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. 2019 Jan 30;47(5):2216–2228. doi: 10.1093/nar/gkz033

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© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 3. — Distribution of S. cerevisiae CSCg values compared with a shuffled version of the genome. (A) The frequency distribution of CSCgs calculated from Coller's CSC is shown in black. The upper panel shows a cumulative distribution of this dataset. A shuffled version of the genome was generated by maintaining the same codon bias and protein sequence but randomizing the codon usage in each mRNA. The resulting CSCg distribution of the shuffled dataset is shown in blue. The frequency of the distribution of individual CSC values is shown on the right; this distribution was maintained in the shuffled version of the genome. (B) The subset of genes with CSCg values below zero (black lines) was compared to another shuffled mRNA dataset (blue line). This new shuffled dataset was generated as described in A, but this time the frequency of codons derived from the mRNA population with negative CSCg values (shown in the right panel) was used in the calculation. A ratio between the actual genome and the shuffled distribution is shown in the inset; note that the frequency of genes with CSCg values lower than 0 is ten times higher in the S. cerevisiae genome than in the shuffled genome. The P-values were calculated with the Kolmogorov–Smirnov test for both panels. The raw data, sample size, P values, and statistical analyses are presented in Supplementary Table S3.