cis eQTL were penalized if their binding target region contained a B6/D2 polymorphism. As Affymetrix probe sequences were designed against the B6 genome, probe SNPs primarily reduce binding avidity with D2 transcripts. Therefore, this penalty was only applied to cis eQTL if B6 was the increaser allele. A full list of SNPs identified within probe sequences are contained in Table S8. Candidates were prioritized further if they belonged to the same network as constituents of the linked trans-band, taking into account the relative importance of a gene in the resident network by using the connectivity and centrality measures from the hub gene analysis. Genes identified as significantly ethanol-responsive across the BXD lines received additional scoring.
