Estimating accuracy of RNA-Seq and microarrays with proteomics.
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.


CONCLUSIONS
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.
Key lab of Systems Biology, Shanghai Institutes for Biological Sciences, China Academy of Sciences, Shanghai, 200031, PR China. xfu@sibs.ac.cn
Xing
X
Fu
Ning
N
Fu
Song
S
Guo
Zheng
Z
Yan
Ying
Y
Xu
Hao
H
Hu
Corinna
C
Menzel
Wei
W
Chen
Yixue
Y
Li
Rong
R
Zeng
Philipp
P
Khaitovich
D020869:Gene Expression Profiling; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D012333:RNA, Messenger / Q000032:analysis* / Q000378:metabolism; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods*
D012333:RNA, Messenger