Fig. 4
Gene promoters in most cancer pathways are significantly enriched for repeat instability. Box plots of the proportion of promoters in five different cancer-associated signaling pathways with a) unstable repeats in their promoters and b) orphan repeats in their promoters, for normal-normal genome pairs (left boxes, n = 595) and for tumor-matched normal genome pairs (right boxes, n = 35). The pathways are: MAPK (number of genes in the pathway, N = 113), mTOR (N = 44), p53 (N = 98), TGF beta (N = 29), and Wnt (N = 87). Thick horizontal lines in each box mark the median, edges of boxes correspond to the 25th and 75th percentiles, and whiskers cover 99.3 % of the data’s range. In panel a repeat instability is significantly different in tumor genomes for the MAPK, p53, and Wnt signaling pathways (WRS test, P = 0.03, P < 10−8, P < 10−5, respectively, after Bonferroni correction). In panel b repeat instability is significantly different in tumor genomes for the MAPK, mTOR, p53, and Wnt signaling pathways (WRS Test, P < 10−31, P < 10−24, P < 10−9, P < 10−18, respectively after Bonferroni, correction)