The networks are generated by first mapping the uploaded list of genes to the selected underlying database. By default, a search algorithm is then performed to identify proteins that directly interact with the uploaded genes/proteins (“seeds”). The seeds and their interaction partners are returned to build the subnetworks (first-order network).
This approach will typically return one giant subnetwork (“continent”) with multiple smaller ones (“islands”). Most subsequent analysis is performed on the continent. Note, networks with less than 3 nodes will be excluded.
Note that NetworkAnalyst offers many different functions to allow users to further customize the default network (expand, reduce or other node filtering)