Overlap and differences between AP1 and SEP3 DNA binding. (A) Overview of AP1 and SEP3 common target genes obtained from the ChIP-seq datasets at the same time points. The figure shows the ratio between the observed number of common target genes divided by the expected number when the location of AP1 and SEP3 BSs are independent, this expected number was estimated by multiplying the proportion of AP1 BSs by the proportion of SEP3 BSs and by the total number of BSs. The x-axis and y-axis represent the threshold values for declaring a given region as significantly bound by AP1 and SEP3, respectively. (B) Changes in AP1 and SEP3 binding at common time points. ‘Higher AP1 peaks’ are genomic regions with AP1 peaks that are at least two-fold higher than the SEP3 peaks, while ‘higher SEP3 peaks’ are genomic regions with AP1 peaks at least two-fold lower than the SEP3 peaks. Only significant peaks (FDR <0.001) located in a region comprising 3 kb upstream and 1 kb downstream of a gene are considered. (Additional file 2: Table S2). (C) AP1 and SEP3 binding profiles for selected target genes. SHINE 1 (SHN1) is an example of an AP1 target gene that is most strongly bound at day 4, whereas TGA9, a gene involved in anther development, and CRC, a gene involved in carpel development, are preferentially SEP3 targets.