The expression values of the 23,574 transcripts were treated as quantitative traits and fitted to the same linear regression models used to compute LOD scores for clinical traits (eQTLs). The FDR at each threshold was determined by permuting the data 100 times and taking the mean number of QTLs detected over all of the permuted datasets at a given threshold, and dividing this count by the number of QTLs detected at the same threshold in the observed data. At the threshold for significant linkage (p < 5 × 10−5, genome-wide p < 0.05, based on a single trait), the FDR was estimated at 3.4% for the standard QTL model not accounting for any sex terms, 3.1% for the QTL model accounting for additive sex effects, and 3.2% for the QTL model accounting for additive sex effects and allowing for the sex interaction terms to enter the model. A list of all detected suggestive (p < 1 × 10−3) and significant eQTLs (p < 5 × 10−5) detected in the BXH.ApoE−/− intercross is provided in Table S1.