Figure 7

A. amnicola transcriptome co-expression networks. (A) Visualization of the 18 co-expression modules among the differentially expressed genes detected by WGCNA. Each node represents an individual differentially expressed gene (10,440) and each edge (577,405) represents a co-expression measure between two connected nodes, with shorter edges indicating higher co-expression. Nodes are colored by co-expression module membership and labeled M1 through M18 (Supplementary Fig. S2). (B) Transcription factors connected to at least two flavonoid biosynthesis unigenes when analyzing the top ten transcription factors with the highest co-expression values for each flavonoid unigene. Flavonoid biosynthesis unigenes (11) are shown as circles, and transcription factors (30) are shown as diamonds and labeled as their transcription factor class. Nodes are colored by their co-expression module membership. Edges connecting each transcription factor to a flavonoid unigene are weighted by topological overlap measures with shorter edges indicating stronger co-expression. Flavonoid biosynthesis unigene IDs are shown in Supplementary Table S5 and transcription factor unigene IDs are shown in Supplementary Table S7.