Figure 1
From: Combined logical and data-driven models for linking signalling pathways to cellular response
Experimental and Computational workflow: (a) The "signalling" dataset monitors the activity of 16 different key phosphoproteins (blue nodes) under the combinatorial treatment of stimuli (green nodes) and inhibitors (red circles). (b) The response dataset can include any quantifiable cellular response such as cytokine releases (22 pink nodes) that are monitored under similar treatments. (c) A canonical pathway that incorporates the stimuli and key phosphoproteins is constructed from the literature (d) Data-driven approach is used to connect the signalling nodes via "non-canonical" edges to cytokine releases. (e) Canonical and non-canonical edges that fit the experimental data are selected using an ILP optimisation formulation and thus, the extended pathway topology is constructed.