Subnetworks are generated by first mapping the genes/metabolites (also known as “seeds” or “baits” ) to the underlying gene-metabolite-disease interaction database. A search algorithm is then performed to identify and extract first-order neighbours (nodes that directly interact with those seeds) to build the subnetworks.
The above approach will typically return one giant subnetwork (“continent”) with multiple smaller ones (“islands”). Most subsequent analyses are performed on the continent. Note, networks with less than 3 nodes will be excluded .