Fig. 4

Combination analyses of epigenomic and transcriptomic data of the kaku4-2 mutant and WT. A Heatmap showing relative expression levels of differentially expressed genes in different replicates of the kaku4-2 mutant and WT. B GO enrichment analyses for genes upregulated in kaku4-2 mutant by agriGOv2 and REVIGO. The scatter plot shows the cluster representatives in two-dimensional space derived by applying multidimensional scaling to a matrix of the significant GO terms with semantic similarities. The color and size of the bubble indicate the log₁₀FDR (a legend in the bottom right-hand corner). The colors from red to green represent the significance level of the GO terms, from high to low. Fisher's exact test was conducted, and the P-value was adjusted using the Benjamini-Yekutieli method, FDR ≤ 0.05. C GO enrichment analyses for genes downregulated in kaku4-2 mutant by agriGOv2 and REVIGO. D GO enrichment analyses for genes upregulated in the kaku4-2 mutant and with higher deposition of H3K27me3 in the WT by agriGO and REVIGO