As an example of a single-trait analysis in the newly expanded strain set, we performed an analysis of mechanical nociception, the latency to respond to a plastic-coated smooth alligator clip placed on the tail. Previous studies of this trait in inbred mouse strains show high heritability of 0.69 (Lariviere et al. 2002). Analysis in MouseTrack using the RI analysis tool showed that this measure has statistically significant main effects of sex and strain ( ), and interaction effects ( ). The variances accounted for by strain are 0.32 and 0.27 in females and males, respectively. BXD sub-population effects on females and males were non-significant (P-value sub- populaton(Female) = 0.68,P-value sub- populaton(Male) = 0.93). Because the main effect of sex was significant, male and female data were exported separately for analysis in GeneNetwork, which uses a single vector of strain means as input. Permutation thresholds for significant and suggestive LOD scores were 3.78 and 2.21, respectively, in males and 3.6 and 2.27, respectively, in females. Interval mapping of tail clip latency for males of the full BXD RI panel shows suggestive
