Fig. 5: TWAS analysis results by different methods for GERA traits.

Compared methods include CoMM (turquoise), PMR-Egger (magenta), TWAS (blue), LDA MR-Egger (black), SMR (orange), and PrediXcan (purple). a Quantile–quantile plot of −log10 p-values from different methods for testing the causal effect for an exemplary trait irritable bowel syndrome. b Quantile–quantile plot of −log10 p-values from different methods for testing the causal effect for another exemplary trait asthma. c Genomic inflation factor for testing the causal effect for each of the 22 traits by different methods. d Number of causal genes identified for each of the 22 traits by different methods. e Quantile–quantile plot of −log10 p-values from different methods for testing the horizontal pleiotropic effect for an exemplary trait irritable bowel syndrome. f Quantile–quantile plot of −log10 p-values from different methods for testing the horizontal pleiotropic effect for another exemplary trait Asthma. g Genomic inflation factor for testing the horizontal pleiotropic effect for each of the 22 traits by different methods. h Number of genes identified to have significant horizontal pleiotropic effect for each of the 22 traits by different methods. For c, d, g, h, the number on the x axis represents 22 traits in order: asthma, allergic rhinitis, CARD, cancers, depressive disorder, dermatophytosis, T2D, dyslipidemia, HT, hemorrhoids, abdominal hernia, insomnia, iron deficiency, irritable bowel syndrome, macular degeneration, osteoarthritis, osteoporosis, PVD, peptic ulcer, psychiatric disorders, stress disorders, varicose veins.