Determination and application of a disruption frequency threshold. (A) Results of the analyses of ten simulated datasets. Aggregating the results of the simulated analyses, the proportion of genes in random simulations at the observed frequency thresholds are shown. From these analysis, approximately 2% of the simulations were ≥ 6/9. (B) Using a frequency cut-off of 6/9, the number of genes disrupted at that frequency using a single or combination of DNA dimensions. With a single dimension alone, we can maximally identify 437 genes which are differentially expressed and exhibit a concerted change at the DNA level in a minimum of 6/9 samples. However, using all three dimensions, we find that 1162 genes are in fact differentially expressed and contain at least one concerted change in one of the DNA dimensions. This represents over a two-fold increase in the number of genes identified.