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Fig. 3 | Genome Biology

Fig. 3

From: Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution

Fig. 3

Validation of promoter–enhancer interactions by gene expression perturbation. Functional tests evaluating the predictive capabilities of HiCap- or Hi-C-mapped promoter–enhancer interactions. Transcription factor binding sites (TFBSs) were associated with promoters using either HiCap or Hi-C [12] interactions and compared with the set of genes closest to each TFBS. Gene sets were compared with upregulated genes from TF over-expression experiments, and fold improvement was computed based on the fraction of upregulated genes with HiCap (black) or Hi-C (red) interaction support over comparison gene sets (i.e., closest genes). a Comparison of only closest genes (to mapped TFBSs ) with interaction support with closest genes without interaction support. b Fold improvement in the fraction of upregulated genes among the closest genes with interaction support divided by the fraction of closest genes lacking interaction support. Significant (Fisher’s exact test) comparisons are indicated with asterisks: *P < 0.05, **P < 0.01; ***P < 0.001. c Like (b) but using a minimum 15-kb interaction distance. d Comparison between only non-closest genes (to mapped TFBSs ) with interaction support and closest genes (irrespective of interaction support). e, f Fold improvement in the fraction of upregulated genes among genes identified based on interactions with the set of closest genes. Details as in (b-c). Promoter–promoter interactions were excluded in all analyses for this figure

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