also corrects for physical proximity along the chromosome retaining only one gene per cluster of genes in a category of genes. The nominal GSEA p-value is calculated by comparing the extent of the “leading edge fraction” (i.e., the subset of genes whose corrected p-values are among the 95th percentile) of each category of genes (of size n), to the one observed in 10,000 random samples of n genes. Finally, the method uses Bonferroni multiple test correction (p-value = 0.05), and also computes the false discovery rate, a less stringent approach to correct for the burden of testing multiple hypotheses.
