These simulated data sets could also be used for assessing whether several other genomic annotations were enriched in our observed dataset compared to what would be expected by randomly choosing regions matched for appropriate parameters, as discussed in subsequent subsections.
Only four function annotations were enriched in both gF and gC, including 'microtubule dynamics' and 'chemotaxis of neurons', which could be generally categorized as architectural features of neuronal development.
To determine if any annotations were enriched in both mouse and human, even though individual genes were not shared, separate lists of genes nominally significant in human (915 genes p ≤ 0.05) and human homologues of the 42 mouse genes with p ≤ 0.05 were entered into DAVID.
Nevertheless, functions of the 550 transcripts having GO annotation are enriched in 3 GO terms, prolyl oligopeptidase activity (GO 0004287, P = 3.5e-6), nucleic acid binding (GO: 0003676, P = 5.1e-5), anDNANA binding (GO: 0003677, P = 1.7e-3), withethe most enriched category being prolyl oligopeptidase activity.
GO terms and functional annotations that are enriched in gene families that were identified to be expanded or contracted in D. suzukii based on all three comparisons are more likely related to adaptation specific to the D. suzukii lineage, whereas those that are only present or absent in more restrictive comparisons may reflect gene family evolution events in a larger group of species.
Other notable functional annotations that are enriched in gene families expanded in D. suzukii, especially when compared to more basal Drosophila species, include "detection of stimulus," "sensory transduction," "G-protein-coupled receptor protein signaling," "proton-transporting ATP synthase activity," and "endopeptidase inhibitor".
We find that a subset of 22,534 TSSs from 13,542 genes from our 'all' gene annotation dataset are enriched in H3K4me3.
Using DAVID [ 50, 51], we found that these lists of genes are enriched in annotations like cytoskeleton, intracellular non-membrane-bounded organelle, microtubule, cell projection, cilium and related terms, with annotation clusters enrichment scores between 1.53 and 4.39.
Disease phenotypes consistent with cancers, as well as inflammation are enriched in annotation for the OI-MET-TF set.
