Extended Data Fig. 10: Browning et al. 2018 introgressed phenotype enrichment.
From: Resurrecting the alternative splicing landscape of archaic hominins using machine learning
(A) Phenotype associations enriched among genes with48 introgressed SAVs based on annotations from the 2019 GWAS Catalog. Phenotypes are ordered by increasing enrichment within manually curated systems. Circle size indicates enrichment magnitude. Enrichment and p-values were calculated from a one-sided permutation test based on an empirical null distribution generated from 10,000 shuffles of maximum ∆ across the entire dataset (Methods). Dotted and dashed lines represent false-discovery rate (FDR) corrected p-value thresholds at FDR = 0.05 and 0.1, respectively. At least one example phenotype with a p-value ≤ the stricter FDR threshold (0.05) is annotated per system. CEA = carcinoembryonic antigen, FGF = fibroblast growth factor. (B) Phenotypes enriched among genes with48 introgressed SAVs based on annotations from the Human Phenotype Ontology (HPO). Data were generated and visualized as in A. See Supplementary Data 2 for all phenotype enrichment results.
