Model checking of apoptosis signaling pathways in lung cancers

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Tezin Türü: Yüksek Lisans

Tezin Yürütüldüğü Kurum: Orta Doğu Teknik Üniversitesi, Enformatik Enstitüsü, Bilişim Sistemleri Anabilim Dalı, Türkiye

Tezin Onay Tarihi: 2011

Öğrenci: MEHTAP AYFER PARLAK

Danışman: AYSU BETİN CAN

Özet:

Model checking is a formal verification technique which is widely used in different areas for automated verification and analysis. In this study, we applied a Model Checking method to a biological system. Firstly we constructed a single-cell, Boolean network model for the signaling pathways of apoptosis (programmed cell death) in lung cancers by combining the intrinsic and extrinsic Apoptosis pathways, p53 signaling pathway and p53 - DAP Kinase pathway in Lung cancers. We translated this model to the NuSMV input language. Then we converted known experimental results to CTL properties and checked the conformance of our model with respect to biological experimental results. We examined the dynamics of the apoptosis in lung cancer using NuSMV symbolic model checker and identified the relationship between apoptosis and lung cancer. Finally we generalized the whole process by introducing translation rules and CTL property patterns for biological queries so that model checking any signaling pathway can be automated.