MIRTFnet: analysis of miRNA regulated transcription factors.

<h4>Background</h4>Several expression datasets of miRNA transfection experiments are available to analyze the regulatory mechanisms downstream of miRNA effects. The miRNA induced regulatory effects can be propagated via transcription factors (TFs). We propose the method MIRTFnet to ident...

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Autores principales:	Haroon Naeem, Robert Küffner, Ralf Zimmer
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/714ca0bfb22c4cdf8eaf356379161d3f
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spelling	oai:doaj.org-article:714ca0bfb22c4cdf8eaf356379161d3f2021-11-18T06:47:51ZMIRTFnet: analysis of miRNA regulated transcription factors.1932-620310.1371/journal.pone.0022519https://doaj.org/article/714ca0bfb22c4cdf8eaf356379161d3f2011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21857930/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Several expression datasets of miRNA transfection experiments are available to analyze the regulatory mechanisms downstream of miRNA effects. The miRNA induced regulatory effects can be propagated via transcription factors (TFs). We propose the method MIRTFnet to identify miRNA controlled TFs as active regulators if their downstream target genes are differentially expressed.<h4>Methodology/principal findings</h4>MIRTFnet enables the determination of active transcription factors (TFs) and is sensitive enough to exploit the small expression changes induced by the activity of miRNAs. For this purpose, different statistical tests were evaluated and compared. Based on the identified TFs, databases, computational predictions and the literature we construct regulatory models downstream of miRNA actions. Transfecting miRNAs are connected to active regulators via a network of miRNA-TF, miRNA-kinase-TF as well as TF-TF relationships. Based on 43 transfection experiments involving 17 cancer relevant miRNAs we show that MIRTFnet detects active regulators reliably.<h4>Conclusions/significance</h4>The consensus of the individual regulatory models shows that the examined miRNAs induce activity changes in a common core of transcription factors involved in cancer related processes such as proliferation or apoptosis.Haroon NaeemRobert KüffnerRalf ZimmerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 8, p e22519 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Haroon Naeem Robert Küffner Ralf Zimmer MIRTFnet: analysis of miRNA regulated transcription factors.
description	<h4>Background</h4>Several expression datasets of miRNA transfection experiments are available to analyze the regulatory mechanisms downstream of miRNA effects. The miRNA induced regulatory effects can be propagated via transcription factors (TFs). We propose the method MIRTFnet to identify miRNA controlled TFs as active regulators if their downstream target genes are differentially expressed.<h4>Methodology/principal findings</h4>MIRTFnet enables the determination of active transcription factors (TFs) and is sensitive enough to exploit the small expression changes induced by the activity of miRNAs. For this purpose, different statistical tests were evaluated and compared. Based on the identified TFs, databases, computational predictions and the literature we construct regulatory models downstream of miRNA actions. Transfecting miRNAs are connected to active regulators via a network of miRNA-TF, miRNA-kinase-TF as well as TF-TF relationships. Based on 43 transfection experiments involving 17 cancer relevant miRNAs we show that MIRTFnet detects active regulators reliably.<h4>Conclusions/significance</h4>The consensus of the individual regulatory models shows that the examined miRNAs induce activity changes in a common core of transcription factors involved in cancer related processes such as proliferation or apoptosis.
format	article
author	Haroon Naeem Robert Küffner Ralf Zimmer
author_facet	Haroon Naeem Robert Küffner Ralf Zimmer
author_sort	Haroon Naeem
title	MIRTFnet: analysis of miRNA regulated transcription factors.
title_short	MIRTFnet: analysis of miRNA regulated transcription factors.
title_full	MIRTFnet: analysis of miRNA regulated transcription factors.
title_fullStr	MIRTFnet: analysis of miRNA regulated transcription factors.
title_full_unstemmed	MIRTFnet: analysis of miRNA regulated transcription factors.
title_sort	mirtfnet: analysis of mirna regulated transcription factors.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/714ca0bfb22c4cdf8eaf356379161d3f
work_keys_str_mv	AT haroonnaeem mirtfnetanalysisofmirnaregulatedtranscriptionfactors AT robertkuffner mirtfnetanalysisofmirnaregulatedtranscriptionfactors AT ralfzimmer mirtfnetanalysisofmirnaregulatedtranscriptionfactors
_version_	1718424356851286016

MIRTFnet: analysis of miRNA regulated transcription factors.

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