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. 2014 Nov 5;9(3):555–568. doi: 10.1016/j.molonc.2014.10.012

Figure 5.

Figure 5

Patterns of DNA copy number changes associated with Epi‐LumB and Epi‐Basal tumors revealing divergent tumor evolutionary paths and candidate tumor suppressor genes. A) Frequencies of DNA copy number gains and losses in Epi‐LumB tumors are displayed as proportions on the y‐axis (positive and negative signs represent gains and losses, respectively) according to genomic position along the x‐axis from p‐arm to q‐arm (left to right, respectively) for all 23 chromosomes. The blue and red lines are frequencies derived from the PEBC and TCGA cohorts, respectively. The bars (black) on top and below the frequency plot indicate positions wherein copy number gains and losses, respectively, were found to be associated with Epi‐LumB tumors (comparing Epi‐LumB against all other tumors). Only regions wherein the statistical significance achieved less than 5% FDR in both the PEBC and TCGA cohorts are shown. A subset of the genes found within significant regions of copy number loss were also found to be promoter methylated in association with the Epi‐LumB subtype. The identity of these candidate tumor suppressor genes are given below the frequency plot. B) Event frequency plot for Epi‐Basal tumors (upper), with the corresponding significance analysis (black bars above and below the frequency plot indicative of significant copy number gains and losses, respectivley). Epi‐Basal associated promoter methylation events (gene symbols) found within significant regions of copy number losses are shown.