RT Journal Article SR Electronic T1 Inferring intracellular signal transduction circuitry from molecular perturbation experiments JF bioRxiv FD Cold Spring Harbor Laboratory SP 107730 DO 10.1101/107730 A1 Michelle L. Wynn A1 Megan Egbert A1 Nikita Consul A1 Jungsoo Chang A1 Zhi-Fen Wu A1 Sofia D. Meravjer A1 Santiago Schnell YR 2017 UL http://biorxiv.org/content/early/2017/02/10/107730.abstract AB The development of network inference methodologies that accurately predict connectivity in dysregulated pathways may enable the rational selection of patient therapies. However, accurately inferring an intracellular network from data remains a very challenging problem in molecular systems biology. Living cells integrate extremely robust circuits that exhibit significant heterogeneity, but still respond to external stimuli in predictable ways. This phenomenon allows us to introduce a network inference methodology that integrates measurements of protein activation from perturbation experiments. The methodology relies on logic-based networks to provide a predictive approximation of the transfer of signals in a network. The approach presented was validated in silico with a set of test networks and applied to investigate the epidermal growth factor receptor signaling of a breast epithelial cell line, MFC10A. In our analysis, we predict the potential signaling circuitry most likely responsible for the experimental readouts of several proteins in the mitogen activated protein kinase and phosphatidylinositol-3 kinase pathways. The approach can also be used to identify additional necessary perturbation experiments to distinguish between a set of possible candidate networks.