Skewed monoallelic expression in the mouse. (a) Examples of genes with apparent skewed monoallelic expression. Same display conventions as Figure 1a. For a subset of random monoallelic expression (RMAE) genes, such as those shown here, we only observed RMAE in one direction (either monoallelic maternal or monoallelic paternal). (b) Skewed genes. For any given gene, the number of clones is too low to make an observation of skewed RMAE significant. When considering the genome-wide data, however, it becomes apparent that an observation of bias in the direction of RMAE occurs more often than can be explained by chance. When examining genes that show RMAE in only one direction, we can compare the number of genes observed (green) to that which would be expected by chance (blue) for genes with two, three or four monoallelic clones. In each case, the number of genes with RMAE clones solely in one direction is higher than expected (two clones, P = 1.92 × 10-2; three clones, P = 9 × 10-4). See main text and Note 6 in Additional file 1 for details. (c) The observed skewed RMAE is consistent with a range of simple models. By varying the percentage of genes subject to skewed RMAE, and by varying the probability of seeing one allele rather than the other allele for those genes with skewed RMAE, we estimated how closely simple models approximate the observed numbers of genes with monoallelic clones all in one direction. Shown in each cell is the sum of squares of differences between the observed and expected number of genes with two, three, and four clones all in one direction; the smaller the value is, the more closely the model approximates the actual observed values.