Based on superior performance in cross-validation analysis, the PAM method [ 18] was selected for all downstream class prediction analyses.
Further, the GRMs for both the upstream and downstream classes are very similar, indicating that variants annotated in the upstream class are potentially annotated in the downstream class, further emphasizing the need to have accurately defined annotations in these regions.
Similarly for the beef traits we see significant enrichment in the upstream class for most traits, with the downstream class having equal highest level of enrichment to the intragenic and intron classes,.
In the context of the role of PI3K/Akt/mTOR autophagy pathway in oncogenic regulation, Akt as the major player downstream class I PI3K can activate mTOR and lead to inhibition of autophagy.
The results from the enrichment or depletion analysis were not in complete agreement with the results from variance component analysis, where the missense and synonymous classes gave the greatest increase in variance explained, while the upstream and downstream classes showed a more modest increase in the variance explained.
In the upstream and downstream classes, there are a very large number of SNP, so that the chance of at least one of them being in high linkage disequilibrium with a causal mutation (a TAV) is higher than for classes with a lower number of SNP.
Of all dairy traits, only fat percent was significant in both the upstream and downstream classes, although there was a trend for the other annotations to explain more of the variance when compared to the random intergenic set for the traits fat percent, milk production and protein percent (Table 5, Figure 3).
We also observe very similar matrices between the upstream and downstream classes.
We also found significant enrichment of TAVs in upstream and downstream classes suggesting that these classes can have potentially important regulatory functions.
In the TAV enrichment or depletion analysis we observed that the upstream and downstream classes were significantly enriched for most dairy traits and many beef traits, while the protein coding classes are also enriched in dairy, but for fewer traits.
The missense class, however, had one of the highest levels of enrichment after the upstream and downstream classes in dairy with 7 traits to be significantly enriched for TAVs, while in beef we see no enrichment or depletion.
