Gene regulatory networks analysis of muscle-invasive bladder cancer subtypes using differential graphical model

Abstract Background Recently, erdafitinib (Balversa), the first targeted therapy drug for genetic alteration, was approved to metastatic urothelial carcinoma. Cancer genomics research has been greatly encouraged. Currently, a large number of gene regulatory networks between different states have bee...

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Autores principales:	Yongqing Zhang, Qingyuan Chen, Meiqin Gong, Yuanqi Zeng, Dongrui Gao
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Muscle-invasive bladder cancer Molecular subtypes Gene regulatory networks Differential networks Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/1d67f4700f7a45789b9f3f6ba0db20b3
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spelling	oai:doaj.org-article:1d67f4700f7a45789b9f3f6ba0db20b32021-12-05T12:17:09ZGene regulatory networks analysis of muscle-invasive bladder cancer subtypes using differential graphical model10.1186/s12864-021-08113-z1471-2164https://doaj.org/article/1d67f4700f7a45789b9f3f6ba0db20b32021-12-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08113-zhttps://doaj.org/toc/1471-2164Abstract Background Recently, erdafitinib (Balversa), the first targeted therapy drug for genetic alteration, was approved to metastatic urothelial carcinoma. Cancer genomics research has been greatly encouraged. Currently, a large number of gene regulatory networks between different states have been constructed, which can reveal the difference states of genes. However, they have not been applied to the subtypes of Muscle-invasive bladder cancer (MIBC). Results In this paper, we propose a method that construct gene regulatory networks under different molecular subtypes of MIBC, and analyse the regulatory differences between different molecular subtypes. Through differential expression analysis and the differential network analysis of the top 100 differential genes in the network, we find that SERPINI1, NOTUM, FGFR1 and other genes have significant differences in expression and regulatory relationship between MIBC subtypes. Conclusions Furthermore, pathway enrichment analysis and differential network analysis demonstrate that Neuroactive ligand-receptor interaction and Cytokine-cytokine receptor interaction are significantly enriched pathways, and the genes contained in them are significant diversity in the subtypes of bladder cancer.Yongqing ZhangQingyuan ChenMeiqin GongYuanqi ZengDongrui GaoBMCarticleMuscle-invasive bladder cancerMolecular subtypesGene regulatory networksDifferential networksBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss S1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Muscle-invasive bladder cancer Molecular subtypes Gene regulatory networks Differential networks Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Muscle-invasive bladder cancer Molecular subtypes Gene regulatory networks Differential networks Biotechnology TP248.13-248.65 Genetics QH426-470 Yongqing Zhang Qingyuan Chen Meiqin Gong Yuanqi Zeng Dongrui Gao Gene regulatory networks analysis of muscle-invasive bladder cancer subtypes using differential graphical model
description	Abstract Background Recently, erdafitinib (Balversa), the first targeted therapy drug for genetic alteration, was approved to metastatic urothelial carcinoma. Cancer genomics research has been greatly encouraged. Currently, a large number of gene regulatory networks between different states have been constructed, which can reveal the difference states of genes. However, they have not been applied to the subtypes of Muscle-invasive bladder cancer (MIBC). Results In this paper, we propose a method that construct gene regulatory networks under different molecular subtypes of MIBC, and analyse the regulatory differences between different molecular subtypes. Through differential expression analysis and the differential network analysis of the top 100 differential genes in the network, we find that SERPINI1, NOTUM, FGFR1 and other genes have significant differences in expression and regulatory relationship between MIBC subtypes. Conclusions Furthermore, pathway enrichment analysis and differential network analysis demonstrate that Neuroactive ligand-receptor interaction and Cytokine-cytokine receptor interaction are significantly enriched pathways, and the genes contained in them are significant diversity in the subtypes of bladder cancer.
format	article
author	Yongqing Zhang Qingyuan Chen Meiqin Gong Yuanqi Zeng Dongrui Gao
author_facet	Yongqing Zhang Qingyuan Chen Meiqin Gong Yuanqi Zeng Dongrui Gao
author_sort	Yongqing Zhang
title	Gene regulatory networks analysis of muscle-invasive bladder cancer subtypes using differential graphical model
title_short	Gene regulatory networks analysis of muscle-invasive bladder cancer subtypes using differential graphical model
title_full	Gene regulatory networks analysis of muscle-invasive bladder cancer subtypes using differential graphical model
title_fullStr	Gene regulatory networks analysis of muscle-invasive bladder cancer subtypes using differential graphical model
title_full_unstemmed	Gene regulatory networks analysis of muscle-invasive bladder cancer subtypes using differential graphical model
title_sort	gene regulatory networks analysis of muscle-invasive bladder cancer subtypes using differential graphical model
publisher	BMC
publishDate	2021
url	https://doaj.org/article/1d67f4700f7a45789b9f3f6ba0db20b3
work_keys_str_mv	AT yongqingzhang generegulatorynetworksanalysisofmuscleinvasivebladdercancersubtypesusingdifferentialgraphicalmodel AT qingyuanchen generegulatorynetworksanalysisofmuscleinvasivebladdercancersubtypesusingdifferentialgraphicalmodel AT meiqingong generegulatorynetworksanalysisofmuscleinvasivebladdercancersubtypesusingdifferentialgraphicalmodel AT yuanqizeng generegulatorynetworksanalysisofmuscleinvasivebladdercancersubtypesusingdifferentialgraphicalmodel AT dongruigao generegulatorynetworksanalysisofmuscleinvasivebladdercancersubtypesusingdifferentialgraphicalmodel
_version_	1718372062665375744

Gene regulatory networks analysis of muscle-invasive bladder cancer subtypes using differential graphical model

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