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Table 2 Test for associations between the inhibitory codon pairs and various gene expression variables

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
  1. (A) Spearman’s and Kendall’s correlation coefficients to assess an association between the fraction of the inhibitory codon pairs 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 the presence/absence of the inhibitory codon pairs. (C) Spearman’s and Kendall’s partial correlation coefficients controlled for GC content, tAI, dipeptide content, coding length to assess an association between the fraction of the inhibitory codon pairs and various gene expression variables. (D) Same as (C) but for the presence/absence of the inhibitory codon pairs