Figure 1. The user interface of the KeyPathwayMiner Cytoscape app is located in the control panel.

The user sets the analysis up as follows (omitting the ‘Pos/Neg’ tab, where nodes can be specified for inclusion or exclusion): ( A) one or several dataset files are selected from the disk. ( B) Several dataset files can be logically connected via a formula editor. ( C) The run parameters are configured, most importantly the enrichment strategy (INES or GLONE), the search algorithm, the input network and the search parameters K and/or L, which can also be defined as a range. ( D) Network perturbation settings used in robustness or validation runs.