Figure 2

Identification of REBs and DNA copy number abnormalities from individual HCC samples. 39 HCC samples were analyzed for REBs from gene expression data using IR-CGMA and for DNA copy number abnormalities from aCGH data using hidden Markov modelling. Corresponding chromosome ideograms for chromosomes 1, 4, 6, 8, 13, and 17 are also shown to scale. The red bars in the ideogram highlight the centromere. A. IR-CGMA estimations were plotted as a heatmap to indicate significant expression biases as described in Figure 1. For consistent plotting, z-scores > 4 and z-scores < -4 were set to 4 and -4 respectively. Scales ranging from 4 to -4 are shown adjacent to each graph. Data for all autosomal chromosomes for all samples was also generated [see Additional file 1]. B. aCGH predictions of genomic deletions (s ≤ -0.225, blue) and amplifications (s ≥ 0.225, red). The highest intensity blue color indicates a s ≤ -1 while highest intensity red indicates s ≥ 1. Scales ranging from 1 to -1 are shown adjacent to each graph. Data for all autosomal chromosomes was also generated [see Additional file 2].