We extracted and quality-controlled currently known protein interactors (PPIs) for the proteins (seeds) encoded by the genes prioritized in this article (Coloc protein network), using a previously described custom-weighted protein-protein interaction (WPPINA) pipeline (eAppendix in Supplement 1), and performed functional enrichment analysis on the relevant genes prioritized through the WPPINA.25 For comparison, a similar network (mendelian protein network) was prepared for mendelian PD and parkinsonism genes (SNCA [OMIM 163890], LRRK2 [OMIM 609007], GBA [OMIM 606463], SMPD1 [OMIM 607608], VPS35 [OMIM 601501], DNAJC13 [OMIM 614334], PINK1 [OMIM 608309], PRKN [OMIM 602544], DJ1 [OMIM 602533], FBX07 [OMIM 605648], SYNJ1 [OMIM 604297], DNAJC6 [OMIM 608375], WDR45 [OMIM 300526], PLA2G6 [OMIM 603604], ATP13A2 [OMIM 610513], RAB39B [OMIM 300774], SPG11 [OMIM 610844], PANK2 [OMIM 606157], C19orf12 [OMIM 614297], and PRKRA [OMIM 603424]; eTable 1 in Supplement 2). The number of interactions between the Coloc protein network and the mendelian protein network were quantified. To assess the probability that the number of connections between the 2 networks was more than would be expected by chance, we performed random simulations with 1000 control networks characterized by the
