Identification of candidate genes in prominent trans-band eQTLs based on dynamic expression patterns.

Strain differences in temporal gene expression are informative for predicting regulatory genes underlying trans-band eQTLs. Multiple criteria were established to identify the best candidate genes in the trans-band eQTLs mapped in Munger et al. [1]. First, the putative regulatory gene must be expressed above background at or before E11.5 to exert any effects on downstream target genes. Genes implicated in the list of target genes that exhibited a sexually-dimorphic expression pattern consistent with the sexual differentiation pathway (male or female) were prioritized. Genes that met both of the above criteria, and exhibited strain expression differences (either in overall levels of transcript abundance or in timing of onset of sexual dimorphism) in a pattern consistent with the observed allelic effects for that eQTL, were prioritized as the highest candidates. A few eQTLs harbor genes in which abnormal sex determination phenotypes have been noted in the null mutant mouse, and these genes were given similar high priority. Using these criteria, confidence intervals containing 60–526 protein coding genes were narrowed down to eight or fewer high priority candidates.