eADAGE features constructed from publicly available P. aeruginosa expression data describe known KEGG pathway-pathway relationships. a The glycerolipid metabolism, Entner-Doudoroff, glycolysis/gluconeogenesis, and pentose phosphate, pathways share common functions related to glucose catabolism. b Organophosphate and inorganic phosphate transport- and metabolism-related processes frequently co-occur with bacterial secretion systems. Here, we observe pairwise relationships between type II general secretion and phosphate-related processes. c Pathways involved in the catabolism of sulfur-containing molecules—taurine (NitT/TauT family transport) and methionine (D-Methionine transport), and the general sulfur metabolism process—are functionally linked. d The zinc transport, iron complex transport, and MacAB-TolC transporter systems are pairwise connected. The fully labeled network can be viewed at https://pathcore-demo.herokuapp.com/PAO1. The list of KEGG pathway-pathway relationships visualized in the network is available at the specified link (Ctrl + L for list view) and as a Additional file 2 for this paper.