Fig 1.
META-GSA: a tool for meta-analysis based on GSAs for GWASs.
Genome-wide association study (GWAS); gene-set analysis (GSA); meta-analysis of GSAs (META-GSA); gene set of interest (GS, containing genes 3,5,…); complementary gene set (GS’, containing genes 1, 2, 4,…); gene-level statistic of gene g and study s (Γg,s); “enrichment score” (ES) as test statistic for GSA in study s.
Table 1.
Notation.
Table 2.
Power of META-GSA, pooledGWAS-GSA and SPP across all studies, based on 100 genes with 1 marker each.
Fig 2.
Correlation of pMETA-GSA and pSPP in scenario no. 1.
The numbers of simulations out of a total of 500 are depicted. Gene sets are classified as significant (p ≤ 0.05) or not significant using SPP and META-GSA.
Table 3.
Comparing the number of significant findings of META-GSA with SPP in selected scenarios.
Fig 3.
Correlation of pMETA-GSA and pSPP in scenario no. 8.
The numbers of simulations out of a total of 500 are depicted. Gene sets are classified as significant (p ≤ 0.05) or not significant using SPP and META-GSA.
Table 4.
META-GSA vs. SPP: Number of nominally significant gene sets by GSA methods.
Table 5.
Rank correlation of p-values comparing GSA methods (best SNP approach).