (Coller) | 0.17 | 5.1E-25 | 1.0E-04 | 0.13 | 0.0E + 00 | 1.0E-04 |
Protein per mRNA | −0.31 | 2.9E-70 | 1.0E-04 | −0.24 | 1.4E-67 | 1.0E-04 |
Ribosome occupancy | −0.34 | 1.2E-120 | 1.0E-04 | −0.25 | 8.3E-112 | 1.0E-04 |
Protein decay rate | 0.10 | 1.7E-08 | 1.0E-04 | 0.08 | 1.4E-08 | 1.0E-04 |
(B) Correlation based on the presence/absence of the inhibitory codon pairs | ||||||
Spearman | Kendall | |||||
ρ | P value | Permutation P value | τ | P value | Permutation P value | |
mRNA synthesis rate (Cramer 1) | −0.23 | 2.1E-49 | 1.0E-04 | −0.19 | 3.6E-48 | 1.0E-04 |
mRNA synthesis rate (Cramer 2) | −0.22 | 7.7E-41 | 1.0E-04 | −0.18 | 6.1E-40 | 1.0E-04 |
mRNA synthesis rate (Gresham) | −0.19 | 1.3E-36 | 1.0E-04 | −0.15 | 5.5E-36 | 1.0E-04 |
mRNA synthesis rate (Coller) | −0.31 | 3.2E-83 | 1.0E-04 | −0.25 | 2.4E-79 | 1.0E-04 |
mRNA decay rate (Cramer 1) | 0.36 | 6.3E-122 | 1.0E-04 | 0.29 | 0.0E + 00 | 1.0E-04 |
mRNA decay rate (Cramer 2) | 0.35 | 1.8E-110 | 1.0E-04 | 0.29 | 0.0E + 00 | 1.0E-04 |
mRNA decay rate (Gresham) | 0.30 | 7.8E-88 | 1.0E-04 | 0.25 | 0.0E + 00 | 1.0E-04 |
mRNA decay rate (Coller) | 0.14 | 3.2E-17 | 1.0E-04 | 0.11 | 0.0E + 00 | 1.0E-04 |
Protein per mRNA | −0.30 | 1.0E-62 | 1.0E-04 | −0.24 | 5.2E-60 | 1.0E-04 |
Ribosome occupancy | −0.39 | 2.5E-162 | 1.0E-04 | −0.32 | 7.5E-150 | 1.0E-04 |
Protein decay rate | 0.10 | 3.1E-08 | 1.0E-04 | 0.08 | 3.3E-08 | 1.0E-04 |
(C) Partial correlation based on the fraction of the inhibitory codon pairs | ||||||
Spearman | Kendall | |||||
ρ | P value | Permutation P value | τ | P value | Permutation P value | |
mRNA synthesis rate (Cramer 1) | −0.01 | 5.1E-01 | 2.6E-01 | −0.06 | 8.4E-09 | 1.0E-04 |
mRNA synthesis rate (Cramer 2) | −0.05 | 8.7E-04 | 3.0E-04 | −0.08 | 1.7E-13 | 1.0E-04 |
mRNA synthesis rate (Gresham) | −0.04 | 1.2E-02 | 5.9E-03 | −0.07 | 3.0E-11 | 1.0E-04 |
mRNA synthesis rate (Coller) | −0.02 | 2.3E-01 | 1.1E-01 | −0.08 | 7.3E-13 | 1.0E-04 |
mRNA decay rate (Cramer 1) | 0.14 | 2.1E-18 | 1.0E-04 | 0.15 | 2.4E-48 | 1.0E-04 |
mRNA decay rate (Cramer 2) | 0.15 | 1.2E-20 | 1.0E-04 | 0.16 | 9.8E-49 | 1.0E-04 |
mRNA decay rate (Gresham) | 0.07 | 9.0E-06 | 1.0E-04 | 0.10 | 7.9E-22 | 1.0E-04 |
mRNA decay rate (Coller) | 0.06 | 2.0E-04 | 1.0E-04 | 0.07 | 6.2E-10 | 1.0E-04 |
Protein per mRNA | −0.07 | 4.9E-05 | 1.0E-04 | −0.11 | 7.3E-20 | 1.0E-04 |
Ribosome occupancy | −0.06 | 8.8E-05 | 1.0E-04 | −0.11 | 1.3E-30 | 1.0E-04 |
Protein decay rate | −0.01 | 6.4E-01 | 3.3E-01 | 0.02 | 7.7E-02 | 6.2E-02 |
(D) Partial correlation based on the presence/absence of the inhibitory codon pairs | ||||||
Spearman | Kendall | |||||
ρ | P value | Permutation P value | τ | P value | Permutation P value | |
mRNA synthesis rate (Cramer 1) | 0.00 | 8.0E-01 | 4.1E-01 | −0.06 | 5.7E-09 | 1.0E-04 |
mRNA synthesis rate (Cramer 2) | −0.05 | 3.3E-03 | 1.3E-03 | −0.09 | 1.2E-15 | 1.0E-04 |
mRNA synthesis rate (Gresham) | −0.03 | 5.0E-02 | 2.7E-02 | −0.06 | 1.3E-09 | 1.0E-04 |
mRNA synthesis rate (Coller) | −0.02 | 1.9E-01 | 9.6E-02 | −0.10 | 2.6E-18 | 1.0E-04 |
mRNA decay rate (Cramer 1) | 0.13 | 2.8E-16 | 1.0E-04 | 0.16 | 1.1E-50 | 1.0E-04 |
mRNA decay rate (Cramer 2) | 0.14 | 8.6E-19 | 1.0E-04 | 0.17 | 2.7E-57 | 1.0E-04 |
mRNA decay rate (Gresham) | 0.07 | 2.2E-05 | 1.0E-04 | 0.12 | 8.3E-29 | 1.0E-04 |
mRNA decay rate (Coller) | 0.04 | 7.5E-03 | 3.8E-03 | 0.06 | 5.9E-08 | 1.0E-04 |
Protein per mRNA | −0.07 | 6.3E-05 | 1.0E-04 | −0.12 | 3.2E-23 | 1.0E-04 |
Ribosome occupancy | −0.06 | 1.6E-05 | 2.0E-04 | −0.14 | 3.7E-44 | 1.0E-04 |
Protein decay rate | 0.00 | 7.8E-01 | 3.9E-01 | 0.02 | 3.6E-02 | 5.0E-02 |