Equilibria decomposition-based comparison of reaction networks of Wnt signaling
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| Format: | Preprint |
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2023
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| _version_ | 1866909153361920000 |
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| author | Hernandez, Bryan S. Lubenia, Patrick Vincent N. Mendoza, Eduardo R. |
| author_facet | Hernandez, Bryan S. Lubenia, Patrick Vincent N. Mendoza, Eduardo R. |
| contents | The Wnt signaling pathway plays a critical role in various biochemical processes, including embryonic development, tissue homeostasis, and cancer progression. In this paper, we conduct a comparative analysis of $β$-catenin-dependent Wnt signaling reaction networks, which we refer to as the Feinberg, Schmitz, and MacLean models, based on the previous study by MacLean et al. (PNAS USA 2015). Our analysis is based on the (unique) finest independent decomposition (FID) of each reaction network and our comparative techniques include equilibria parametrizations (EP) and the newly developed methods of Common Reactions Equilibria (CORE) analysis and Concordance Profile (CP) analysis. Our investigation yields three interesting results concerning the equilibria sets of these models. Firstly, we explore the concept of absolute concentration robustness (ACR), wherein a system exhibits ACR in a specific species if the equilibrium value for that species is the same for any positive equilibrium. Through ACR analysis employing FID and EP, we observe that both the Schmitz and MacLean models lack ACR, whereas the Feinberg model demonstrates ACR in a single species. Second, our analyses using FID and CORE reveal important relationships within the equilibria sets of the augmented Schmitz and MacLean models. Furthermore, FID and CORE identify the lack of a substantial relationship between the equilibria sets of the Feinberg and MacLean models. Hence, these methods detect subtle differences between the Feinberg and MacLean models and also between the Schmitz and MacLean models, which are not evident in the standard reaction network analysis. Finally, based on the concordance levels, CP analysis indicates that the MacLean and Schmitz models are more similar than the MacLean and Feinberg models. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2310_18931 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Equilibria decomposition-based comparison of reaction networks of Wnt signaling Hernandez, Bryan S. Lubenia, Patrick Vincent N. Mendoza, Eduardo R. Dynamical Systems The Wnt signaling pathway plays a critical role in various biochemical processes, including embryonic development, tissue homeostasis, and cancer progression. In this paper, we conduct a comparative analysis of $β$-catenin-dependent Wnt signaling reaction networks, which we refer to as the Feinberg, Schmitz, and MacLean models, based on the previous study by MacLean et al. (PNAS USA 2015). Our analysis is based on the (unique) finest independent decomposition (FID) of each reaction network and our comparative techniques include equilibria parametrizations (EP) and the newly developed methods of Common Reactions Equilibria (CORE) analysis and Concordance Profile (CP) analysis. Our investigation yields three interesting results concerning the equilibria sets of these models. Firstly, we explore the concept of absolute concentration robustness (ACR), wherein a system exhibits ACR in a specific species if the equilibrium value for that species is the same for any positive equilibrium. Through ACR analysis employing FID and EP, we observe that both the Schmitz and MacLean models lack ACR, whereas the Feinberg model demonstrates ACR in a single species. Second, our analyses using FID and CORE reveal important relationships within the equilibria sets of the augmented Schmitz and MacLean models. Furthermore, FID and CORE identify the lack of a substantial relationship between the equilibria sets of the Feinberg and MacLean models. Hence, these methods detect subtle differences between the Feinberg and MacLean models and also between the Schmitz and MacLean models, which are not evident in the standard reaction network analysis. Finally, based on the concordance levels, CP analysis indicates that the MacLean and Schmitz models are more similar than the MacLean and Feinberg models. |
| title | Equilibria decomposition-based comparison of reaction networks of Wnt signaling |
| topic | Dynamical Systems |
| url | https://arxiv.org/abs/2310.18931 |