A concern when adding pleiotropic terms was that large semantic distances may be more likely to arise in larger pathways with more genes, resulting in less specific pathway functions.
Three students in our sample explained the difference between low- and high-intensity pigmented plants, saying that low-intensity pigmentation resulted from plants inheriting fewer genes involved in anthocyanin biosynthesis, whereas high-intensity pigmented plants inherited more genes, resulting in a higher "gene dose".
Testing the alternative hypothesis that apicomplexan-specific genes were more expression-diverged than more phyletically-unrestricted genes resulted in a p-value of 0.115 using the Kolmogorov-Smironov test while the alternative hypothesis that Plasmodium-specific genes were more diverged than phyletically-unrestricted genes resulted in a p-value of 0.003.
Removing genes whose expression profiles consist entirely of samples which are among the lowest 5th percentile and 10th percentile of genes assayed in a particular sample in either species and then re-testing the hypothesis that Plasmodium-specific genes were more expression-diverged than more phyletically-unrestricted genes resulted in p-values of 0.013 and 0.003 respectively.
This adjustment can result in more or less reported results, by favoring higher level parent nodes with more associated genes, resulting in up to an 80% reduction in the number of reported terms (Supplementary Table).
Given these expectations and observations of more duplicate genes in regions of high recombination, we hypothesize that species with higher global recombination rates may have more duplicate genes, resulting in larger gene families.
Interestingly, this higher level of connectivity between smaller numbers of genes resulted in more MCL modules ranging from 39,931 (at 0%) to 47,623 (at 100%) as well as more total enriched function terms ranging from 37,614 (at 0%) to 64,236 (at 100%) (Additional file 1: Figure S2).
The use of fewer genes resulted in more accurate prediction for non-local-recurrence patients, but less accuracy for local-recurrence patients.
The selection was restricted to pathways with 4 or more genes represented, resulting in identification of 72 KEGG pathways.
Consequently, there is little selective pressure for more efficient sulfate reduction genes resulting in more variants and no dominant variants.
