Identifying Cancer-Related Signaling Pathways Using Formal Methods

Methods called pathway analysis have emerged whose purpose is to identify significantly impacted signaling pathways in a given condition. Most of these methods employ graphs to model the interactions between genes. Graphs have some limitations in accurately modeling various aspects of the interactions in the signaling pathways. As a result, formal methods as practiced in computer science is suggested for modeling signaling pathways. Using formal methods, various types of interactions among biological components are modeled, which can reduce the false-positive rates compared to other methods. Formal methods can also model the concurrent and stochastic behavior of signaling pathways.