Fig. 4

Identification and functional enrichment analysis of differently expressed genes (DEGs). a Venn plot analysis of common and uniquely expressed genes in leaves of wild type (WT) and PbrGA2ox1-overexpressing (OE) seedlings at 35 days after vernalization (DAV) under long-day conditions. b The number of up-regulated and down-regulated DEGs in the comparison group namely OE vs. WT. c The expression heatmap of DEGs across total samples. The color indicates the expression level in the form of log₂|FPKM| values. Blue represents a high expression level, and red represents a low expression level. Numbers above the groups indicate corresponding subclusters from one to eight. d Expression profile clustering of the DEGs in OE vs. WT. The red line indicates the average expression level of all DEGs in a subcluster. e Enriched gene ontology (GO) terms for DEGs identified from the RNA-seq data of the leaves from WT and OE seedlings. The DEGs were classified based on GO annotation and were categorized into biological process (BP), molecular function (MF), and cellular component (CC). The values indicate the number of genes in each classification, and the red marks highlight the most enriched category. f A bubble map of the top 20 KEGG enrichments for DEGs. The ordinate denotes the pathway name, the abscissa describes the richness factor, each circle in the map represents a pathway, the size of a circle indicates the number of DEGs in the pathway, and the color of a circle corresponds to different p-value ranges