ABSTRACT

This chapter focuses on signaling pathways, specifically, their analysis with high level models, striving primarily to elucidate pathway structures, and discusses modeling techniques primarily used for genetic regulatory or metabolic pathways. Signaling pathways constitute the primary mechanism by which cells response to cues. They sense external cues and orchestrate the downstream response, by engaging relevant parts of the cellular machinery to bring about the desired outcome. The achieve a desired outcome, the signaling pathway often involves other pathway types, such as metabolic and genetic regulatory pathways. The chapter describes signaling pathways and their importance in biological systems, and provides a brief introduction to Bayesian networks. The Bayesian network represents relationships among variables in a signaling pathway, where the variables can represent signaling molecules, small molecules, lipids, or any biologically relevant molecule. Most of the work aimed at elucidating signaling pathways fits the category of elucidation of protein protein interaction networks.