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First, a component due to relatedness,, which represents the proportion of selection acting directly on the G-values of individuals, and which is always positive.
We show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs.
For instance, when the simulated proportion of selection target is 0.05 with a certain recombination environment--Rec rate = 10-8, the PPV of the empirical distribution ranges from 0.50 to 0.90 under the selection strength 20-200).
The proportion of selection genes was not obviously enriched compared with the permutation in genes with very high degrees (degree > 20, fig. 2 A), likely due to the limited number of high degree genes (only 8.8% of genes had a degree > 20).
For each interval of DC and BC, a Z-score of the proportion of positive selection was obtained as follows: (3) Z − score S, i = P S, i − Expected (P N, i ) Standard deviation (P N, i ) Where i is the interval index, P S, i is the empirical proportion of selection, and P N, i is the proportion of randomly sampled proteins under the null hypothesis.
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Figure 2 displays a stacked accumulation of the selections of formality level per factor, providing an easier method of comparing the proportion of selections overall.
If these answers were not considered, the proportion of selections of logistical/practical reasons would be 13.31%95%5% CI 9.9 17.62) during first-order treatments and 11.82% (95% 8.92 15.46) overall.
To look into more details, we calculated the proportions of selection genes within different intervals of centrality scores.
A similar pattern was observed when the proportions of selection were conditioned on the BC score of global centrality (fig. 2 B).
The observed proportions of selection genes were normalized by 10,000 random permutations to derive a Z-score for each interval, and then they were ranked against the null distribution generated by permutation for statistical significance (see Materials and Methods).
In EAS, the proportions of selection increased from a significant underrepresentation at the very periphery of the network (BC = 0; nominal P = 0.001, FDR corrected P = 0.007) to a marginally significant overrepresentation with high BC scores of 2,001 20,000 (nominal P = 0.008, FDR corrected P = 0.025).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com