Supportness of the protein complex standards in PPI networks

A protein complex is a collection of two or more associated proteins that interact with each other in a stable long-term interaction. Protein complexes have essential roles in regulatory processes, cellular functions and signaling cascades. This paper examines how well-known collections of protein c...

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Autores principales:	Milana Grbić, Vukašin Crnogorac, Milan Predojević, Aleksandar Kartelj, Dragan Matić
Formato:	article
Lenguaje:	EN
Publicado:	Taylor & Francis Group 2021
Materias:	variable neighbourhood search ppi networks protein complexes network connectivity Telecommunication TK5101-6720 Information technology T58.5-58.64
Acceso en línea:	https://doaj.org/article/38c118f13b43433682c0609e88639af7
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spelling	oai:doaj.org-article:38c118f13b43433682c0609e88639af72021-11-04T15:51:57ZSupportness of the protein complex standards in PPI networks2475-18392475-184710.1080/24751839.2021.1989241https://doaj.org/article/38c118f13b43433682c0609e88639af72021-10-01T00:00:00Zhttp://dx.doi.org/10.1080/24751839.2021.1989241https://doaj.org/toc/2475-1839https://doaj.org/toc/2475-1847A protein complex is a collection of two or more associated proteins that interact with each other in a stable long-term interaction. Protein complexes have essential roles in regulatory processes, cellular functions and signaling cascades. This paper examines how well-known collections of protein complexes are supported in protein–protein interaction (PPI) networks, i.e. whether they form connected subnetworks in a particular PPI network. For that purpose, we apply a variable neighbourhood search (VNS) metaheuristic algorithm for adding the minimum number of interactions in order to support protein complexes. Experimental results obtained on several PPI networks (BioGRID, WI-PHI and String) and four protein complex standards (MIPS, TAP06, SGD and CYC2008) show that considered networks do not include enough PPIs to support all complexes from complex standards. Deeper analysis indicates that there exists common PPIs which are probably missing in the considered networks. These findings can be useful for further biological interpretation and developing of PPI prediction models.Milana GrbićVukašin CrnogoracMilan PredojevićAleksandar KarteljDragan MatićTaylor & Francis Grouparticlevariable neighbourhood searchppi networksprotein complexesnetwork connectivityTelecommunicationTK5101-6720Information technologyT58.5-58.64ENJournal of Information and Telecommunication, Vol 0, Iss 0, Pp 1-21 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	variable neighbourhood search ppi networks protein complexes network connectivity Telecommunication TK5101-6720 Information technology T58.5-58.64
spellingShingle	variable neighbourhood search ppi networks protein complexes network connectivity Telecommunication TK5101-6720 Information technology T58.5-58.64 Milana Grbić Vukašin Crnogorac Milan Predojević Aleksandar Kartelj Dragan Matić Supportness of the protein complex standards in PPI networks
description	A protein complex is a collection of two or more associated proteins that interact with each other in a stable long-term interaction. Protein complexes have essential roles in regulatory processes, cellular functions and signaling cascades. This paper examines how well-known collections of protein complexes are supported in protein–protein interaction (PPI) networks, i.e. whether they form connected subnetworks in a particular PPI network. For that purpose, we apply a variable neighbourhood search (VNS) metaheuristic algorithm for adding the minimum number of interactions in order to support protein complexes. Experimental results obtained on several PPI networks (BioGRID, WI-PHI and String) and four protein complex standards (MIPS, TAP06, SGD and CYC2008) show that considered networks do not include enough PPIs to support all complexes from complex standards. Deeper analysis indicates that there exists common PPIs which are probably missing in the considered networks. These findings can be useful for further biological interpretation and developing of PPI prediction models.
format	article
author	Milana Grbić Vukašin Crnogorac Milan Predojević Aleksandar Kartelj Dragan Matić
author_facet	Milana Grbić Vukašin Crnogorac Milan Predojević Aleksandar Kartelj Dragan Matić
author_sort	Milana Grbić
title	Supportness of the protein complex standards in PPI networks
title_short	Supportness of the protein complex standards in PPI networks
title_full	Supportness of the protein complex standards in PPI networks
title_fullStr	Supportness of the protein complex standards in PPI networks
title_full_unstemmed	Supportness of the protein complex standards in PPI networks
title_sort	supportness of the protein complex standards in ppi networks
publisher	Taylor & Francis Group
publishDate	2021
url	https://doaj.org/article/38c118f13b43433682c0609e88639af7
work_keys_str_mv	AT milanagrbic supportnessoftheproteincomplexstandardsinppinetworks AT vukasincrnogorac supportnessoftheproteincomplexstandardsinppinetworks AT milanpredojevic supportnessoftheproteincomplexstandardsinppinetworks AT aleksandarkartelj supportnessoftheproteincomplexstandardsinppinetworks AT draganmatic supportnessoftheproteincomplexstandardsinppinetworks
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Supportness of the protein complex standards in PPI networks

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