Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity

Abstract Intestinal epithelial cells, like Caco-2, are commonly used to study the interaction between food, other luminal factors and the host, often supported by microarray analysis to study the changes in gene expression as a result of the exposure. However, no compiled dataset for Caco-2 has ever...

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Autores principales:	Prashanna Balaji Venkatasubramanian, Gamze Toydemir, Nicole de Wit, Edoardo Saccenti, Vitor A. P. Martins dos Santos, Peter van Baarlen, Jerry M. Wells, Maria Suarez-Diez, Jurriaan J. Mes
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2e6ba67a3f444e8ea2dc6fd556c631c5
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spelling	oai:doaj.org-article:2e6ba67a3f444e8ea2dc6fd556c631c52021-12-02T12:32:29ZUse of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity10.1038/s41598-017-06355-02045-2322https://doaj.org/article/2e6ba67a3f444e8ea2dc6fd556c631c52017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-06355-0https://doaj.org/toc/2045-2322Abstract Intestinal epithelial cells, like Caco-2, are commonly used to study the interaction between food, other luminal factors and the host, often supported by microarray analysis to study the changes in gene expression as a result of the exposure. However, no compiled dataset for Caco-2 has ever been initiated and Caco-2-dedicated gene expression networks are barely available. Here, 341 Caco-2-specific microarray samples were collected from public databases and from in-house experiments pertaining to Caco-2 cells exposed to pathogens, probiotics and several food compounds. Using these datasets, a gene functional association network specific for Caco-2 was generated containing 8937 nodes 129711 edges. Two in silico methods, a modified version of biclustering and the new Differential Expression Correlation Analysis, were developed to identify Caco-2-specific gene targets within a pathway of interest. These methods were subsequently applied to the AhR and Nrf2 signalling pathways and altered expression of the predicted target genes was validated by qPCR in Caco-2 cells exposed to coffee extracts, known to activate both AhR and Nrf2 pathways. The datasets and in silico method(s) to identify and predict responsive target genes can be used to more efficiently design experiments to study Caco-2/intestinal epithelial-relevant biological processes.Prashanna Balaji VenkatasubramanianGamze ToydemirNicole de WitEdoardo SaccentiVitor A. P. Martins dos SantosPeter van BaarlenJerry M. WellsMaria Suarez-DiezJurriaan J. MesNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Prashanna Balaji Venkatasubramanian Gamze Toydemir Nicole de Wit Edoardo Saccenti Vitor A. P. Martins dos Santos Peter van Baarlen Jerry M. Wells Maria Suarez-Diez Jurriaan J. Mes Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity
description	Abstract Intestinal epithelial cells, like Caco-2, are commonly used to study the interaction between food, other luminal factors and the host, often supported by microarray analysis to study the changes in gene expression as a result of the exposure. However, no compiled dataset for Caco-2 has ever been initiated and Caco-2-dedicated gene expression networks are barely available. Here, 341 Caco-2-specific microarray samples were collected from public databases and from in-house experiments pertaining to Caco-2 cells exposed to pathogens, probiotics and several food compounds. Using these datasets, a gene functional association network specific for Caco-2 was generated containing 8937 nodes 129711 edges. Two in silico methods, a modified version of biclustering and the new Differential Expression Correlation Analysis, were developed to identify Caco-2-specific gene targets within a pathway of interest. These methods were subsequently applied to the AhR and Nrf2 signalling pathways and altered expression of the predicted target genes was validated by qPCR in Caco-2 cells exposed to coffee extracts, known to activate both AhR and Nrf2 pathways. The datasets and in silico method(s) to identify and predict responsive target genes can be used to more efficiently design experiments to study Caco-2/intestinal epithelial-relevant biological processes.
format	article
author	Prashanna Balaji Venkatasubramanian Gamze Toydemir Nicole de Wit Edoardo Saccenti Vitor A. P. Martins dos Santos Peter van Baarlen Jerry M. Wells Maria Suarez-Diez Jurriaan J. Mes
author_facet	Prashanna Balaji Venkatasubramanian Gamze Toydemir Nicole de Wit Edoardo Saccenti Vitor A. P. Martins dos Santos Peter van Baarlen Jerry M. Wells Maria Suarez-Diez Jurriaan J. Mes
author_sort	Prashanna Balaji Venkatasubramanian
title	Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity
title_short	Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity
title_full	Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity
title_fullStr	Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity
title_full_unstemmed	Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity
title_sort	use of microarray datasets to generate caco-2-dedicated networks and to identify reporter genes of specific pathway activity
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/2e6ba67a3f444e8ea2dc6fd556c631c5
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Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity

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