Ideas for integrating transcriptomic data/co-expression network and genome-scale metabolic networks

Question

[pixie@bioinfo]

Hello, I have RNA-seq time-series data from various stress conditions of a plant. I have the stress and time-point specific DEGs, as well as co-expression networks of the DEGs. I need some idea as to how I can use the genome-scale metabolic network (GEM) of the given plant for an integrated analysis? Any idea will be highly appreciated.