Detection of simultaneous group effects in microRNA expression and related target gene sets.

Expression levels of mRNAs are among other factors regulated by microRNAs. A particular microRNA can bind specifically to several target mRNAs and lead to their degradation. Expression levels of both, mRNAs and microRNAs, can be obtained by microarray experiments. In order to increase the power of d...

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Autores principales:	Stephan Artmann, Klaus Jung, Annalen Bleckmann, Tim Beissbarth
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/88f5c784dcb042eda27b8df602cb9b91
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spelling	oai:doaj.org-article:88f5c784dcb042eda27b8df602cb9b912021-11-18T07:15:03ZDetection of simultaneous group effects in microRNA expression and related target gene sets.1932-620310.1371/journal.pone.0038365https://doaj.org/article/88f5c784dcb042eda27b8df602cb9b912012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22723856/?tool=EBIhttps://doaj.org/toc/1932-6203Expression levels of mRNAs are among other factors regulated by microRNAs. A particular microRNA can bind specifically to several target mRNAs and lead to their degradation. Expression levels of both, mRNAs and microRNAs, can be obtained by microarray experiments. In order to increase the power of detecting microRNAs that are differentially expressed between two different groups of samples, we incorporate expression levels of their related target gene sets. Group effects are determined individually for each microRNA, and by enrichment tests and global tests for target gene sets. The resulting lists of p-values from individual and set-wise testing are combined by means of meta analysis. We propose a new approach to connect microRNA-wise and gene set-wise information by means of p-value combination as often used in meta-analysis. In this context, we evaluate the usefulness of different approaches of gene set tests. In a simulation study we reveal that our combination approach is more powerful than microRNA-wise testing alone. Furthermore, we show that combining microRNA-wise results with 'competitive' gene set tests maintains a pre-specified false discovery rate. In contrast, a combination with 'self-contained' gene set tests can harm the false discovery rate, particularly when gene sets are not disjunct.Stephan ArtmannKlaus JungAnnalen BleckmannTim BeissbarthPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 6, p e38365 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Stephan Artmann Klaus Jung Annalen Bleckmann Tim Beissbarth Detection of simultaneous group effects in microRNA expression and related target gene sets.
description	Expression levels of mRNAs are among other factors regulated by microRNAs. A particular microRNA can bind specifically to several target mRNAs and lead to their degradation. Expression levels of both, mRNAs and microRNAs, can be obtained by microarray experiments. In order to increase the power of detecting microRNAs that are differentially expressed between two different groups of samples, we incorporate expression levels of their related target gene sets. Group effects are determined individually for each microRNA, and by enrichment tests and global tests for target gene sets. The resulting lists of p-values from individual and set-wise testing are combined by means of meta analysis. We propose a new approach to connect microRNA-wise and gene set-wise information by means of p-value combination as often used in meta-analysis. In this context, we evaluate the usefulness of different approaches of gene set tests. In a simulation study we reveal that our combination approach is more powerful than microRNA-wise testing alone. Furthermore, we show that combining microRNA-wise results with 'competitive' gene set tests maintains a pre-specified false discovery rate. In contrast, a combination with 'self-contained' gene set tests can harm the false discovery rate, particularly when gene sets are not disjunct.
format	article
author	Stephan Artmann Klaus Jung Annalen Bleckmann Tim Beissbarth
author_facet	Stephan Artmann Klaus Jung Annalen Bleckmann Tim Beissbarth
author_sort	Stephan Artmann
title	Detection of simultaneous group effects in microRNA expression and related target gene sets.
title_short	Detection of simultaneous group effects in microRNA expression and related target gene sets.
title_full	Detection of simultaneous group effects in microRNA expression and related target gene sets.
title_fullStr	Detection of simultaneous group effects in microRNA expression and related target gene sets.
title_full_unstemmed	Detection of simultaneous group effects in microRNA expression and related target gene sets.
title_sort	detection of simultaneous group effects in microrna expression and related target gene sets.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/88f5c784dcb042eda27b8df602cb9b91
work_keys_str_mv	AT stephanartmann detectionofsimultaneousgroupeffectsinmicrornaexpressionandrelatedtargetgenesets AT klausjung detectionofsimultaneousgroupeffectsinmicrornaexpressionandrelatedtargetgenesets AT annalenbleckmann detectionofsimultaneousgroupeffectsinmicrornaexpressionandrelatedtargetgenesets AT timbeissbarth detectionofsimultaneousgroupeffectsinmicrornaexpressionandrelatedtargetgenesets
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Detection of simultaneous group effects in microRNA expression and related target gene sets.

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