Table 5 Nucleotide substitution rates among GW-572016 nmr different epitope and non-epitope regions. dN SE# dS SE P-value* Associated epitopes 0.01062 0.00952 0.20969 0.07091 < 0.001 Non-associated epitopes 0.02387 0.02537 0.24220 0.12666 < 0.001 Not included epitopes 0.10532 0.01277 0.29085 0.04305 < 0.001
GSK126 chemical structure Non-epitopes 0.09793 0.01653 0.27329 0.04665 < 0.001 Average pairwise number of nonsynonymous (d N ) and synonymous (d S ) substitutions per nonsynonymous and synonymous site, respectively, estimated at different categories of epitope and non-epitope regions among reference sequences of M group are given. # Standard errors were estimated with 100 bootstrap replications in MEGA4. * In pairwise t-tests, the null hypothesis of dS = dN was rejected in all four comparisons. The average dN and dS values for each category of sites obtained from the pairwise comparisons of the reference sequences from the M group are shown in Table 5. Notably, associated epitopes have significantly smaller dN
and dS values than respective dN and dS values at other categories of sites, including non-epitopes (one-way ANOVA and nonparametric Kruskal-Wallis tests, p < 0.001) (see also Additional file 8). While significantly lower dN values at associated epitopes can be attributed to BYL719 cell line strong purifying selection operating to reduce amino acid diversity at these highly conserved epitope regions, in agreement with our previous results [44, 78], the significantly
lower dS values indicate that the high degree Tolmetin of sequence conservation exist not only at the amino acid level, but also at the nucleotide level in these associated regions. Notably, when we consider correlations between the levels of synonymous and nonsynonymous sequence divergence from different site categories for the same pair of sequences, relatively strong and statistically significant positive correlations (Pearson correlation coefficient values between 0.67 and 0.77, p < 0.01) exist between dN and dS values for both non-epitope and epitope regions that were not included in the association rule mining, including variable epitopes, but not for associated epitopes. Similar trends are detected using non-parametric correlation (Kendall’s tau values between 0.34 and 0.45, p < 0.001). This may be attributed to common factors (such as functional and structural constraints and mutation rate) influencing evolution of these regions, so that the regions with higher dS values are also likely to have higher dN values. On the other hand, the levels of synonymous and nonsynonymous sequence divergence at the associated epitopes have only weak or non-significant correlation both with each other (r = -0.14, p < 0.01), as well as with dN and dS values at other regions within the same genomes (see Additional file 9).