Unsupervised hierarchical clustering. Overall patterns of expression of genes across the 14 HCV-related HCC and non-HCC counterpart, as well as 7 HCV-negative control patients. Red indicates over-expression; green indicates under-expression; black indicates unchanged expression; gray indicates no detection of expression (intensity of both Cy3 and Cy5 below the cutoff value). Each row represents a single gene; each column represents a single sample. The dendrogram at the left of matrix indicates the degree of similarity among the genes examined by expression patterns. The dendrogram at the top of the matrix indicates the degree of similarity between samples. Panel A, unsupervised analysis including all three set of samples; Panel B, unsupervised analysis including HCV-related HCC and normal control liver samples; Panel C, unsupervised analysis including HCV-related non-HCC counterpart and normal control liver samples.