Figure 2

Frequency of differentially expressed genes on different haplotypes and attributable to haplotype difference. The proportion of the genes that were differentially expressed and also on different haplotypes in the parental C57BL/6 and A/J mice was obtained for all combinations of the three tissues at pplr thresholds of 0.005 (see Fig 3a for numbers). The percentages of genes that were differentially expressed and on different haplotypes are shown by the solid black bars, the percentages of genes that were estimated using Bayes Theorem to be differentially expressed due to haplotype differences are shown by the grey bars. 30% of the genes in A/J mice were on different haplotypes from C57BL/6, indicated by the horizontal bar on the plot. There was a significant excess of differentially expressed genes on different haplotypes in the parental mice but not in the congenic mice when the congenic region was excluded. Key "3 tissues" (kidney, liver, spleen) in parental mice (C57BL/6 and A/J); "2 tissues" - mean of the three combinations of two out of three tissues from the parental Mice; "1 tissue" - mean of individual tissues from the parental mice; "Congenics" - mean of the genes that were differentially expressed in the congenic mice and on different haplotypes in the parents for for the Tir1 (liver and spleen) and for Tir3 (liver) congenic excluding the congenic region. The percentage of genes that are differentially expressed in the congenic mice and on different haplotypes in the parents is expected to approximate to the percentage of genes on different haplotypes in the parents as was found to be the case.