What is QTL heatmap?

The upper part of this page includes a hierarchical cluster tree of the set of traits you selected in the previous window. To generate this plot, we initially compute distances between pairs of traits using (1 - r) where r is the Pearson product-moment correlation. The hierarchy is assembled by successively linking traits and groups of traits.

The lower part of this page provides a QTL heat map for all members of the Cluster Tree, extending from proximal Chr 1 at the top to distal Chr X at the bottom. Each vertical column or stripe encodes the genome-wide p value computed on the basis of 1000 permutations. Orange triangles mark the approximate location of genes.

These QTL heat maps can be redrawn using alternative color assignments using the "Redraw Cluster Tree" option. The default heat map is "Grey + Blue + Red" in which more intense colors mark chromosomal regions with comparatively high linkage statistics and the spectrum encodes the allelic effect. For example, blue-green regions are those in which one of the parental alleles (e.g., C57BL/6J) is associated with higher trait values, whereas red-yellow regions are those in which the other parental allele is associated with higher trait values. Grey and black regions have insignfiicant linkage to trait variance. The "Blue + Red" option is similar but the entire genome is encoded for allele polarity, including regions without significant linkage. Finally, " Single Spectrum" provides a plot that does not distinguish between allelic effects and encodes the p values, ranging from insignificant (dark blue) to genome-wide significant (bright red).