Codon preference of the slow-translating genes.

(A) Codon preference of low EVI genes in the four cell lines based on Preference Score analysis. For details, please refer to Materials and Methods section. Favored and disfavored codons are shown in red and grey bars, respectively. (B) Mutual correlation of PS_Low-EVI of codons among all four analyzed cell lines. (C) Percentage of variance explained in the principle component analysis (PCA) on RSCU. (D) Principle component (PC) based clustering analysis. The PCs with the summed explained variance greater than 80% were taken for clustering analyses based on the standardized Euclidean distances. For each cell line, four groups of genes were analyzed. They were low EVI genes, high TR genes, all genes and a random subset of genes that were inside the 95% confidence ellipse (Fig 2A and 2B). The clusters with multiple gene groups are indicated by grey ellipses.