Fig. 5

Co-expression analysis of auxin-, TFs- and secondary metabolism-related DEGs during the four main SE phases. Four clusters of genes were generated corresponding to the four developmental phases: Leaf, Dedifferentiation, Embryogenic callus and Redifferentiation. Auxin-related genes are in green, transcription factor-related genes in violet and secondary metabolite-related genes in orange. An average expression profile of the genes present in each cluster was also generated (bar diagrams). For each cluster, a gene co-expression network was inferred using the ARACNE algorithm. All the networks were visualized in Cytoscape. Co-expressed genes share edges. Schematic kinetics of IAA and secondary metabolite endogenous content are also presented (Fig. S2)