Fig. 4
From: SCEPTRE improves calibration and sensitivity in single-cell CRISPR screen analysis
Application of SCEPTRE to Gasperini et al. data yields biologically plausible gene-enhancer links. a Comparison of the original empirical p-values to those obtained from SCEPTRE. The two analysis methods differed substantially, with 200 gene-enhancer links discovered only by SCEPTRE and 107 discovered only by the original analysis. Annotations correspond to pairs in panel (e). b Distribution of distances from TSS to upstream paired enhancers. Compared to Monocle NB (original) and improved NB analyses, SCEPTRE paired genes with nearer enhancers on average. c For those gene-enhancer pairs falling in the same TAD, the cumulative distribution of the fractional rank of the HI-C interaction frequency compared to other distance-matched loci pairs within the same TAD. SCEPTRE showed similar enrichment despite finding 25% more within-TAD pairs compared to the original analysis. Inset table shows gene-enhancer pairs falling in the same TAD. SCEPTRE found 93 more total pairs compared to the original analysis, and a higher percentage of pairs fell within the same TAD. d Enrichment of ChIP-seq signal from seven cell-type relevant transcription factors and one histone mark (H3K27ac) among paired enhancers. SCEPTRE showed stronger enrichment across all ChIP-seq targets. e Five gene-enhancer pairs discovered by SCEPTRE but not the original analysis, each supported by a whole blood GTEx eQTL or FANTOM enhancer RNA correlation p-value