variancePartition: Interpreting drivers of variation in complex gene expression studies

58Citations
Citations of this article
121Readers
Mendeley users who have this article in their library.

Abstract

Background: As large-scale studies of gene expression with multiple sources of biological and technical variation become widely adopted, characterizing these drivers of variation becomes essential to understanding disease biology and regulatory genetics. Results: We describe a statistical and visualization framework, variancePartition, to prioritize drivers of variation based on a genome-wide summary, and identify genes that deviate from the genome-wide trend. Using a linear mixed model, variancePartition quantifies variation in each expression trait attributable to differences in disease status, sex, cell or tissue type, ancestry, genetic background, experimental stimulus, or technical variables. Analysis of four large-scale transcriptome profiling datasets illustrates that variancePartition recovers striking patterns of biological and technical variation that are reproducible across multiple datasets. Conclusions: Our open source software, variancePartition, enables rapid interpretation of complex gene expression studies as well as other high-throughput genomics assays. variancePartition is available from Bioconductor: http://bioconductor.org/packages/variancePartition.

Cite

CITATION STYLE

APA

Hoffman, G. E., & Schadt, E. E. (2016). variancePartition: Interpreting drivers of variation in complex gene expression studies. BMC Bioinformatics, 17(1). https://doi.org/10.1186/s12859-016-1323-z

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free