Impact of multi-dimensional analysis on low frequency events. (A) Box plot analysis of the frequency distribution of single and multi-dimensional analyses (MDA) of the 1162 genes differentially expressed with a concerted change in one of the DNA dimensions. The area in red represents the number of genes (of the 1162) that would be missed if only a single DNA dimension was examined, while the area in blue represents the genes that would be detected. Examining the median values for the three right-most boxes, we see that by even using the box with the highest median (copy number), we would not be able to detect about 50% of the 1162 genes. (B) Two specific examples highlighting the importance of multi-dimensional genomic analysis. Using single dimensional analyses (green shade) alone, CD70 (blue line graph) and ENG (red line graph) disruption occur at very low frequencies (44% and 33% respectively). However, when examining two (red shade) or three genomic dimensions (blue shade), the disruption of these genes occurs at very high frequencies, 88% and 77% respectively. Frequency threshold of 6/9 is denoted with a black dotted line.