Figure 4

Functional enrichment analysis of transcriptome data. The enrichment map (EM) shows biological processes occurring under G510 and G520 light. Hypergeometric tests of gene ontology (GO) terms were performed using BiNGO software⁶⁹. The map shows enriched GO terms related to differences in transcriptome between G510 and G520. Comparison is against FL. Nodes indicate the GO terms and edges between nodes; the gene overlap in GO terms is shown. The inner circle size of each node indicates the number of differentially expressed genes (DEGs) in ‘comparison 1’ (G510 vs. FL) within the GO term in the biological process. The node border size represents the number of DEGs in and ‘comparison 2’ (G520 vs. FL) within the GO term in the biological process. The colour of the node and its border shows the significance based on the BiNGO FDR of the GO term for ‘comparison 1’ and ‘comparison 2’, respectively. Solid red nodes indicate major GO functional terms. The edge size represents the number of DEGs that overlap between two linked GO terms (Jaccard coefficient, cutoff = 0.25). Sole green edges correspond to both data sets when it is the only colour edge. Green and blue edges represent ‘comparison 1’ and ‘comparison 2,’ respectively. Blue dotted circles show summarised GO term clusters based on AutoAnnotate⁷⁰. Enrichment maps were created using the Cytoscape (v3.2.1) Enrichment Map plugin^41,42.