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Fig. 2 | Genome Biology

Fig. 2

From: A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

Fig. 2

Characteristics of BENGI datasets. Six datasets in GM12878 or other LCLs were evaluated: RNAPII ChIA-PET (red), CTCF ChIA-PET (orange), Hi-C (green), CHi-C (blue), GEUVADIS eQTLs (purple), and GTEx eQTLs (pink), and the same color scheme is used for all panels. a Heatmap depicting the overlap coefficients between positive cCRE-gene pairs in each BENGI dataset. The datasets were clustered using the hclust algorithm, and the clustered datasets are outlined in black. b Violin plots depicting the distance distributions of positive cCRE-gene pairs for each BENGI dataset. The 95th percentile of each distribution is indicated by a star and presented above each plot. c Violin plots depicting the expression levels of genes in positive cCRE-gene pairs (in transcripts per million, TPM). d Violin plots depicting CTCF signal levels at cCREs-ELSs in positive cCRE-gene pairs. A dashed box indicates cCREs-ELS with a signal >‚ÄČ5. e Distributions of the number of genes positively linked with a cCRE-ELS across datasets

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