Fig. 11.

Collinear control by amino acid frequency and synonymous codon preference. a The frequency of a codon in a gene is the product of its cognate amino acid frequency (AA) and its synonymous codon preference (syn.codon), where the latter = (number of occurrences of the codon)/(number of occurrences all codons for the cognate amino acid). Examples for the two codons for phenylalanine (Phe) are shown. A priori, there is no necessity for “AA” and “syn.codon” to be correlated. b A model was built for control of translation rates (TR) by the combination of “syn.codon” (61 features) and “AA” (20 features). The R² coefficients for this model are given (top). The percent of the unique and collinear contributions of “AA” and “syn.codon” to the total variance in log₁₀ TR explained by the combined model is shown by length on the y-axis. The percent control of TR by “syn.codon” that is collinear with that by “AA” is shown in red text. The percent of the dataset that contains all 20 amino acids and thus could be used to calculate “syn.codon” is also shown (top). This set of genes was used for all analyses