Table 1.
Voltage-gated ion channel genes involved in this study.
Figure 1.
Odds ratio (OR1) versus codon optimality.
With the exception of human, all organisms show a significant correlation between these two quantities. OR1 measures whether the codon is preferred at transmembrane sites, compared to all other codons encoding the same amino acid.
Table 2.
Example of a 2×2 contingency table for codon GCC in one particular gene in human.
Table 3.
Example of a 2×2 contingency table for amino acid Ala in one particular gene in human.
Table 4.
Odds ratio of optimal codon usage between transmembrane and non-transmembrane sites.
Figure 2.
Joint odds ratio of optimal codon usage between transmembrane and non-transmembrane sites for each type of voltage-gated ion channel.
The odds ratios were calculated by the Mantel-Haenszel procedure.
Figure 3.
Odds ratio (OR2) versus codon optimality.
With the exception of human, all organisms show a significant correlation between these two quantities. OR2 measures whether the codon is preferred at channel-forming sites, compared to all other codons encoding the same amino acid.
Table 5.
Odds ratio of optimal codon usage between channel-forming and non-channel-forming sites.
Table 6.
Example of a 2×2 contingency table for the conserved/non-conserved codon pattern in one particular gene in human.
Figure 4.
Distribution of the mean number of conserved codons across all the voltage-gated ion channel genes.
The black arrows indicate the real mean number of conserved codons across all the voltage-gated ion channel genes. The gray histograms show the random sampling distribution of the same quantity under the null hypothesis, which were generated 1,000 resampled sequences for each gene by randomly reshuffling synonymous codons among sites with identical amino acid. The P-value was obtained by one-tailed test.