Extended Data Fig. 4: Properties of SCENT peaks.
From: Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles
a. The number of significant SCENT peaks per gene across genes we investigated in at least one dataset-cell type pair. b. The number of significant gene-peak pairs discovered by SCENT with FDR < 10% in each dataset (y-axis) as a function of the total number of ATAC-seq fragments in each dataset (x-axis), colored by the dataset. c. The number of significant gene-peak pairs discovered by SCENT with FDR < 10% in each dataset (y-axis) as a function of the total number of unique RNA molecules in each dataset (x-axis), colored by the dataset. d. The effect size correlation r by Pearson’s correlation between arthritis-tissue dataset and the other dataset for the same cell type (left) and the directional (sign) concordance between arthritis-tissue dataset and the other dataset for the same cell type (right). e. Fraction of overlap with ENCODE cCREs in SCENT (teal) or non-SCENT peaks (orange) in each dataset and random set of cis-non-coding regions (pink). f. The mean Δ phastCons score for SCENT with excluding promoter peaks (teal) and all cis-ATAC peaks with excluding promoter peaks (yellow) in each of the three example multimodal datasets. The bars indicate the 95% CI by bootstrapping genes (nbootstrap=1000). g. The mean Δ phastCons score between SCENT peaks and TSS-distance-matched non-SCENT peaks across all the genes. The bars indicate the 95% CI by bootstrapping genes (nbootstrap=1000).
