Static Analysis of Dengue Biological Regulatory Network’s
DOI:
https://doi.org/10.55006/biolsciences.2023.3203Keywords:
Automata Networks Model, DENGUE Model Analysis, Computational Biology, Logical Modeling Analysis, Clearance DENV ModelAbstract
Dengue is an acute viral illness caused by the RNA virus of the family Flaviviridae and spread by Aedes mosquitoes. Intense dengue is a spreading cause of serious disease and death in some ’Asian and South American’ countries. Pathogenesis is associated with the amended functioning of our innate immune system during infection. Toll Like Receptor is influential for the involucre of innate immunity able to cause dengue infection disease like pattern receptor recognition. Toll-like receptors induced by injury of a certain severity arbitrate activation of interferons and Fc receptors arbitrate the involucre of cytokines. Clearance of dengue virus is associated with interferon protein; however regulatory mechanisms have been adopted against this modified effect. The clearance is considered to be a steady state known to be characterized by a low threshold level of DENV. The pathogenic state is characterized by a high threshold level of SOCS. SOCS protein is also induced due to interferon and cytokine-amended signaling, which can subsequently play its part in the regulation of interferon and cytokine production. Our hypothesis in this research the innate immunity system is associated between the pathogenesis of the dengue virus and the SOCS-amended inhibition. We used the static formalism model of the biological regulatory network of Toll-like receptors induced by the pathogenesis of dengue amended signaling pathway. A model verification method used in GINsim was used to deduce the logical parameters for the qualitative modelling. Therefore, a multidisciplinary and translational study we constructed a formal model constraint the approach with a static and integrative computational analysis, which may identify new immunopathological mechanisms and biomarkers for differential diagnosis, opening the way for the development of specific therapies that will reduce mortality and induce morbidity by dengue virus.
Downloads
References
B. Aslam et al., “On the modelling and analysis of the regulatory network of dengue virus pathogenesis and clearance,” Comput. Biol. Chem., vol. 53, pp. 277–291, Dec. 2014, doi: 10.1016/j.compbiolchem.2014.10.003.
B. E. E. Martina, P. Koraka, and A. D. M. E. Osterhaus, “Dengue Virus Pathogenesis: an Integrated View,” Clin. Microbiol. Rev., vol. 22, no. 4, pp. 564–581, Oct. 2009, doi: 10.1128/CMR.00035-09.
S. K. Roy and S. Bhattacharjee, “Dengue virus: epidemiology, biology, and disease aetiology,” Can. J. Microbiol., vol. 67, no. 10, pp. 687–702, Oct. 2021, doi: 10.1139/cjm-2020-0572.
T. Chareonsirisuthigul, S. Kalayanarooj, and S. Ubol, “Dengue virus (DENV) antibody-dependent enhancement of infection upregulates the production of anti-inflammatory cytokines, but suppresses anti-DENV free radical and pro-inflammatory cytokine production, in THP-1 cells,” J. Gen. Virol., vol. 88, no. 2, pp. 365–375, Feb. 2007, doi: 10.1099/vir.0.82537-0.
M. G. Guzman, D. J. Gubler, A. Izquierdo, E. Martinez, and S. B. Halstead, “Dengue infection,” Nat. Rev. Dis. Prim., vol. 2, no. 1, p. 16055, Aug. 2016, doi: 10.1038/nrdp.2016.55.
C. Suharti et al., “Cytokine patterns during dengue shock syndrome.” [Online]. Available: http://www.john-libbey-eurotext.fr/fr/revues/bio_rech/ecn/e-docs/00/03/FA/D6/article.phtml
P. K. Sorger and B. Schoeberl, “An expanding role for cell biologists in drug discovery and pharmacology,” Mol. Biol. Cell, vol. 23, no. 21, pp. 4162–4164, Nov. 2012, doi: 10.1091/mbc.e12-05-0394.
Z. Ji, K. Yan, W. Li, H. Hu, and X. Zhu, “Mathematical and Computational Modeling in Complex Biological Systems,” Biomed Res. Int., vol. 2017, pp. 1–16, 2017, doi: 10.1155/2017/5958321.
D. J. Gubler, “Dengue/Dengue Haemorrhagic Fever: History and Current Status,” 2008, pp. 3–22. doi: 10.1002/0470058005.ch2.
K. S. Abhishek, A. Chakravarti, C. P. Baveja, N. Kumar, O. Siddiqui, and S. Kumar, “Association of interleukin-2, -4 and -10 with dengue severity.,” Indian J. Pathol. Microbiol., vol. 60, no. 1, pp. 66–69, 2017, doi: 10.4103/0377-4929.200027.
N. Azim et al., “A Static Analysis of Wnt / β -Catenin and Wnt / Ca 2+ Biological Regulatory Networks for ARVC Using Automata Network Model,” IEEE Access, vol. 9, pp. 107611–107624, 2021, doi: 10.1109/ACCESS.2021.3097550.
N. Azim et al., “Petri Net modelling approach for analysing the behaviour of Wnt/ ‐catenin and Wnt/ Ca 2+ signalling pathways in arrhythmogenic right ventricular cardiomyopathy,” IET Syst. Biol., vol. 14, no. 6, pp. 350–367, Dec. 2020, doi: 10.1049/iet-syb.2020.0038.
A. Naldi, D. Berenguier, A. Fauré, F. Lopez, D. Thieffry, and C. Chaouiya, “Logical modelling of regulatory networks with GINsim 2.3,” Biosystems, vol. 97, no. 2, pp. 134–139, Aug. 2009, doi: 10.1016/j.biosystems.2009.04.008.
L. Paulevé, G. Andrieux, and H. Koeppl, “Under-Approximating Cut Sets for Reachability in Large Scale Automata Networks,” 2013, pp. 69–84. doi: 10.1007/978-3-642-39799-8_4.
