Fig. 3

HDACi effects on 1-cell stage embryos. (a) Volcano plot of differentially expressed genes (DEGs), with colors representing the relationships between the DEGs in the two HDACi treatments, and point shapes indicating the HDACi treatment from which the corresponding DEGs stem. To display all data clearly, the point sizes were linearly scaled along the slopes using the same absolute values on both the positive and negative x-axes. (b) Heatmap of DEGs prepared using the hierarchical clustering method to divide the differential genes into two clusters. (c) Results of predicted transcription factors (TFs) that regulated DEGs, ranked in descending order of NES, with the color representing the ratio of DEGs among the gene set that was regulated by the corresponding TFs. (d) protein–protein interaction (PPI) network of HDACi-affected minor zygotic gene activation (ZGA) genes, with yellow nodes representing core proteins. (e) Hexagonal Venn diagram showing the presence of DEGs in the strictly filtered minor ZGA gene set. The color of the frame indicates the type of HDACi, and the genes within the frame represent the minor ZGA genes that were affected by the corresponding HDACi treatment. (f) Differential expression results of HDAC-family genes after HDACi treatment, where the open circles represent adjusted P-values < 0.05 and LFC represents the log2 fold change