The presented Pearson's chi-squared formulation is slightly modified to determine whether the ICU (CC) is significantly different between high-expression genes and all genes in the genome.
Similarly, more than 80% of the amino acids (pairs) show significant difference in ICU and CC distributions between high-expression genes and all genes in the genomes of these three microbes.
Contrastingly, 80% amino acids did not show significant difference in CC distributions between high-expression genes and all genes in L. lactis, suggesting that the selection of highly expressed genes may not be required to establish the CC preference of L. lactis.
By substituting E ij H with E ˜ ij H in the expression for Χ j, the chi-squared statistic to test the difference in ICU (CC) distribution between high-expression genes and all genes in the host's genome can be calculated.
There is a strong variation in codon frequencies between low and high expression genes, where highly expressed genes have a codon usage that is biased toward codons corresponding to frequent tRNAs.
Using this approach I identified 24 codons showing significant ΔRSCU values between low and high expression genes in four or more species.
First, the overall distribution in GC3 values is shifted towards the left (namely lower values), and second the difference in GC3 preference between low and high expression genes is less pronounced than that observed in the other trypanosome.
Optimal codons appear to be largely the same across the five species used in this analysis, and most of the differences between species can be explained by codons with low ΔRSCU values, where the statistical power to detect changes in codon usage between low and high expression genes may be low.
Based on the median expression level in nonsmokers, expressed genes were further divided into "low" (RPKM 0.125 to 1), "medium" (RPKM between 1 and 10) and "high" expression genes (RPKM > 10).
In the present study, the high expression of SE observed in root tissue was in corroboration with the data of Sabir et al. [ 8], who reported a correlation between high expression of the genes for squalene epoxidase and squalene synthase and relatively higher accumulation of withanolide in field-grown root tissues.
Despite the correlation between high expression of these genes and the MDR, some studies suggest that using agents that increase GSH, GSH-Px and GSTs levels during drug treatment is a promising way to reduce oxidative stress, thus reducing the collateral effects of chemotherapy in breast cancer patients [ 24- 26].
