Genetic and nongenetic variation revealed for the principal components of human gene expression.

ABSTRACT: Principal components analysis has been employed in gene expression studies to correct for population substructure and batch and environmental effects. This method typically involves the removal of variation contained in as many as 50 principal components (PCs), which can constitute a large proportion of total variation present in the data. Each PC, however, can detect many sources of variation, including gene expression networks and genetic variation influencing transcript levels. We demonstrate that PCs generated from gene expression data can simultaneously contain both genetic and nongenetic factors. From heritability estimates we show that all PCs contain a considerable portion of genetic variation while nongenetic artifacts such as batch effects were associated to varying degrees with

SUBMITTER: Goldinger A 

PROVIDER: S-EPMC3813841 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature