Dissecting the global variation of gene expression for the functional interpretation of transcriptome data

Abstract

To perform their biological functions, individual genes exhibit varying ranges of expression levels. Thus, considering the intrinsic variability of gene expression can improve geneset-based functional analyses which are typically used to interpret transcriptome data. Through the extensive quantitative analysis of the expressional variability of individual genes using large collections of transcriptome and proteome data, we found the existence of the intrinsic variability of gene expression at the transcriptional level. Interestingly, genes under post-translational regulation were not sensitively regulated at the transcriptional level. Because genes have intrinsically different levels of regulation at the transcription and translation stages, the functional geneset-based interpretation of transcriptome data should only include genes that are significantly varied at the transcriptional level. Thus, by removing genes with low transcriptional variation from the DNA microarray data, we showed that geneset enrichment analysis could provide improved resolution in prioritizing target functional pathways in several different experimental datasets.

Keywords: DNA microarray; Geneset enrichment analysis; Pathway analysis; Proteome; Transcriptome.