Skip to main content

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
  1. (A) Spearman’s partial correlation coefficients controlled for GC content, tAI, dipeptide content, and coding length to assess an association between the fraction of hexanucleotide sequences corresponding to the inhibitory codon pairs in the 0, +1, and +2 frames 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 Kendall’s partial correlation coefficients. (C) Same as (A) but for the presence/absence of the hexanucleotide sequences. (D) Same as (B) but for the presence/absence of the hexanucleotide sequences