Hierarchical clustering and functional classification of differentially expressed genes. Genome-wide expression analysis was performed for two different experimental groups (G) of chondrocytes stimulated with supernatant of a synovial fibroblast cell line derived from a patient with rheumatoid arthritis (RASFsn) and chondrocytes stimulated with supernatant of a synovial fibroblast cell line derived from normal donor (NDSFsn) (n = 2). Each experimental group was a pool of RNA isolated from stimulated chondrocytes that originated from three different donors; that is, group 1 (G1) consisted of equal amounts of RNA from stimulated chondrocytes of donors 1 to 3 and group 2 (G2) of donors 4 to 6. Genes that displayed ≥2-fold increase or ≤-2-fold decrease in RASFsn-stimulated compared with NDSFsn-stimulated chondrocytes determined by both analyses with GeneChip Operating Software and Robust Multi-array Analysis were hierarchically clustered and functionally classified into six groups. Colors represent relative levels of gene expression: bright red indicates the highest level of expression and bright green indicates the lowest level of expression. Expression data from the different experimental groups were compared and showed that the expression patterns were similar for the corresponding experimental groups of both RASFsn-stimulated and NDSFsn-stimulated chondrocytes because they clustered and were therefore most similar to each other, showing little variability.