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Estimating accuracy of RNA-Seq and microarrays with proteomics
1Key lab of Systems Biology, Shanghai Institutes for Biological Sciences, China Academy of Sciences, Shanghai, 200031, PR China. xfu@sibs.ac.cn
BMC Genomics
|April 18, 2009
Summary
High throughput sequencing (RNA-Seq) offers a more accurate method for quantifying absolute gene expression levels compared to microarrays. Proteomics confirmed RNA-Seq as the superior technique for transcriptome studies needing precise expression measurements.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Microarrays enabled transcriptome-wide gene expression comparisons but lack accuracy in estimating absolute levels.
- High throughput sequencing (RNA-Seq) is an emerging alternative for transcriptome studies.
- The accuracy of RNA-Seq for absolute transcript level estimation was previously unknown.
Purpose of the Study:
- To evaluate the relative accuracy of microarrays and RNA-Seq for estimating absolute transcript levels.
- To compare the technical performance of microarrays and RNA-Seq using proteomics as a validation method.
Main Methods:
- Comparative analysis of gene expression data from microarrays and RNA-Seq.
- Utilizing proteomics data to validate and assess the accuracy of transcript level estimations.
Main Results:
- RNA-Seq provides a more accurate estimate of absolute transcript levels compared to microarrays.
- Proteomics data supported the superior accuracy of RNA-Seq.
Conclusions:
- RNA-Seq is the preferred technique for transcriptome studies requiring precise absolute expression quantification.
- RNA-Seq demonstrates superior overall technical performance for accurate transcript level estimation.
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