Differentially expressed genes in the DBA/1 strain during collagen-induced arthritis (CIA). Three experimental conditions, post-immunisation (PI), onset of arthritis (OA) and chronic arthritis (CA), were compared with naïve control (NC) to search for differentially expressed genes. (a) Venn diagram indicating the number of overlapping genes differentially expressed at three phases of CIA. (b) Hierarchical clustering of the 310 differentially expressed genes. The left panel shows the distribution of relative gene expression across the hierarchical tree structure. Rows represent individual genes; columns represent individual value of triplicate samples for each experimental group. Each cell in the matrix represents the expression level of a gene, with red and green indicating transcription levels above and below the normal values for that gene, respectively. Four sample groups are indicated above the expression matrix. Six basic gene clusters (clusters I to VI) were yielded by the analysis according to the gene expression pattern during CIA. The expression patterns of the gene cluster are graphed and the major biological activities for each cluster that were examined by functional clustering analysis are indicated on the right.