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. 2023 Aug 11;42(19):e113639. doi: 10.15252/embj.2023113639

Figure 4. WRKY11 and OBE1 co‐occupy chromatin and repress gene expression.

Figure 4

  1. Distribution of WRKY11 and OBE1 ChIP‐seq peaks in distal promoter, proximal promoter, 5′ UTR, CDS (coding sequence), 3′ UTR, and intergenic regions. Distal and proximal promoters represent 401–1,000 and 0–400 bp upstream of transcription start sites, respectively. The distribution of random genomic regions is shown as a control.
  2. Metaplots showing WRKY11 and OBE1 ChIP‐seq occupancy over protein‐coding genes. TSS, transcription start site; TES, transcription end site. The ChIP‐seq data of WRKY11 and OBE1 are from two independent biological replicates. The input genomic DNA is shown as a negative control.
  3. Heatmaps showing the enrichment of WRKY11 and OBE1 ChIP‐seq reads over protein‐coding genes. TSS, transcription start site; TES, transcription end site.
  4. Venn diagram showing the overlap between WRKY11‐ and OBE1‐enriched genes. The overlapping genes are defined as group A genes. P‐values were determined by the hypergeometric test (one‐tailed). RF (representation factor) represents the number of observed overlapping genes divided by the number of expected overlapping genes drawn from two independent groups.
  5. Venn diagrams showing the overlap between WRKY11 and OBE1 co‐enriched genes and up‐ or downregulated genes in the wrky‐qm/15 +/− and obe1/2 mutants. Group B and group C genes represent the overlap between WRKY11 and OBE1 co‐enriched genes and co‐upregulated genes (left) or co‐downregulated genes (right) in the wrky‐qm/15 +/− and obe1/2 mutants. P‐values were determined by the hypergeometric test (one‐tailed). RF (representation factor) represents the number of observed overlapping genes divided by the number of expected overlapping genes drawn from two independent groups.
  6. Box plots of WRKY11‐ and OBE1‐enriched levels at group A, group B, and group C genes. Sample size of each box plot: group A (n = 6,498), group B (n = 979), and group C (n = 434). In box plots, center lines and box edges are medians and the interquartile range (IQR), respectively. Whiskers extend within 1.5 times the IQR. P‐values were determined by two‐tailed Mann–Whitney U‐test (unpaired) for non‐normally distributed data.

Source data are available online for this figure.