The overall gene expression profile of GC-Th cells (GC-Th) versus naive CD4⁺CD45RA⁺ (naive), CD4⁺CXCR5⁺CCR7⁺ “early memory” (CXCR5), and CD4⁺CCR7^– “effector memory” (CCR7N) CD4⁺ cells. (A) Depicted are the 20 000 measurements of gene expression filtered from 12 microarray analyses of the 4 T-cell subsets (3 independent arrays per subset using cells from different donors, indicated as 1-3). Hierarchical clustering was performed to arrange genes based on their patterns of expression. Each row represents a separate cDNA clone on the microarray and each column a separate mRNA or T-cell subset. The results presented represent the ratio of hybridization of fluorescent cDNA probes prepared from each mRNA sample isolated from naive or memory/effector cells to reference mRNA samples from naive CD4⁺ T cells. These ratios are measures of relative gene expression in each mRNA sample and were depicted according to the color scale shown at the right. As indicated, the scale extends from fluorescence ratios of 0.25 to 6.25 (–2.5 to +2.5 in log base 2 units). Gray indicates missing or excluded data. (B) Individual expression patterns of several marker genes in the T-cell subsets. beta indicates beta-1,3-glucoronyltransferase 1. (C) Relationship between T-cell subsets as a function of similarity of gene expression programs shown in hierarchical dendrogram. Average linkage clustering based on Pearson correlation was performed to compare similarities among the T-cell subsets. The r values represent the correlation between gene expression profiles of T-cell subsets (+1 being a perfect positive linear relationship, 0 meaning no linear relationship, and –1 being a perfect negative linear relationship).