Validation of signalling pathways: Case study of the p16-mediated pathway

• Published in: Journal of bioinformatics and computational biology Vol. 13; no. 2; p. 1550007
• Main Authors: Akçay, Nimet İlke, Bashirov, Rza, Tüzmen, Şükrü
• Format: Journal Article
• Language: English
• Published: Singapore 01-04-2015
• Subjects: Cell Cycle Checkpoints - genetics; Computational Biology; Computer Simulation; Cyclin-Dependent Kinase Inhibitor p16 - genetics; Cyclin-Dependent Kinase Inhibitor p16 - metabolism; DNA Damage; Genes, p16; Humans; Models, Biological; Neoplasms - genetics; Neoplasms - metabolism; Neoplasms - pathology; Retinoblastoma Protein - metabolism; Signal Transduction - genetics; quantitative modeling; p16-mediated pathway; Signaling pathway; hybrid functional Petri net
• ISSN: 1757-6334
• DOI: 10.1142/S0219720015500079

p16 is recognized as a tumor suppressor gene due to the prevalence of its genetic inactivation in all types of human cancers. Additionally, p16 gene plays a critical role in controlling aging, regulating cellular senescence, detection and maintenance of DNA damage. The molecular mechanism behind these events involves p16-mediated signaling pathway (or p16- Rb pathway), the focus of our study. Understanding functional dependence between dynamic behavior of biological components involved in the p16-mediated pathway and aforesaid molecular-level events might suggest possible implications in the diagnosis, prognosis and treatment of human cancer. In the present work, we employ reverse-engineering approach to construct the most detailed computational model of p16-mediated pathway in higher eukaryotes. We implement experimental data from the literature to validate the model, and under various assumptions predict the dynamic behavior of p16 and other biological components by interpreting the simulation results. The quantitative model of p16-mediated pathway is created in a systematic manner in terms of Petri net technologies.