Incorporating regulatory interactions into gene-set analyses for GWAS data: A controlled analysis with the MAGMA tool
Fig 6
Significant gene sets that gain from augmentation, often gain no more from genuine augmentation than from matched, random augmentation.
Left panel: the numbers of gaining (bars directed rightwards and positive values) and non-gaining (bars directed leftwards and negative values) gene sets amongst significant gene sets detected for atrial fibrillation with selected augmentations (note, this is similar to the graph for atrial fibrillation in Fig 5). Right panel: significant gene sets that gained from augmentation were stratified and counted according to three validation categories (strongly validated, mildly validated, and invalidated), which defined how pronounced a gain was with genuine augmentation, over that with matched, random augmentation. The augmentation, “Big Flanks”, refers to gene bodies with 100kb upstream- and downstream flanks (note, as part of the baseline model, the first 10kb on either side of a gene body were not permuted by EPVP). Mapping abbreviations: H-Muscle Cells (heart-muscle cells). Refer to S4 Fig for similar graphs for the other phenotypes.