Protein Interaction Networks

1st Edition, Volume 131 - July 7, 2022
Editor: Rossen Donev
Language: English
Hardback ISBN:
9 7 8 - 0 - 3 2 3 - 9 9 2 3 1 - 2
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 9 9 2 3 2 - 9

Protein Interaction Networks, Volume 131 in the Advances in Protein Chemistry and Structural Biology series, highlights new advances in the field, with this new volume presen… Read more

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Protein Interaction Networks, Volume 131 in the Advances in Protein Chemistry and Structural Biology series, highlights new advances in the field, with this new volume presenting interesting chapters written by an international board of authors.

Cover image
Title page
Table of Contents
Copyright
Contributors
Chapter One: On the current failure—but bright future—of topology-driven biological network alignment
Abstract
1: Introduction
2: Preliminaries
3: Testing hypotheses R1 and R3
4: Addressing R2: Measuring functional relevance of topological objective functions
5: Discussion
6: Methods
7: Data availability
Author contributions
References
Chapter Two: From single-omics to interactomics: How can ligand-induced perturbations modulate single-cell phenotypes?
Abstract
1: Introduction
2: Single-cell omics: From unimodal to multimodal analysis
3: Bridging structure and cell data as drivers to understand ligand-induced perturbations
4: Conclusion
References
Chapter Three: A review of bioinformatics tools and web servers in different microarray platforms used in cancer research
Abstract
1: Microarray and bioinformatics
2: Application of microarray data
3: Classification of microarray data in cancer
4: Microarray data expression repositories
5: Gene expression profiling (GEP)
6: Tools available to analyze microarray data
7: Biological networks
8: Pathway databases and analysis
9: Gene and transcriptional regulatory networks
10: Metabolic networks
11: Drug-drug interaction networks
12: Clustering, classification, and comparison of microarray data
13: Methodology and results
14: Limitations
15: Conclusion and future perspectives
References
Further reading
Chapter Four: Fusion proteins mediate alternation of protein interaction networks in cancers
Abstract
1: Introduction
2: Structural features of fusion proteins in cancers
3: How do fusion proteins alter the protein interaction network?
4: How to analyze the fusion proteins mediated alternation of PPI networks?
5: Identifying altered fusion PPI networks and targeting fusion proteins in cancers could help to develop the precision medicine platform
6: Concluding remarks
Acknowledgments
References
Chapter Five: Integrative ontology and pathway-based approach identifies distinct molecular signatures in transcriptomes of esophageal squamous cell carcinoma
Abstract
1: Introduction
2: Materials and methods
3: Principal component analysis (PCA) of hub genes
4: Results
5: Discussion
6: Conclusion
References
Chapter Six: Protein interaction networks of the mammalian core clock proteins
Abstract
1: Introduction
2: Circadian rhythm in mammals
3: Protein–protein interaction network
4: Conclusion
Acknowledgment
References
Chapter Seven: Investigation of differentially expressed genes and dysregulated pathways involved in multiple sclerosis
Abstract
1: Introduction
2: Methodology
3: Results
4: Discussion
5: Conclusion
References
Chapter Eight: Viral hijacking mechanism in humans through protein–protein interactions
Abstract
1: Introduction
2: Human–virus protein–protein interactions
3: Interfaces of protein interactions in virus-host systems
4: Protein domains in the context of virus–host interactions
5: Protein interaction networks underlying viral processes
6: Intraviral interactomes
7: Different patterns of virus interaction
8: Viral protein interaction with human cellular proteins
9: HIV infection role through proteins
10: SARS-CoV-2 infection role through proteins
11: Conclusion
Acknowledgment
Reference
Chapter Nine: Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study
Abstract
1: Introduction
2: Methods
3: Trajectory file analysis (RMSD/RMSF/H-bridges)
4: SASA/AbASA calculations and analysis
5: Results and discussion
6: Conclusions
Acknowledgments
References
Chapter Ten: Exploring COVID-19 pathogenesis on command-line: A bioinformatics pipeline for handling and integrating omics data
Abstract
1: Introduction
2: Applications
3: Methodologies
4: Results
5: Discussion
6: Conclusions
References

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Rossen Donev