Fig. 2.

Global genome expression reveals extensive similarities between CD1d^indNKT and NK cells that surpass similarities between iNKT and NK cells. (A) Splenic NK (NK1.1⁺DX5⁺CD3⁻CD1d tetramer⁻), CD1d^indNKT (NK1.1⁺DX5⁺CD3⁺CD1d tetramer⁻), iNKT (NK1.1⁺DX5⁻CD3⁺CD1d tetramer⁺), and conventional T (NK1.1⁻DX5⁻CD3⁺CD1d tetramer⁻) cells were sorted, and RNA was extracted and hybridized to the mouse 1.0 ST array. Ratios were generated using normalized raw expression values and then log₂ transformed. Total genes were first filtered based on an expression value of at least 16 in one of the four cell populations. Ratios of NK relative to T cells (NK/T), CD1d^indNKT relative to T cells (CD1d^indNKT/T), and iNKT relative to T cells (iNKT/T) were compared, and the genes that did not have a larger than twofold change in at least one of the three ratios were filtered out. The remaining genes were ranked by the SD of the three values, and k-means (k = 15) clustering was performed in the top 20%. The blowout shows two clusters of genes with higher differential expression in NK/T and CD1d^indNKT/T but not in iNKT/T cells. (B) Heat map of hierarchical clustering of the killer cell lectin-like (Ly49) family of receptors. (C) Heat map of hierarchical clustering of various selected genes commonly found in T cells. (D) Heat map showing genes that are selectively up-regulated or down-regulated (more than twofold) in CD1d^indNKT but not in NK or iNKT cells (less than twofold) relative to T cells. We subtracted the absolute expression change values in NK and iNKT from the values in CD1d^indNKT, sorted the selected genes by this value from high to low, and displayed the top 16 genes as a heat map. A more complete set of genes is shown in Fig. S7. Colors indicate up-regulation (green) and down-regulation (red) relative to T cells. (E–G) Pair-wise Euclidean distance of expression levels between NK, CD1d^indNKT, iNKT, and T-cell subsets. E shows the same selected set of genes shown in A, F shows genes with at least twofold differential expression in at least one of these cell subsets, and G shows all expressed genes (with expression levels higher than 16). Colors indicate long (yellow) and short (dark red) distance. Gene chip data are from cell subsets sorted from n = 7 mice.