Figure 14. QTL cluster map for coat color in the BXD RI strains. Chromosomes are listed along the bottom of the figure from 1 to X. Each row corresponds to a QTL map for a single transcript. The intense red and blue bands on Chr 4 correspond to significant QTLs on Chr 4 centered at approximately 80 Mb—the location of Tyrp1. The lower blue section of this Chr 4 band corresponds to transcripts whose expression is higher in strains with a B haplotype on Chr 4, whereas the upper red section corresponds to transcripts whose expression is higher in strains with the mutant D haplotype. In addition, there are distinct but less intense bands on Chrs 6, 9, 15, and 18. How to extract data based upon phenotype using “Coat Color” to determine the possibility that the Chr 4 trans-acting band is related to pigmentation: Step 1. Open either the main website GeneNetwork. Step 2. Set up the Find Records field to read “Choose Species=Mouse, Group=BXD, Type=Phenotypes, Database=BXD Published Phenotypes. Step 3. Enter the search term “Coat Color” in the ANY field and click on the 'Search' button. Step 4. Select RecordID/11280-Coat Color to generate the Trait Data and Analysis page. Step 6. In the Analysis Tools section, locate the options for Trait Correlations. There are several options in this area: Choose Database, Calculate, and Return. Under Choose Database select the Eye M430V2 (Sep 08) RMA database, under Return select top 200, and finally select 'Trait Correlations'. The Correlation Table is constructed listing the top 200 correlates that are associated with the eye and coat color. Step 7. Click on a limit of 100 of the highest correlates, making sure that you include genes that are known to be associated with coat color and the eye. After 100 probe sets are chosen, select the 'QTL Heat Map' function.