Correlated patterns of gene expression using WGCNA
Weighted gene correlation network analysis (WGCNA) allows for the identification of genes with expression correlated and significantly associated with experimental factors. We identified 25 modules containing genes with highly correlated expression, and several of these modules significantly correlated with one or more experimental factors (OP Regime, Pyr Regime, OP PTx, Pyr PTx, BtTx; Suppl. Fig. 7). We mapped differentially expressed transcripts to each gene module and identified one that was significantly associated with all five experimental factors (Suppl. Fig. 7; magenta module) and was also associated with a high number of significantly differentially expressed transcripts (Fig. 4; Suppl. Fig. 7; 201 DE transcripts/ 258 total). Thus, genes in this module displayed common expression patterns and were overall upregulated with both OP and Pyr selection regimes and downregulated with OP, Pyr, and Btt exposure (Suppl. Fig. 7). GO enrichment analysis of the magenta module transcripts revealed the importance of genes involved in hydrolase activity (GO:0016787; FDR = 6.07*10-7) and monooxygenase activity (GO:0004497; FDR = 1.81*10-6).