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. 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. © 2022 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.

Citation

Apurva Badkas, Sébastien De Landtsheer, Thomas Sauter. Construction and contextualization approaches for protein-protein interaction networks. Computational and structural biotechnology journal. 2022;20:3280-3290

PMID: 35832626

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