Unsupervised hierarchic clustering of gene expression data generated from non-Hodgkin and AIDS-related lymphomas.

RNA extracted from 62 cases was converted into labeled cRNA and hybridized to U95A Affymetrix Gene Chips. AIDS-related NHL is indicated by a yellow rectangle; PEL, a black rectangle; centroblastic DLBCL, a blue rectangle; immunoblastic DLBCL, a green rectangle; and BL, a red rectangle. Unsupervised clustering can identify distinct cell types (eg, AIDS-NHL subtypes) that have not been classified a priori. The hierarchic clustering algorithm used to generate the dendrogram is based on the average-linkage method.17 18 For construction of the dendrogram, see “Materials and methods.” The matrix below the dendrogram depicts the gene expression values of the individual samples, with columns representing individual tumor samples and rows representing individual genes ordered according to hierarchic clustering. The color scale identifies relative gene expression changes normalized by the standard deviation, with 0 representing the mean expression level of a given gene across the panel. Of note, the BL panel from immunocompetent patients included “classical” BL as well as atypical Burkitt/Burkitt-like tumors from elderly persons (see “Materials and methods”); this heterogeneity among the BL group may explain the apparent intermingled clustering in the dendrogram.