Supplementary Figure 4: Pathway-centric PLIER eQTLs have a higher replication rate.
From: Pathway-level information extractor (PLIER) for gene expression data
We compare trans-eQTL discovered with the standard gene-centric approach to those discovered by PLIER with respect to independent replication in the NESDA dataset. While gene-centric approach considers all possible SNP-gene associations that satisfy valid trans-eQTL criteria (see Methods) the pathway-centric approach only considers those gene-level effects that are associated with pathway-level eQTLs. We find that at the same raw p-value threshold, pathway-centric eQTLs have a notably higher replication rate. Since pathway-centric associations are by construction linked to a pathway-level effect, they are more likely to represent real and replicable indirect associations. Statistics were computed using Spearman rank correlation across 922 subjects with a two-sided test. P-values indicated on the x-axis are uncorrected.
