In the cellular component category, transcripts for the "light-harvesting complex" have the highest level of enrichment among light-induced transcripts (Figure 2A).
The five BP terms displaying the highest level of enrichment corresponded to "ribosome biogenesis", "translation", "response to cold", "response to water deprivation" and "response to cadmium ion".
The MF categories displaying the highest level of enrichment were "carboxylesterase activity", "lipid binding", "microtubule motor activity", "DNA-dependent ATPase activity" and "cyclin-dependent protein kinase regulator activity".
Thus we see that two of the TEs showing the highest level of enrichment in our datasets host a collection of TFBSs located at a fixed distance among them, whose relative position seems to be carefully conserved by evolution.
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,.
The five BP categories displaying the highest level of enrichment were "DNA-dependent DNA replication initiation", "regulation of cell cycle", "DNA unwinding involved in replication", "cell cycle and microtubule-based movement activity".
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.
The highest levels of enrichment were observed in the promoters of Pho7-regulated genes identified in the microarray analysis (for a complete list of the identified peaks, see Additional file 5).
Of all chromatin marks we investigated, only H3K4me1 consistently showed its highest levels of enrichment within HMRs relative to up- and downstream regions (where it was consistently depleted; fig. 3 c and supplementary fig. S5, Supplementary Material online).
He added, however, that the Iranians, while showing the skills to achieve that high level of enrichment, had little of the manufacturing expertise needed to turn the enriched material into safe reactor fuel.
