Although the two trans-effects identified (IL1RAP and CASP8AP2) are interestingly both involved in an apoptosis pathway, these trans-eQTLs were not detected in the HapMap B cell line dataset. These trans-eQTL results are in strong contrast to the number of cis-eQTLs we detected within the two data sets. This results primarily from the limited statistical power to detect trans-eQTLs, due to the number of statistical tests that need to be performed. Additionally, in order to cause a trans-effect, more intermediate biological steps are required that introduces additional biological noise, lessening the correlation between genotype and trans-gene expression. Cis-eQTLs can have a significant impact on the co-expression of genes; this genotypic variation may hinder the identification of significant trans effects. This adds an additional layer of complexity to the analysis of genotypic effects on gene expression in outbred populations.
