Fig. 4: In silico perturbations reveal TF target enhancers.
From: Mechanistic analysis of enhancer sequences in the estrogen receptor transcriptional program
Results of in silico knock-down experiments using a representative GEMSTAT model for ERα (a), NKX3-1 (b), and ERα-FOXA1 interaction (c). d, e Bars depict the extent to which in silico perturbations of TFs or TF-TF interactions affect enhancers, shown separately for positive (eRNA expressing) and negative (silent) enhancer classes. Bar height represents the average over 244 top ranking models (shown as individual points), and error bars represent the standard deviation. The extent of perturbation effect is shown as (d) the fraction of enhancers whose expression changes by at least 5 percentile points in each perturbation experiment, and (e) the percentile change in expression after perturbation, averaged over enhancers that were affected by at least 5 percentile points. Pairs with statistically significant difference between positive and negative group enhancers (adjusted Wilcoxon p value < 1e−6) are marked with asterisks (*).
