Fig. 1

CyTRANSFINDER overview. a The main plugin control panel. It allows the user to set the source and destination list of genes and the specific pattern of regulators to search. b Shows the graphical output of the plugin that consists of a network connecting source genes with destination genes. Nodes of this network represent genes, TFs and miRNAs. c This panel allows to define a set of parameters related to the integration of miRNAs into the generated STPs. They can be used to control the size of the generated networks. d This panel allows the user to export the results in the form of a text file including all identified circuits or to delete the current experiment and start with a new one. e The Cytoscape node and edge tables. They can be used to access detailed information on the nodes and arcs of the identified STPs