title: Topology and dynamics of signaling networks: in search of transcriptional control of the inflammatory response.
abstract: Over the past several decades, to develop a fundamental understanding of inflammation's progression, research has focused on extracellular mediators, such as cytokines, as characteristic components of inflammatory response. These efforts have recently been complemented by advances in proteomics that allow analysis of multiple signaling proteins in parallel, to provide more complete mechanistic models of inflammation. In this review, we discuss various techniques for assessing protein activity, as well as computational techniques that are well suited for interpreting large amounts of proteomic data to generate signaling networks or for modeling the dynamics of known network interactions. We also discuss examples that explore these experimental and computational techniques in tandem to generate signaling networks under various conditions and that link those networks to transcriptional activity. Further advancements in this field will likely provide an explicit description of inflammatory response, paving the way for better diagnostics and therapies in clinic.
authors.affiliation: Chemical & Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854, USA. yannis@rci.rutgers.edu
authors.forename: Ioannis P
authors.initials: IP
authors.lastname: Androulakis
authors.forename: Kubra
authors.initials: K
authors.lastname: Kamisoglu
authors.forename: John S
authors.initials: JS
authors.lastname: Mattick
mesh_terms: D000818:Animals; D017209:Apoptosis; D001499:Bayes Theorem; D045744:Cell Line, Tumor; D019295:Computational Biology; D016207:Cytokines / Q000378:metabolism; D005456:Fluorescent Dyes / Q000737:chemistry; D053263:Gene Regulatory Networks; D006801:Humans; D007113:Immunity, Innate; D007249:Inflammation / Q000378:metabolism*; D013058:Mass Spectrometry; D040081:Protein Array Analysis; D040901:Proteomics; D012044:Regression Analysis; D015398:Signal Transduction; D014158:Transcription, Genetic
chemical_list: D016207:Cytokines; D005456:Fluorescent Dyes