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Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context

At the heart of the cellular machinery through the regulation of cellular functions, protein–protein interactions (PPIs) have a significant role. PPIs can be analyzed with network approaches. Construction of a PPI network requires prediction of the interactions. All PPIs form a network. Different bi...

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Autores principales: Robin, Vivian, Bodein, Antoine, Scott-Boyer, Marie-Pier, Leclercq, Mickaël, Périn, Olivier, Droit, Arnaud
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9494275/
https://www.ncbi.nlm.nih.gov/pubmed/36158572
http://dx.doi.org/10.3389/fmolb.2022.962799
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author Robin, Vivian
Bodein, Antoine
Scott-Boyer, Marie-Pier
Leclercq, Mickaël
Périn, Olivier
Droit, Arnaud
author_facet Robin, Vivian
Bodein, Antoine
Scott-Boyer, Marie-Pier
Leclercq, Mickaël
Périn, Olivier
Droit, Arnaud
author_sort Robin, Vivian
collection PubMed
description At the heart of the cellular machinery through the regulation of cellular functions, protein–protein interactions (PPIs) have a significant role. PPIs can be analyzed with network approaches. Construction of a PPI network requires prediction of the interactions. All PPIs form a network. Different biases such as lack of data, recurrence of information, and false interactions make the network unstable. Integrated strategies allow solving these different challenges. These approaches have shown encouraging results for the understanding of molecular mechanisms, drug action mechanisms, and identification of target genes. In order to give more importance to an interaction, it is evaluated by different confidence scores. These scores allow the filtration of the network and thus facilitate the representation of the network, essential steps to the identification and understanding of molecular mechanisms. In this review, we will discuss the main computational methods for predicting PPI, including ones confirming an interaction as well as the integration of PPIs into a network, and we will discuss visualization of these complex data.
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spelling pubmed-94942752022-09-23 Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context Robin, Vivian Bodein, Antoine Scott-Boyer, Marie-Pier Leclercq, Mickaël Périn, Olivier Droit, Arnaud Front Mol Biosci Molecular Biosciences At the heart of the cellular machinery through the regulation of cellular functions, protein–protein interactions (PPIs) have a significant role. PPIs can be analyzed with network approaches. Construction of a PPI network requires prediction of the interactions. All PPIs form a network. Different biases such as lack of data, recurrence of information, and false interactions make the network unstable. Integrated strategies allow solving these different challenges. These approaches have shown encouraging results for the understanding of molecular mechanisms, drug action mechanisms, and identification of target genes. In order to give more importance to an interaction, it is evaluated by different confidence scores. These scores allow the filtration of the network and thus facilitate the representation of the network, essential steps to the identification and understanding of molecular mechanisms. In this review, we will discuss the main computational methods for predicting PPI, including ones confirming an interaction as well as the integration of PPIs into a network, and we will discuss visualization of these complex data. Frontiers Media S.A. 2022-09-08 /pmc/articles/PMC9494275/ /pubmed/36158572 http://dx.doi.org/10.3389/fmolb.2022.962799 Text en Copyright © 2022 Robin, Bodein, Scott-Boyer, Leclercq, Périn and Droit. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Robin, Vivian
Bodein, Antoine
Scott-Boyer, Marie-Pier
Leclercq, Mickaël
Périn, Olivier
Droit, Arnaud
Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context
title Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context
title_full Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context
title_fullStr Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context
title_full_unstemmed Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context
title_short Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context
title_sort overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9494275/
https://www.ncbi.nlm.nih.gov/pubmed/36158572
http://dx.doi.org/10.3389/fmolb.2022.962799
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