Temporal Logic based Framework to Model and Analyse Gene Networks with Alternative Splicing

Toward system-level understanding of biological systems, we need a formalism to model and analyse them. Due to incompleteness of knowledge about quantitative parameters and molecular mechanisms, qualitative methods have been useful alternatives. We have been working on temporal logic-based approach for qualitative modelling and analysis of gene regulatory networks. Although our framework is well-established to model several aspects of gene regulation, we still lack treatment of alternative splicing, which contributes to proteomic diversity of eukaryotic organisms. In this paper we extend our logic-based qualitative framework to be able to capture alternative splicing, which is crucial to model the gene regulatory networks in eukaryotic organisms. We study mechanisms of alternative splicing and propose how we model each mechanism, then demonstrate the modelling method by analysing the regulatory network of sex determination in Drosophila and verify that the network ensures sex determination.