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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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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. |
format | Online Article Text |
id | pubmed-9494275 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
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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