An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk.
Sci Rep
; 11(1): 7272, 2021 03 31.
Article
em En
| MEDLINE
| ID: mdl-33790340
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.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
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Software
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Neoplasias da Mama
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Receptores do Ácido Retinoico
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Redes Reguladoras de Genes
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Proteínas de Neoplasias
Limite:
Female
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Humans
Idioma:
En
Ano de publicação:
2021
Tipo de documento:
Article