Figure 2.
Strong gametic phase disequilibrium between genes with significant cis-acting eQTLs simulates independence events. (a) The Ppox and Ifi203 gene expression traits have strong cis-acting eQTLs with lod scores of 29.2 and 17.4, respectively, at the positions indicated. The physical locations of these genes on chromosome 1 are also shown aligned next to the genetic map. (b) Scatter plot of the mean-log (ML) expression ratios for Ppox and Ifi203 in the BXD data set. The two genes are positively correlated, with a correlation coefficient of 0.75. This correlation is probably induced by the two genes having closely linked eQTLs and not a result of any functional relationship. (c) Twenty-one genes physically residing on chromosome 1 were identified with strong cis-acting eQTL (corresponding lod scores > 10.0)3. Pearson correlation coefficients were computed for the mean log expression ratios between each of the 210 possible pairs of genes. The absolute value of each of the correlations is plotted here against the distance (cM) separating the cis-acting eQTLs for each pair. The pattern in this plot indicates that the magnitude of correlation is directly proportional to the distance between the cis-acting eQTLs, which are coincident with the physical locations of the genes (correlation coefficient = 0.82). This is precisely the relationship we would expect if the correlation structures were attributed to linkage disequilibrium between the eQTLs. The Ppox-Ifi203 pair is highlighted by the red dot.