Modelling Signalling Networks from Perturbation Data
Mathurin Dorel, Bertram Klinger, Anja Sieber, Anirudh Prahallad, Torsten Groß, Evert Bosdriesz, Lodewyk F.A. Wessels, Nils Blüthgen · bioRxiv (Cold Spring Harbor Laboratory) · 2018
Abstract Motivation Intracellular signalling is realized by complex signalling networks which are almost impossible to understand without network models, especially if feedbacks are involved. Modular Response Analysis (MRA) is a convenient modelling method to study signalling networks in various contexts. Results We developed a derivative of MRA that is suited to model signalling networks from incomplete perturbation schemes and multi-perturbation data. We applied the method to study the effect of SHP2, a protein that has been implicated in resistance to targeted therapy in colon cancer, using data from a knock out and parental colon cancer cell line. We find that SHP2 is required for MAPK signalling, whereas AKT signalling only partially depends on SHP2. Availability An R-package is available at https://github.com/MathurinD/STASNet Contact [email protected]