Figure 11. Genetic linkage maps of Tyrp1 and Tyr. A: Tyrp1 expression is controlled by a cis QTL located on Chr 4 at 80 Mb. This location corresponds to the location of the Tyrp1 itself (triangle on x-axis and the LRS of 57) on Chr 4 at 80 Mb. B: A similar map for Tyr, a gene that is located on Chr 7 but that has a strong trans-acting QTL. The numbers along the top of each plot represent chromosomes. The y-axis and the bold blue function provides the likelihood ratio statistic (LRS=4.6 x LOD). The two horizontal lines across these plots mark genome significance thresholds at p<0.05 (genome-wide significant, red line) and suggestive threshold (p<0.63, gray line). The thin red and green functions summarize the average additive effects of D and B alleles among all BXD strains at particular markers. If BXD strains with a D allele have higher values than those with a B allele at a particular marker then the line is colored green. In contrast, if strains with the B allele have higher mean values, the line is colored red. This additive effect size is measure in log2 units per allele. In other words, an additive effect of 0.5 signifies a twofold difference in expression level between strains with BB and DD genotypes at a marker (log 2 raised to the power of 2×0.5). How to generate QTL maps: Step 1. Link to expression data for a gene of interest using steps in Figure 1. For example, enter the search term “Tyrp1” in the ANY field and click the 'Search' button. Step 2. Click on Tyrp1 in the Search Results (probe set 1415862_at) to generate the Trait Data and Analysis Form (Figure 4). Step 3. Select the 'Interval Mapping' button in this form (Figure 4). This will initiate the analysis and display the whole-genome interval map for Tyrp1. The steps can be repeated with Tyr (1417717_a_at) to generate (panel B). You can now zoom in on a single chromosome (e.g., Chr 4) by clicking on the chromosome numbers along at the top of the plot. You can also customize the scale and features of the plot by entering appropriate parameters in the control box.