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In this study, we investigate the impact that the degree of LD, marker allele frequency, and association type have on estimating the probabilities of sharing alleles identical by descent in multipoint calculations and hence on type I error rates of different sib-pair linkage approaches that assume LE.
Values indicate the probabilities of sharing the same structure.
They are the population probabilities of sharing 2, 1 and 0 genes IBD for relative pair (i, j), without regard to their particular genotypes, but only (i, j)'s kinship relationships, under the Mendelian inheritance.
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One analysis is based on indicator probabilities of shared gene function that were previously reported in Ref. (Sykacek et al., 2007).
These initial steps provide indicator probabilities of shared gene activity and 2245 GO terms which we use as inputs for inferring GO term activity.
We can, for example, use the marginal probabilities over gene indicators as they arise from Bayesian variable selection in (Bae & Mallick, 2004; Lee et al. 2003) or the posterior probabilities of shared gene function proposed in (Sykacek et al., 2007).
The observation that active GO terms from these indicator probabilities of shared gene function point to several cell death-related terms is in line with the Fishers exact test-based inference in (Sykacek et al., 2007).
Our assessment that GO term activity can be more reliably inferred by quantitatively combining probabilities of gene activity is also supported by analysing probabilities of shared gene function (Sykacek et al., 2007) in mammary gland development (Clarkson et al., 2004) and endothelial cell apoptosis (Johnson et al., 2004).
Considering only the silent polymorphisms, to avoid confounding any effects of positive or balancing selection, we examined the probabilities of shared SNPs arising among the hsp70S genes via independent mutation or gene conversion using the method of Rozas and Aguade [ 26].
In these three localities, the number of species reported surpasses 130, therefore, the probability of sharing species between these three sites increases, and this is probably the reason why they are grouped together.
In comparison, the backup link mapping is much more complicated and the probability of sharing resources among backup links of different VNs is much higher.
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