A comparison of global gene expression measurement technologies in Arabidopsis thaliana
Article first published online: 7 APR 2004
Copyright © 2004 John Wiley & Sons, Ltd.
Comparative and Functional Genomics
Volume 5, Issue 3, pages 245–252, April 2004
How to Cite
Coughlan, S. J., Agrawal, V. and Meyers, B. (2004), A comparison of global gene expression measurement technologies in Arabidopsis thaliana. Comp Funct Genom, 5: 245–252. doi: 10.1002/cfg.397
- Issue published online: 7 APR 2004
- Article first published online: 7 APR 2004
- Manuscript Revised: 12 FEB 2004
- Manuscript Accepted: 12 FEB 2004
- Manuscript Received: 10 FEB 2004
- NSF Plant Genome Research. Grant Number: 0110528
- gene expression;
- cross-platform comparisons
Microarrays and tag-based transcriptional profiling technologies represent diverse but complementary data types. We are currently conducting a comparison of high-density in situ synthesized microarrays and massively-parallel signature sequencing (MPSS) data in the model plant, Arabidopsis thaliana. The MPSS data (available at http://mpss.udel.edu/at) and the microarray data have been compiled using the same RNA source material. In this review, we outline the experimental strategy that we are using, and present preliminary data and interpretations from the transcriptional profiles of Arabidopsis leaves and roots. The preliminary data indicate that the log ratio differences of transcripts between leaves and roots measured by microarray data are in better agreement with the MPSS data than the absolute intensities measured for individual microarrays hybridized to only one of the cRNA populations. The correlation was substantially improved by focusing on a subset of genes excluding those with very low expression levels; this selection may have removed noisy data. Future reports will incorporate more than 10 tissues that have been sampled by MPSS. Copyright © 2004 John Wiley & Sons, Ltd.