Enrichment plots for statistically significant gene sets identified by GSEA. User-defined gene sets enriched with the DEX or vehicle conditions are depicted. Black bars illustrate the position of probe sets belonging to metabolic, extracellular matrix (A), cytokine and growth factor (B) gene sets in the context of all probes on the DEX array. The running enrichment score (RES) plotted as a function of the position within the ranked list of array probes is shown in green. The ranked list metric shown in gray illustrates the correlation between the signal to noise values of all individually ranked genes according and the class labels (experimental conditions). Metabolic and ECM genes are overrepresented in the left side of the enrichment plot indicating correlation to differential expression in DEX-treated chondrocytes. In contrast, cytokines and growth factor genes are enriched in the right side of the plots and correspond to the vehicle control. Significantly enriched data sets are defined according to GSEA default settings i.e., a p < 0.001 and a false discovery rate (FDR) < 0.25. Individual expression profiles for probe sets contributing to the normalized enrichment score are shown in the right panel. R.L.M = ranked list metric, E.S. = enrichment score.
James et al. BMC Genomics 2007 8:205 doi:10.1186/1471-2164-8-205