Extended Data Fig. 4: Re-analysis of PIF4 ChIP seq data.

Re-analysis of PIF4 ChIP seq data. a, Positional distribution of PIF4-binding peaks on Arabidopsis genes. The observed distribution (black), the 95% confidence interval (shaded blue) and mean (dashed line) of 1,000 random peak sets are shown. b, Histogram showing the positional distribution of G-boxes relative to the peak centre (E-value = 3.5e-39). c, Histogram showing the number of PIF4 peaks with different numbers of G-box motifs. d, The distance between consecutive G-box motifs in a single PIF4 peak. The density of the distance between consecutive G-boxes in the promoters of all non-PIF targets was used as a control. e, Overlapping gene set between PIF4 and CDF2 peaks. Note that in a limited number of cases, multiple peaks in a single sample (merged peaks) overlap with a single peak in the other sample. f, Overlapping gene set between PIF4 peaks and CDF2 peaks with significantly reduced binding affinity in the pif4 mutant. Similar to in e, multiple peaks in a single sample can overlap with a single peak in the other sample. g, GO-term enrichment based on the gene set between PIF4 peaks and CDF2 peaks with significantly reduced binding affinity in the pif4 mutant. Enrichment tests were performed with topGO for each GO term separately using the Fisher Exact test. Raw p-values were adjusted using the Benjamini-Hochberg procedure. GO terms with adjusted p-values < 0.05 were considered significantly enriched.