Fig. 3

Topology designs for pathway deregulation. a Example of a particular pathway with 30 genes. In order to deregulate this pathway on detection call level e.g. DC = 50 % (+/− 5 %) we needed to assign 14–16 affected gene to this pathway and allocate them on the pathway graph according to 3 topology approaches. b In the community design two gene communities were selected to be affected (depicted in red). c Top scored betweenness genes were depicted in red. d Gene neighbourhood of order 2 of the blue gene was affected (in red). The colour coding of graph edges represents activation (green) and inhibition (red) interactions between the nodes