Fig. 3. Placental MOSTWAS prediction and association test results.

a Overview of TWAS association testing pipeline with number of gene-trait associations (GTAs) across unique genes over various levels of TWAS tests. b Kernel density plots of in- (through cross-validation in ELGAN, red) and out-sample (external validation in RICHS, blue) McNemar’s adjusted $R^2$ between predicted and observed expression. Dotted and solid lines represent the mean and median of the respective distribution, respectively. c Bar graph of numbers of TWAS GTAs at overall TWAS $P<2.5\times {10}^{-6}$ (for two-sided weighted burden Z-test) and two-sided permutation test FDR-adjusted $P<0.05$ (x-axis) across traits (y-axis). The total number of GTAs per trait are labeled, colored by the category of each trait. The bar is broken down by numbers of GTAs with (orange) and without (green) significant distal expression-mediated associations, as indicated by FDR-adjusted $P<0.05$ for the distal-SNPs added-last test. d Enrichment plot of over-representation in 176 TWAS genes of PANTHER pathways (y-axis) with -log₁₀ FDR-adjusted P-value (x-axis) of one-sided Fisher’s exact test. The size of the point gives the relative enrichment ratio for the given pathway.