PCA and supervised HCA of gene and miRNA expression accurately cluster the trisomy 8, disomy 8, and reference cultures. (A) The PCA identified 1,650 probes that displayed significant expression differences among the trisomy 8, disomy 8, and reference groups (left). Supervised HCA of these probes accurately clustered the subgroups, as illustrated in the heat map to the right. (B) A similar pattern was observed when analyzing only chr8 data, with the PCA identifying 87 genes (left) and HCA accurately clustering the subgroups (right), placing the trisomy 8 cultures in a single branch. (C) Median-centered gene expression of chr8 demonstrated that the majority of the genes on this chromosome in the trisomy 8 cultures were upregulated compared with the disomy 8 cultures (left), whereas few differences were observed when comparing the disomy 8 cultures with the reference cultures (right). (D) The PCA identified 108 miRNA probes that displayed significant expression differences between the trisomy 8, disomy 8, and reference groups (left). Supervised HCA of these probes grouped the cultures correctly (right). chr8, chromosome 8; HCA, hierarchical cluster analysis; miRNA, microRNA; PCA, principal component analysis.