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Analysis of all possible 3721 codon pairs. (A) Plotted are ordered Kendall’s correlation coefficients between the fraction of individual codon pairs and mRNA decay rates in the “Cramer 1” data. The 17 inhibitory codon pairs are labeled. Also shown is the P value from Wilcoxon rank sum test with an alternative hypothesis that correlation coefficients are greater for the 17 inhibitory codon pairs than for other pairs. (B) Same as (A) but for the “Cramer 2” data. (C) Same as (A) but for the “Gresham” data. (D) Same as (C) but for the “Coller” data. (PDF 56 kb)

Correlations between the CSC values obtained from different RNA kinetic datasets in S. cerevisiae (“Cramer (1),” “Cramer (2),” “Gresham,” and “Coller (1)”) (A-F) and S. pombe (“Mata (5)” and “Gagneur”) (G). Spearman's ρ and P value are shown. The circles and cross signs represent optimal and non-optimal codons, respectively. (PDF 38 kb)

Correlations between mRNA half-lives, synthesis rates, and abundance in S. cerevisiae. (A) Scatterplot comparing mRNA half-lives and abundance in the “Cramer (1)” data. Spearman's ρ and P value are shown. (B) Same as (A) but for the “Cramer (2)” data. (C) Same as (A) but for the “Gresham” data. (D) Scatterplot comparing mRNA synthesis rates and abundance in the “Cramer (1)” data. (E) Same as (D) but for the “Cramer (2)” data. (F) Same as (D) but for the “Gresham” data. (G) Scatterplot comparing mRNA half-lives and synthesis rates in the “Cramer (1)” data. (H) Same as (G) but for the “Cramer (2)” data. (I) Same as (G) but for the “Gresham” data. (PDF 1187 kb)

Comparison of mRNA synthesis rates with ChIP intensity signals for RNAPII in S. pombe. (A-G) Scatterplot comparing mRNA synthesis rates [RNA/min] in seven datasets and RNAPII ChIP signals in an arbitrary unit (a. u.) obtained by Bahler and colleagues [55]. Spearman's Ď and P value are shown. (PDF 984 kb)

Codon optimality and mRNA synthesis rates are significantly associated in S. cerevisiae. (A) The CPC plotted for each codon based on mRNA synthesis rates in the “Cramer (1)” dataset. The white and gray bars represent optimal and non-optimal codons, respectively. The classification of codon optimality is based on the S. cerevisiae cTE. (B) Same as (A) but based on the “Cramer (2)” dataset. (C) Scatterplot comparing tAIg and mRNA synthesis rates in the “Cramer (1)” dataset. Spearman's ρ and P value are shown. (D) Same as (C) but for the “Cramer (2)” dataset. (PDF 275 kb)

Comparison of mRNA half-life measurements in S. pombe. The pairwise scatterplots compare mRNA half-lives in seven datasets. The datasets are ordered as in Fig. 1d. The upper triangle panels show Spearman correlation coefficients (top) and P values (bottom). The axis range is from 0 to 120 min. (PDF 456 kb)

Comparison of mRNA synthesis rates in S. cerevisiae. The pairwise scatterplots compare mRNA synthesis rates in 14 datasets. The datasets are ordered as in Fig. 2c. The upper triangle panels show Spearman correlation coefficients (top) and P values (bottom). The axis range is from 0 to 1 RNA per minute. (PDF 1203 kb)

Comparison of mRNA synthesis rates in S. pombe. The pairwise scatterplots compare mRNA half-lives in seven datasets. The datasets are ordered as in Fig. 2d. The upper triangle panels show Spearman correlation coefficients (top) and P values (bottom). The axis range is from 0 to 1 RNA per minute. (PDF 434 kb)

Correlations between mRNA half-lives, synthesis rates, and abundance in S. pombe. (A) Scatterplot comparing mRNA half-lives in the “Mata (5)” data and mRNA abundance [RNA/cell] obtained by Bahler and colleagues [72]. Spearman's ρ and P value are shown. (B) Same as (A) but for mRNA half-lives in the “Gagneur” data. (C) Scatterplot comparing mRNA synthesis rates computed from the “Mata (5)” data and mRNA abundance as shown in (A). (D) Same as (C) but for mRNA synthesis rates in the “Gagneur” data. (E) Scatterplot comparing mRNA half-lives and synthesis rates in the “Mata (5)” data. (F) Same as (E) but for the “Gagneur” data. (PDF 818 kb)

Codon optimality and mRNA half-lives are significantly associated in S. cerevisiae and S. pombe. (A) The CSC plotted for each codon based on S. cerevisiae mRNA half-lives in the “Cramer (1)” dataset. The white and gray bars represent optimal and non-optimal codons, respectively. The classification of codon optimality is based on the S. cerevisiae cTE. (B) Same as (A) but for the “Cramer (2)” dataset. (C) The CSC plotted for each codon based on S. pombe mRNA half-lives in the “Mata (5)” dataset. The classification of codon optimality is based on the S. pombe cTE. (D) Scatterplot comparing tAIg and mRNA half-lives in the “Cramer (1)” dataset in S. cerevisiae. Spearman's ρ and P value are shown. (E) Same as (D) but for the “Cramer (2)” data. (F) Same as (D) but for the “Mata (5)” dataset in S. pombe. (PDF 427 kb)