Modelling and analysis of the complement system signalling pathways: roles of C3, C5a and pro-inflammatory cytokines in SARS-CoV-2 infection

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Bioinformatics and Genomics

Main article text

 

Introduction

Materials and Methods

Reduction of complement system signalling pathways

Computational tree logic development

Model checking and logical parameters inference

Network analysis

Results

Signalling in normal condition

Signalling in pathogenic condition

Intervention modelling

Case-1 (Intervention in C3 mediated upregulation of C5a and PICyts)

Case-2 (Intervention in C5a mediated upregulation of PICyts)

Discussion

Conclusions

Supplemental Information

Examples of dummy BRNs.

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Normal condition parameters set heatmap.

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Normal condition parameters set dummy tentency graphs.

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Normal condition state graph.

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Pathogenic condition parameters sets heatmap.

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Pathogenic condition state graph.

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Intervention Case 1 parameters sets heatmap.

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Intervention Case 1 state graph.

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Intervention Case 2 parameters sets heatmap.

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Intervention Case 2 state graph.

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CTL Fundamentals.

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Normal condition parameters sets.

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Logical Parameters Evidences.

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Normal state graph model code.

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Pathogenic condition parameters sets.

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Pathogenic state graph.

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Intervention Case 1.

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Intervention Case 1 BRN.

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Intervention Case 2 state graph.

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Intervention Case 2.

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Intervention Case 2 BRN.

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SMBioNet and GINSim kinetic parameters entry.

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Dummy model parameters set.

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Experimental observations.

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Normal condition state graph rendered in cytoscape (CYS).

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Normal condition state graph rendered in cytoscape (SIF).

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Pathogenic condition state graph rendered in cytoscape (CYS).

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Pathogenic condition state graph rendered in cytoscape (SIF).

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Intervention Case 1 state graph rendered in cytoscape (CYS).

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Intervention Case 1 state graph rendered in cytoscape (SIF).

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Intervention Case 2 state graph rendered in cytoscape (CYS).

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Intervention Case 2 state graph rendered in cytoscape (SIF).

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Additional Information and Declarations

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Didar Murad conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Rehan Zafar Paracha conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Muhammad Tariq Saeed performed the experiments, analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Jamil Ahmad analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Ammar Mushtaq analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Maleeha Humayun analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The model codes, algorithm of model checker in the SMBioNet tool code along with logical parameters sets and the BRN simulated to state graphs rendered in cytoscape are available in the Supplemental Files.

Funding

The authors received no funding for this work.

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