Incorporating regulatory interactions into gene-set analyses for GWAS data: A controlled analysis with the MAGMA tool
Fig 3
Genuine augmentations are associated with more significant genes than matched, random augmentations.
The number of significant genes detected for selected, genuine augmentations (saturated bars), in comparison to matched, random augmentations (desaturated bars). For random augmentations, counts and error bars represent the mean and standard deviation, respectively (based on 20 independent permutations of EPVP). Red, dashed line shows the number of significant genes detected with the baseline model itself. We tested (T-test) if there were more significant genes with genuine augmentation than with matched, random augmentation (a above a saturated bar indicates that the p-value of the test, which was FDR-adjusted across all mappings within each phenotype, was smaller than 0.05). We then tested, in a similar way, if there were more significant genes with the baseline model than with random augmentation of the baseline model (b above a desaturated bar for an FDR-adjusted p-value smaller than 0.05). 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). Phenotype abbreviations: C-Artery Disease (coronary-artery disease); Mac. Degeneration (macular degeneration). Mapping abbreviations: Br-Neuronal Cells (brain-neuronal cells); H-Muscle Cells (heart-muscle cells); NP Cells (neural-progenitor cells); Pa-Islet Cells (pancreatic-islet cells); Pr-Gland Cells (prostate-gland cells).