Fibrosis protein-protein interactions from Google matrix analysis of MetaCore network

Kotelnikova, Ekaterina; Frahm, Klaus M.; Shepelyansky, Dima L.; Kunduzova, Oksana

doi:10.1101/2021.10.20.465138

2021

DOI: 10.1101/2021.10.20.465138

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Fibrosis protein-protein interactions from Google matrix analysis of MetaCore network

Ekaterina Kotelnikova¹,

Klaus M. Frahm

Dima L. Shepelyansky

et al.

Abstract: Protein-protein interactions is a longstanding challenge in cardiac remodeling processes and heart failure. Here we use the MetaCore network and the Google matrix algorithms for prediction of protein-protein interactions dictating cardiac fibrosis, a primary causes of end-stage heart failure. The developed algorithms allow to identify interactions between key proteins and predict new actors orchestrating fibroblast activation linked to fibrosis in mouse and human tissues. These data hold great promise for unco… Show more

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Cited by 3 publications

References 23 publications

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Fibroblast-Specific Protein-Protein Interactions for Myocardial Fibrosis from MetaCore Network

Frahm,

Kotelnikova,

Kunduzova

et al. 2024

Biomolecules

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Myocardial fibrosis is a major pathologic disorder associated with a multitude of cardiovascular diseases (CVD). The pathogenesis is complex and encompasses multiple molecular pathways. Integration of fibrosis-associated genes into the global MetaCore network of protein-protein interactions (PPI) offers opportunities to identify PPI with functional and therapeutic significance. Here, we report the generation of a fibrosis-focused PPI network and identification of fibroblast-specific arbitrators driving reparative and reactive myocardial fibrosis. In TGF-β-mediated fibroblast activation, developed network analysis predicts new regulatory mechanisms for fibrosis-associated genes. We introduce an efficient Erdös barrage approach to suppress activation of a number of fibrosis-associated nodes in order to reverse fibrotic cascades. In the network model each protein node is characterized by an Ising up or down spin corresponding to activated or repairing state acting on other nodes being initially in a neutral state. An asynchronous Monte Carlo process describes fibrosis progression determined by a dominant action of linked proteins. Our results suggest that the constructed Ising Network Fibrosis Interaction model offers network insights into fibrosis mechanisms and can complement future experimental efforts to counteract cardiac fibrosis.

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Fibroblast-Specific Protein-Protein Interactions for Myocardial Fibrosis from MetaCore Network

Frahm,

Kotelnikova,

Kunduzova

et al. 2024

Biomolecules

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Opinion Formation in the World Trade Network

Coquidé,

Lages,

Shepelyansky

2024

Entropy

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We extend the opinion formation approach to probe the world influence of economical organizations. Our opinion formation model mimics a battle between currencies within the international trade network. Based on the United Nations Comtrade database, we construct the world trade network for the years of the last decade from 2010 to 2020. We consider different core groups constituted by countries preferring to trade in a specific currency. We will consider principally two core groups, namely, five Anglo-Saxon countries that prefer to trade in US dollar and the 11 BRICS+ that prefer to trade in a hypothetical currency, hereafter called BRI, pegged to their economies. We determine the trade currency preference of the other countries via a Monte Carlo process depending on the direct transactions between the countries. The results obtained in the frame of this mathematical model show that starting from the year 2014, the majority of the world countries would have preferred to trade in BRI than USD. The Monte Carlo process reaches a steady state with three distinct groups: two groups of countries preferring to trade in whatever is the initial distribution of the trade currency preferences, one in BRI and the other in USD, and a third group of countries swinging as a whole between USD and BRI depending on the initial distribution of the trade currency preferences. We also analyze the battle between three currencies: on one hand, we consider USD, BRI and EUR, the latter currency being pegged by the core group of nine EU countries. We show that the countries preferring EUR are mainly the swing countries obtained in the frame of the two currencies model. On the other hand, we consider USD, CNY (Chinese yuan), OPE, the latter currency being pegged to the major OPEC+ economies for which we try to probe the effective economical influence within international trade. Finally, we present the reduced Google matrix description of the trade relations between the Anglo-Saxon countries and the BRICS+.

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Recent Advances in Protein–Protein Interactions

Sedov

Zuev²

2023

IJMS

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Fibrosis protein-protein interactions from Google matrix analysis of MetaCore network

Cited by 3 publications

References 23 publications

Fibroblast-Specific Protein-Protein Interactions for Myocardial Fibrosis from MetaCore Network

Fibroblast-Specific Protein-Protein Interactions for Myocardial Fibrosis from MetaCore Network

Opinion Formation in the World Trade Network

Recent Advances in Protein–Protein Interactions

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