Comparisons between scaffold (3D) and monolayer (ML) cultures were performed for chondrocytes obtained from osteoarthritic (OA) and normal donors (ND) (see Figure 1 for experimental setup). Genes were functionally filtered by annotations of the Gene Ontology Database according to their association with skeletal development and extracellular matrix formation [see Additional data file 2 for full list]. Genes were regarded as differentially expressed when fulfilling specific change call criteria provided by GeneChip Operating Software (GCOS, Affymetrix). The limit was set to at least eight (of nine possible) significant change calls. Further significance levels were determined applying the Welch's t-test of the SiPaGene database . Numbers in brackets represent the total number of genes regulated without functional filtering [see Additional data file 1 for full list].