Jacobsen A, Ivanova O, Amini S, Heringa J, Kemmeren P, Feenstra KA. A framework for exhaustive modelling of genetic interaction patterns using Petri nets.
Bioinformatics 2020;
36:2142-2149. [PMID:
31845959 DOI:
10.1093/bioinformatics/btz917]
[Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 07/09/2019] [Accepted: 12/13/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION
Genetic interaction (GI) patterns are characterized by the phenotypes of interacting single and double mutated gene pairs. Uncovering the regulatory mechanisms of GIs would provide a better understanding of their role in biological processes, diseases and drug response. Computational analyses can provide insights into the underpinning mechanisms of GIs.
RESULTS
In this study, we present a framework for exhaustive modelling of GI patterns using Petri nets (PN). Four-node models were defined and generated on three levels with restrictions, to enable an exhaustive approach. Simulations suggest ∼5 million models of GIs. Generalizing these we propose putative mechanisms for the GI patterns, inversion and suppression. We demonstrate that exhaustive PN modelling enables reasoning about mechanisms of GIs when only the phenotypes of gene pairs are known. The framework can be applied to other GI or genetic regulatory datasets.
AVAILABILITY AND IMPLEMENTATION
The framework is available at http://www.ibi.vu.nl/programs/ExhMod.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
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