The two subsets of transcripts—those with trans-QTLs in Qrr1p and those with trans-QTLs in Qrr1d—were analyzed for overrepresented gene functions using the DAVID functional annotation tool (http://david.abcc.ncifcrf.gov/). This revealed distinct gene ontology (GO) categories enriched in the two subsets (dataset S2). Enriched GOs among the transcripts modulated by Qrr1p include GTPase-mediate signal transduction (modified Fisher's exact test p = 0.001), and structural constituents of ribosomes (p = 0.003). Transcripts modulated by Qrr1d are highly enriched in genes involved in RNA metabolism (p = 4×10−7), tRNA aminoacylation (p = 1×10−5) and translation (p = 2×10−5), RNA transport (p = 0.003), cell cycle (p = 0.004), and ubiquitin mediated protein catabolism (p = 0.006). Other GO categories show enrichment in both Qrr1p and Qrr1d. For example, genes involved in RNA metabolism and ubiquitin-mediated protein catabolism are also overrepresented among the transcripts modulated by Qrr1p (p = 0.002 for RNA metabolism and p = 0.005 for ubiquitin-protein ligases). This may either be due to limitations in QTL resolution, or due to multiple loci in Qrr1p and Qrr1d controlling these subsets of transcripts.
