Generation of the CD40 gene expression signature. Six samples of each type of CD40-stimulated and unstimulated Ramos cells were studied by DNA microarray analysis. Genes differentially expressed in the 2 groups were identified by supervised analysis by means of the Genes@Work software platform. In the matrix, columns represent samples and rows correspond to genes. Red and green indicate up-regulated and down-regulated expression, respectively. Values are quantified by the scale bar, which visualizes the difference in the ζ-score (expression difference/standard deviation) relative to the mean. Genes are ranked based on the z score (mean expression difference of the respective gene in phenotype and control group/standard deviation). (A) The CD40 gene expression signature comprised 106 up-regulated and 73 down-regulated genes. Some of the genes whose expression is known to change upon CD40 activation are indicated. (B) A subset of the CD40 signature genes is shown according to their distribution in functional categories. For the complete list of genes, including GenBank Accession numbers and Affymetrix codes, see Table S1, available on the Blood website (click the Supplemental Materials link at the top of the online article).