The Library
The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance
Tools
(2014) The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nature Biotechnology, Volume 32 (Number 9). pp. 926-932. doi:10.1038/nbt.3001 ISSN 1087-0156.
Research output not available from this repository.
Request-a-Copy directly from author or use local Library Get it For Me service.
Official URL: http://dx.doi.org/10.1038/nbt.3001
Abstract
The concordance of RNA-sequencing (RNA-seq) with microarrays for genome-wide analysis of differential gene expression has not been rigorously assessed using a range of chemical treatment conditions. Here we use a comprehensive study design to generate Illumina RNA-seq and Affymetrix microarray data from the same liver samples of rats exposed in triplicate to varying degrees of perturbation by 27 chemicals representing multiple modes of action (MOAs). The cross-platform concordance in terms of differentially expressed genes (DEGs) or enriched pathways is linearly correlated with treatment effect size (R2≈0.8). Furthermore, the concordance is also affected by transcript abundance and biological complexity of the MOA. RNA-seq outperforms microarray (93% versus 75%) in DEG verification as assessed by quantitative PCR, with the gain mainly due to its improved accuracy for low-abundance transcripts. Nonetheless, classifiers to predict MOAs perform similarly when developed using data from either platform. Therefore, the endpoint studied and its biological complexity, transcript abundance and the genomic application are important factors in transcriptomic research and for clinical and regulatory decision making.
Item Type: | Journal Article | ||||||||
---|---|---|---|---|---|---|---|---|---|
Divisions: | Faculty of Science, Engineering and Medicine > Science > Computer Science | ||||||||
Journal or Publication Title: | Nature Biotechnology | ||||||||
Publisher: | Nature Publishing Group | ||||||||
ISSN: | 1087-0156 | ||||||||
Official Date: | 24 August 2014 | ||||||||
Dates: |
|
||||||||
Volume: | Volume 32 | ||||||||
Number: | Number 9 | ||||||||
Page Range: | pp. 926-932 | ||||||||
DOI: | 10.1038/nbt.3001 | ||||||||
Status: | Peer Reviewed | ||||||||
Publication Status: | Published | ||||||||
Access rights to Published version: | Restricted or Subscription Access | ||||||||
Embodied As: | 1 |
Request changes or add full text files to a record
Repository staff actions (login required)
View Item |