Among the BXD strains, differential expression of any given gene can be attributed to polymorphisms (referred to as expression quantitative trait loci or eQTLs) driving that gene’s expression. eQTL mapping was used to identify chromosomal locations associated with differential expression of genes. We performed eQTL analysis using the WebQTL module on GeneNetwork (www.genenetwork.org) according to our published methods [29]. Simple interval mapping was used to identify potential eQTLs regulating Cd14 expression levels and to estimate the significance at each location using known genotypic data for those sites. Composite interval mapping was also used to control for genetic variance associated with major eQTLs and therefore identify any secondary eQTLs that may have been otherwise masked. Each of these analyses produced a likelihood ratio statistic (LRS) score, providing us with a quantitative measure of confidence of linkage between the observed phenotype—in this case variation in the expression level of Cd14—and known genetic markers. The significance of the eQTLs was calculated using more than 2000 permutations tests. Loci were considered statistically significant if genome-wide p < 0.05. Sequence variability between B6 and D2 was then determined using the SNP variant browser link on GeneNetwork.
