Hierarchical cluster analysis of chondrocytes from osteoarthritic and normal donors cultured in monolayer and Hyaff-11 scaffolds. Genes that were differentially expressed between normal donors (ND) chondrocytes cultured in monolayer (ML) and scaffold (3D) cultures, functionally filtered by their association with skeletal development and extracellular matrix (ECM) formation, were used to assess chondrogenic capacity of chondrocytes from osteoarthritic (OA) patients. Green bars depict a repressed and red bars an induced expression of genes normalized to the mean. The clustering gave two main groups classified as monolayer chondrocytes and scaffold-cultured chondrocytes. The separate OA monolayer cluster clearly indicated a differential expression pattern between OA and ND chondrocytes. In scaffold cultures on the other hand, no OA-related cluster separation was observed demonstrating a loss of differences between OA and ND chondrocytes during scaffold culture.