An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
31 03 2021
31 03 2021
Historique:
received:
09
10
2020
accepted:
09
03
2021
entrez:
1
4
2021
pubmed:
2
4
2021
medline:
21
10
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 33790340
doi: 10.1038/s41598-021-86544-0
pii: 10.1038/s41598-021-86544-0
pmc: PMC8012374
doi:
Substances chimiques
Neoplasm Proteins
0
Receptors, Retinoic Acid
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
7272Références
Mol Endocrinol. 2013 Sep;27(9):1429-41
pubmed: 23885094
J Theor Biol. 2005 Feb 7;232(3):427-41
pubmed: 15572066
Nucleic Acids Res. 2012 May;40(10):4288-97
pubmed: 22287627
Physiol Rev. 2007 Jul;87(3):905-31
pubmed: 17615392
J Biol Chem. 2003 Nov 7;278(45):43889-92
pubmed: 14506269
J Biol Chem. 2005 Mar 4;280(9):7829-35
pubmed: 15632153
Transl Oncol. 2018 Oct;11(5):1090-1096
pubmed: 30007204
Bioinformatics. 2018 Sep 1;34(17):i997-i1004
pubmed: 30423075
Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12841-6
pubmed: 12242336
Genome Biol. 2013 Apr 25;14(4):R36
pubmed: 23618408
Mol Cell. 2003 Jan;11(1):139-50
pubmed: 12535528
Bioinformatics. 2015 Jan 15;31(2):166-9
pubmed: 25260700
Bioinformatics. 2011 Feb 1;27(3):431-2
pubmed: 21149340
Nat Cell Biol. 2007 Mar;9(3):324-30
pubmed: 17310240
Mol Syst Biol. 2012;8:601
pubmed: 22864383
Cell. 2009 Jun 26;137(7):1259-71
pubmed: 19563758
J Steroid Biochem Mol Biol. 2003 Jul;86(1):1-14
pubmed: 12943740
Luminescence. 2001 Mar-Apr;16(2):153-8
pubmed: 11312541
Mol Syst Biol. 2013 Jun 18;9:676
pubmed: 23774759
Mol Syst Biol. 2013;9:673
pubmed: 23752269
Bioinformatics. 2018 Dec 1;34(23):4079-4086
pubmed: 29931053
Mol Endocrinol. 2005 Jun;19(6):1584-92
pubmed: 15831516
Sci Rep. 2018 Nov 1;8(1):16217
pubmed: 30385767
NPJ Syst Biol Appl. 2019 May 23;5:19
pubmed: 31149348
BMC Syst Biol. 2013 Jul 06;7:57
pubmed: 23829771
EMBO J. 1995 Aug 1;14(15):3741-51
pubmed: 7641693
Genes Dev. 2010 Jan 15;24(2):171-82
pubmed: 20080953
Oncogene. 2017 Aug 17;36(33):4790-4801
pubmed: 28414308