Fig. 5

Example of GSEA enrichment plot for Mitotic Sister Chromatid Segregation in SW480. a The x axis lists all microarray genes ranked based on their association with the comparison treated SW480 versus control. The black vertical bars indicate candidate genes in the target gene set. The ES profile (green trace) records the cumulative score of the gene ranks from the target gene set. Here, a majority of gene ranks from the candidate gene set are low (i.e., toward the down-regulated genes of the ranking) compared to the rest of genes, and the cumulative ranking score (ES profile) will have a negative peak, suggesting a significant enrichment of this gene set. The significant genes are determined by the position of the peak of the profile. There are 8 candidate genes up to this peak position that are claimed as significant (leading-edge subset). They are plotted in the heatmap shown in b (red means high expression level, and blue means low expression level) (color figure online)