Comparison of DEX-treated primary chondrocytes to a time course of chondrocyte differentiation in micromass culture. The Venn diagram depicts probe sets that are common between the list of 2119 probe sets differentially expressed between days 3 and 15 of micromass culture and the list of 22 091 significantly expressed probe sets in primary chondrocyte monolayer cultures (A). The matrix of 77 user-defined gene sets are used to interrogate microarray data from days 15 and day 3 of micromass culture. Normalized enrichment scores (NES) generated from this analysis are then compared to NES scores derived from the DEX study to evaluate similarities in the regulation of different groups of genes in chondrocytes (B). Positive enrichment scores (ES) indicate gene sets that are enriched and up-regulated in DEX-treated chondrocytes or d15 of micromass culture. Negative ES indicate gene set enrichment and down-regulation in the DEX-treatment or up-regulation in the day 3 samples of the micromass (MM) culture data set.
James et al. BMC Genomics 2007 8:205 doi:10.1186/1471-2164-8-205