ArticleNucleic acids research2011
A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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91 citing papers in PubMed, 140 citations in OpenAlex.
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31 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
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.
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