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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 161.
Published online 2009 April 16. doi:  10.1186/1471-2164-10-161
PMCID: PMC2676304
Copyright © 2009 Fu et al; licensee BioMed Central Ltd.
Estimating accuracy of RNA-Seq and microarrays with proteomics
Xing Fu,#1 Ning Fu,#1 Song Guo,2 Zheng Yan,2 Ying Xu,2 Hao Hu,2,3 Corinna Menzel,3 Wei Chen,corresponding author3 Yixue Li,1 Rong Zeng,1 and Philipp Khaitovichcorresponding author2,4
1Key lab of Systems Biology, Shanghai Institutes for Biological Sciences, China Academy of Sciences, Shanghai, 200031, PR China
2Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, PR China
3Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany
4Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
corresponding authorCorresponding author.
#Contributed equally.
Xing Fu: xfu/at/sibs.ac.cn; Ning Fu: nfu/at/sibs.ac.cn; Song Guo: song/at/picb.ac.cn; Zheng Yan: zhengyan/at/picb.ac.cn; Ying Xu: bio_xy/at/hotmail.com; Hao Hu: hhu/at/picb.ac.cn; Corinna Menzel: menzel/at/molgen.mpg.de; Wei Chen: wei/at/molgen.mpg.de; Yixue Li: yxli/at/sibs.ac.cn; Rong Zeng: zr/at/sibs.ac.cn; Philipp Khaitovich: khaitovich/at/eva.mpg.de
Received November 13, 2008; Accepted April 16, 2009.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Abstract
Background
Microarrays revolutionized biological research by enabling gene expression comparisons on a transcriptome-wide scale. Microarrays, however, do not estimate absolute expression level accurately. At present, high throughput sequencing is emerging as an alternative methodology for transcriptome studies. Although free of many limitations imposed by microarray design, its potential to estimate absolute transcript levels is unknown.
Results
In this study, we evaluate relative accuracy of microarrays and transcriptome sequencing (RNA-Seq) using third methodology: proteomics. We find that RNA-Seq provides a better estimate of absolute expression levels.
Conclusion
Our result shows that in terms of overall technical performance, RNA-Seq is the technique of choice for studies that require accurate estimation of absolute transcript levels.
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