A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships.

Inferring gene regulatory relationships from observational data is challenging. Manipulation and intervention is often required to unravel causal relationships unambiguously. However, gene copy number changes, as they frequently occur in cancer cells, might be considered natural manipulation experim...

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Autores principales:	Richard Newton, Lorenz Wernisch
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4fb5bc19ecb549448f9bece64c9285be
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spelling	oai:doaj.org-article:4fb5bc19ecb549448f9bece64c9285be2021-11-25T06:03:32ZA meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships.1932-620310.1371/journal.pone.0105522https://doaj.org/article/4fb5bc19ecb549448f9bece64c9285be2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25148247/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Inferring gene regulatory relationships from observational data is challenging. Manipulation and intervention is often required to unravel causal relationships unambiguously. However, gene copy number changes, as they frequently occur in cancer cells, might be considered natural manipulation experiments on gene expression. An increasing number of data sets on matched array comparative genomic hybridisation and transcriptomics experiments from a variety of cancer pathologies are becoming publicly available. Here we explore the potential of a meta-analysis of thirty such data sets. The aim of our analysis was to assess the potential of in silico inference of trans-acting gene regulatory relationships from this type of data. We found sufficient correlation signal in the data to infer gene regulatory relationships, with interesting similarities between data sets. A number of genes had highly correlated copy number and expression changes in many of the data sets and we present predicted potential trans-acted regulatory relationships for each of these genes. The study also investigates to what extent heterogeneity between cell types and between pathologies determines the number of statistically significant predictions available from a meta-analysis of experiments.Richard NewtonLorenz WernischPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 8, p e105522 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Richard Newton Lorenz Wernisch A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships.
description	Inferring gene regulatory relationships from observational data is challenging. Manipulation and intervention is often required to unravel causal relationships unambiguously. However, gene copy number changes, as they frequently occur in cancer cells, might be considered natural manipulation experiments on gene expression. An increasing number of data sets on matched array comparative genomic hybridisation and transcriptomics experiments from a variety of cancer pathologies are becoming publicly available. Here we explore the potential of a meta-analysis of thirty such data sets. The aim of our analysis was to assess the potential of in silico inference of trans-acting gene regulatory relationships from this type of data. We found sufficient correlation signal in the data to infer gene regulatory relationships, with interesting similarities between data sets. A number of genes had highly correlated copy number and expression changes in many of the data sets and we present predicted potential trans-acted regulatory relationships for each of these genes. The study also investigates to what extent heterogeneity between cell types and between pathologies determines the number of statistically significant predictions available from a meta-analysis of experiments.
format	article
author	Richard Newton Lorenz Wernisch
author_facet	Richard Newton Lorenz Wernisch
author_sort	Richard Newton
title	A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships.
title_short	A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships.
title_full	A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships.
title_fullStr	A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships.
title_full_unstemmed	A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships.
title_sort	meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/4fb5bc19ecb549448f9bece64c9285be
work_keys_str_mv	AT richardnewton ametaanalysisofmultiplematchedcopynumberandtranscriptomicsdatasetsforinferringgeneregulatoryrelationships AT lorenzwernisch ametaanalysisofmultiplematchedcopynumberandtranscriptomicsdatasetsforinferringgeneregulatoryrelationships AT richardnewton metaanalysisofmultiplematchedcopynumberandtranscriptomicsdatasetsforinferringgeneregulatoryrelationships AT lorenzwernisch metaanalysisofmultiplematchedcopynumberandtranscriptomicsdatasetsforinferringgeneregulatoryrelationships
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A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships.

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