k-core genes underpin structural features of breast cancer

Abstract Gene co-expression networks (GCNs) have been developed as relevant analytical tools for the study of the gene expression patterns behind complex phenotypes. Determining the association between structure and function in GCNs is a current challenge in biomedical research. Several structural d...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Rodrigo Dorantes-Gilardi, Diana García-Cortés, Enrique Hernández-Lemus, Jesús Espinal-Enríquez
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8a77833741c94473b5b282636b778343
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:8a77833741c94473b5b282636b778343
record_format	dspace
spelling	oai:doaj.org-article:8a77833741c94473b5b282636b7783432021-12-02T15:08:23Zk-core genes underpin structural features of breast cancer10.1038/s41598-021-95313-y2045-2322https://doaj.org/article/8a77833741c94473b5b282636b7783432021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-95313-yhttps://doaj.org/toc/2045-2322Abstract Gene co-expression networks (GCNs) have been developed as relevant analytical tools for the study of the gene expression patterns behind complex phenotypes. Determining the association between structure and function in GCNs is a current challenge in biomedical research. Several structural differences between GCNs of breast cancer and healthy phenotypes have been reported. In a previous study, using co-expression multilayer networks, we have shown that there are abrupt differences in the connectivity patterns of the GCN of basal-like breast cancer between top co-expressed gene-pairs and the remaining gene-pairs. Here, we compared the top-100,000 interactions networks for the four breast cancer phenotypes (Luminal-A, Luminal-B, Her2+ and Basal), in terms of structural properties. For this purpose, we used the graph-theoretical k-core of a network (maximal sub-network with nodes of degree at least k). We developed a comprehensive analysis of the network k-core ( $$k=30$$ k = 30 ) structures in cancer, and its relationship with biological functions. We found that in the Top-100,000-edges networks, the majority of interactions in breast cancer networks are intra-chromosome, meanwhile inter-chromosome interactions serve as connecting bridges between clusters. Moreover, core genes in the healthy network are strongly associated with processes such as metabolism and cell cycle. In breast cancer, only the core of Luminal A is related to those processes, and genes in its core are over-expressed. The intersection of the core nodes in all subtypes of cancer is composed only by genes in the chr8q24.3 region. This region has been observed to be highly amplified in several cancers before, and its appearance in the intersection of the four breast cancer k-cores, may suggest that local co-expression is a conserved phenomenon in cancer. Considering the many intricacies associated with these phenomena and the vast amount of research in epigenomic regulation which is currently undergoing, there is a need for further research on the epigenomic effects on the structure and function of gene co-expression networks in cancer.Rodrigo Dorantes-GilardiDiana García-CortésEnrique Hernández-LemusJesús Espinal-EnríquezNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-17 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Rodrigo Dorantes-Gilardi Diana García-Cortés Enrique Hernández-Lemus Jesús Espinal-Enríquez k-core genes underpin structural features of breast cancer
description	Abstract Gene co-expression networks (GCNs) have been developed as relevant analytical tools for the study of the gene expression patterns behind complex phenotypes. Determining the association between structure and function in GCNs is a current challenge in biomedical research. Several structural differences between GCNs of breast cancer and healthy phenotypes have been reported. In a previous study, using co-expression multilayer networks, we have shown that there are abrupt differences in the connectivity patterns of the GCN of basal-like breast cancer between top co-expressed gene-pairs and the remaining gene-pairs. Here, we compared the top-100,000 interactions networks for the four breast cancer phenotypes (Luminal-A, Luminal-B, Her2+ and Basal), in terms of structural properties. For this purpose, we used the graph-theoretical k-core of a network (maximal sub-network with nodes of degree at least k). We developed a comprehensive analysis of the network k-core ( $$k=30$$ k = 30 ) structures in cancer, and its relationship with biological functions. We found that in the Top-100,000-edges networks, the majority of interactions in breast cancer networks are intra-chromosome, meanwhile inter-chromosome interactions serve as connecting bridges between clusters. Moreover, core genes in the healthy network are strongly associated with processes such as metabolism and cell cycle. In breast cancer, only the core of Luminal A is related to those processes, and genes in its core are over-expressed. The intersection of the core nodes in all subtypes of cancer is composed only by genes in the chr8q24.3 region. This region has been observed to be highly amplified in several cancers before, and its appearance in the intersection of the four breast cancer k-cores, may suggest that local co-expression is a conserved phenomenon in cancer. Considering the many intricacies associated with these phenomena and the vast amount of research in epigenomic regulation which is currently undergoing, there is a need for further research on the epigenomic effects on the structure and function of gene co-expression networks in cancer.
format	article
author	Rodrigo Dorantes-Gilardi Diana García-Cortés Enrique Hernández-Lemus Jesús Espinal-Enríquez
author_facet	Rodrigo Dorantes-Gilardi Diana García-Cortés Enrique Hernández-Lemus Jesús Espinal-Enríquez
author_sort	Rodrigo Dorantes-Gilardi
title	k-core genes underpin structural features of breast cancer
title_short	k-core genes underpin structural features of breast cancer
title_full	k-core genes underpin structural features of breast cancer
title_fullStr	k-core genes underpin structural features of breast cancer
title_full_unstemmed	k-core genes underpin structural features of breast cancer
title_sort	k-core genes underpin structural features of breast cancer
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/8a77833741c94473b5b282636b778343
work_keys_str_mv	AT rodrigodorantesgilardi kcoregenesunderpinstructuralfeaturesofbreastcancer AT dianagarciacortes kcoregenesunderpinstructuralfeaturesofbreastcancer AT enriquehernandezlemus kcoregenesunderpinstructuralfeaturesofbreastcancer AT jesusespinalenriquez kcoregenesunderpinstructuralfeaturesofbreastcancer
_version_	1718388133160026112

k-core genes underpin structural features of breast cancer

Ejemplares similares