Cells communicate through cascades where a single receptor-binding event is amplified through a chain of intracellular messengers, ultimately switching gene expression on or off. This 2D view lays the same pathway graph flat, so every node and connection is visible at once.
activity_i(t+1) = activity_i(t)(1-decay) + ligand*sensitivity*sum(w_ij*activity_j)
- Signalling nodes — receptors and intracellular effectors (kinases, transcription factors) in the pathway.
- Pathway connectivity — how many downstream effectors each upstream node feeds into — pathway branching.
- Ligand concentration — extracellular signal molecule (hormone, cytokine, growth factor) available to bind receptors.
- Receptor sensitivity — how readily a bound receptor triggers its intracellular cascade.
This kind of node-and-edge signalling logic is exactly what underlies drugs like trastuzumab (blocking HER2 receptor nodes) and MEK inhibitors (blocking a downstream cascade node) in cancer therapy.