iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections
Figure 4
Validation of the p53 regulon by ChIP-Seq.
A. Integrative Genomic Viewer (IGV) [131] screenshot for CDKN1A, a known p53 target gene, showing up-regulation by RNA-seq (red arrowhead) and ChIP peaks in the upstream region (green and blue arrowhead). IGV is free software under GNU Lesser General Public License, version 2.1 (LGPL-2.1). B. Gene Set Enrichment analysis, with on the x-axis all genes in the genome ranked according to their maximum ChIP-Seq peak (20 kb around TSS). The p53 targets (green curve) show higher enrichment than the total set of up-regulated genes (blue curve), approaching the previously known curated targets (red curve), while the non-predicted p53 targets (magenta curve) and the set of down-regulated genes (cyan curve) show no enrichment. The initial two steps in the magenta curve represent two false negative predictions of iRegulon (they fall just below the optimal cutoff), namely PLK3 and DDB2, which are up-regulated and have a ChIP peak. P-values in the legend are calculated by the hypergeometric formula of the leading edge determined by GSEA. C. Comparison between annotated up-regulated p53 targets and predicted p53 targets by iRegulon and ChIP-Seq, indicating the number of previously known p53 targets. See also Figure S6.