Extended Data Fig. 6: Causal variant enrichment for eQTLs.
From: Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles
a. The mean causal variant enrichment for eQTL within SCENT peaks with excluding all promoters (teal) or cis-regulatory ATAC-seq peaks with excluding all promoters (yellow) in each dataset. b. The mean causal variant enrichment for eQTL within SCENT peaks (teal) or non-SCENT peaks with matching distance to TSS (pink). c. Comparison of the mean causal variant enrichment for eQTL (y-axis) among SCENT (teal), ArchR (pink), and Signac (purple) as a function of the number of significant peak-gene pairs at each threshold of significance by FDR in SCENT and correlation r in ArchR and Signac. d. Comparison of the mean causal variant enrichment for eQTL among SCENT, ArchR, and Signac as a function of the number of significant peak-gene pairs at each threshold of FDR in SCENT, ArchR and Signac. The ArchR results with > 180,000 peak-gene linkages are omitted. e. Comparison of the mean causal variant enrichment for eQTL among SCENT, ArchR, and ArchR filtered on RNA expression as a function of the number of significant peak-gene pairs. f. Comparison of the mean causal variant enrichment for eQTL among SCENT, Signac, and Signac filtered on RNA expression as a function of the number of significant peak-gene pairs. g. Comparison of the mean causal variant enrichment for eQTL among SCENT, the default Pearson’s correlation version of Signac, and the optional Spearman’s correlation version of Signac as a function of the number of significant peak-gene pairs. h. Comparison of the mean causal variant enrichment for eQTL among original SCENT (Poisson regression + non-parametric bootstrapping), Poisson-only strategy without bootstrapping, and Cicero (correlation method using sc-ATAC-seq alone) as a function of the number of significant peak-gene pairs up to 100,000 peak-gene linkages. i. Comparison of the mean causal variant enrichment for eQTL between SCENT and Cicero peaks with adding all accessible promoter regions (1 kb regions from TSS) to account for potential promoter bias. j. Tissue-specific causal variant enrichment within SCENT peaks. The dots and lines are colored by the eQTL source tissue in GTEx that we assessed. In all panels, the bars indicate 95% confidence intervals by bootstrapping genes (nbootstrap=1000).
