iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections
Figure 3
Using iRegulon to map a p53-dependent gene regulatory network.
A. MCF-7 breast cancer cells were treated with Nutlin-3a to stabilize p53, followed by RNA-Seq after 24 h. iRegulon results shows p53 as top regulator in a set of 801 up-regulated genes, represented by 6 significantly enriched motifs, and 307 predicted direct targets. The top regulator in the set of down-regulated genes is E2F, with 653/790 predicted direct targets. B. Regulatory network for up-regulated target genes showing the overlap between the p53 regulon and regulons of predicted co-factors (AP-1, NFY, FOX) and regulatory network for down-regulated target genes showing a strong overlap between the predicted E2F and NF-Y regulons. Targets are in grey circle nodes and TF in black hexagon nodes. Regulons for each TF are represented by different edge colours. See also Tables S2–S5.