Construction and contextualization approaches for protein-protein interaction networks
Protein-protein interaction network (PPIN) analysis is a widely used method to study the contextual role of proteins of interest, to predict novel disease genes, disease or functional modules, and to identify novel drug targets. PPIN-based analysis uses both generic and context-specific networks. Mu...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-01-01
|
| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037022002549 |
| _version_ | 1828088008325201920 |
|---|---|
| author | Apurva Badkas Sébastien De Landtsheer Thomas Sauter |
| author_facet | Apurva Badkas Sébastien De Landtsheer Thomas Sauter |
| author_sort | Apurva Badkas |
| collection | DOAJ |
| description | Protein-protein interaction network (PPIN) analysis is a widely used method to study the contextual role of proteins of interest, to predict novel disease genes, disease or functional modules, and to identify novel drug targets. PPIN-based analysis uses both generic and context-specific networks. Multiple contextualization methodologies have been described, such as shortest-path algorithms, neighborhood-based methods, and diffusion/propagation algorithms. This review discusses these methods, provides intuitive representations of PPIN contextualization, and also examines how the quality of such context-specific networks could be improved by considering additional sources of evidence. As a heuristic, we observe that tasks such as identifying disease genes, drug targets, and protein complexes should consider local neighborhoods, while uncovering disease mechanisms and discovering disease-pathways would gain from diffusion-based construction. |
| first_indexed | 2024-04-11T05:20:04Z |
| format | Article |
| id | doaj.art-edaba2f452b94c79a26e3bad88364d67 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:20:04Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-edaba2f452b94c79a26e3bad88364d672022-12-24T04:53:06ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-012032803290Construction and contextualization approaches for protein-protein interaction networksApurva Badkas0Sébastien De Landtsheer1Thomas Sauter2Department of Life Sciences and Medicine, University of Luxembourg, Belval Campus, 2, avenue de l’Université, L-4365 Esch-sur-Alzette, LuxembourgDepartment of Life Sciences and Medicine, University of Luxembourg, Belval Campus, 2, avenue de l’Université, L-4365 Esch-sur-Alzette, LuxembourgCorresponding author.; Department of Life Sciences and Medicine, University of Luxembourg, Belval Campus, 2, avenue de l’Université, L-4365 Esch-sur-Alzette, LuxembourgProtein-protein interaction network (PPIN) analysis is a widely used method to study the contextual role of proteins of interest, to predict novel disease genes, disease or functional modules, and to identify novel drug targets. PPIN-based analysis uses both generic and context-specific networks. Multiple contextualization methodologies have been described, such as shortest-path algorithms, neighborhood-based methods, and diffusion/propagation algorithms. This review discusses these methods, provides intuitive representations of PPIN contextualization, and also examines how the quality of such context-specific networks could be improved by considering additional sources of evidence. As a heuristic, we observe that tasks such as identifying disease genes, drug targets, and protein complexes should consider local neighborhoods, while uncovering disease mechanisms and discovering disease-pathways would gain from diffusion-based construction.http://www.sciencedirect.com/science/article/pii/S2001037022002549Protein-protein interaction networkNeighborhoodDiffusionContext-specific network |
| spellingShingle | Apurva Badkas Sébastien De Landtsheer Thomas Sauter Construction and contextualization approaches for protein-protein interaction networks Computational and Structural Biotechnology Journal Protein-protein interaction network Neighborhood Diffusion Context-specific network |
| title | Construction and contextualization approaches for protein-protein interaction networks |
| title_full | Construction and contextualization approaches for protein-protein interaction networks |
| title_fullStr | Construction and contextualization approaches for protein-protein interaction networks |
| title_full_unstemmed | Construction and contextualization approaches for protein-protein interaction networks |
| title_short | Construction and contextualization approaches for protein-protein interaction networks |
| title_sort | construction and contextualization approaches for protein protein interaction networks |
| topic | Protein-protein interaction network Neighborhood Diffusion Context-specific network |
| url | http://www.sciencedirect.com/science/article/pii/S2001037022002549 |
| work_keys_str_mv | AT apurvabadkas constructionandcontextualizationapproachesforproteinproteininteractionnetworks AT sebastiendelandtsheer constructionandcontextualizationapproachesforproteinproteininteractionnetworks AT thomassauter constructionandcontextualizationapproachesforproteinproteininteractionnetworks |