Cluster analysis and validation of gene expression profile. (A) Separation of samples by unsupervised hierarchical clustering. The groups are: day 0 to 3, week 1 to 2 and week 3 to 4 after onset of arthritis, and joints with declining clinical disease activity. Colours and colour intensity indicate upregulation (red) or downregulation (green) regulation of genes. (B) Venn diagram of the gene expression study showing the number of genes differentially expressed at the time points: day 0 to 3, week 1 to 2, week 3 to 4, and in the declining disease phase in comparison to control. (C) The results from the microarray study were validated with qPCR. Bmp1 was normalised to Gapdh expression and compared to a control sample from non-immunised mice. Statistically significant differences between group means (δ-ct-values) are indicated with lines above the bars (Bonferroni’s multiple comparison test, *P <0.05, **P <0.01). (D) The gene expression level of Bmp1 assessed by qPCR correlated significantly (r2 = 0.7, P <0.0002) with the corresponding microarray data (linear regression test).