NALT transcript analysis identifying genes that differentiate between mock-infected and pneumococcal-infected mice. Comparisons were made between infected samples and mock-infected controls using Statistical Analysis for Microarrays (SAM) and the Fligner-Killeen Test for equality of variance. These analyses identified 112 transcripts that consistently differed during infection [SAM (FDR = 5%)] and the 358 transcripts (top 5%) that varied more during carriage as compared to control mice. (A) A union of the gene sets was clustered using a self-organizing map algorithm; each row represents a single gene, and each column a single animal. Black indicates the median level of expression, red indicates greater expression than the median, green less expression, and gray missing data. Numerically labeled horizontal gray bars above the samples indicate day post-colonization. (B) Expression profiles for the five functional categories identified. Heat maps illustrating the individual genes comprising each category are shown. An average expression profile for each category was calculated and plotted to illustrate the temporal characteristics of each category. Purple: Early Immune Response; Green: Immune System Process; Orange: Response to Wounding; Blue: Basement Membrane; Yellow: Cell Cycle/DNA Replication.