A new algorithm for integrated analysis of miRNA-mRNA interactions based on individual classification reveals insights into bladder cancer.

<h4>Background</h4>MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression. It has been proposed that miRNAs play an important role in cancer development and progression. Their ability to affect multiple gene pathways by targeting various mRNAs makes them an interestin...

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Autores principales:	Nikolai Hecker, Carsten Stephan, Hans-Joachim Mollenkopf, Klaus Jung, Robert Preissner, Hellmuth-A Meyer
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7bcbe37186fb490f95b924c9eedef52a
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spelling	oai:doaj.org-article:7bcbe37186fb490f95b924c9eedef52a2021-11-18T07:44:18ZA new algorithm for integrated analysis of miRNA-mRNA interactions based on individual classification reveals insights into bladder cancer.1932-620310.1371/journal.pone.0064543https://doaj.org/article/7bcbe37186fb490f95b924c9eedef52a2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23717626/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression. It has been proposed that miRNAs play an important role in cancer development and progression. Their ability to affect multiple gene pathways by targeting various mRNAs makes them an interesting class of regulators.<h4>Methodology/principal findings</h4>We have developed an algorithm, Classification based Analysis of Paired Expression data of RNA (CAPE RNA), which is capable of identifying altered miRNA-mRNA regulation between tissues samples that assigns interaction states to each sample without preexisting stratification of groups. The distribution of the assigned interaction states compared to given experimental groups is used to assess the quality of a predicted interaction. We demonstrate the applicability of our approach by analyzing urothelial carcinoma and normal bladder tissue samples derived from 24 patients. Using our approach, normal and tumor tissue samples as well as different stages of tumor progression were successfully stratified. Also, our results suggest interesting differentially regulated miRNA-mRNA interactions associated with bladder tumor progression.<h4>Conclusions/significance</h4>The need for tools that allow an integrative analysis of microRNA and mRNA expression data has been addressed. With this study, we provide an algorithm that emphasizes on the distribution of samples to rank differentially regulated miRNA-mRNA interactions. This is a new point of view compared to current approaches. From bootstrapping analysis, our ranking yields features that build strong classifiers. Further analysis reveals genes identified as differentially regulated by miRNAs to be enriched in cancer pathways, thus suggesting biologically interesting interactions.Nikolai HeckerCarsten StephanHans-Joachim MollenkopfKlaus JungRobert PreissnerHellmuth-A MeyerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 5, p e64543 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nikolai Hecker Carsten Stephan Hans-Joachim Mollenkopf Klaus Jung Robert Preissner Hellmuth-A Meyer A new algorithm for integrated analysis of miRNA-mRNA interactions based on individual classification reveals insights into bladder cancer.
description	<h4>Background</h4>MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression. It has been proposed that miRNAs play an important role in cancer development and progression. Their ability to affect multiple gene pathways by targeting various mRNAs makes them an interesting class of regulators.<h4>Methodology/principal findings</h4>We have developed an algorithm, Classification based Analysis of Paired Expression data of RNA (CAPE RNA), which is capable of identifying altered miRNA-mRNA regulation between tissues samples that assigns interaction states to each sample without preexisting stratification of groups. The distribution of the assigned interaction states compared to given experimental groups is used to assess the quality of a predicted interaction. We demonstrate the applicability of our approach by analyzing urothelial carcinoma and normal bladder tissue samples derived from 24 patients. Using our approach, normal and tumor tissue samples as well as different stages of tumor progression were successfully stratified. Also, our results suggest interesting differentially regulated miRNA-mRNA interactions associated with bladder tumor progression.<h4>Conclusions/significance</h4>The need for tools that allow an integrative analysis of microRNA and mRNA expression data has been addressed. With this study, we provide an algorithm that emphasizes on the distribution of samples to rank differentially regulated miRNA-mRNA interactions. This is a new point of view compared to current approaches. From bootstrapping analysis, our ranking yields features that build strong classifiers. Further analysis reveals genes identified as differentially regulated by miRNAs to be enriched in cancer pathways, thus suggesting biologically interesting interactions.
format	article
author	Nikolai Hecker Carsten Stephan Hans-Joachim Mollenkopf Klaus Jung Robert Preissner Hellmuth-A Meyer
author_facet	Nikolai Hecker Carsten Stephan Hans-Joachim Mollenkopf Klaus Jung Robert Preissner Hellmuth-A Meyer
author_sort	Nikolai Hecker
title	A new algorithm for integrated analysis of miRNA-mRNA interactions based on individual classification reveals insights into bladder cancer.
title_short	A new algorithm for integrated analysis of miRNA-mRNA interactions based on individual classification reveals insights into bladder cancer.
title_full	A new algorithm for integrated analysis of miRNA-mRNA interactions based on individual classification reveals insights into bladder cancer.
title_fullStr	A new algorithm for integrated analysis of miRNA-mRNA interactions based on individual classification reveals insights into bladder cancer.
title_full_unstemmed	A new algorithm for integrated analysis of miRNA-mRNA interactions based on individual classification reveals insights into bladder cancer.
title_sort	new algorithm for integrated analysis of mirna-mrna interactions based on individual classification reveals insights into bladder cancer.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/7bcbe37186fb490f95b924c9eedef52a
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A new algorithm for integrated analysis of miRNA-mRNA interactions based on individual classification reveals insights into bladder cancer.

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