Table 5.

Results of combining GSEA P-values using 4 meta-analysis approaches for Alzheimer’s data

The 5 top ranked pathways and FDR-corrected P-values obtained by combining the P-values of GSEA using 4 meta-analysis approaches: Fisher’s, Stouffer’s, the additive method and bi-level meta-analysis. In the first three approaches, the 7 P-values for a pathway (one of each of the 7 datasets) were combined into a single P-value using Fisher’s, Stouffer’s and the additive method. This is done for all of the 150 signaling pathways in KEGG. The P-values are then adjusted for multiple comparisons using FDR. The pathways are sorted by the combined P-values, from low to high. The horizontal lines show the 5% significance threshold. The target pathway Alzheimer’s disease and two neurological disease pathways, Parkinson’s disease and Huntington’s disease, are highlighted in green. Only the bi-level meta-analysis identifies all three neurological disease pathways, Alzheimer’s disease, Parkinson’s disease and Huntington’s disease, as significant.