Cargando…

A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species

RNA-Seq has emerged as a revolutionary technology for transcriptome analysis. In this article, we report a systematic comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. On a panel of human/chimpanzee/rhesus cerebellum RNA sam...

Descripción completa

Detalles Bibliográficos
Autores principales: Liu, Song, Lin, Lan, Jiang, Peng, Wang, Dan, Xing, Yi
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025565/
https://www.ncbi.nlm.nih.gov/pubmed/20864445
http://dx.doi.org/10.1093/nar/gkq817
_version_ 1782196924780118016
author Liu, Song
Lin, Lan
Jiang, Peng
Wang, Dan
Xing, Yi
author_facet Liu, Song
Lin, Lan
Jiang, Peng
Wang, Dan
Xing, Yi
author_sort Liu, Song
collection PubMed
description RNA-Seq has emerged as a revolutionary technology for transcriptome analysis. In this article, we report a systematic comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. On a panel of human/chimpanzee/rhesus cerebellum RNA samples previously examined by the high-density human exon junction array (HJAY) and real-time qPCR, we generated 48.68 million RNA-Seq reads. Our results indicate that RNA-Seq has significantly improved gene coverage and increased sensitivity for differentially expressed genes compared with the high-density HJAY array. Meanwhile, we observed a systematic increase in the RNA-Seq error rate for lowly expressed genes. Specifically, between-species DEGs detected by array/qPCR but missed by RNA-Seq were characterized by relatively low expression levels, as indicated by lower RNA-Seq read counts, lower HJAY array expression indices and higher qPCR raw cycle threshold values. Furthermore, this issue was not unique to between-species comparisons of gene expression. In the RNA-Seq analysis of MicroArray Quality Control human reference RNA samples with extensive qPCR data, we also observed an increase in both the false-negative rate and the false-positive rate for lowly expressed genes. These findings have important implications for the design and data interpretation of RNA-Seq studies on gene expression differences between and within species.
format Text
id pubmed-3025565
institution National Center for Biotechnology Information
language English
publishDate 2011
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-30255652011-01-24 A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species Liu, Song Lin, Lan Jiang, Peng Wang, Dan Xing, Yi Nucleic Acids Res Genomics RNA-Seq has emerged as a revolutionary technology for transcriptome analysis. In this article, we report a systematic comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. On a panel of human/chimpanzee/rhesus cerebellum RNA samples previously examined by the high-density human exon junction array (HJAY) and real-time qPCR, we generated 48.68 million RNA-Seq reads. Our results indicate that RNA-Seq has significantly improved gene coverage and increased sensitivity for differentially expressed genes compared with the high-density HJAY array. Meanwhile, we observed a systematic increase in the RNA-Seq error rate for lowly expressed genes. Specifically, between-species DEGs detected by array/qPCR but missed by RNA-Seq were characterized by relatively low expression levels, as indicated by lower RNA-Seq read counts, lower HJAY array expression indices and higher qPCR raw cycle threshold values. Furthermore, this issue was not unique to between-species comparisons of gene expression. In the RNA-Seq analysis of MicroArray Quality Control human reference RNA samples with extensive qPCR data, we also observed an increase in both the false-negative rate and the false-positive rate for lowly expressed genes. These findings have important implications for the design and data interpretation of RNA-Seq studies on gene expression differences between and within species. Oxford University Press 2011-01 2010-09-22 /pmc/articles/PMC3025565/ /pubmed/20864445 http://dx.doi.org/10.1093/nar/gkq817 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genomics
Liu, Song
Lin, Lan
Jiang, Peng
Wang, Dan
Xing, Yi
A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species
title A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species
title_full A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species
title_fullStr A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species
title_full_unstemmed A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species
title_short A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species
title_sort comparison of rna-seq and high-density exon array for detecting differential gene expression between closely related species
topic Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025565/
https://www.ncbi.nlm.nih.gov/pubmed/20864445
http://dx.doi.org/10.1093/nar/gkq817
work_keys_str_mv AT liusong acomparisonofrnaseqandhighdensityexonarrayfordetectingdifferentialgeneexpressionbetweencloselyrelatedspecies
AT linlan acomparisonofrnaseqandhighdensityexonarrayfordetectingdifferentialgeneexpressionbetweencloselyrelatedspecies
AT jiangpeng acomparisonofrnaseqandhighdensityexonarrayfordetectingdifferentialgeneexpressionbetweencloselyrelatedspecies
AT wangdan acomparisonofrnaseqandhighdensityexonarrayfordetectingdifferentialgeneexpressionbetweencloselyrelatedspecies
AT xingyi acomparisonofrnaseqandhighdensityexonarrayfordetectingdifferentialgeneexpressionbetweencloselyrelatedspecies
AT liusong comparisonofrnaseqandhighdensityexonarrayfordetectingdifferentialgeneexpressionbetweencloselyrelatedspecies
AT linlan comparisonofrnaseqandhighdensityexonarrayfordetectingdifferentialgeneexpressionbetweencloselyrelatedspecies
AT jiangpeng comparisonofrnaseqandhighdensityexonarrayfordetectingdifferentialgeneexpressionbetweencloselyrelatedspecies
AT wangdan comparisonofrnaseqandhighdensityexonarrayfordetectingdifferentialgeneexpressionbetweencloselyrelatedspecies
AT xingyi comparisonofrnaseqandhighdensityexonarrayfordetectingdifferentialgeneexpressionbetweencloselyrelatedspecies