Figure 5.

Application to childhood ALL data. To verify the ability of the proposed method to identify genomic regions with expected increases/decreases in average gene expression, we applied it to the data set by Ross et al [26] (Affymetrix U133A+B arrays). Each case was normalized and segmented as described in Materials and methods. Blue solid: Average segmentation result across all cases of each leukemic subtype (Table 1). Orange: Average DNA copy number profile across within each class, as determined from the Mullighan et al data set [29] (Affymetrix 250 k SNP arrays). Key observation: The method successfully identified several regions with altered gene expression (details in Results). The case-specific segmentations are provided in Additional file 3. In this example, T_μ = 0.25 (similar results for other reasonable values).