Fig. 5 | Nature Communications

Fig. 5

From: Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution

Fig. 5The alternative text for this image may have been generated using AI.

Spearman correlation of computational scores with measured expression effects. The figure reports Spearman correlation coefficients (in percent) of the absolute expression effect for all SNVs with at least ten tags in each region with various measures agnostic to the cell type, like conservation (mammalian PhyloP, mammalian PhastCons, and GERP++), overlapping TFBS as predicted in JASPAR 2018 (counting those in the top 10th percentile of motif scores across all elements, all motifs, and additional percentiles are available in Supplementary Table 15), and computational tools that integrate large sets of functional genomics data in combined scores (CADD v1.4, DeepSEA, Eigen, FATHMM-MKL, FunSeq2, GWAVA region model, LINSIGHT, and ReMM). In addition, we compared a subset of experiments (10/21) to absolute deltaSVM scores available for specific cell types (HEK293T, HeLa S3, HepG2, K562, and LNCaP). In cases where an annotation is based on positions rather than alleles, we assumed the same value for all substitutions at each position. The column Type assigns each region as either enhancer (enh.), promoter (prom.), or ultraconserved element (UC). MYC (rs11986220) and MYC (rs6983267) are abbreviated to MYCs1 and MYCs2, respectively. Blue bars denote positive and red bars negative correlation

Back to article page