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Addressing confounding artifacts in reconstruction of gene co-expression networks

Gene co-expression networks capture biological relationships between genes and are important tools in predicting gene function and understanding disease mechanisms. We show that technical and biological artifacts in gene expression data confound commonly used network reconstruction algorithms. We de...

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Detalles Bibliográficos
Autores principales: Parsana, Princy, Ruberman, Claire, Jaffe, Andrew E., Schatz, Michael C., Battle, Alexis, Leek, Jeffrey T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6521369/
https://www.ncbi.nlm.nih.gov/pubmed/31097038
http://dx.doi.org/10.1186/s13059-019-1700-9
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author Parsana, Princy
Ruberman, Claire
Jaffe, Andrew E.
Schatz, Michael C.
Battle, Alexis
Leek, Jeffrey T.
author_facet Parsana, Princy
Ruberman, Claire
Jaffe, Andrew E.
Schatz, Michael C.
Battle, Alexis
Leek, Jeffrey T.
author_sort Parsana, Princy
collection PubMed
description Gene co-expression networks capture biological relationships between genes and are important tools in predicting gene function and understanding disease mechanisms. We show that technical and biological artifacts in gene expression data confound commonly used network reconstruction algorithms. We demonstrate theoretically, in simulation, and empirically, that principal component correction of gene expression measurements prior to network inference can reduce false discoveries. Using data from the GTEx project in multiple tissues, we show that this approach reduces false discoveries beyond correcting only for known confounders. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1700-9) contains supplementary material, which is available to authorized users.
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spelling pubmed-65213692019-05-23 Addressing confounding artifacts in reconstruction of gene co-expression networks Parsana, Princy Ruberman, Claire Jaffe, Andrew E. Schatz, Michael C. Battle, Alexis Leek, Jeffrey T. Genome Biol Short Report Gene co-expression networks capture biological relationships between genes and are important tools in predicting gene function and understanding disease mechanisms. We show that technical and biological artifacts in gene expression data confound commonly used network reconstruction algorithms. We demonstrate theoretically, in simulation, and empirically, that principal component correction of gene expression measurements prior to network inference can reduce false discoveries. Using data from the GTEx project in multiple tissues, we show that this approach reduces false discoveries beyond correcting only for known confounders. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1700-9) contains supplementary material, which is available to authorized users. BioMed Central 2019-05-16 /pmc/articles/PMC6521369/ /pubmed/31097038 http://dx.doi.org/10.1186/s13059-019-1700-9 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Short Report
Parsana, Princy
Ruberman, Claire
Jaffe, Andrew E.
Schatz, Michael C.
Battle, Alexis
Leek, Jeffrey T.
Addressing confounding artifacts in reconstruction of gene co-expression networks
title Addressing confounding artifacts in reconstruction of gene co-expression networks
title_full Addressing confounding artifacts in reconstruction of gene co-expression networks
title_fullStr Addressing confounding artifacts in reconstruction of gene co-expression networks
title_full_unstemmed Addressing confounding artifacts in reconstruction of gene co-expression networks
title_short Addressing confounding artifacts in reconstruction of gene co-expression networks
title_sort addressing confounding artifacts in reconstruction of gene co-expression networks
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6521369/
https://www.ncbi.nlm.nih.gov/pubmed/31097038
http://dx.doi.org/10.1186/s13059-019-1700-9
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