The gene-set that remains is the Regulation of AMPK via LKB1 (REACTOME) set. For two additional gene sets, Cell Adhesion Molecules (KEGG) and ECM-receptor Interaction (KEGG), the competitive p-value also drops below the significance threshold (Table 4 and S12 Fig) if the correction for gene size and gene density is turned off. This suggests that these gene sets do in fact contain significantly elevated levels of association, but that this is partially caused by confounding effects of the size and density of the genes they contain. Given the strength of the confounding effect it is evident that gene-set analyses should always be corrected for these and other potential confounders, to avoid false positive results. Full results for the analyses can be found in Table S5 in S2 File.
