Fig. 1

Integrating multiple GSEA into a BubbleMap. GSEA output is a bar code (1) corresponding to the projection of the gene set on the blue-to-red gradient representing all the genes of the chip ranked from high expression in the population on the left to high expression in the population on the right. The more the gene set is regulated, the more the bar code is shifted to one side. This is measured by two parameters. The normalized enrichment score (NES) integrates the number and differential expression intensity of the assessed genes. NES > 0: the gene set is enriched in the population on the left. NES < 0: it is enriched in the population on the right. The FDR is the likelihood that the gene set enrichment represents a false-positive finding (2). Here, the FDR is different from the one calculated by GSEA, because it is corrected for multiple testing across the gene sets and across the pairwise comparisons, thus allowing the user to compare all the bubbles in a BubbleMap. Each enrichment is summarized as a bubble, bigger and darker as the enrichment was stronger and more significant, in a color matching the population in which the gene set was enriched (3). Final output is a BubbleMap (4) with legend (5). Gene sets are either generated by GeneSign or retrieved from public gene set databases (6)