Fig. 5: Candidate genes and pathways for LDL discovered by cTWAS.

a, PIPs of 9,881 liver genes from cTWAS analysis of LDL cholesterol. The labeled genes have PIP > 0.8, colored based on existing evidence for LDL function: silver standard genes (green); nearest genes of genome-wide significant loci but not in silver standard (orange); or otherwise new (purple). b, GO biological process terms enriched (FDR < 0.05) among 35 detected LDL genes at PIP > 0.8. Redundant terms were omitted for clarity (Methods). Gene count means the number of detected genes associated with a GO term. c, cTWAS results at the ACVR1C locus. Description is the same as in Fig. 4b,c. d, Summary of cTWAS outcomes for all 69 silver standard genes into the following categories: detected by cTWAS at PIP > 0.8 (‘detected (PIP > 0.8)’); significant by TWAS (Bonferroni threshold), but not detected by cTWAS (‘significant by TWAS but undetected’); insignificant by TWAS and not detected by cTWAS, with a genome-wide significant GWAS variant within 500 kb (‘insignificant by TWAS’); gene does not have any expression prediction model (‘not imputed’); not detected by cTWAS and TWAS, and no genome-wide significant GWAS variant within 500 kb (‘no GWAS signal’).