An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk

Abstract Modular response analysis (MRA) is a widely used inference technique developed to uncover directions and strengths of connections in molecular networks under a steady-state condition by means of perturbation experiments. We devised several extensions of this methodology to search genomic da...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Gabriel Jimenez-Dominguez, Patrice Ravel, Stéphan Jalaguier, Vincent Cavaillès, Jacques Colinge
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d94098b1f0d3446eb30d3bf3eb359a2a
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:d94098b1f0d3446eb30d3bf3eb359a2a
record_format	dspace
spelling	oai:doaj.org-article:d94098b1f0d3446eb30d3bf3eb359a2a2021-12-02T13:27:04ZAn R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk10.1038/s41598-021-86544-02045-2322https://doaj.org/article/d94098b1f0d3446eb30d3bf3eb359a2a2021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-86544-0https://doaj.org/toc/2045-2322Abstract Modular response analysis (MRA) is a widely used inference technique developed to uncover directions and strengths of connections in molecular networks under a steady-state condition by means of perturbation experiments. We devised several extensions of this methodology to search genomic data for new associations with a biological network inferred by MRA, to improve the predictive accuracy of MRA-inferred networks, and to estimate confidence intervals of MRA parameters from datasets with low numbers of replicates. The classical MRA computations and their extensions were implemented in a freely available R package called aiMeRA ( https://github.com/bioinfo-ircm/aiMeRA/ ). We illustrated the application of our package by assessing the crosstalk between estrogen and retinoic acid receptors, two nuclear receptors implicated in several hormone-driven cancers, such as breast cancer. Based on new data generated for this study, our analysis revealed potential cross-inhibition mediated by the shared corepressors NRIP1 and LCoR. We designed aiMeRA for non-specialists and to allow biologists to perform their own analyses.Gabriel Jimenez-DominguezPatrice RavelStéphan JalaguierVincent CavaillèsJacques ColingeNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Gabriel Jimenez-Dominguez Patrice Ravel Stéphan Jalaguier Vincent Cavaillès Jacques Colinge An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk
description	Abstract Modular response analysis (MRA) is a widely used inference technique developed to uncover directions and strengths of connections in molecular networks under a steady-state condition by means of perturbation experiments. We devised several extensions of this methodology to search genomic data for new associations with a biological network inferred by MRA, to improve the predictive accuracy of MRA-inferred networks, and to estimate confidence intervals of MRA parameters from datasets with low numbers of replicates. The classical MRA computations and their extensions were implemented in a freely available R package called aiMeRA ( https://github.com/bioinfo-ircm/aiMeRA/ ). We illustrated the application of our package by assessing the crosstalk between estrogen and retinoic acid receptors, two nuclear receptors implicated in several hormone-driven cancers, such as breast cancer. Based on new data generated for this study, our analysis revealed potential cross-inhibition mediated by the shared corepressors NRIP1 and LCoR. We designed aiMeRA for non-specialists and to allow biologists to perform their own analyses.
format	article
author	Gabriel Jimenez-Dominguez Patrice Ravel Stéphan Jalaguier Vincent Cavaillès Jacques Colinge
author_facet	Gabriel Jimenez-Dominguez Patrice Ravel Stéphan Jalaguier Vincent Cavaillès Jacques Colinge
author_sort	Gabriel Jimenez-Dominguez
title	An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk
title_short	An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk
title_full	An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk
title_fullStr	An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk
title_full_unstemmed	An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk
title_sort	r package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/d94098b1f0d3446eb30d3bf3eb359a2a
work_keys_str_mv	AT gabrieljimenezdominguez anrpackageforgenericmodularresponseanalysisanditsapplicationtoestrogenandretinoicacidreceptorcrosstalk AT patriceravel anrpackageforgenericmodularresponseanalysisanditsapplicationtoestrogenandretinoicacidreceptorcrosstalk AT stephanjalaguier anrpackageforgenericmodularresponseanalysisanditsapplicationtoestrogenandretinoicacidreceptorcrosstalk AT vincentcavailles anrpackageforgenericmodularresponseanalysisanditsapplicationtoestrogenandretinoicacidreceptorcrosstalk AT jacquescolinge anrpackageforgenericmodularresponseanalysisanditsapplicationtoestrogenandretinoicacidreceptorcrosstalk AT gabrieljimenezdominguez rpackageforgenericmodularresponseanalysisanditsapplicationtoestrogenandretinoicacidreceptorcrosstalk AT patriceravel rpackageforgenericmodularresponseanalysisanditsapplicationtoestrogenandretinoicacidreceptorcrosstalk AT stephanjalaguier rpackageforgenericmodularresponseanalysisanditsapplicationtoestrogenandretinoicacidreceptorcrosstalk AT vincentcavailles rpackageforgenericmodularresponseanalysisanditsapplicationtoestrogenandretinoicacidreceptorcrosstalk AT jacquescolinge rpackageforgenericmodularresponseanalysisanditsapplicationtoestrogenandretinoicacidreceptorcrosstalk
_version_	1718393062698254336

An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk

Ejemplares similares