Fig. 1
From: PINES: phenotype-informed tissue weighting improves prediction of pathogenic noncoding variants
Overview of the PINES framework. PINES aims to systematically predict and rank the functional relevance of noncoding genomic variants. It can either work in a default (“unweighted”) mode and compare user-defined variants against the genomic background. Alternatively, users can customize searches towards annotations considered as of highest relevance to a phenotype of interest, for instance by providing a list of SNPs associated with a disease of interest through GWAS, or by highlighting disease-relevant tissues (“weighted” PINES mode). Scores of genomic background variants serve as an empirical null distribution against which significance levels for each variant of interest are computed and scored in an output file