Robust meta-analysis of gene expression using the elastic net

Meta-analysis of gene expression has enabled numerous insights into biological systems, but current methods have several limitations. We developed a method to perform a meta-analysis using the elastic net, a powerful and versatile approach for classification and regression. To demonstrate the utilit...

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Bibliographic Details
Published in:Nucleic acids research 2015-07, Vol.43 (12), p.e79-e79
Main Authors: Hughey, Jacob J, Butte, Atul J
Format: Article
Language:English
Subjects:
Female
Gene Expression
Humans
Lung Neoplasms - classification
Lung Neoplasms - genetics
Lung Neoplasms - metabolism
Male
Meta-Analysis as Topic
Methods Online
Regression Analysis
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Summary:Meta-analysis of gene expression has enabled numerous insights into biological systems, but current methods have several limitations. We developed a method to perform a meta-analysis using the elastic net, a powerful and versatile approach for classification and regression. To demonstrate the utility of our method, we conducted a meta-analysis of lung cancer gene expression based on publicly available data. Using 629 samples from five data sets, we trained a multinomial classifier to distinguish between four lung cancer subtypes. Our meta-analysis-derived classifier included 58 genes and achieved 91% accuracy on leave-one-study-out cross-validation and on three independent data sets. Our method makes meta-analysis of gene expression more systematic and expands the range of questions that a meta-analysis can be used to address. As the amount of publicly available gene expression data continues to grow, our method will be an effective tool to help distill these data into knowledge.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkv229