The figure summarizes the results of a genome-wide search through all pairs of genetic loci for associations with a trait 'percent fat'. In this figure we see strong associations on chromosomes 5+12, and on 12+18 that appear to be additive. An interacting pair is indicated for chromosomes 12+14. The x and y axes are genetic markers arranged in order along the chromosomes from 1 to X. Each 'pixel' represents a marker pair. We did not look at pairs within chromosomes due to numerical difficulties, thus there are blank spaces running up the main diagonal which are labeled with chromosome numbers. The size of these boxes reflects the number of markers typed and not the actual size of the chromosomes.
There are two portions the figure, above and below the diagonal. Below the diagonal, color scale* indicates the strength of evidence for an association of the locus pair with the trait. This is assessed assuming that the pair can potentially interact, i.e. that their effects don't simply add up. Above the diagonal the color scale indicates evidence for non-additive interaction. Interacting pairs are detected when 1) there is a red peak in the lower triangle and 2) there is a corresponding peak in the upper triangle.
Peaks in the upper half without a peak in the lower half are artifacts. Peaks in the lower half only indicate pairs of loci that act additively. The stripes in the figure are due to the strong effect of only of the loci in a pair and these can be screened out using additional statistical tests.
*The scale is -log_10 of the p-value from a likelihood ratio test.Gary Churchill
Courtesy Gary Churchill