Based on the definition of four different poly(A) site categories (i.e., constitutive, strong, median and weak poly(A) sites, see the section Materials and Methods for definition), the numbers and percentages of the four different PAC sites and corresponding genes are shown in Table 3.
Irrespective of the substitution model (GTR nt, JTT) used for the analysis, the phylogenetic model additionally involved four discrete categories of gamma distributed rates across sites (denoted + Γ4, [ 42]), plus an invariant site category (denoted + I).
The WAG amino acid substitution model [ 92] with gamma distributed site rates and an invariable site category was used in all phylogenetic analyses as the Prottest software [ 93] indicated that this model provided the best fit to the data.
Model A can be compared with its site-specific counterpart (model M1) using the LRT with df = 2. In addition, the lineage and site-specific model model A null was applied as a second LRT with model A. In model A null, the additional site category is fixed at neutral rather than being estimated from the data, and this LRT provides an additional test for model A (Zhang et al., 2005).
For each tumour site category, an alphanumeric value is assigned reflecting the burden, or prognostic significance of the disease identified, with a higher value representing more advanced disease, or a worse prognosis.
Each site category has an estimated proportion (p0, p1, p2) and their ω values (ω0, ω1, ω2) are estimated from the data.
In subsequent analyses we treated sites with a BEB posterior for the divergent site category 2 (ω2) of >0.5 as being under diversifying selection.
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Survival estimates and 95% confidence intervals from each database were compared by state and primary site category.
So the frequency we would expect in the internal jugular site category is 1305 × (934/1706) = 714.5.
