Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach

Abstract In this study, we investigated cancer cellular networks in the context of gene interactions and their associated patterns in order to recognize the structural features underlying this disease. We aim to propose that the quest of understanding cancer takes us beyond pairwise interactions bet...

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Autores principales:	Hosein Masoomy, Behrouz Askari, Samin Tajik, Abbas K. Rizi, G. Reza Jafari
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4c30b04e5ac44b70a69771449d5bd380
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spelling	oai:doaj.org-article:4c30b04e5ac44b70a69771449d5bd3802021-12-02T15:08:38ZTopological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach10.1038/s41598-021-94847-52045-2322https://doaj.org/article/4c30b04e5ac44b70a69771449d5bd3802021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-94847-5https://doaj.org/toc/2045-2322Abstract In this study, we investigated cancer cellular networks in the context of gene interactions and their associated patterns in order to recognize the structural features underlying this disease. We aim to propose that the quest of understanding cancer takes us beyond pairwise interactions between genes to a higher-order construction. We characterize the most prominent network deviations in the gene interaction patterns between cancer and normal samples that contribute to the complexity of this disease. What we hope is that through understanding these interaction patterns we will notice a deeper structure in the cancer network. This study uncovers the significant deviations that topological features in cancerous cells show from the healthy one, where the last stage of filtration confirms the importance of one-dimensional holes (topological loops) in cancerous cells and two-dimensional holes (topological voids) in healthy cells. In the small threshold region, the drop in the number of connected components of the cancer network, along with the rise in the number of loops and voids, all occurring at some smaller weight values compared to the normal case, reveals the cancerous network tendency to certain pathways.Hosein MasoomyBehrouz AskariSamin TajikAbbas K. RiziG. Reza JafariNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hosein Masoomy Behrouz Askari Samin Tajik Abbas K. Rizi G. Reza Jafari Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach
description	Abstract In this study, we investigated cancer cellular networks in the context of gene interactions and their associated patterns in order to recognize the structural features underlying this disease. We aim to propose that the quest of understanding cancer takes us beyond pairwise interactions between genes to a higher-order construction. We characterize the most prominent network deviations in the gene interaction patterns between cancer and normal samples that contribute to the complexity of this disease. What we hope is that through understanding these interaction patterns we will notice a deeper structure in the cancer network. This study uncovers the significant deviations that topological features in cancerous cells show from the healthy one, where the last stage of filtration confirms the importance of one-dimensional holes (topological loops) in cancerous cells and two-dimensional holes (topological voids) in healthy cells. In the small threshold region, the drop in the number of connected components of the cancer network, along with the rise in the number of loops and voids, all occurring at some smaller weight values compared to the normal case, reveals the cancerous network tendency to certain pathways.
format	article
author	Hosein Masoomy Behrouz Askari Samin Tajik Abbas K. Rizi G. Reza Jafari
author_facet	Hosein Masoomy Behrouz Askari Samin Tajik Abbas K. Rizi G. Reza Jafari
author_sort	Hosein Masoomy
title	Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach
title_short	Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach
title_full	Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach
title_fullStr	Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach
title_full_unstemmed	Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach
title_sort	topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/4c30b04e5ac44b70a69771449d5bd380
work_keys_str_mv	AT hoseinmasoomy topologicalanalysisofinteractionpatternsincancerspecificgeneregulatorynetworkpersistenthomologyapproach AT behrouzaskari topologicalanalysisofinteractionpatternsincancerspecificgeneregulatorynetworkpersistenthomologyapproach AT samintajik topologicalanalysisofinteractionpatternsincancerspecificgeneregulatorynetworkpersistenthomologyapproach AT abbaskrizi topologicalanalysisofinteractionpatternsincancerspecificgeneregulatorynetworkpersistenthomologyapproach AT grezajafari topologicalanalysisofinteractionpatternsincancerspecificgeneregulatorynetworkpersistenthomologyapproach
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Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach

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