Inferring domain-domain interactions from protein-protein interactions with formal concept analysis.

Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain...

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Autor principal:	Susan Khor
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/168c3c70b2aa4554acb6a6f0f68ac31f
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spelling	oai:doaj.org-article:168c3c70b2aa4554acb6a6f0f68ac31f2021-11-18T08:32:02ZInferring domain-domain interactions from protein-protein interactions with formal concept analysis.1932-620310.1371/journal.pone.0088943https://doaj.org/article/168c3c70b2aa4554acb6a6f0f68ac31f2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24586450/?tool=EBIhttps://doaj.org/toc/1932-6203Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain interactions is domain promiscuity. Promiscuous domains are domains that can occur in many domain architectures and are therefore found in many proteins. This becomes a problem for a method where the score of a domain-pair is the ratio between observed and expected frequencies because the protein-protein interaction network is sparse. As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized. This domain promiscuity challenge to the problem of inferring reliable domain-domain interactions from protein-protein interactions has been recognized, and a number of work-arounds have been proposed. This paper reports on an application of Formal Concept Analysis to this problem. It is found that the relationship between formal concepts provides a natural way for rare domains to elevate the rank of promiscuous domain-pairs and enrich highly ranked domain-pairs with reliable domain-domain interactions. This piggybacking of promiscuous domain-pairs onto less promiscuous domain-pairs is possible only with concept lattices whose attribute-labels are not reduced and is enhanced by the presence of proteins that comprise both promiscuous and rare domains.Susan KhorPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 2, p e88943 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Susan Khor Inferring domain-domain interactions from protein-protein interactions with formal concept analysis.
description	Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain interactions is domain promiscuity. Promiscuous domains are domains that can occur in many domain architectures and are therefore found in many proteins. This becomes a problem for a method where the score of a domain-pair is the ratio between observed and expected frequencies because the protein-protein interaction network is sparse. As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized. This domain promiscuity challenge to the problem of inferring reliable domain-domain interactions from protein-protein interactions has been recognized, and a number of work-arounds have been proposed. This paper reports on an application of Formal Concept Analysis to this problem. It is found that the relationship between formal concepts provides a natural way for rare domains to elevate the rank of promiscuous domain-pairs and enrich highly ranked domain-pairs with reliable domain-domain interactions. This piggybacking of promiscuous domain-pairs onto less promiscuous domain-pairs is possible only with concept lattices whose attribute-labels are not reduced and is enhanced by the presence of proteins that comprise both promiscuous and rare domains.
format	article
author	Susan Khor
author_facet	Susan Khor
author_sort	Susan Khor
title	Inferring domain-domain interactions from protein-protein interactions with formal concept analysis.
title_short	Inferring domain-domain interactions from protein-protein interactions with formal concept analysis.
title_full	Inferring domain-domain interactions from protein-protein interactions with formal concept analysis.
title_fullStr	Inferring domain-domain interactions from protein-protein interactions with formal concept analysis.
title_full_unstemmed	Inferring domain-domain interactions from protein-protein interactions with formal concept analysis.
title_sort	inferring domain-domain interactions from protein-protein interactions with formal concept analysis.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/168c3c70b2aa4554acb6a6f0f68ac31f
work_keys_str_mv	AT susankhor inferringdomaindomaininteractionsfromproteinproteininteractionswithformalconceptanalysis
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Inferring domain-domain interactions from protein-protein interactions with formal concept analysis.

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