Codon usage similarity between viral and some host genes suggests a codon-specific translational regulation

Figures

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  Figure 1. The PCA of the RSCU. The RSCU of human genes and RNA viruses were subjected to PCA. Then, the simplified RSCU values of human genes and RNA viruses were plotted on the graph as the coordinates of component 1 (x) and 2 (y). The color keys indicate the groups of RNA viruses. Human genes are represented using transparent black dots.

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  Figure 2. The correlation between principal components (PC1, PC2), codon adaptive index (CAI), and percentage of GC content at the third position of codon (%G+C(3)) were determined using simple linear regression and Pearson correlation coefficient. (A) CAI was plotted with either PC1 (R2 = 0.7958, PCC = -0.8921, p < 0.001) or PC2 (R2 0.5824, PCC = 0.7631, p < 0.001). (B) %G+C(3) was plotted with either PC1 (R2 = 0.9459, PCC = -0.9726, p < 0.001) or PC2 (R2 = 0.4373, PCC = 0.6613, p < 0.001).

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  Figure 3. The human genes with RSCUs similar to RNA viruses in each subgroup are represented using transparent colored dots.

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  Figure 4. GO terms enrichment in the biological processes from human genes with RSCUs similar to RNA viruses. GO terms with p ≤ 0.01 were taken as a significant enrichment and represented with -Log10 (p-value). The bold alphabets indicate GO terms that were found to be identical to the enriched GO terms of upregulated protein profiles in viral infections, determined by high-throughput quantitative proteomics; H (HIV-1), Z (Zika virus), F (influenza A virus), and D (dengue virus serotype 2).

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  Figure 5. The graph shows the RSCUs of human cell cycle regulated (CCR) genes and non-cell cycle regulated (NCCR) genes, compared with the RSCUs of RNA viruses.