R. Thomas, “Boolean formalization of genetic control circuits,” J. Theor. Biol., vol. 42, no. 3, pp. 563–585, Dec. 1973, doi: 10.1016/0022-5193(73)90247-6.
L. Pauleve, “Reduction of Qualitative Models of Biological Networks for Transient Dynamics Analysis,” IEEE/ACM Trans. Comput. Biol. Bioinforma., vol. 15, no. 4, pp. 1167–1179, Jul. 2018, doi: 10.1109/TCBB.2017.2749225.
L. PAULEVÉ, M. MAGNIN, and O. ROUX, “Static analysis of Biological Regulatory Networks dynamics using abstract interpretation,” Math. Struct. Comput. Sci., vol. 22, no. 4, pp. 651–685, Aug. 2012, doi: 10.1017/S0960129511000739.
K. Kobayashi, “Design of Fixed Points in Boolean Networks Using Feedback Vertex Sets and Model Reduction,” Complexity, vol. 2019, pp. 1–9, Mar. 2019, doi: 10.1155/2019/9261793.
N. Levy et al., “Prediction of Mutations to Control Pathways Enabling Tumor Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial),” Front. Physiol., vol. 9, Jul. 2018, doi: 10.3389/fphys.2018.00787.
L. Paulevé, “Pint: A Static Analyzer for Transient Dynamics of Qualitative Networks with IPython Interface,” 2017, pp. 309–316. doi: 10.1007/978-3-319-67471-1_20.
L. F. Fitime, O. Roux, C. Guziolowski, and L. Paulevé, “Identification of bifurcation transitions in biological regulatory networks using Answer-Set Programming,” Algorithms Mol. Biol., vol. 12, no. 1, p. 19, Dec. 2017, doi:10.1186/s13015-017-0110-3.
R. M. Borisyuk and A. B. Kirillov, “Bifurcation analysis of a neural network model,” Biol. Cybern., vol. 66, no. 4, pp. 319–325, Feb. 1992, doi: 10.1007/BF00203668.
D. Bryce and S. Kambhampati, “A Tutorial on Planning Graph Based Reachability Heuristics,” 2007.
J. J. Tyson, T. Laomettachit, and P. Kraikivski, “Modeling the dynamic behavior of biochemical regulatory networks,” J. Theor. Biol., vol. 462, pp. 514–527, Feb. 2019, doi: 10.1016/j.jtbi.2018.11.034.
L. Paulevé, C. Chancellor, M. Folschette, M. Magnin, and O. Roux, “Analyzing Large Network Dynamics with Process Hitting,” in Logical Modeling of Biological Systems, Hoboken, NJ, USA: John Wiley & Sons, Inc., 2014, pp. 125–166. doi: 10.1002/9781119005223.ch4.
A. G. Gonzalez, A. Naldi, L. Sánchez, D. Thieffry, and C. Chaouiya, “GINsim: A software suite for the qualitative modelling, simulation and analysis of regulatory networks,” Biosystems, vol. 84, no. 2, pp. 91–100, May 2006, doi: 10.1016/j.biosystems.2005.10.003.
L. Calzone, E. Barillot, and A. Zinovyev, “Predicting genetic interactions from Boolean models of biological networks,” Integr. Biol., vol. 7, no. 8, pp. 921–929, 2015, doi: 10.1039/C5IB00029G.
M. Folschette, L. Paulevé, M. Magnin, and O. Roux, “Sufficient conditions for reachability in automata networks with priorities,” Theor. Comput. Sci., vol. 608, pp. 66–83, Dec. 2015, doi: 10.1016/j.tcs.2015.08.040.
R. Thomas, “Logical analysis of systems comprising feedback loops,” J. Theor. Biol., vol. 73, no. 4, pp. 631–656, Aug. 1978, doi: 10.1016/0022-5193(78)90127-3.
L. Paulevé and A. Richard, “Static Analysis of Boolean Networks Based on Interaction Graphs: A Survey,” Electron. Notes Theor. Comput. Sci., vol. 284, pp. 93–104, Jun. 2012, doi: 10.1016/j.entcs.2012.05.017.
S. Klamt and E. D. Gilles, “Minimal cut sets in biochemical reaction networks,” Bioinformatics, vol. 20, no. 2, pp. 226–234, Jan. 2004, doi: 10.1093/bioinformatics/btg395.
N. W. Paton et al., “Conceptual modelling of genomic information,” Bioinformatics, vol. 16, no. 6, pp. 548–557, Jun. 2000, doi: 10.1093/bioinformatics/16.6.548.
D. A. Muller, A. C. I. Depelsenaire, and P. R. Young, “Clinical and Laboratory Diagnosis of Dengue Virus Infection,” J. Infect. Dis., vol. 215, no. suppl_2, pp. S89–S95, Mar. 2017, doi: 10.1093/infdis/jiw649.
M. Kotlyar, C. Pastrello, Z. Ahmed, J. Chee, Z. Varyova, and I. Jurisica, “IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis,” Nucleic Acids Res., vol. 50, no. D1, pp. D640–D647, Jan. 2022, doi: 10.1093/nar/gkab1034.
S. Khalid, R. Hanif, S. H. K. Tareen, A. Siddiqa, Z. Bibi, and J. Ahmad, “Formal modeling and analysis of ER- α associated Biological Regulatory Network in breast cancer,” PeerJ, vol. 4, p. e2542, Oct. 2016, doi: 10.7717/peerj.2542.
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2023 Abdullah Khan, Shmmon Ahmad, Bibi Tahira, Amina Khalid

This work is licensed under a Creative Commons Attribution 4.0 International License.
-
Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
- No additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.

