Hierarchical classification of mouse-strain-specific and CM-R/CM-S genes according to the time of infection. A. Hierarchical clustering of the 58 brain tissue samples, using expression levels of 327 significant genes differentially expressed between the mouse strains at early and late stages of infection. This set of genes was extracted from the full data set (n = 2012) by use of a SAM procedure and a false discovery rate of 0%. Each row represents a gene and each column represents a sample. Red and green indicate expression levels above and below the median, respectively. Grey indicates missing data. Dendograms of samples (above matrix) and genes (to the left of matrix) represent overall similarities in gene expression profiles. B. Dendogram of samples representing the results of the same global hierarchical clustering applied to the 58 brain tissue samples. Clustering of technical replicates (CBA/J-5, C57BL6-20 and BALB/c-13) is shown: the samples taken from a CBA/J mouse on day 2, a C57L/6 mouse on day 7, and a BALB/c mouse on day 7 were run on 5, 2, and 2 microarrays, respectively. Samples taken from mice on days 2, 5, 7, 9, and 15 post-infection are coded D2, D5, D7, D9, and D15, respectively.