Fig. 3: Gene Set Enrichment Analysis (GSEA) of differential gene expression in SK-N-BE(2)-C cells following co-treatment with verlindamycin (2d) and ATRA.
Gene expression data generated by expression microarray analysis following 6 days of co-treatment with 1 μM ATRA and 0.5× Gi50 verlindamycin versus untreated (DMSO) control were analyzed using GSEA to extract biological knowledge and highly significantly enriched gene sets are shown. The most upregulated genes in vehicle control are shown on the left side (red), while the most upregulated genes following ATRA + 2d treatment are shown on the right side (blue). Black bars represent the positions of the vehicle control versus ATRA + 2d upregulated signature genes in the ranked list. Green curves represent the evolution gene density. Normalized enrichment scores (NES) reflect the degree to which genes are overrepresented. When the distribution is random, the enrichment score is zero. Enrichment of signature genes at the top of the ranked list results in a large positive deviation of the NES from zero. q-value false discovery rate (FDR)-adjusted q-value.
