Figure 2
From: Sequence signatures extracted from proximal promoters can be used to predict distal enhancers
Genome-wide enhancer predictions. (A) The number of enhancer predictions in the loci of highly expressed genes divided by the total number of sequences scanned in the loci of highly expressed genes (in red), as compared to the number of enhancer predictions in the loci of lowly expressed genes divided by the total number of sequences scanned in the loci of lowly expressed genes (in black), for 71 promoter-based models. Statistically significant differences are indicated by asterisks (P-values ≤0.05, Fisher’s exact test). (B) Correlation between the fold enrichment between the proportions of enhancer predictions in the loci of highly expressed and lowly expressed genes with the cross-validation accuracy of the corresponding promoter-based models. (C) Overlap of liver enhancer predictions with strong enhancers predicted by ChromHMM in HepG2 cell lines [51], compared to random sequences with similar length in the loci of genes highly expressed in liver. (D) Overlap of liver enhancer predictions with DNase I hypersensitivity sites (DHS) in HepG2 cell lines from the ENCODE project, compared to random sequences with similar length in the loci of genes highly expressed in liver.