Extended Data Fig. 10: Cells to be included in the regression framework.
From: Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles
a. An example situation of correlated gene expression without biological regulatory function. b. Benchmarking models for statistical power to define biologically plausible peak-gene linkage over false-associations due to correlated genes. c. Benchmarking results regarding cells and covariates included in the SCENT regression model. The x-axis represents the number of statistically significant peak-gene linkages among 5,000 randomly selected peak-gene linkages in cis, and the y-axis represents the number of statistically significant peak-gene linkages in cis divided by the number of statistically significant peak-gene linkages in trans among 5,000 randomly selected peak-gene linkages on different chromosomes, as a proxy metric for capability of identifying regulatory elements over ‘correlated’ elements. Red dots indicate the analyses conducted in all cells including different cell types (n = 8,881), whereas blue dots indicate the analyses conducted in only T cells (n = 8,881). d and e. False positive rate and precision for peak-gene linkages from analyses conducted in all cells (teal) or in only T cells (orange) by using experimentally validated enhancer-gene linkages (that is, CRISPR-Flow FISH data in d and H3K27ac data in e). False negative rate and precision were defined as follows: \(false\,negative\,rate=\#\,false\,negative/(\#\,true\,positive+\#\,false\,negative)=1-recall\).
