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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
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Zinc proteome interaction network as a model to identify nutrient-affected pathways in human pathologies.
Guido Leoni1, Antonio Rosato, Giuditta Perozzi
1CRA-NUT, Food and Nutrition Research Center, Agricultural Research Council, Via Ardeatina 546, 00178, Rome, Italy.
Genes & Nutrition
|November 5, 2014
Summary
This study defines the zinc proteome (ZNP) and identifies cellular processes affected by zinc availability. It highlights zinc
Area of Science:
- Biochemistry and Molecular Biology
- Nutritional Science
- Computational Biology
Background:
- Zinc is a vital micronutrient essential for numerous cellular processes, including cell division, growth, and differentiation.
- Zinc-binding proteins constitute approximately 10% of the human proteome, with zinc ions critical for enzyme function and regulatory protein activity.
- Understanding the comprehensive network of zinc-binding proteins and their interactions is crucial for elucidating zinc's role in health and disease.
Purpose of the Study:
- To define the zinc proteome (ZNP) by identifying all zinc-binding proteins and their direct interactors.
- To computationally identify cellular processes influenced by zinc availability and homeostasis.
- To investigate the potential role of the ZNP network in the pathogenesis of Crohn's disease.
Main Methods:
- Systematic annotation and integration of known zinc-binding proteins and their interactors to construct the ZNP.
- Application of pathway analysis and network enrichment tools to predict cellular processes affected by zinc dysregulation.
- Case study analysis correlating ZNP network alterations with gene expression data from Crohn's disease patients.
Main Results:
- The study established a comprehensive zinc proteome (ZNP) network.
- Pathway and network analyses identified key biological processes sensitive to zinc homeostasis.
- A specific ZNP network associated with Crohn's disease pathogenesis was identified, implicating zinc in intestinal inflammation and tissue remodeling.
Conclusions:
- The computational approach successfully identified pathways influenced by zinc availability and linked to disease.
- Zinc plays a significant role in the tissue remodeling processes during gut inflammation, suggesting novel disease mechanisms.
- The developed ZNP network provides a valuable resource for mechanistic research into various pathological conditions, including Crohn's disease.
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