Article (Scientific journals)
Construction and contextualization approaches for protein-protein interaction networks.
BADKAS, Apurva; DE LANDTSHEER, Sébastien; SAUTER, Thomas
2022In Computational and Structural Biotechnology Journal, 20, p. 3280-3290
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Keywords :
Context-specific network; Diffusion; Neighborhood; Protein-protein interaction network
Abstract :
[en] 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.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
BADKAS, Apurva ;  University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Life Sciences and Medicine (DLSM)
DE LANDTSHEER, Sébastien ;  University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Life Sciences and Medicine (DLSM)
SAUTER, Thomas ;  University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Life Sciences and Medicine (DLSM)
External co-authors :
no
Language :
English
Title :
Construction and contextualization approaches for protein-protein interaction networks.
Publication date :
2022
Journal title :
Computational and Structural Biotechnology Journal
eISSN :
2001-0370
Publisher :
Research Network of Computational and Structural Biotechnology, Sweden
Volume :
20
Pages :
3280-3290
Peer reviewed :
Peer Reviewed verified by ORBi
Commentary :
© 2022 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
Available on ORBilu :
since 19 July 2022

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