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).