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Lookup NU author(s): Dr Ana ViñuelaORCiD
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
© 2015 Brown et al. Statistical factor analysis methods have previously been used to remove noise components from high-dimensional data prior to genetic association mapping and, in a guided fashion, to summarize biologically relevant sources of variation. Here, we show how the derived factors summarizing pathway expression can be used to analyze the relationships between expression, heritability, and aging. We used skin gene expression data from 647 twins from the MuTHER Consortium and applied factor analysis to concisely summarize patterns of gene expression to remove broad confounding influences and to produce concise pathway-level phenotypes. We derived 930 "pathway phenotypes" that summarized patterns of variation across 186 KEGG pathways (five phenotypes per pathway). We identified 69 significant associations of age with phenotype from 57 distinct KEGG pathways at a stringent Bonferroni threshold (P<5:38×10-5). These phenotypes are more heritable (h2 = 0:32) than gene expression levels. On average, expression levels of 16% of genes within these pathways are associated with age. Several significant pathways relate to metabolizing sugars and fatty acids; others relate to insulin signaling. We have demonstrated that factor analysis methods combined with biological knowledge can produce more reliable phenotypes with less stochastic noise than the individual gene expression levels, which increases our power to discover biologically relevant associations. These phenotypes could also be applied to discover associations with other environmental factors.
Author(s): Brown AA, Ding Z, Vinuela A, Glass D, Parts L, Spector T, Winn J, Durbin R
Publication type: Article
Publication status: Published
Journal: G3: Genes, Genomes, Genetics
Year: 2015
Volume: 5
Issue: 5
Pages: 839-847
Online publication date: 11/05/2015
Acceptance date: 05/03/2015
Date deposited: 29/06/2020
ISSN (electronic): 2160-1836
Publisher: Genetics Society of America
URL: https://doi.org/10.1534/g3.114.011411
DOI: 10.1534/g3.114.011411
PubMed id: 25758824
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