Extended Data Fig. 5: Colocalization scores. | Nature Genetics

Extended Data Fig. 5: Colocalization scores.

From: Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes

Extended Data Fig. 5

a, Genes with maximum colocalization H4 probability >0.9 have higher Pagerank percentile (left boxplot) and higher total score (sum of the four non-coloc predictors, right boxplot) than do genes without colocalisation (<0.5). Genes with intermediate colocalisation evidence (bins 0.5 - 0.8 and 0.8 - 0.9) show little evidence of having higher scores by the other metrics. Based on this, we chose a maxColoc probability of 0.9 as the lower bound for our colocalization score. b, Boxplot of the total score (excluding coloc) for genes that have a colocalisation probability > 0.9 in at least one QTL dataset within each tissue group. The most significant difference is between totalScore for genes with microglial colocalizations vs. the genes with colocalization in ‘other’ tissues (non-immune GTEx tissues), but the difference is weak (P = 0.041, Wilcoxon rank sum test). In all cases, boxplots show the 25th, median, and 75th percentile of the distribution, with whiskers extending to the largest (and smallest) value no further than 1.5 times the interquartile range from the boxplot hinge.

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