Transcriptional profiling of CD4+CD25+ TReg and CD4+CD25- naïve T cells. To identify molecular differences between regulatory and naïve human T cells, differential expression of 350 genes was investigated by application of our Human TReg Chip. Following data normalization, Statistical Analysis of Microarrays (SAM) was applied as a data mining tool to ascertain gene expression changes, identifying 62 significantly altered genes between both T cell subpopulations (delta = 2.46, median FDR [false discovery rate] = 0.48). After entering the generated data set into Genesis software, a two-dimensional hierarchical clustering analysis yielded the displayed transcriptional pattern, which discriminates between human regulatory and naïve T cells, and consists of 32 upregulated and 30 downregulated genes. Each row represents a gene probed on the Human TReg Chip; each column shows expression of the 62 genes measured for each individual in the study. Red indicates genes that are expressed at higher levels compared with the mean signal intensities of all experiments, whereas downregulated genes are colored in green and black indicates signal intensities near the mean expression level.
Pfoertner et al. Genome Biology 2006 7:R54 doi:10.1186/gb-2006-7-7-r54