Link clustering reveals structural characteristics and biological contexts in signed molecular networks.

Many biological networks are signed molecular networks which consist of positive and negative links. To reveal the distinct features between links with different signs, we proposed signed link-clustering coefficients that assess the similarity of inter-action profiles between linked molecules. We fo...

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Autores principales:	Chen-Ching Lin, Chia-Hsien Lee, Chiou-Shann Fuh, Hsueh-Fen Juan, Hsuan-Cheng Huang
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/334e932c93934de284f05b93415605c7
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spelling	oai:doaj.org-article:334e932c93934de284f05b93415605c72021-11-18T07:40:21ZLink clustering reveals structural characteristics and biological contexts in signed molecular networks.1932-620310.1371/journal.pone.0067089https://doaj.org/article/334e932c93934de284f05b93415605c72013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23826198/?tool=EBIhttps://doaj.org/toc/1932-6203Many biological networks are signed molecular networks which consist of positive and negative links. To reveal the distinct features between links with different signs, we proposed signed link-clustering coefficients that assess the similarity of inter-action profiles between linked molecules. We found that positive links tended to cluster together, while negative links usually behaved like bridges between positive clusters. Positive links with higher adhesiveness tended to share protein domains, be associated with protein-protein interactions and make intra-connections within protein complexes. Negative links that were more bridge-like tended to make interconnections between protein complexes. Utilizing the proposed measures to group positive links, we observed hierarchical modules that could be well characterized by functional annotations or known protein complexes. Our results imply that the proposed sign-specific measures can help reveal the network structural characteristics and the embedded biological contexts of signed links, as well as the functional organization of signed molecular networks.Chen-Ching LinChia-Hsien LeeChiou-Shann FuhHsueh-Fen JuanHsuan-Cheng HuangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 6, p e67089 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Chen-Ching Lin Chia-Hsien Lee Chiou-Shann Fuh Hsueh-Fen Juan Hsuan-Cheng Huang Link clustering reveals structural characteristics and biological contexts in signed molecular networks.
description	Many biological networks are signed molecular networks which consist of positive and negative links. To reveal the distinct features between links with different signs, we proposed signed link-clustering coefficients that assess the similarity of inter-action profiles between linked molecules. We found that positive links tended to cluster together, while negative links usually behaved like bridges between positive clusters. Positive links with higher adhesiveness tended to share protein domains, be associated with protein-protein interactions and make intra-connections within protein complexes. Negative links that were more bridge-like tended to make interconnections between protein complexes. Utilizing the proposed measures to group positive links, we observed hierarchical modules that could be well characterized by functional annotations or known protein complexes. Our results imply that the proposed sign-specific measures can help reveal the network structural characteristics and the embedded biological contexts of signed links, as well as the functional organization of signed molecular networks.
format	article
author	Chen-Ching Lin Chia-Hsien Lee Chiou-Shann Fuh Hsueh-Fen Juan Hsuan-Cheng Huang
author_facet	Chen-Ching Lin Chia-Hsien Lee Chiou-Shann Fuh Hsueh-Fen Juan Hsuan-Cheng Huang
author_sort	Chen-Ching Lin
title	Link clustering reveals structural characteristics and biological contexts in signed molecular networks.
title_short	Link clustering reveals structural characteristics and biological contexts in signed molecular networks.
title_full	Link clustering reveals structural characteristics and biological contexts in signed molecular networks.
title_fullStr	Link clustering reveals structural characteristics and biological contexts in signed molecular networks.
title_full_unstemmed	Link clustering reveals structural characteristics and biological contexts in signed molecular networks.
title_sort	link clustering reveals structural characteristics and biological contexts in signed molecular networks.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/334e932c93934de284f05b93415605c7
work_keys_str_mv	AT chenchinglin linkclusteringrevealsstructuralcharacteristicsandbiologicalcontextsinsignedmolecularnetworks AT chiahsienlee linkclusteringrevealsstructuralcharacteristicsandbiologicalcontextsinsignedmolecularnetworks AT chioushannfuh linkclusteringrevealsstructuralcharacteristicsandbiologicalcontextsinsignedmolecularnetworks AT hsuehfenjuan linkclusteringrevealsstructuralcharacteristicsandbiologicalcontextsinsignedmolecularnetworks AT hsuanchenghuang linkclusteringrevealsstructuralcharacteristicsandbiologicalcontextsinsignedmolecularnetworks
_version_	1718423089122902016

Link clustering reveals structural characteristics and biological contexts in signed molecular networks.

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