Cluster analysis of mature miRNA levels in KS and PEL. Data were first normalized relative to U6 to yield delta cycle threshold (dCT). dCT data were clustered using a correlation metric. (A) Principal component analysis (PCA) of the data identified 7 clusters as well as miRNAs that did not fall into any of the clusters (red crosses). PCA is a statistical tool of reducing multidimensional datasets. For instance, many miRNA genes are correlated. The PCAs can be derived from gene expression data and form an artificial coordinate system, in which coregulated genes cluster together. (A) Plot of the first 3 PCAs to visually assess the goodness of our cluster algorithm Clean clustering will result in nonoverlapping clusters. (B, C) Heatmap depiction of individual (duplicate) miRNA measurements. Red represents increase relative to all data in this set; blue, decrease relative to all data in this set. Only cluster members are shown, not unclassified miRNAs. PEL indicates primary effusion lymphoma; T, tonsil; K, KS; and H, EC. KS biopsies were from male AIDS-KS patients seen in the United States after 2004. The rightmost lane represents KSHV latently infected ECs. miRNAs that are discussed in the text are in large font.