Table 3 Test for associations of the out-of-frame inhibitory codon pairs with mRNA decay rate, protein per mRNA, and ribosome occupancy
From: The link between adjacent codon pairs and mRNA stability
(A) Spearman’s partial correlation based on the fraction of the inhibitory codon pairs | |||||||||
Frame 0 | Frame 1 | Frame 2 | |||||||
ρ | P value | Perm. P value | ρ | P value | Perm. P value | ρ | P value | Perm. P value | |
mRNA decay rate (Cramer 1) | 0.14 | 2.1E-18 | 1.0E-04 | 0.05 | 1.0E-03 | 7.0E-04 | 0.02 | 3.4E-01 | 1.7E-01 |
mRNA decay rate (Cramer 2) | 0.15 | 1.2E-20 | 1.0E-04 | 0.02 | 2.4E-01 | 1.3E-01 | 0.03 | 3.8E-02 | 1.8E-02 |
mRNA decay rate (Gresham) | 0.07 | 9.0E-06 | 1.0E-04 | 0.06 | 2.0E-04 | 2.0E-04 | 0.01 | 5.2E-01 | 2.6E-01 |
mRNA decay rate (Coller) | 0.06 | 2.0E-04 | 1.0E-04 | 0.02 | 2.2E-01 | 1.1E-01 | 0.03 | 4.6E-02 | 2.4E-02 |
Protein per mRNA | −0.07 | 4.9E-05 | 1.0E-04 | 0.03 | 8.6E-02 | 4.3E-02 | 0.01 | 7.2E-01 | 3.6E-01 |
Ribosome occupancy | −0.06 | 8.8E-05 | 1.0E-04 | 0.02 | 2.0E-01 | 9.9E-02 | 0.01 | 5.2E-01 | 2.7E-01 |
(B) Kendall’s partial correlation based on the fraction of the inhibitory codon pairs | |||||||||
Frame 0 | Frame 0 | Frame 0 | |||||||
τ | P value | Perm. P value | τ | P value | Perm. P value | τ | P value | Perm. P value | |
mRNA decay rate (Cramer 1) | 0.15 | 2.4E-48 | 1.0E-04 | 0.04 | 6.7E-04 | 1.0E-04 | 0.00 | 7.7E-01 | 3.8E-01 |
mRNA decay rate (Cramer 2) | 0.16 | 9.8E-49 | 1.0E-04 | 0.02 | 2.5E-02 | 9.7E-03 | 0.02 | 7.1E-02 | 3.2E-02 |
mRNA decay rate (Gresham) | 0.10 | 7.9E-22 | 1.0E-04 | 0.08 | 2.6E-13 | 1.0E-04 | 0.03 | 1.3E-02 | 4.0E-03 |
mRNA decay rate (Coller) | 0.07 | 6.2E-10 | 1.0E-04 | 0.01 | 6.1E-01 | 3.1E-01 | 0.01 | 3.8E-01 | 2.0E-01 |
Protein per mRNA | −0.11 | 7.3E-20 | 1.0E-04 | 0.01 | 3.7E-01 | 1.7E-01 | 0.01 | 6.2E-01 | 3.1E-01 |
Ribosome occupancy | −0.11 | 1.3E-30 | 1.0E-04 | −0.02 | 2.2E-02 | 3.9E-03 | −0.01 | 4.6E-01 | 2.0E-01 |
(C) Spearman’s partial correlation based on the presence/absence of the inhibitory codon pairs | |||||||||
Frame 0 | Frame 1 | Frame 2 | |||||||
ρ | P value | Perm. P value | ρ | P value | Perm. P value | ρ | P value | Perm. P value | |
mRNA decay rate (Cramer 1) | 0.13 | 2.8E-16 | 1.0E-04 | 0.04 | 1.1E-02 | 7.3E-03 | 0.00 | 8.7E-01 | 4.3E-01 |
mRNA decay rate (Cramer 2) | 0.14 | 8.6E-19 | 1.0E-04 | 0.01 | 4.0E-01 | 2.0E-01 | 0.01 | 5.5E-01 | 2.7E-01 |
mRNA decay rate (Gresham) | 0.07 | 2.2E-05 | 1.0E-04 | 0.06 | 2.9E-04 | 3.0E-04 | 0.01 | 6.0E-01 | 3.0E-01 |
mRNA decay rate (Coller) | 0.04 | 7.5E-03 | 3.8E-03 | 0.02 | 1.7E-01 | 8.1E-02 | 0.02 | 2.7E-01 | 1.4E-01 |
Protein per mRNA | −0.07 | 6.3E-05 | 1.0E-04 | 0.03 | 1.6E-01 | 8.1E-02 | 0.00 | 9.9E-01 | 4.9E-01 |
Ribosome occupancy | −0.06 | 1.6E-05 | 2.0E-04 | 0.01 | 4.1E-01 | 2.0E-01 | 0.00 | 9.6E-01 | 4.8E-01 |
(D) Kendall’s partial correlation based on the presence/absence of the inhibitory codon pairs | |||||||||
Frame 0 | Frame 0 | Frame 0 | |||||||
τ | P value | Perm. P value | τ | P value | Perm. P value | τ | P value | Perm. P value | |
mRNA decay rate (Cramer 1) | 0.16 | 1.1E-50 | 1.0E-04 | 0.03 | 1.2E-03 | 1.5E-03 | 0.00 | 1.0E + 00 | 4.9E-01 |
mRNA decay rate (Cramer 2) | 0.17 | 2.7E-57 | 1.0E-04 | 0.04 | 8.8E-04 | 2.1E-03 | 0.02 | 6.1E-02 | 5.1E-02 |
mRNA decay rate (Gresham) | 0.12 | 8.3E-29 | 1.0E-04 | 0.12 | 7.0E-31 | 1.0E-04 | 0.07 | 1.4E-10 | 1.0E-04 |
mRNA decay rate (Coller) | 0.06 | 5.9E-08 | 1.0E-04 | 0.00 | 9.8E-01 | 4.9E-01 | 0.00 | 6.6E-01 | 3.5E-01 |
Protein per mRNA | −0.12 | 3.2E-23 | 1.0E-04 | 0.01 | 3.2E-01 | 2.0E-01 | 0.00 | 9.6E-01 | 4.8E-01 |
Ribosome occupancy | −0.14 | 3.7E-44 | 1.0E-04 | −0.07 | 3.4E-11 | 1.0E-04 | −0.05 | 2.6E-07 | 1.0E-04 |